"<div> <div> <div> <div>In prokaryotes there is no <span class=cloze>[...]</span>, so <span style=""font-weight: 700; font-style: italic;"">transcription </span>and <span style=""font-weight: 700; font-style: italic;"">translation </span>are <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div>In prokaryotes there is no <span class=cloze>nucleus</span>, so <span style=""font-weight: 700; font-style: italic;"">transcription </span>and <span style=""font-weight: 700; font-style: italic;"">translation </span>are <span class=cloze>transiently linked</span>&nbsp;</div> </div> </div></div><br> "
<div> <div> <div>In eukaryotes, transcription occurs in the <span class=cloze>[...]</span> and translation occurs in the <span class=cloze>[...]</span> so they are separated by the <span class=cloze>[...]</span></div> </div> </div> <div> <div> <div>In eukaryotes, transcription occurs in the <span class=cloze>nucleus</span> and translation occurs in the <span class=cloze>cytosol</span> so they are separated by the <span class=cloze>nuclear membrane&nbsp;</span></div> </div> </div><br> " <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Chargaff’s Rules </span>for nucleotide composition (1950)<br> (1) Base composition varies across species<br> (2) All tissues within a species will have the same % composition of all 4 nucleotides (3) Base composition is consistent with age, nutritional status, &amp; environment<br> (4) The % of purines = the % of pyrimidines </div> <div>The %A = %<span class=cloze>[...]</span> and the %G = %<span class=cloze>[...]</span> <br>So <span class=cloze>[...]</span>&nbsp;= <span class=cloze>[...]</span><br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Chargaff’s Rules </span>for nucleotide composition (1950)<br> (1) Base composition varies across species<br> (2) All tissues within a species will have the same % composition of all 4 nucleotides (3) Base composition is consistent with age, nutritional status, &amp; environment<br> (4) The % of purines = the % of pyrimidines </div> <div>The %A = %<span class=cloze>T</span> and the %G = %<span class=cloze>C</span> <br>So <span class=cloze>A+G</span>&nbsp;= <span class=cloze>T+C&nbsp;</span><br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Watson-Crick DNA Model (1953) </span></div> <div>Determined through fiber diffraction (from Franklin &amp; Wilkins) and X-ray data <br><br>1962 Nobel prize<br><br>&nbsp;Identified the <span class=cloze>[...]</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>model </div> <div><br>2 strands running in opposite directions (<span class=cloze>[...]</span>) with complimentary base pairs joined by <span class=cloze>[...]</span> </div> <div><br>The original strand serves as the template in <span class=cloze>[...]</span> </div> <div><br>Phosphodiester linkages between <span class=cloze>[...]</span> for the sugar-phosphate backbone <br><br><b><font color=""#f75538"">Read from&nbsp;</font></b><span class=cloze>[...]</span></div> </div> </div> <div> <div> <div><br>The bases are staked perpendicular to the helical axis<br><span class=cloze>[...]</span> in van der Waals &amp; dipole-dipole attractions<br><span class=cloze>[...]</span> in water interactions<br> Vertically stacked bases are 3.4 Å apart&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Watson-Crick DNA Model (1953) </span></div> <div>Determined through fiber diffraction (from Franklin &amp; Wilkins) and X-ray data <br><br>1962 Nobel prize<br><br>&nbsp;Identified the <span class=cloze>double helix</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>model </div> <div><br>2 strands running in opposite directions (<span class=cloze>antiparallel</span>) with complimentary base pairs joined by <span class=cloze>hydrogen bonds</span> </div> <div><br>The original strand serves as the template in <span class=cloze>replication</span> </div> <div><br>Phosphodiester linkages between <span class=cloze>nucleotides</span> for the sugar-phosphate backbone <br><br><b><font color=""#f75538"">Read from&nbsp;</font></b><span class=cloze>5' --&gt; 3'</span></div> </div> </div> <div> <div> <div><br>The bases are staked perpendicular to the helical axis<br><span class=cloze>HIGH</span> in van der Waals &amp; dipole-dipole attractions<br><span class=cloze>LOW</span> in water interactions<br> Vertically stacked bases are 3.4 Å apart&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>A &amp; T connected by <span class=cloze>[...]</span> <br>G &amp; C connected by <span class=cloze>[...]</span>&nbsp;<br><br>*not COVALENT bonds*</div> </div> </div></div><div> <div> <div> <div>A &amp; T connected by <span class=cloze>2 H bonds</span> <br>G &amp; C connected by <span class=cloze>3 H bonds</span>&nbsp;<br><br>*not COVALENT bonds*</div> </div> </div></div><br> <div> <div> <div> <div>DNA and RNA will be <span class=cloze>[...]</span> charged at physiological pH<br><br>The <span class=cloze>[...]</span> group is acidic at low pH&nbsp;</div> </div> </div></div><div> <div> <div> <div>DNA and RNA will be <span class=cloze>negatively</span> charged at physiological pH<br><br>The <span class=cloze>phosphate</span> group is acidic at low pH&nbsp;</div> </div> </div></div><br> "<div> <div> <div> <div><u><span style=""font-weight: 700; font-style: italic;"">B-DNA </span>conformation</u><br><br>This is the Watson-Crick structure<br><br><span class=cloze>[...]</span> double helix<br><br>Most <span class=cloze>[...]</span> under <span class=cloze>[...]</span></div> <div><br>&gt; 99% of DNA in this form in living cells Majority of <span class=cloze>[...]</span> recognize the <span class=cloze>[...]</span></div> <div><br>Base pairs are exposed in <span class=cloze>[...]</span> 10.5 base pairs per turn </div> <div><br>Base pairs are flat and perpendicular to axis with a propeller twist of about <b>1 ̊&nbsp;</b></div> </div> </div></div>""<div> <div> <div> <div><u><span style=""font-weight: 700; font-style: italic;"">B-DNA </span>conformation</u><br><br>This is the Watson-Crick structure<br><br><span class=cloze>Right-handed</span> double helix<br><br>Most <span class=cloze>stable form</span> under <span class=cloze>physiological conditions</span></div> <div><br>&gt; 99% of DNA in this form in living cells Majority of <span class=cloze>proteins</span> recognize the <span class=cloze>major groove</span></div> <div><br>Base pairs are exposed in <span class=cloze>both grooves</span> 10.5 base pairs per turn </div> <div><br>Base pairs are flat and perpendicular to axis with a propeller twist of about <b>1 ̊&nbsp;</b></div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">A-DNA </span>conformation <br><span class=cloze>[...]</span> double helix </div> <div>Favored form in <span class=cloze>[...]</span> conditions (<span class=cloze>[...]</span>) <br>Good model for RNA-DNA hybrids </div> <div><span style=""font-weight: 700; font-style: italic;""><br>Z-DNA </span>conformation <br><div> <div> <div> <div><span class=cloze>[...]</span> double helix<br></div></div></div></div></div> <div>Active role in <span class=cloze>[...]</span> of cellular DNA </div> <div><br><br>Small amounts of DNA in eukaryotic cells exist in other conformations <br><u>Cruciform, triplex, quadruplex&nbsp;</u><br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">A-DNA </span>conformation <br><span class=cloze>Right-handed</span> double helix </div> <div>Favored form in <span class=cloze>anhydrous</span> conditions (<span class=cloze>not physiological conditions</span>) <br>Good model for RNA-DNA hybrids </div> <div><span style=""font-weight: 700; font-style: italic;""><br>Z-DNA </span>conformation <br><div> <div> <div> <div><span class=cloze>Left-handed</span> double helix<br></div></div></div></div></div> <div>Active role in <span class=cloze>gene expression &lt; 1%</span> of cellular DNA </div> <div><br><br>Small amounts of DNA in eukaryotic cells exist in other conformations <br><u>Cruciform, triplex, quadruplex&nbsp;</u><br></div> </div> </div><br> "
"<img src=""paste-0fa5c346ef676197e81054374787e261e8b25c41.jpg""><br>Left: <span class=cloze>[...]</span><br>Middle: <span class=cloze>[...]</span><br>Right: <span class=cloze>[...]</span><div></div><div></div>""<img src=""paste-0fa5c346ef676197e81054374787e261e8b25c41.jpg""><br>Left: <span class=cloze>A</span><br>Middle: <span class=cloze>B</span><br>Right: <span class=cloze>Z</span><div></div><div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">DNA Denaturation</span></div> <div><br>When DNA strands separate (<span class=cloze>[...]</span>), only the <span class=cloze>[...]</span>, not the covalent bonds, are disrupted <br>&nbsp; &nbsp;This is referred to as <span class=cloze>[...]</span> the DNA </div> <div><br>The DNA strand melts in <span class=cloze>[...]</span> conditions, <span class=cloze>[...]</span> conditions, and at <span class=cloze>[...]</span> temperature <br>&nbsp; &nbsp;Each species of DNA has a characteristic Tm where <span class=cloze>[...]</span> of the DNA is <span class=cloze>[...]</span></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">DNA Denaturation</span></div> <div><br>When DNA strands separate (<span class=cloze>melt</span>), only the <span class=cloze>H-bonds</span>, not the covalent bonds, are disrupted <br>&nbsp; &nbsp;This is referred to as <span class=cloze>denaturing</span> the DNA </div> <div><br>The DNA strand melts in <span class=cloze>acidic</span> conditions, <span class=cloze>alkali</span> conditions, and at <span class=cloze>increased</span> temperature <br>&nbsp; &nbsp;Each species of DNA has a characteristic Tm where <span class=cloze>1⁄2</span> of the DNA is <span class=cloze>single-stranded</span></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Renaturation (Annealing)</span></div> <div><br>Complimentary strands can associate (<span class=cloze>[...]</span>) once stabilized&nbsp; &nbsp; &nbsp; &nbsp; When ≈<span class=cloze>[...]</span> below Tmin ≈<span class=cloze>[...]</span> </div> <div><br>High <span class=cloze>[...]</span> stabilizes the duplex and <span class=cloze>[...]</span> <span style=""font-weight: 700; font-style: italic;"">T</span><span style=""font-weight: 700; font-style: italic;"">m </span>through <span class=cloze>[...]</span> interactions and <span class=cloze>[...]</span> shielding </div> <div><br>The higher the <span class=cloze>[...]</span> content, the higher the <span class=cloze>[...]</span></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Renaturation (Annealing)</span></div> <div><br>Complimentary strands can associate (<span class=cloze>anneal</span>) once stabilized&nbsp; &nbsp; &nbsp; &nbsp; When ≈<span class=cloze>20 ̊C</span> below Tmin ≈<span class=cloze>0.15M NaCl</span> </div> <div><br>High <span class=cloze>salt</span> stabilizes the duplex and <span class=cloze>increases</span> <span style=""font-weight: 700; font-style: italic;"">T</span><span style=""font-weight: 700; font-style: italic;"">m </span>through <span class=cloze>hydrophobic</span> interactions and <span class=cloze>phosphate</span> shielding </div> <div><br>The higher the <span class=cloze>G-C</span> content, the higher the <span class=cloze>melting point</span></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Ribonucleic Acid (RNA) </span></div> <div>A linear, single-stranded polynucleotide with a <span class=cloze>[...]</span> backbone <br><br>Thymine is replaced with <span class=cloze>[...]</span><br><br>Read from <span class=cloze>[...]</span><br><br><span class=cloze>[...]</span> and <span class=cloze>[...]</span> resemble A-DNA structure <br><br>Complex secondary and tertiary structures </div> <div><span class=cloze>[...]</span> and <span class=cloze>[...]</span> turns</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Ribonucleic Acid (RNA) </span></div> <div>A linear, single-stranded polynucleotide with a <span class=cloze>ribose-phosphate</span> backbone <br><br>Thymine is replaced with <span class=cloze>Uracil (U)</span><br><br>Read from <span class=cloze>5’ --&gt; 3’</span><br><br><span class=cloze>Double-stranded RNA</span> and <span class=cloze>DNA-RNA hybrids</span> resemble A-DNA structure <br><br>Complex secondary and tertiary structures </div> <div><span class=cloze>Loops</span> and <span class=cloze>hairpin</span> turns</div> </div> </div></div><br> "
<div> <div> <div> <div><b><u>Enzymatic Synthesis of Polynucleotides </u></b></div> <div><br><span class=cloze>[...]</span> catalyze the extension (synthesize) of the strand by adding nucleoside-<span class=cloze>[...]</span>-triphosphate groups to the <span class=cloze>[...]</span> of the strand </div> <div><br>The <span class=cloze>[...]</span> is a strand that is complimentary to the template with a free 3’-hydrozyl group where the nucleotide can be <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div><div> <div> <div> <div><b><u>Enzymatic Synthesis of Polynucleotides </u></b></div> <div><br><span class=cloze>Polymerases</span> catalyze the extension (synthesize) of the strand by adding nucleoside-<span class=cloze>5’</span>-triphosphate groups to the <span class=cloze>3’ end</span> of the strand </div> <div><br>The <span class=cloze>primer</span> is a strand that is complimentary to the template with a free 3’-hydrozyl group where the nucleotide can be <span class=cloze>added</span>&nbsp;</div> </div> </div></div><br> <div> <div><div><span class=cloze>[...]</span> - Primed DNA template is used to synthesize DNA&nbsp;</div> </div> </div> <div> <div><div><span class=cloze>DNA polymerase</span> - Primed DNA template is used to synthesize DNA&nbsp;</div> </div> </div><br> " <div> <div><div><span class=cloze>[...]</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– DNA template is used to synthesize RNA </div> <div>No <span class=cloze>[...]</span> needed<br> </div> </div> </div>"" <div> <div><div><span class=cloze>RNA polymerase</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– DNA template is used to synthesize RNA </div> <div>No <span class=cloze>primer</span> needed<br> </div> </div> </div><br> "
" <div> <div><div><span class=cloze>[...]</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– Primed RNA template is used to synthesize DNA&nbsp;</div> </div> </div>"" <div> <div><div><span class=cloze>Reverse transcriptase</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– Primed RNA template is used to synthesize DNA&nbsp;</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;""><u>Endonucleases </u></span></div> <div>Cut the sugar-phosphate backbone on the polynucleotide chain <br>Gives <span class=cloze>[...]</span> or <span class=cloze>[...]</span> </div> <div><br>Can be a <span class=cloze>[...]</span> or <span class=cloze>[...]</span> or both<br><br>DNase may cut only one strand (<span class=cloze>[...]</span>) or both strands (<span class=cloze>[...]</span>) </div> <div><br>Can be sequence independent (<span class=cloze>[...]</span>) or sequence dependent (<span class=cloze>[...]</span>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;""><u>Endonucleases </u></span></div> <div>Cut the sugar-phosphate backbone on the polynucleotide chain <br>Gives <span class=cloze>fragments</span> or <span class=cloze>individual nucleotides</span> </div> <div><br>Can be a <span class=cloze>DNase</span> or <span class=cloze>RNase</span> or both<br><br>DNase may cut only one strand (<span class=cloze>a <span style=""font-weight: 700; font-style: italic;"">nick</span></span>) or both strands (<span class=cloze>a <span style=""font-weight: 700; font-style: italic;"">double-strand break</span></span>) </div> <div><br>Can be sequence independent (<span class=cloze>reduce to individual nucleotides</span>) or sequence dependent (<span class=cloze>cut at a specific location</span>)&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Exonucleases </span></div> <div><span class=cloze>[...]</span> nucleotides from the end of a polynucleotide chain<br><br>Can go either from <span class=cloze>[...]</span>&nbsp;or 3' --&gt; 5’ of a <span class=cloze>[...]</span> depending on the specific exonuclease <br><br>Can be a <span class=cloze>[...]</span> or <span class=cloze>[...]</span> or both&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Exonucleases </span></div> <div><span class=cloze>Cuts</span> nucleotides from the end of a polynucleotide chain<br><br>Can go either from <span class=cloze>5’ --&gt; 3’</span>&nbsp;or 3' --&gt; 5’ of a <span class=cloze>single strand</span> depending on the specific exonuclease <br><br>Can be a <span class=cloze>DNase</span> or <span class=cloze>RNase</span> or both&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Ligase </span></div> <div><br>Joins together the nucleotides end-to-end to give a <span class=cloze>[...]</span>&nbsp;<br>&nbsp; &nbsp; &nbsp;Can use either <span class=cloze>[...]</span> or <span class=cloze>[...]</span> ends </div> <div><br>Primary function within cells is to <span class=cloze>[...]</span> “nicks” in DNA&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Ligase </span></div> <div><br>Joins together the nucleotides end-to-end to give a <span class=cloze>continuous 5’ --&gt; 3’ strand</span>&nbsp;<br>&nbsp; &nbsp; &nbsp;Can use either <span class=cloze>sticky</span> or <span class=cloze>blunt</span> ends </div> <div><br>Primary function within cells is to <span class=cloze>repair</span> “nicks” in DNA&nbsp;</div> </div> </div></div><br> "
<div> <div><div><span class=cloze>[...]</span> are the unit of heredity<br><br>Encodes functional RNA or protein or regulatory elements controlling <span class=cloze>[...]</span> </div> <div><br>Each gene has a specific location on the <span class=cloze>[...]</span> <br><br>Genome size is not related to species <span class=cloze>[...]</span>&nbsp;</div> </div> </div> <div> <div><div><span class=cloze>Genes</span> are the unit of heredity<br><br>Encodes functional RNA or protein or regulatory elements controlling <span class=cloze>expression</span> </div> <div><br>Each gene has a specific location on the <span class=cloze>genome</span> <br><br>Genome size is not related to species <span class=cloze>complexity</span>&nbsp;</div> </div> </div><br> "<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Genomes </span></div> <div><br><span class=cloze>[...]</span> genes on both strands<br><br>Highly compact structure with lots of coding or regulatory information<br><br>Still must be <span class=cloze>[...]</span> to fit in the cell<br><br>Circular DNA can be relaxed or supercoiled </div> <div><br><span class=cloze>[...]</span> supercoils twist in the opposite direction as the helical turns <span class=cloze>[...]</span> </div> <div><br><span class=cloze>[...]</span> supercoils twist in the same direction as the helical turns <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Genomes </span></div> <div><br><span class=cloze>Structural</span> genes on both strands<br><br>Highly compact structure with lots of coding or regulatory information<br><br>Still must be <span class=cloze>compacted</span> to fit in the cell<br><br>Circular DNA can be relaxed or supercoiled </div> <div><br><span class=cloze>Negative</span> supercoils twist in the opposite direction as the helical turns <span class=cloze>Underwound</span> </div> <div><br><span class=cloze>Positive</span> supercoils twist in the same direction as the helical turns <span class=cloze>Overwound</span>&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Human Genomes </span></div> <div>Eukaryotic genomes are not compact <br>About half of the genome is repetitive </div> <div><br>The human genome contains 46 linear chromosones<br> 22 pairs of autosomes + 1 pair of sex chromosomes </div> <div><br>The mitochondrial genome is circular and compact<br> Encodes for 37 genes (13 proteins, 22 tRNA, &amp; 2 rRNAs) <br>Gene coding on both strands with overlapping genes <br>Maternal inheritance </div> <div><br><br><u>Structural Elements in Human Chromosomes <br></u><br>Centromeres </div> <div>Replicated <span class=cloze>[...]</span> are separated into 2 daughter cells<br> The centromere contains repetitive DNA elements (<span class=cloze>[...]</span>) </div> <div><span class=cloze>[...]</span> bp <br><br>Telomeres </div> <div>Protect the ends of linear chromosomes<br> Telomeric repeats - about <span class=cloze>[...]</span> times<br> Ends contain <span class=cloze>[...]</span> DNA that is stabilized by telomeric proteins (<span class=cloze>[...]</span>)&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Human Genomes </span></div> <div>Eukaryotic genomes are not compact <br>About half of the genome is repetitive </div> <div><br>The human genome contains 46 linear chromosones<br> 22 pairs of autosomes + 1 pair of sex chromosomes </div> <div><br>The mitochondrial genome is circular and compact<br> Encodes for 37 genes (13 proteins, 22 tRNA, &amp; 2 rRNAs) <br>Gene coding on both strands with overlapping genes <br>Maternal inheritance </div> <div><br><br><u>Structural Elements in Human Chromosomes <br></u><br>Centromeres </div> <div>Replicated <span class=cloze>chromatids</span> are separated into 2 daughter cells<br> The centromere contains repetitive DNA elements (<span class=cloze>a-satellite DNA</span>) </div> <div><span class=cloze>170 repeated</span> bp <br><br>Telomeres </div> <div>Protect the ends of linear chromosomes<br> Telomeric repeats - about <span class=cloze>2500</span> times<br> Ends contain <span class=cloze>triplex</span> DNA that is stabilized by telomeric proteins (<span class=cloze>D-loop</span>)&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Human Genomes </span></div> <div>Eukaryotic genomes are not <span class=cloze>[...]</span> <br>About <span class=cloze>[...]</span> of the genome is <span class=cloze>[...]</span> </div> <div><br>The human genome contains <span class=cloze>[...]</span> chromosones<br> <span class=cloze>[...]</span> pairs of autosomes + 1 pair of sex chromosomes </div> <div><br>The <span class=cloze>[...]</span> genome is circular and compact<br> Encodes for 37 genes (13 proteins, 22 tRNA, &amp; 2 rRNAs) <br>Gene coding on both strands with overlapping genes <br><span class=cloze>[...]</span> inheritance </div> <div><br><br><u>Structural Elements in Human Chromosomes <br></u><br>Centromeres </div> <div>Replicated chromatids are separated into 2 daughter cells<br> The centromere contains repetitive DNA elements (a-satellite DNA) </div> <div>170 repeated bp <br><br>Telomeres </div> <div>Protect the ends of linear chromosomes<br> Telomeric repeats - about 2500 times<br> Ends contain triplex DNA that is stabilized by telomeric proteins (D-loop)&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Human Genomes </span></div> <div>Eukaryotic genomes are not <span class=cloze>compact</span> <br>About <span class=cloze>half</span> of the genome is <span class=cloze>repetitive</span> </div> <div><br>The human genome contains <span class=cloze>46 linear</span> chromosones<br> <span class=cloze>22</span> pairs of autosomes + 1 pair of sex chromosomes </div> <div><br>The <span class=cloze>mitochondrial</span> genome is circular and compact<br> Encodes for 37 genes (13 proteins, 22 tRNA, &amp; 2 rRNAs) <br>Gene coding on both strands with overlapping genes <br><span class=cloze>Maternal</span> inheritance </div> <div><br><br><u>Structural Elements in Human Chromosomes <br></u><br>Centromeres </div> <div>Replicated chromatids are separated into 2 daughter cells<br> The centromere contains repetitive DNA elements (a-satellite DNA) </div> <div>170 repeated bp <br><br>Telomeres </div> <div>Protect the ends of linear chromosomes<br> Telomeric repeats - about 2500 times<br> Ends contain triplex DNA that is stabilized by telomeric proteins (D-loop)&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Condensing DNA </span></div> <div>2 meters of genetic material into a nucleus averaging 6μm in diameter<br><br>Parts of the genome not in use are highly condensed (<span class=cloze>[...]</span>) and stored separately </div> <div>from the portion being actively used (<span class=cloze>[...]</span>)<br> <span style=""font-weight: 700; font-style: italic;""><br></span><span class=cloze>[...]</span> = DNA that is heterochromatin in one cell type but euchromatin in </div> <div>another&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Condensing DNA </span></div> <div>2 meters of genetic material into a nucleus averaging 6μm in diameter<br><br>Parts of the genome not in use are highly condensed (<span class=cloze>heterochromatin</span>) and stored separately </div> <div>from the portion being actively used (<span class=cloze>euchromatin</span>)<br> <span style=""font-weight: 700; font-style: italic;""><br></span><span class=cloze>Facultative heterochromatin</span> = DNA that is heterochromatin in one cell type but euchromatin in </div> <div>another&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Nucleosomes </span></div> <div>the building blocks for <span class=cloze>[...]</span> <br>Defined as core particle + one linker </div> <div>Repeating unit is ~200 bp<br> 146 bp wrapping twice around histone core<br>&nbsp;~ 50 bp spacer </div> <div><br>Most DNA-protein contacts are <span class=cloze>[...]</span><br>Preference for areas rich in <span class=cloze>[...]</span> </div> <div><br>Electrostatic and H-bonds between histone proteins (<span class=cloze>[...]</span>) and DNA sugar-phosphate backbone (<span class=cloze>[...]</span>) </div> <div><br>Each histone core is an <span class=cloze>[...]</span> with 2 copies each of H2A, H2B, H3, and H4 <br><br>Eukaryotic DNA wraps around a histone core in 1.67 left-handed superhelical turns&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Nucleosomes </span></div> <div>the building blocks for <span class=cloze>chromatin</span> <br>Defined as core particle + one linker </div> <div>Repeating unit is ~200 bp<br> 146 bp wrapping twice around histone core<br>&nbsp;~ 50 bp spacer </div> <div><br>Most DNA-protein contacts are <span class=cloze>sequence independent</span><br>Preference for areas rich in <span class=cloze>AT</span> </div> <div><br>Electrostatic and H-bonds between histone proteins (<span class=cloze>basic</span>) and DNA sugar-phosphate backbone (<span class=cloze>acidic</span>) </div> <div><br>Each histone core is an <span class=cloze>octomer</span> with 2 copies each of H2A, H2B, H3, and H4 <br><br>Eukaryotic DNA wraps around a histone core in 1.67 left-handed superhelical turns&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>Naked DNA --&gt; Nucleosomes --&gt; 30-nm solenoid --&gt; Extended chromatin --&gt; Condensed chromatin --&gt; Mitotic chromosome&nbsp;</div> </div> </div></div>
"<div> <div> <div> <div><span style=""font-weight: 700;"">Organization and Variations </span></div> <div>Chromosomes are organized into DNA “neighborhoods” <br>Topologically Associated Domains (TADs) </div> <div><br>Single nucleotide polymorphisms (SNPs) are variations in the sequence that set apart one individual from another </div> <div>Currently about 1.4 million recognized in human genome <br>Accounts for more than 90% of genetic diversity </div> <div>Found in bond coding and non-coding regions<br> Can be used to identify <span class=cloze>[...]</span> or determine <span class=cloze>[...]</span> </div> <div><br>76% of <span class=cloze>[...]</span> information is copied into RNA molecules <br>Long non-coding RNAs (<span class=cloze>[...]</span>)<br> microRNAs (<span class=cloze>[...]</span>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Organization and Variations </span></div> <div>Chromosomes are organized into DNA “neighborhoods” <br>Topologically Associated Domains (TADs) </div> <div><br>Single nucleotide polymorphisms (SNPs) are variations in the sequence that set apart one individual from another </div> <div>Currently about 1.4 million recognized in human genome <br>Accounts for more than 90% of genetic diversity </div> <div>Found in bond coding and non-coding regions<br> Can be used to identify <span class=cloze>racial groups</span> or determine <span class=cloze>disease risk</span> </div> <div><br>76% of <span class=cloze>non-coding</span> information is copied into RNA molecules <br>Long non-coding RNAs (<span class=cloze>lncRNA</span>)<br> microRNAs (<span class=cloze>miRNAs</span>)&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>Before a cell can divide, the genetic material must be <span class=cloze>[...]</span> through <span class=cloze>[...]</span> <br>Each daughter cell will have a complete copy of the genetic code&nbsp;</div> </div> </div></div><div> <div> <div> <div>Before a cell can divide, the genetic material must be <span class=cloze>duplicated</span> through <span class=cloze>replication</span> <br>Each daughter cell will have a complete copy of the genetic code&nbsp;</div> </div> </div></div><br> "<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Polymerase </span></div> <div>DNA <span class=cloze>[...]</span> catalyzes DNA strand extension in the <span class=cloze>[...]</span>&nbsp;direction only <br>They are actually <span class=cloze>[...]</span> fron 3’ --&gt; 5’<br> <span style=""font-style: italic;"">Note that this is not de novo synthesis. You can only add to an existing strand </span></div> <div><br>Requirements for DNA synthesis:<br> A DNA template strand with an annealed <span class=cloze>[...]</span> <br>Reaction substrates are deoxyribonucleotide triphosphates </div> <div><br>The catalytic site is located in the “<span class=cloze>[...]</span>” of the enzyme&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Polymerase </span></div> <div>DNA <span class=cloze>polymerase</span> catalyzes DNA strand extension in the <span class=cloze>5’ --&gt; 3’</span>&nbsp;direction only <br>They are actually <span class=cloze>reading</span> fron 3’ --&gt; 5’<br> <span style=""font-style: italic;"">Note that this is not de novo synthesis. You can only add to an existing strand </span></div> <div><br>Requirements for DNA synthesis:<br> A DNA template strand with an annealed <span class=cloze>primer</span> <br>Reaction substrates are deoxyribonucleotide triphosphates </div> <div><br>The catalytic site is located in the “<span class=cloze>palm</span>” of the enzyme&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">3 possibilities for DNA synthesis </span></div> <div>(1) Conservative replication<br> Original strand is intact + 1 <span class=cloze>[...]</span> strand </div> <div><br>(2) Semiconservative replication<br> 2 new DNA molecules – each have 1 <span class=cloze>[...]</span> strand &amp; 1 new strand </div> <div><br>(3) Non-conservative replication<br> 2 new DNA molecules – parent strand is <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">3 possibilities for DNA synthesis </span></div> <div>(1) Conservative replication<br> Original strand is intact + 1 <span class=cloze>new</span> strand </div> <div><br>(2) Semiconservative replication<br> 2 new DNA molecules – each have 1 <span class=cloze>paternal</span> strand &amp; 1 new strand </div> <div><br>(3) Non-conservative replication<br> 2 new DNA molecules – parent strand is <span class=cloze>destroyed</span>&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">The Messelson &amp; Stahl Experiment </span></div> <div>DNA synthesis is <span class=cloze>[...]</span> <br><br>Procedure: </div> <div>E.Coli grown in 15N medium --&gt; DNA prepared --&gt; density gradient centrifuge<br>E.Coli grown in 14N medium --&gt; transferred to 15N medium --&gt; DNA prepared --&gt; density gradient centrifuge&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">The Messelson &amp; Stahl Experiment </span></div> <div>DNA synthesis is <span class=cloze>semiconservative</span> <br><br>Procedure: </div> <div>E.Coli grown in 15N medium --&gt; DNA prepared --&gt; density gradient centrifuge<br>E.Coli grown in 14N medium --&gt; transferred to 15N medium --&gt; DNA prepared --&gt; density gradient centrifuge&nbsp;</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">The Replication Fork </span></div> <div>The replication fork is where the parental strand <span class=cloze>[...]</span> and the new strands <span class=cloze>[...]</span><br>A <span class=cloze>[...]</span> is used to separate the DNA strands </div> <div><br><span class=cloze>[...]</span> – synthesis occurs <span class=cloze>[...]</span> from 5’ --&gt; 3’ <br>Primed only once </div> <div><br><span class=cloze>[...]</span> – synthesis occurs <span class=cloze>[...]</span> from 5’ --&gt;3'</div> <div>Okazaki fragments<br>Each fragment must be <span class=cloze>[...]</span> <br>Fragments must later be joined&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">The Replication Fork </span></div> <div>The replication fork is where the parental strand <span class=cloze>is separated</span> and the new strands <span class=cloze>are synthesized</span><br>A <span class=cloze>helicase</span> is used to separate the DNA strands </div> <div><br><span class=cloze>Leading strand</span> – synthesis occurs <span class=cloze>continuously</span> from 5’ --&gt; 3’ <br>Primed only once </div> <div><br><span class=cloze>Lagging strand</span> – synthesis occurs <span class=cloze>discontinuously</span> from 5’ --&gt;3'</div> <div>Okazaki fragments<br>Each fragment must be <span class=cloze>primed</span> <br>Fragments must later be joined&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Circular DNA </span></div> <div><span class=cloze>[...]</span> genomes and <span class=cloze>[...]</span> are circular<br> Circular DNA can be found in a relaxed or supercoiled state <br><br><u>Positive</u> supercoils result from overwinding </div> <div>Winds the cord in the <span class=cloze>[...]</span> direction as the helix <br><br><u>Negative</u> supercoils result from underwinding </div> <div>Winds the cord in the <span class=cloze>[...]</span> direction as the helix <br><br>Most biological molecules have <span class=cloze>[...]</span> supercoils&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Circular DNA </span></div> <div><span class=cloze>Bacterial</span> genomes and <span class=cloze>plasmids</span> are circular<br> Circular DNA can be found in a relaxed or supercoiled state <br><br><u>Positive</u> supercoils result from overwinding </div> <div>Winds the cord in the <span class=cloze>same</span> direction as the helix <br><br><u>Negative</u> supercoils result from underwinding </div> <div>Winds the cord in the <span class=cloze>opposite</span> direction as the helix <br><br>Most biological molecules have <span class=cloze>negative</span> supercoils&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Replication of circular DNA </span></div> <div>Replication is semiconservative &amp; bidirectional<br><br>Origin of replication – where DNA synthesis begins <br>Bidirectional synthesis – replication forks go in both directions </div> <div><br>DNA polymerase is not able to link the 5’ and 3’ ends <br>DNA ligase is needed to repair the nick </div> <div><br>Strand separation creates <span class=cloze>[...]</span> stress, which leads to <span class=cloze>[...]</span>, which creates a <span class=cloze>[...]</span> supercoil </div> <div><br>Topoisomerases are used to <span class=cloze>[...]</span> supercoils&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Replication of circular DNA </span></div> <div>Replication is semiconservative &amp; bidirectional<br><br>Origin of replication – where DNA synthesis begins <br>Bidirectional synthesis – replication forks go in both directions </div> <div><br>DNA polymerase is not able to link the 5’ and 3’ ends <br>DNA ligase is needed to repair the nick </div> <div><br>Strand separation creates <span class=cloze>torsional</span> stress, which leads to <span class=cloze>overwinding</span>, which creates a <span class=cloze>positive</span> supercoil </div> <div><br>Topoisomerases are used to <span class=cloze>relieve</span> supercoils&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Replication of circular DNA </span></div> <div>Replication is <span class=cloze>[...]</span> &amp; <span class=cloze>[...]</span><br><br>Origin of replication – where DNA <span class=cloze>[...]</span> begins <br>Bidirectional synthesis – replication forks go in both directions </div> <div><br>DNA <span class=cloze>[...]</span> is not able to link the 5’ and 3’ ends <br>DNA <span class=cloze>[...]</span> is needed to repair the nick </div> <div><br>Strand separation creates torsional stress, which leads to overwinding, which creates a positive supercoil </div> <div><br>Topoisomerases are used to relieve supercoils&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Replication of circular DNA </span></div> <div>Replication is <span class=cloze>semiconservative</span> &amp; <span class=cloze>bidirectional</span><br><br>Origin of replication – where DNA <span class=cloze>synthesis</span> begins <br>Bidirectional synthesis – replication forks go in both directions </div> <div><br>DNA <span class=cloze>polymerase</span> is not able to link the 5’ and 3’ ends <br>DNA <span class=cloze>ligase</span> is needed to repair the nick </div> <div><br>Strand separation creates torsional stress, which leads to overwinding, which creates a positive supercoil </div> <div><br>Topoisomerases are used to relieve supercoils&nbsp;</div> </div> </div></div><br> "
Bidirectional, semi-conservative replication will give....2 DNA molecules with the same nucleotide sequence
"<div> <div> <div> <div><span style=""font-weight: 700;"">Topoisomerases </span></div> <div>DNA polymerase’s helicase activity will separate the two strands <br><br><u>Topoisomerase type I </u></div> <div>Breaks <span class=cloze>[...]</span> strand, passes the <span class=cloze>[...]</span> strand through, rejoins the ends <br><br><u>Topoisomerase type II </u></div> <div>Breaks <span class=cloze>[...]</span> strands, passes <span class=cloze>[...]</span> DNA through the break, rejoins the ends <br><span class=cloze>[...]</span> is a topoisomerase type II that runs in the <span class=cloze>[...]</span> direction </div> <div>Adds <span class=cloze>[...]</span> supercoils ahead of the replication fork&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Topoisomerases </span></div> <div>DNA polymerase’s helicase activity will separate the two strands <br><br><u>Topoisomerase type I </u></div> <div>Breaks <span class=cloze>1</span> strand, passes the <span class=cloze>unbroken</span> strand through, rejoins the ends <br><br><u>Topoisomerase type II </u></div> <div>Breaks <span class=cloze>2</span> strands, passes <span class=cloze>intact</span> DNA through the break, rejoins the ends <br><span class=cloze>Gyrase</span> is a topoisomerase type II that runs in the <span class=cloze>opposite</span> direction </div> <div>Adds <span class=cloze>negative</span> supercoils ahead of the replication fork&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerases </span></div> <div>DNA polymerase I – Roles in replication, recombination, &amp; DNA repair DNA polymerase II – 2 other functions in DNA repair<br><font color=""#5073fa""> DNA polymerase III</font> – <span class=cloze>[...]</span> replication in bacteria&nbsp;<br><br>All three have <span class=cloze>[...]</span> polymerases</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerases </span></div> <div>DNA polymerase I – Roles in replication, recombination, &amp; DNA repair DNA polymerase II – 2 other functions in DNA repair<br><font color=""#5073fa""> DNA polymerase III</font> – <span class=cloze>Genomic</span> replication in bacteria&nbsp;<br><br>All three have <span class=cloze>HIGH FIDELITY</span> polymerases</div> </div> </div></div><br> "
"<img src=""paste-7733a202dda29f33e75b43131c2d180e3b75330f.jpg""><br><br>3-200: <span class=cloze>[...]</span> off<br>&gt;500,000: holds on <span class=cloze>[...]</span>""<img src=""paste-7733a202dda29f33e75b43131c2d180e3b75330f.jpg""><br><br>3-200: <span class=cloze>falls</span> off<br>&gt;500,000: holds on <span class=cloze>tight</span><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure </span></div> <div><span class=cloze>[...]</span> – acts as a scaffold for DNA polymerase III complex &amp; to assemble the clamp onto DNA&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure </span></div> <div><span class=cloze>Clamp loader (ttgdd’)</span> – acts as a scaffold for DNA polymerase III complex &amp; to assemble the clamp onto DNA&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure</span></div> <div><span class=cloze>[...]</span> – moves along the strand and separates it&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure</span></div> <div><span class=cloze>DnaB helicase</span> – moves along the strand and separates it&nbsp;</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure</span></div><div><span class=cloze>[...]</span> – catalyzes DNA synthesis </div> <div>2 of them: 1 for the leading strand &amp; 1 for the lagging<br><br> </div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure</span></div><div><span class=cloze>Core polymerase (aew)</span> – catalyzes DNA synthesis </div> <div>2 of them: 1 for the leading strand &amp; 1 for the lagging<br><br> </div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure </span></div> <div><span class=cloze>[...]</span> – keeps the polymerase in contact with the DNA so multiple cycles can occur<br></div> <div><br>Encircles the DNA<br> Provides means for high processivity &amp; rapid DNA polymerization<br>Has 2 identical subunits&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic DNA Polymerase III Structure </span></div> <div><span class=cloze>beta clamp (sliding clamp)</span> – keeps the polymerase in contact with the DNA so multiple cycles can occur<br></div> <div><br>Encircles the DNA<br> Provides means for high processivity &amp; rapid DNA polymerization<br>Has 2 identical subunits&nbsp;<br></div> </div> </div><br> "
<div> <div> <div> <div><span class=cloze>[...]</span> binding to the clamp loader causes it to open &amp; bind to the clamp <br><br>Once open, it can associate with the DNA strand<br><br>ATP <span class=cloze>[...]</span> causes the clamp to close around DNA&nbsp;</div> </div> </div></div><div> <div> <div> <div><span class=cloze>ATP</span> binding to the clamp loader causes it to open &amp; bind to the clamp <br><br>Once open, it can associate with the DNA strand<br><br>ATP <span class=cloze>hydrolysis</span> causes the clamp to close around DNA&nbsp;</div> </div> </div></div><br> "<div> <div> <div> <div><span style=""font-weight: 700;"">3 STAGES OF REPLICATION </span></div> <div>(1) Initiation <br>(2) Elongation <br>(3) Termination </div> <div><span style=""font-weight: 700;""><br>Initiation </span></div> <div>Replication initiation occurs at oriC<br><br>oriC = the origin of replication </div> <div>DNA unwinding element (DUE) is the A•T rich segment where strand separation happens </div> <div><br>The protein DnaA binds to a site at the <span class=cloze>[...]</span>, which induces a supercoil. The strain of the supercoil <span class=cloze>[...]</span> the DUE region<br> After separation, DnaC loads <span class=cloze>[...]</span> onto the strand. </div> <div><br>The interaction between DnaC-DnaB opens DnaB and 1 hexamer adds to each strand </div> <div><br>DnaC is <b>hydrolyzed</b> and leaves<br> DnaB helicase travels down the strand from <span class=cloze>[...]</span></div> <div>So the 2 DnaBs are traveling in opposite directions<br><br>After separation, SSBs bind to stabilize &amp; DNA gyrase <span class=cloze>[...]</span> the stress <span class=cloze>[...]</span> of the fork </div> <div>SSB = single strand binding protein<br><br><span class=cloze>[...]</span> of DnaB is the key step in initiation – binding commits the cell to replication &amp; division&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">3 STAGES OF REPLICATION </span></div> <div>(1) Initiation <br>(2) Elongation <br>(3) Termination </div> <div><span style=""font-weight: 700;""><br>Initiation </span></div> <div>Replication initiation occurs at oriC<br><br>oriC = the origin of replication </div> <div>DNA unwinding element (DUE) is the A•T rich segment where strand separation happens </div> <div><br>The protein DnaA binds to a site at the <span class=cloze>oriC</span>, which induces a supercoil. The strain of the supercoil <span class=cloze>denatures</span> the DUE region<br> After separation, DnaC loads <span class=cloze>DnaB</span> onto the strand. </div> <div><br>The interaction between DnaC-DnaB opens DnaB and 1 hexamer adds to each strand </div> <div><br>DnaC is <b>hydrolyzed</b> and leaves<br> DnaB helicase travels down the strand from <span class=cloze>5’ --&gt;3’</span></div> <div>So the 2 DnaBs are traveling in opposite directions<br><br>After separation, SSBs bind to stabilize &amp; DNA gyrase <span class=cloze>relieves</span> the stress <span class=cloze>ahead</span> of the fork </div> <div>SSB = single strand binding protein<br><br><span class=cloze>Loading</span> of DnaB is the key step in initiation – binding commits the cell to replication &amp; division&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">3 STAGES OF REPLICATION </span></div> <div>(1) Initiation <br>(2) Elongation <br>(3) Termination </div> <div><span style=""font-weight: 700;""><br>Initiation </span></div> <div>Replication initiation occurs at oriC<br><br>oriC = <span class=cloze>[...]</span> </div> <div>DNA unwinding element (DUE) is the <span class=cloze>[...]</span> segment where strand separation happens </div> <div><br>The protein DnaA binds to a site at the oriC, which induces a supercoil. The strain of the supercoil denatures the DUE region<br> After separation, DnaC loads DnaB onto the strand. </div> <div><br>The interaction between DnaC-DnaB opens DnaB and 1 hexamer adds to each strand </div> <div><br>DnaC is <b>hydrolyzed</b> and leaves<br> DnaB helicase travels down the strand from 5’ --&gt;3’</div> <div>So the 2 DnaBs are traveling in opposite directions<br><br>After separation, SSBs bind to stabilize &amp; DNA gyrase relieves the stress ahead of the fork </div> <div>SSB = single strand binding protein<br><br>Loading of DnaB is the key step in initiation – binding commits the cell to replication &amp; division&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">3 STAGES OF REPLICATION </span></div> <div>(1) Initiation <br>(2) Elongation <br>(3) Termination </div> <div><span style=""font-weight: 700;""><br>Initiation </span></div> <div>Replication initiation occurs at oriC<br><br>oriC = <span class=cloze>the origin of replication</span> </div> <div>DNA unwinding element (DUE) is the <span class=cloze>A•T rich</span> segment where strand separation happens </div> <div><br>The protein DnaA binds to a site at the oriC, which induces a supercoil. The strain of the supercoil denatures the DUE region<br> After separation, DnaC loads DnaB onto the strand. </div> <div><br>The interaction between DnaC-DnaB opens DnaB and 1 hexamer adds to each strand </div> <div><br>DnaC is <b>hydrolyzed</b> and leaves<br> DnaB helicase travels down the strand from 5’ --&gt;3’</div> <div>So the 2 DnaBs are traveling in opposite directions<br><br>After separation, SSBs bind to stabilize &amp; DNA gyrase relieves the stress ahead of the fork </div> <div>SSB = single strand binding protein<br><br>Loading of DnaB is the key step in initiation – binding commits the cell to replication &amp; division&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Elongation </span></div> <div>The leading and lagging strands follows different pathways for replication elongation<br><br>For the <span class=cloze>[...]</span> strand... </div> <div>Primase makes a short RNA primer at <span class=cloze>[...]</span><br> Primase is a RNA <span class=cloze>[...]</span> that is <span class=cloze>[...]</span> dependent &amp; primer <span class=cloze>[...]</span> </div> <div>DNA polymerase III <span class=cloze>[...]</span> to the primer </div> <div>Synthesized as a <span class=cloze>[...]</span> chain <br><br>For the <b><u>lagging</u></b> strand... </div> <div>Primase makes a short RNA primer at oriC<br> DNA polymerase III adds nucleotides to the primer<br> Synthesized in Okazaki fragments<br> Single strand binding protein (SSB) works to protect the gaps in the strand&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Elongation </span></div> <div>The leading and lagging strands follows different pathways for replication elongation<br><br>For the <span class=cloze><b><u>leading</u></b></span> strand... </div> <div>Primase makes a short RNA primer at <span class=cloze>oriC</span><br> Primase is a RNA <span class=cloze>polymerase</span> that is <span class=cloze>DNA template</span> dependent &amp; primer <span class=cloze>independent</span> </div> <div>DNA polymerase III <span class=cloze>adds nucleotides</span> to the primer </div> <div>Synthesized as a <span class=cloze>continuous</span> chain <br><br>For the <b><u>lagging</u></b> strand... </div> <div>Primase makes a short RNA primer at oriC<br> DNA polymerase III adds nucleotides to the primer<br> Synthesized in Okazaki fragments<br> Single strand binding protein (SSB) works to protect the gaps in the strand&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Elongation </span></div> <div>The leading and lagging strands follows different pathways for replication elongation<br><br>For the <b><u>leading</u></b> strand... </div> <div>Primase makes a short RNA primer at oriC<br> Primase is a RNA polymerase that is DNA template dependent &amp; primer independent </div> <div>DNA polymerase III adds nucleotides to the primer </div> <div>Synthesized as a continuous chain <br><br>For the <span class=cloze>[...]</span> strand... </div> <div>Primase makes a short RNA primer at <span class=cloze>[...]</span><br> DNA polymerase III <span class=cloze>[...]</span> to the primer<br> Synthesized in <span class=cloze>[...]</span><br> Single strand binding protein (SSB) works to <span class=cloze>[...]</span> the gaps in the strand&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Elongation </span></div> <div>The leading and lagging strands follows different pathways for replication elongation<br><br>For the <b><u>leading</u></b> strand... </div> <div>Primase makes a short RNA primer at oriC<br> Primase is a RNA polymerase that is DNA template dependent &amp; primer independent </div> <div>DNA polymerase III adds nucleotides to the primer </div> <div>Synthesized as a continuous chain <br><br>For the <span class=cloze><b><u>lagging</u></b></span> strand... </div> <div>Primase makes a short RNA primer at <span class=cloze>oriC</span><br> DNA polymerase III <span class=cloze>adds nucleotides</span> to the primer<br> Synthesized in <span class=cloze>Okazaki fragments</span><br> Single strand binding protein (SSB) works to <span class=cloze>protect</span> the gaps in the strand&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>Both strands are using the same, asymmetric DNA polymerase III dimer<br><br>The lagging strand must be looped around so the <span class=cloze>[...]</span> products are together <br><br>On the lagging strand, new <span class=cloze>[...]</span>&nbsp;and <span class=cloze>[...]</span> must be added and the old removed&nbsp;</div> </div> </div></div><div> <div> <div> <div>Both strands are using the same, asymmetric DNA polymerase III dimer<br><br>The lagging strand must be looped around so the <span class=cloze>polymerization</span> products are together <br><br>On the lagging strand, new <span class=cloze>b-clamps</span>&nbsp;and <span class=cloze>primers</span> must be added and the old removed&nbsp;</div> </div> </div></div><br> <div> <div> <div> <div>Once the Okazaki fragments are formed, they must be joined<br><br>DNA polymerase III stops once it reaches the next primer &amp; is sent to the next fragment<br><br>After DNA pol III leaves, <span class=cloze>[...]</span> comes in and removes the <span class=cloze>[...]</span> and replaces it with DNA <br><br>DNA <span class=cloze>[...]</span> is used to repair the nick and join the fragments&nbsp;</div> </div> </div></div><div> <div> <div> <div>Once the Okazaki fragments are formed, they must be joined<br><br>DNA polymerase III stops once it reaches the next primer &amp; is sent to the next fragment<br><br>After DNA pol III leaves, <span class=cloze>DNA pol I</span> comes in and removes the <span class=cloze>primer</span> and replaces it with DNA <br><br>DNA <span class=cloze>ligase</span> is used to repair the nick and join the fragments&nbsp;</div> </div> </div></div><br> <div> <div> <div> <div> <div> <div>Mutations are <span class=cloze>[...]</span> errors in replication that will be <span class=cloze>[...]</span> by subsequent daughter cells <br><br>The average mutation rate is <b>1 per 10^9 to 10^10</b> base pairs&nbsp;</div> </div> </div></div> </div> </div> <div> <div> <div> <div> <div> <div>Mutations are <span class=cloze>permanent</span> errors in replication that will be <span class=cloze>inherited</span> by subsequent daughter cells <br><br>The average mutation rate is <b>1 per 10^9 to 10^10</b> base pairs&nbsp;</div> </div> </div></div> </div> </div><br> " <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors: </span></div> <div><u>(1) Presynthetic error control</u><br> DNA <span class=cloze>[...]</span> demands for the correct base pairs<br> <span class=cloze>[...]</span> base pairs (A•T &amp; G•C) fit well into DNA polymerase’s catalytic site, <span class=cloze>[...]</span> pairs are not a good fit<br><br>Errors occur due to tautomerism</div> <div>1/10,000 bases are in the incorrect form<br> Allows for alternative base pairs to form that are <b>compatible</b> with catalytic site <br>When the base tautomerizes back to the more stable form, there will be a mismatch&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors: </span></div> <div><u>(1) Presynthetic error control</u><br> DNA <span class=cloze>polymerase</span> demands for the correct base pairs<br> <span class=cloze>Correct</span> base pairs (A•T &amp; G•C) fit well into DNA polymerase’s catalytic site, <span class=cloze>mismatched</span> pairs are not a good fit<br><br>Errors occur due to tautomerism</div> <div>1/10,000 bases are in the incorrect form<br> Allows for alternative base pairs to form that are <b>compatible</b> with catalytic site <br>When the base tautomerizes back to the more stable form, there will be a mismatch&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors: </span></div> <div><u>(1) Presynthetic error control</u><br> DNA polymerase demands for the correct base pairs<br> Correct base pairs (A•T &amp; G•C) fit well into DNA polymerase’s catalytic site, mismatched pairs are not a good fit<br><br>Errors occur due to <span class=cloze>[...]</span></div> <div><span class=cloze>[...]</span> bases are in the incorrect form<br> Allows for alternative base pairs to form that are <b>compatible</b> with catalytic site <br>When the base tautomerizes <span class=cloze>[...]</span> form, there will be a mismatch&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors: </span></div> <div><u>(1) Presynthetic error control</u><br> DNA polymerase demands for the correct base pairs<br> Correct base pairs (A•T &amp; G•C) fit well into DNA polymerase’s catalytic site, mismatched pairs are not a good fit<br><br>Errors occur due to <span class=cloze>tautomerism</span></div> <div><span class=cloze>1/10,000</span> bases are in the incorrect form<br> Allows for alternative base pairs to form that are <b>compatible</b> with catalytic site <br>When the base tautomerizes <span class=cloze>back to the more stable</span> form, there will be a mismatch&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors:<br></span>(2) Proofreading<br> <span class=cloze>[...]</span> and <span class=cloze>[...]</span> mistakes<br><br>&nbsp;On high-fidelity DNA polymerases there is both a <span class=cloze>[...]</span> site for DNA synthesis &amp; a <span class=cloze>[...]</span> for proofreading&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors:<br></span>(2) Proofreading<br> <span class=cloze>Recognizes</span> and <span class=cloze>corrects</span> mistakes<br><br>&nbsp;On high-fidelity DNA polymerases there is both a <span class=cloze>catalytic</span> site for DNA synthesis &amp; a <span class=cloze>3’ --&gt;5’ exonuclease</span> for proofreading&nbsp;</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors:<br></span>(3) Mismatch repair&nbsp;</div><div> <div> <div> <div>Scans <span class=cloze>[...]</span> the replication fork<br><br><span class=cloze>[...]</span> newly synthesized DNA and <span class=cloze>[...]</span> the mismatched bases <span class=cloze>[...]</span> the replication fork has passed&nbsp;</div> </div> </div></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">3 mechanisms to avoid replication errors:<br></span>(3) Mismatch repair&nbsp;</div><div> <div> <div> <div>Scans <span class=cloze>behind</span> the replication fork<br><br><span class=cloze>Examines</span> newly synthesized DNA and <span class=cloze>removes</span> the mismatched bases <span class=cloze>after</span> the replication fork has passed&nbsp;</div> </div> </div></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerases </span></div> <div>Replication in eukaryotes is <font color=""#547dfa"">very similar</font> to replication in prokaryotes <br><br>DNA synthesis is semiconservative &amp; bidirectional<br> Mechanism is template &amp; primer <span class=cloze>[...]</span><br><br>Synthesized from <span class=cloze>[...]</span></div> <div>Leading strand is synthesized <span class=cloze>[...]</span> </div> <div>Lagging strand is synthesized <span class=cloze>[...]</span><br><br>There are about 15 DNA polymerases with specialized functions </div> <div><span class=cloze>[...]</span> carry out genome replication<br> Most have both presynthetic error control &amp; proofreading activity </div> <div><br>Replisomes are responsible for <span class=cloze>[...]</span> replication<br> </div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerases </span></div> <div>Replication in eukaryotes is <font color=""#547dfa"">very similar</font> to replication in prokaryotes <br><br>DNA synthesis is semiconservative &amp; bidirectional<br> Mechanism is template &amp; primer <span class=cloze>dependent</span><br><br>Synthesized from <span class=cloze>5’ --&gt;3’</span></div> <div>Leading strand is synthesized <span class=cloze>continuously</span> </div> <div>Lagging strand is synthesized <span class=cloze>discontinuously</span><br><br>There are about 15 DNA polymerases with specialized functions </div> <div><span class=cloze>Replicases</span> carry out genome replication<br> Most have both presynthetic error control &amp; proofreading activity </div> <div><br>Replisomes are responsible for <span class=cloze>genome</span> replication<br> </div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much longer &amp; linear<br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now is in a complex with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are multiple origins of replication whereas prokaryotes have 1 <br>Coordination requires “licensing” </div> <div><u><br>Elongation</u><br> Rate is much slower (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> Removal of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much longer &amp; linear<br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now is in a complex with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are multiple origins of replication whereas prokaryotes have 1 <br>Coordination requires “licensing” </div> <div><u><br>Elongation</u><br> Rate is much slower (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> Removal of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to <span class=cloze>eukaryotes</span>&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much <span class=cloze>[...]</span> &amp; <span class=cloze>[...]</span><br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now <span class=cloze>[...]</span> with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are multiple origins of replication whereas prokaryotes have 1 <br>Coordination requires “licensing” </div> <div><u><br>Elongation</u><br> Rate is much slower (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> Removal of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to eukaryotes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much <span class=cloze>longer</span> &amp; <span class=cloze>linear</span><br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now <span class=cloze>is in a complex</span> with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are multiple origins of replication whereas prokaryotes have 1 <br>Coordination requires “licensing” </div> <div><u><br>Elongation</u><br> Rate is much slower (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> Removal of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to eukaryotes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much longer &amp; linear<br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now is in a complex with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are <span class=cloze>[...]</span> of replication whereas prokaryotes have 1 <br>Coordination requires “<span class=cloze>[...]</span>” </div> <div><u><br>Elongation</u><br> Rate is much slower (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> Removal of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to eukaryotes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much longer &amp; linear<br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now is in a complex with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are <span class=cloze>multiple origins</span> of replication whereas prokaryotes have 1 <br>Coordination requires “<span class=cloze>licensing</span>” </div> <div><u><br>Elongation</u><br> Rate is much slower (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> Removal of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to eukaryotes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much longer &amp; linear<br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now is in a complex with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are multiple origins of replication whereas prokaryotes have 1 <br>Coordination requires “licensing” </div> <div><u><br>Elongation</u><br> Rate is much <span class=cloze>[...]</span> (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> <span class=cloze>[...]</span> of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to eukaryotes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Differences in Eukaryotic Replication </span></div> <div>Eukaryotic chromosomes are much longer &amp; linear<br> Many of the proteins have the same function but with different names<br>Replicase has both DNA polymerase delta and epsilon<br>Primase is still a RNA polymerase but now is in a complex with DNA polymerase A</div> <div><br><u>Initiation</u><br> There are multiple origins of replication whereas prokaryotes have 1 <br>Coordination requires “licensing” </div> <div><u><br>Elongation</u><br> Rate is much <span class=cloze>slower</span> (about 50 nt/s)<br> Okazaki fragments are shorter (100-200 nt)<br> 2 different core enzymes are used by replicase<br> <span class=cloze>Removal</span> of RNA primer and DNA replacement is different </div> <div><u><br>Termination<br></u> Different details </div> <div>Telomeres are unique to eukaryotes&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div>Structure looks very similar to <span class=cloze>[...]</span><br><br><span class=cloze>[...]</span>&nbsp;– Synthesizes the leading strand<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div>Structure looks very similar to <span class=cloze>DNA polymerase III</span><br><br><span class=cloze>DNA polymerase e</span>&nbsp;– Synthesizes the leading strand<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>[...]</span> – Synthesizes the lagging strand<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>DNA polymerase delta</span> – Synthesizes the lagging strand<br></div> </div> </div><br> "
" <div> <div><div><div><div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>[...]</span>&nbsp;– Makes primers for leading &amp; lagging strand synthesis&nbsp;</div></div></div></div> </div> </div> </div> </div>"" <div> <div><div><div><div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>DNA polymerase a primease</span>&nbsp;– Makes primers for leading &amp; lagging strand synthesis&nbsp;</div></div></div></div> </div> </div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>[...]</span> – Mini chromosome maintenance – Helicase</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>MCM</span> – Mini chromosome maintenance – Helicase</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><span class=cloze>[...]</span> – Replication factor C – Clamp loader</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><span class=cloze>RFC</span> – Replication factor C – Clamp loader</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <br><div> <span class=cloze>[...]</span> – Proliferating cell nuclear antigen – Clamp </div> <div>Functions the same as in prokaryotes but there are <b>3 subunits</b> instead of 2&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <br><div> <span class=cloze>PCNA</span> – Proliferating cell nuclear antigen – Clamp </div> <div>Functions the same as in prokaryotes but there are <b>3 subunits</b> instead of 2&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>[...]</span> – Replication protein A – single strand binding protein (SSB)</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <div><br><span class=cloze>RPA</span> – Replication protein A – single strand binding protein (SSB)</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure</span></div><div><br><span class=cloze>[...]</span> – Joins fragments<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure</span></div><div><br><span class=cloze>DNA ligase</span> – Joins fragments<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <br><div> <span class=cloze>[...]</span> – DNase <span style=""font-style: italic;"">endonuclease&nbsp;</span></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic DNA Polymerase Structure </span></div> <br><div> <span class=cloze>FEN1</span> – DNase <span style=""font-style: italic;"">endonuclease&nbsp;</span></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Dealing with multiple origins of replication </span></div> <div><br>All of the origins of replication on all chromosomes must be activated only once per cell cycle <br>All are activated in the S phase but they are <b>not necessarily activated simultaneously </b></div> <div><br>In yeast, origins of replication are called <span class=cloze>[...]</span> (ARS) <br>The ARS are about 150 bp elements that are <span class=cloze>[...]</span> spaced<br> Yeast genome has 16 chromosomes with about 400 ARS </div> <div>Humans have 46 chromosomes with thousands of origins of replication<br>Origins are about 25,000 base pairs apart </div> <div>Location is <span class=cloze>[...]</span>, as it is not defined by specific DNA sequence&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Dealing with multiple origins of replication </span></div> <div><br>All of the origins of replication on all chromosomes must be activated only once per cell cycle <br>All are activated in the S phase but they are <b>not necessarily activated simultaneously </b></div> <div><br>In yeast, origins of replication are called <span class=cloze>autonomously replicating sequences</span> (ARS) <br>The ARS are about 150 bp elements that are <span class=cloze>irregularly</span> spaced<br> Yeast genome has 16 chromosomes with about 400 ARS </div> <div>Humans have 46 chromosomes with thousands of origins of replication<br>Origins are about 25,000 base pairs apart </div> <div>Location is <span class=cloze>not fixed</span>, as it is not defined by specific DNA sequence&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Dealing with multiple origins of replication </span></div> <div><br>All of the origins of replication on all chromosomes must be <span class=cloze>[...]</span> per cell cycle <br>All are activated in the <span class=cloze>[...]</span> but they are <b>not necessarily activated simultaneously </b></div> <div><br>In yeast, origins of replication are called autonomously replicating sequences (ARS) <br>The ARS are about 150 bp elements that are irregularly spaced<br> Yeast genome has 16 chromosomes with about 400 ARS </div> <div>Humans have 46 chromosomes with thousands of origins of replication<br>Origins are about 25,000 base pairs apart </div> <div>Location is not fixed, as it is not defined by specific DNA sequence&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Dealing with multiple origins of replication </span></div> <div><br>All of the origins of replication on all chromosomes must be <span class=cloze>activated only once</span> per cell cycle <br>All are activated in the <span class=cloze>S phase</span> but they are <b>not necessarily activated simultaneously </b></div> <div><br>In yeast, origins of replication are called autonomously replicating sequences (ARS) <br>The ARS are about 150 bp elements that are irregularly spaced<br> Yeast genome has 16 chromosomes with about 400 ARS </div> <div>Humans have 46 chromosomes with thousands of origins of replication<br>Origins are about 25,000 base pairs apart </div> <div>Location is not fixed, as it is not defined by specific DNA sequence&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Replication Initiation </span></div> <div>As with prokaryotes, the key regulation event is <span class=cloze>[...]</span><br><br>Origin of replication complexes (ORC) bind A•T rich DNA tightly immediate after replication =&gt; </div> <div>Cell division cycle 6 (CDC6) joins ORC in G1 phase =&gt; Protein CDT1 brings MCM to the ORC =&gt; Cell cycle dependent kinase (cdk) phosphorylates amino acids in ORC, CDC6, &amp; MCM2-7 =&gt; MCM2 helicase is loaded onto DNA in the S phase =&gt; Replicase is assembled on MCM2-7 helicase&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Replication Initiation </span></div> <div>As with prokaryotes, the key regulation event is <span class=cloze>loading the helicase</span><br><br>Origin of replication complexes (ORC) bind A•T rich DNA tightly immediate after replication =&gt; </div> <div>Cell division cycle 6 (CDC6) joins ORC in G1 phase =&gt; Protein CDT1 brings MCM to the ORC =&gt; Cell cycle dependent kinase (cdk) phosphorylates amino acids in ORC, CDC6, &amp; MCM2-7 =&gt; MCM2 helicase is loaded onto DNA in the S phase =&gt; Replicase is assembled on MCM2-7 helicase&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Replication Elongation</span></div><div><br>Lagging strand is completed differently </div> <div>DNA polymerase is a <span class=cloze>[...]</span> DNA polymerase <br>FEN1 is a <span class=cloze>[...]</span>&nbsp;that digests the primer<br> DNA ligase joins the fragments&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Replication Elongation</span></div><div><br>Lagging strand is completed differently </div> <div>DNA polymerase is a <span class=cloze>strand-displacing</span> DNA polymerase <br>FEN1 is a <span class=cloze>5’ --&gt;3’ exonuclease</span>&nbsp;that digests the primer<br> DNA ligase joins the fragments&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Replication Termination </span></div> <div><br>When 2 replication forks <u>approach</u> each other <b>DNA synthesis stalls</b> <br><br>DNA <span class=cloze>[...]</span>&nbsp;synthesizes DNA across the gap <br>DNA ligase repairs the nick<br><br>Topoisomerase <span class=cloze>[...]</span>&nbsp;the chromosomes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Replication Termination </span></div> <div><br>When 2 replication forks <u>approach</u> each other <b>DNA synthesis stalls</b> <br><br>DNA <span class=cloze>polymerase a-primase</span>&nbsp;synthesizes DNA across the gap <br>DNA ligase repairs the nick<br><br>Topoisomerase <span class=cloze>separates</span>&nbsp;the chromosomes&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div>Gene regulation in single cell organisms (e.g., <span style=""font-style: italic;"">E. Coli</span>) happens mainly in response to environmental changes, such as nutrient availability.&nbsp;<br><br><div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Cis</span><span style=""font-weight: 700;"">- and </span><span style=""font-weight: 700; font-style: italic;"">trans</span><span style=""font-weight: 700;"">-acting factors <br></span><br><u>Trans-acting factors</u><br><span class=cloze>[...]</span> – can function at multiple sites in a genome<br>Examples: DNA binding proteins like transcription factors &amp; some regulatory RNAs&nbsp;</div><div><br><u>Cis-acting elements </u></div> <div>Closely tied to the genome<br> Examples: DNA sequence elements like promoters, terminators, enhancers (for eukaryotes) &amp; binding sites for <span style=""font-style: italic;"">trans</span>-acting factors </div> <div><span style=""font-style: italic;""><br><font color=""#547dfa"">Think “trans is in transit while cis sits”&nbsp;</font></span></div> </div> </div></div></div> </div> </div>"" <div> <div> <div>Gene regulation in single cell organisms (e.g., <span style=""font-style: italic;"">E. Coli</span>) happens mainly in response to environmental changes, such as nutrient availability.&nbsp;<br><br><div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Cis</span><span style=""font-weight: 700;"">- and </span><span style=""font-weight: 700; font-style: italic;"">trans</span><span style=""font-weight: 700;"">-acting factors <br></span><br><u>Trans-acting factors</u><br><span class=cloze>Diffusible</span> – can function at multiple sites in a genome<br>Examples: DNA binding proteins like transcription factors &amp; some regulatory RNAs&nbsp;</div><div><br><u>Cis-acting elements </u></div> <div>Closely tied to the genome<br> Examples: DNA sequence elements like promoters, terminators, enhancers (for eukaryotes) &amp; binding sites for <span style=""font-style: italic;"">trans</span>-acting factors </div> <div><span style=""font-style: italic;""><br><font color=""#547dfa"">Think “trans is in transit while cis sits”&nbsp;</font></span></div> </div> </div></div></div> </div> </div><br> "
" <div> <div> <div>Gene regulation in single cell organisms (e.g., <span style=""font-style: italic;"">E. Coli</span>) happens mainly in response to environmental changes, such as nutrient availability.&nbsp;<br><br><div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Cis</span><span style=""font-weight: 700;"">- and </span><span style=""font-weight: 700; font-style: italic;"">trans</span><span style=""font-weight: 700;"">-acting factors <br></span><br><u>Trans-acting factors</u><br>Diffusible – can function at multiple sites in a genome<br>Examples: DNA binding proteins like transcription factors &amp; some regulatory RNAs&nbsp;</div><div><br><u>Cis-acting elements </u></div> <div>Closely tied to the genome<br> Examples: DNA <span class=cloze>[...]</span> like promoters, terminators, enhancers (for eukaryotes) &amp; binding sites for <span style=""font-style: italic;"">trans</span>-acting factors </div> <div><span style=""font-style: italic;""><br><font color=""#547dfa"">Think “trans is in transit while cis sits”&nbsp;</font></span></div> </div> </div></div></div> </div> </div>"" <div> <div> <div>Gene regulation in single cell organisms (e.g., <span style=""font-style: italic;"">E. Coli</span>) happens mainly in response to environmental changes, such as nutrient availability.&nbsp;<br><br><div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Cis</span><span style=""font-weight: 700;"">- and </span><span style=""font-weight: 700; font-style: italic;"">trans</span><span style=""font-weight: 700;"">-acting factors <br></span><br><u>Trans-acting factors</u><br>Diffusible – can function at multiple sites in a genome<br>Examples: DNA binding proteins like transcription factors &amp; some regulatory RNAs&nbsp;</div><div><br><u>Cis-acting elements </u></div> <div>Closely tied to the genome<br> Examples: DNA <span class=cloze>sequence elements</span> like promoters, terminators, enhancers (for eukaryotes) &amp; binding sites for <span style=""font-style: italic;"">trans</span>-acting factors </div> <div><span style=""font-style: italic;""><br><font color=""#547dfa"">Think “trans is in transit while cis sits”&nbsp;</font></span></div> </div> </div></div></div> </div> </div><br> "
" <div> <div> <div>Gene regulation in single cell organisms (e.g., <span style=""font-style: italic;"">E. Coli</span>) happens mainly in response to environmental changes, such as nutrient availability.&nbsp;<br><br><div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Cis</span><span style=""font-weight: 700;"">- and </span><span style=""font-weight: 700; font-style: italic;"">trans</span><span style=""font-weight: 700;"">-acting factors <br></span><br><u>Trans-acting factors</u><br>Diffusible – can function at multiple sites in a genome<br>Examples: DNA <span class=cloze>[...]</span> like transcription factors &amp; some regulatory RNAs&nbsp;</div><div><br><u>Cis-acting elements </u></div> <div>Closely tied to the genome<br> Examples: DNA sequence elements like promoters, terminators, enhancers (for eukaryotes) &amp; binding sites for <span style=""font-style: italic;"">trans</span>-acting factors </div> <div><span style=""font-style: italic;""><br><font color=""#547dfa"">Think “trans is in transit while cis sits”&nbsp;</font></span></div> </div> </div></div></div> </div> </div>"" <div> <div> <div>Gene regulation in single cell organisms (e.g., <span style=""font-style: italic;"">E. Coli</span>) happens mainly in response to environmental changes, such as nutrient availability.&nbsp;<br><br><div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Cis</span><span style=""font-weight: 700;"">- and </span><span style=""font-weight: 700; font-style: italic;"">trans</span><span style=""font-weight: 700;"">-acting factors <br></span><br><u>Trans-acting factors</u><br>Diffusible – can function at multiple sites in a genome<br>Examples: DNA <span class=cloze>binding proteins</span> like transcription factors &amp; some regulatory RNAs&nbsp;</div><div><br><u>Cis-acting elements </u></div> <div>Closely tied to the genome<br> Examples: DNA sequence elements like promoters, terminators, enhancers (for eukaryotes) &amp; binding sites for <span style=""font-style: italic;"">trans</span>-acting factors </div> <div><span style=""font-style: italic;""><br><font color=""#547dfa"">Think “trans is in transit while cis sits”&nbsp;</font></span></div> </div> </div></div></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Ribonucleic Acid (RNA) </span></div> <div><br>A linear, single-stranded polynucleotide with a ribose-phosphate backbone<br> Read from 5’ --&gt; 3’<br> Contains uracil (U) in place of thymine (T)<br><br><span class=cloze>[...]</span> base pairings can lead to <span class=cloze>[...]</span> structures like RNA folding<br> Uses: <br>(1) genetic material in some viruses <br>(2) for transmission of DNA information <br>(3) for <span class=cloze>[...]</span> acting as a “ribozyme”</div><br> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Ribonucleic Acid (RNA) </span></div> <div><br>A linear, single-stranded polynucleotide with a ribose-phosphate backbone<br> Read from 5’ --&gt; 3’<br> Contains uracil (U) in place of thymine (T)<br><br><span class=cloze>Intramolecular</span> base pairings can lead to <span class=cloze>complex 2 ̊ and 3 ̊</span> structures like RNA folding<br> Uses: <br>(1) genetic material in some viruses <br>(2) for transmission of DNA information <br>(3) for <span class=cloze>catalytic activity</span> acting as a “ribozyme”</div><br> </div> </div><br> "
<div> <div> <div><span class=cloze>[...]</span> = carries genetic information from DNA for encoding an amino acid sequence to form a protein</div> </div> </div> <div> <div> <div><span class=cloze>messenger RNA (mRNA)</span> = carries genetic information from DNA for encoding an amino acid sequence to form a protein</div> </div> </div><br> <div> <div> <div><span class=cloze>[...]</span> = carries an amino acid to the catalytic site of a ribosome. <br><br>Receives the amino acid codon from <span class=cloze>[...]</span>&nbsp;</div> </div> </div> <div> <div> <div><span class=cloze>transfer RNA (tRNA)</span> = carries an amino acid to the catalytic site of a ribosome. <br><br>Receives the amino acid codon from <span class=cloze>mRNA</span>&nbsp;</div> </div> </div><br> <div> <div> <div><span class=cloze>[...]</span> = structural components of the ribosome that catalyze protein synthesis&nbsp;<br></div> </div> </div> <div> <div> <div><span class=cloze>ribosomal RNA (rRNA)</span> = structural components of the ribosome that catalyze protein synthesis&nbsp;<br></div> </div> </div><br> "<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription unit </span></div> <div><br>Codes for a single RNA molecule<br> Transcription starts at a <span class=cloze>[...]</span> and ends at a <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription unit </span></div> <div><br>Codes for a single RNA molecule<br> Transcription starts at a <span class=cloze>promoter</span> and ends at a <span class=cloze>terminator</span>&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">RNA transcript sequence </span></div> <div><span class=cloze>[...]</span> = The DNA strand that serves as a template for the RNA strand <br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">RNA transcript sequence </span></div> <div><span class=cloze>Template strand</span> = The DNA strand that serves as a template for the RNA strand <br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">RNA transcript sequence </span></div> <div><span class=cloze>[...]</span> = The DNA strand that is the complement to the template strand </div> <div><br>Also called the <b>coding strand</b> because it will have the same sequence (except T instead of U) as the RNA being made&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">RNA transcript sequence </span></div> <div><span class=cloze>Non-template strand</span> = The DNA strand that is the complement to the template strand </div> <div><br>Also called the <b>coding strand</b> because it will have the same sequence (except T instead of U) as the RNA being made&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Organization of bacterial genomes </span></div> </div> </div> <div> <div> <div><br><span class=cloze>[...]</span> are transcriptionally linked genes that are regulated together<br><br>Open reading frames (ORFs) = regions of DNA that code for a particular gene (each is one transcription unit) </div> <div>Arranged from 5’ --&gt;3’&nbsp;in a transcription unit<br><br>Using 1 promoter &amp; 1 terminator gives a polycistronic mRNA <br>(Note: prokaryotes <b>don’t </b>have introns, <font color=""#547dfa"">eukaryotes do</font>.)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Organization of bacterial genomes </span></div> </div> </div> <div> <div> <div><br><span class=cloze>Operons</span> are transcriptionally linked genes that are regulated together<br><br>Open reading frames (ORFs) = regions of DNA that code for a particular gene (each is one transcription unit) </div> <div>Arranged from 5’ --&gt;3’&nbsp;in a transcription unit<br><br>Using 1 promoter &amp; 1 terminator gives a polycistronic mRNA <br>(Note: prokaryotes <b>don’t </b>have introns, <font color=""#547dfa"">eukaryotes do</font>.)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Organization of bacterial genomes </span></div> </div> </div> <div> <div> <div><br>Operons are transcriptionally linked genes that are regulated together<br><br><span class=cloze>[...]</span> = regions of DNA that code for a particular gene (each is one transcription unit) </div> <div>Arranged from <span class=cloze>[...]</span>&nbsp;in a transcription unit<br><br>Using 1 promoter &amp; 1 terminator gives a polycistronic mRNA <br>(Note: prokaryotes <b>don’t </b>have introns, <font color=""#547dfa"">eukaryotes do</font>.)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Organization of bacterial genomes </span></div> </div> </div> <div> <div> <div><br>Operons are transcriptionally linked genes that are regulated together<br><br><span class=cloze>Open reading frames (ORFs)</span> = regions of DNA that code for a particular gene (each is one transcription unit) </div> <div>Arranged from <span class=cloze>5’ --&gt;3’</span>&nbsp;in a transcription unit<br><br>Using 1 promoter &amp; 1 terminator gives a polycistronic mRNA <br>(Note: prokaryotes <b>don’t </b>have introns, <font color=""#547dfa"">eukaryotes do</font>.)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A <span class=cloze>[...]</span> is where the RNA polymerase binds to initiate transcription<br>This is a <span class=cloze>[...]</span> element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means <span class=cloze>[...]</span> binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will <span class=cloze>[...]</span> the rate of <span class=cloze>[...]</span> <br><br>The consensus promoter has...</div><div> At -10 region: TATAAT<br> At -35 region: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as CAT sequence (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A <span class=cloze>promoter</span> is where the RNA polymerase binds to initiate transcription<br>This is a <span class=cloze>cis-acting</span> element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means <span class=cloze>stronger</span> binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will <span class=cloze>decrease</span> the rate of <span class=cloze>transcription initiation</span> <br><br>The consensus promoter has...</div><div> At -10 region: TATAAT<br> At -35 region: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as CAT sequence (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A promoter is where the RNA polymerase binds to initiate transcription<br>This is a cis-acting element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means stronger binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will decrease the rate of transcription initiation <br><br>The consensus promoter has...</div><div> At <span class=cloze>[...]</span>: TATAAT<br> At -35 region: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as CAT sequence (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A promoter is where the RNA polymerase binds to initiate transcription<br>This is a cis-acting element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means stronger binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will decrease the rate of transcription initiation <br><br>The consensus promoter has...</div><div> At <span class=cloze>-10 region</span>: TATAAT<br> At -35 region: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as CAT sequence (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A promoter is where the RNA polymerase binds to initiate transcription<br>This is a cis-acting element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means stronger binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will decrease the rate of transcription initiation <br><br>The consensus promoter has...</div><div> At -10 region: TATAAT<br> At <span class=cloze>[...]</span>: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as CAT sequence (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A promoter is where the RNA polymerase binds to initiate transcription<br>This is a cis-acting element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means stronger binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will decrease the rate of transcription initiation <br><br>The consensus promoter has...</div><div> At -10 region: TATAAT<br> At <span class=cloze>-35 region</span>: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as CAT sequence (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A promoter is where the RNA polymerase binds to initiate transcription<br>This is a cis-acting element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means stronger binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will decrease the rate of transcription initiation <br><br>The consensus promoter has...</div><div> At -10 region: TATAAT<br> At -35 region: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as <span class=cloze>[...]</span> (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic promoters </span></div> <div>A promoter is where the RNA polymerase binds to initiate transcription<br>This is a cis-acting element </div> <div>The <b>efficiency</b> of a constitutive promoter depends on how closely it resembles the consensus sequence.</div> <div>Closer resemblance means stronger binding<br><br>&nbsp;A <b>mutation</b> in the promoter that makes it less like the consensus sequence will decrease the rate of transcription initiation <br><br>The consensus promoter has...</div><div> At -10 region: TATAAT<br> At -35 region: TTGACA </div> <div>A spacer between -10 and -35 regions </div> <div><br>Most transcripts start with a <u>purine</u> (+1) – often as <span class=cloze>CAT sequence</span> (know!) <br><br>Constitutive promoters <b>continuously</b> activate transcription for “housekeeping” genes&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>If a mutation occurs in the -10 region that changes A to C, that would <span class=cloze>[...]</span> the rate of transcription because makes the -10 region <span class=cloze>[...]</span>. <br>If weak promoter and mutation happens that makes it more like the normal -10, that <span class=cloze>[...]</span> the rate of transcription.&nbsp;</div> </div> </div></div><div> <div> <div> <div>If a mutation occurs in the -10 region that changes A to C, that would <span class=cloze>reduce</span> the rate of transcription because makes the -10 region <span class=cloze>weaker</span>. <br>If weak promoter and mutation happens that makes it more like the normal -10, that <span class=cloze>increases</span> the rate of transcription.&nbsp;</div> </div> </div></div><br> " <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br><span class=cloze>[...]</span> – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br><span class=cloze>greek o</span> – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div><span class=cloze>[...]</span>– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div><span class=cloze>a2</span>– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div><span class=cloze>[...]</span> – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div><span class=cloze>b &amp; b’</span> – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br><span class=cloze>[...]</span>– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br><span class=cloze>omega w</span>– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from <span class=cloze>[...]</span><br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from <span class=cloze>5’ --&gt; 3’</span><br><br>&nbsp;Transcription is initiated by RNA polymerase holoenzyme, which synthesizes the first 10 nucleotides of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA <span class=cloze>[...]</span>, which synthesizes the <span class=cloze>[...]</span>s of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerase </span></div> </div> <div> <br></div><div> </div> </div> <div> <div> <div>Bacteria, like <span style=""font-style: italic;"">E. coli</span>, have only 1 RNA polymerase<br> Catalyzes transcription from 5’ --&gt; 3’<br><br>&nbsp;Transcription is initiated by RNA <span class=cloze>polymerase holoenzyme</span>, which synthesizes the <span class=cloze>first 10 nucleotide</span>s of the RNA chain <br><br>Subunits of holoenzyme (a2bb’ws)</div> <div>a2– involved in interaction with activators &amp; are essential for enzyme assembly interact<br>with transcription factors </div> <div>b &amp; b’ – catalytic core<br>greek o – recognizes the promoter before binding <br>omega w– provides structural stability </div> <div><br><b>RNA polymerase core enzyme (a2bb’w) caries out the rest of elongation (holoenzyme minus greek o)&nbsp;</b></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-style: italic;"">E. coli </span>has <span class=cloze>[...]</span> subunits (you only need to know s70) </div> <div><br>s70 binds most (<span class=cloze>[...]</span>) of the <span class=cloze>[...]</span> in the <span style=""font-style: italic;"">E. coli </span>genome (for housekeeping)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-style: italic;"">E. coli </span>has <span class=cloze>7 sigma</span> subunits (you only need to know s70) </div> <div><br>s70 binds most (<span class=cloze>80%</span>) of the <span class=cloze>promoters</span> in the <span style=""font-style: italic;"">E. coli </span>genome (for housekeeping)&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>Mechanism for transcription is <b>similar</b> to DNA polymerase<br><br>RNA polymerase requires a DNA template &amp; ribonucleotide triphosphate substrates </div> <div>A primer is <span class=cloze>[...]</span> needed (like it is for DNA polymerase)<br> Does not have <span class=cloze>[...]</span>&nbsp;so the error rate is <span class=cloze>[...]</span> than for DNA </div> <div>1 per 10^4 - 10^5<br>But because all RNAs are eventually degraded or replaced, this isn’t a huge problem&nbsp;</div> </div> </div></div><div> <div> <div> <div>Mechanism for transcription is <b>similar</b> to DNA polymerase<br><br>RNA polymerase requires a DNA template &amp; ribonucleotide triphosphate substrates </div> <div>A primer is <span class=cloze>not</span> needed (like it is for DNA polymerase)<br> Does not have <span class=cloze>proofreading 3’ --&gt; 5’ exonuclease</span>&nbsp;so the error rate is <span class=cloze>higher</span> than for DNA </div> <div>1 per 10^4 - 10^5<br>But because all RNAs are eventually degraded or replaced, this isn’t a huge problem&nbsp;</div> </div> </div></div><br> " <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA polymerase holoenzyme binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the transcription bubble </div> <div>This is now an open complex <br>Holoenzyme initiates RNA synthesis for about the first 10 nucleotides <br>Rate is 1 nucleotides / second</div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to <span class=cloze>[...]</span> nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates <span class=cloze>[...]</span> supercoils <b>behind</b> the transcription bubble and <span class=cloze>[...]</span> supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (RNA and core enzyme) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA polymerase holoenzyme binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the transcription bubble </div> <div>This is now an open complex <br>Holoenzyme initiates RNA synthesis for about the first 10 nucleotides <br>Rate is 1 nucleotides / second</div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to <span class=cloze>50-90</span> nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates <span class=cloze>negative</span> supercoils <b>behind</b> the transcription bubble and <span class=cloze>positive</span> supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (RNA and core enzyme) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA <span class=cloze>[...]</span> binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the transcription bubble </div> <div>This is now an open complex <br>Holoenzyme initiates RNA synthesis for about the first 10 nucleotides <br>Rate is 1 nucleotides / second</div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to 50-90 nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates negative supercoils <b>behind</b> the transcription bubble and positive supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (RNA and core enzyme) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA <span class=cloze>polymerase holoenzyme</span> binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the transcription bubble </div> <div>This is now an open complex <br>Holoenzyme initiates RNA synthesis for about the first 10 nucleotides <br>Rate is 1 nucleotides / second</div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to 50-90 nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates negative supercoils <b>behind</b> the transcription bubble and positive supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (RNA and core enzyme) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA polymerase holoenzyme binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the <span class=cloze>[...]</span> </div> <div>This is now an open complex <br>Holoenzyme initiates <span class=cloze>[...]</span> for about the first 10 nucleotides <br>Rate is <span class=cloze>[...]</span></div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to 50-90 nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates negative supercoils <b>behind</b> the transcription bubble and positive supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (RNA and core enzyme) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA polymerase holoenzyme binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the <span class=cloze>transcription bubble</span> </div> <div>This is now an open complex <br>Holoenzyme initiates <span class=cloze>RNA synthesis</span> for about the first 10 nucleotides <br>Rate is <span class=cloze>1 nucleotides / second</span></div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to 50-90 nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates negative supercoils <b>behind</b> the transcription bubble and positive supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (RNA and core enzyme) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA polymerase holoenzyme binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the transcription bubble </div> <div>This is now an open complex <br>Holoenzyme initiates RNA synthesis for about the first 10 nucleotides <br>Rate is 1 nucleotides / second</div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to 50-90 nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates negative supercoils <b>behind</b> the transcription bubble and positive supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (<span class=cloze>[...]</span>) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-style: italic;""><b>Mechanism of RNA polymerase</b><br><br>(1) Template recognition </span></div> <div>RNA polymerase holoenzyme binds to the promoter<br>Forms the closed complex – DNA is still wound </div> <div><br>(2) <span style=""font-style: italic;"">Initiation<br> </span>A small segment of DNA is unwound (12-15 bp) creating the transcription bubble </div> <div>This is now an open complex <br>Holoenzyme initiates RNA synthesis for about the first 10 nucleotides <br>Rate is 1 nucleotides / second</div> <div><span style=""font-style: italic;""><br>(3) Elongation </span></div> <div>The s factor dissociates to give the core enzyme – allows for promoter clearance<br> The rate accelerates to 50-90 nucleotides / second *Max. speed*<br> Transcription bubble is 12-15 bases<br> The growing strand is temporarily bound to DNA, giving a RNA-DNA hybrid (~ 8 bp) </div> <div>RNA will peel off shortly after it is formed<br> Torsional strain creates negative supercoils <b>behind</b> the transcription bubble and positive supercoils <b>ahead</b> of it – <font color=""#547dfa"">relieved by topoisomerases</font></div> <div><span style=""font-style: italic;""><br>(4) Termination </span></div> <div>Transcription stops &amp; the machinery (<span class=cloze>RNA and core enzyme</span>) dissociates<br>Termination can be either rho-<u style="""">dependent</u> or rho-<u>independent</u>&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Rho-dependent termination </span></div> <div><br>Rho (ρ) is a hexameric protein that binds to RNA chain at a <span style=""font-style: italic;"">rut </span>site<br>&nbsp;<span style=""font-style: italic;"">rut </span>= rho utilization </div> <div><br>Rho is a <span class=cloze>[...]</span> that separates the RNA from the DNA template <span class=cloze>[...]</span> <br>The RNA molecule will be <span class=cloze>[...]</span> when rho (r) reaches the RNA polymerase&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Rho-dependent termination </span></div> <div><br>Rho (ρ) is a hexameric protein that binds to RNA chain at a <span style=""font-style: italic;"">rut </span>site<br>&nbsp;<span style=""font-style: italic;"">rut </span>= rho utilization </div> <div><br>Rho is a <span class=cloze>RNA helicase</span> that separates the RNA from the DNA template <span class=cloze>5’ -&gt; 3’</span> <br>The RNA molecule will be <span class=cloze>released</span> when rho (r) reaches the RNA polymerase&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Rho-independent termination<br><br>Termination signal resides in the nascent RNA chain</span><br> Termination occurs after the <span class=cloze>[...]</span> structure followed by 7 U’s <br>= “Rho-independent terminator”</div><div><br>RNA polymerase pauses at the hairpin which allows the dissociation of the transcript from the </div> <div>template at the weak A•U pairs <br><br>No protein factor needed&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Rho-independent termination<br><br>Termination signal resides in the nascent RNA chain</span><br> Termination occurs after the <span class=cloze>formation of a stable hairpin</span> structure followed by 7 U’s <br>= “Rho-independent terminator”</div><div><br>RNA polymerase pauses at the hairpin which allows the dissociation of the transcript from the </div> <div>template at the weak A•U pairs <br><br>No protein factor needed&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Binding Proteins/ DNA Double Helix </span></div> <div><br>Molecular basis of gene expression comes from the sequence-specific and sequence-independent chemical bonds formed between DNA and DNA binding proteins<br><br>The sugar-phosphate backbone is non-specific – generic protein binding can happen here </div> <div><br>The base pairs each present a unique set of chemical groups in the <span class=cloze>[...]</span> groove<br>CG and AT pairs can be distinguished in the <b>minor</b> groove </div> <div>Can’t tell if CG or GC / AT or TA though&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Binding Proteins/ DNA Double Helix </span></div> <div><br>Molecular basis of gene expression comes from the sequence-specific and sequence-independent chemical bonds formed between DNA and DNA binding proteins<br><br>The sugar-phosphate backbone is non-specific – generic protein binding can happen here </div> <div><br>The base pairs each present a unique set of chemical groups in the <span class=cloze><b>major</b></span> groove<br>CG and AT pairs can be distinguished in the <b>minor</b> groove </div> <div>Can’t tell if CG or GC / AT or TA though&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Binding Proteins/ DNA Double Helix </span></div> <div><br>Molecular basis of gene expression comes from the sequence-specific and sequence-independent chemical bonds formed between DNA and DNA binding proteins<br><br>The sugar-phosphate backbone is non-specific – generic protein binding can happen here </div> <div><br>The base pairs each present a unique set of chemical groups in the <b>major</b> groove<br>CG and AT pairs can be distinguished in the <span class=cloze>[...]</span> groove </div> <div>Can’t tell if CG or GC / AT or TA though&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Binding Proteins/ DNA Double Helix </span></div> <div><br>Molecular basis of gene expression comes from the sequence-specific and sequence-independent chemical bonds formed between DNA and DNA binding proteins<br><br>The sugar-phosphate backbone is non-specific – generic protein binding can happen here </div> <div><br>The base pairs each present a unique set of chemical groups in the <b>major</b> groove<br>CG and AT pairs can be distinguished in the <span class=cloze><b>minor</b></span> groove </div> <div>Can’t tell if CG or GC / AT or TA though&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>The recognition helix&nbsp;is typically an a-helix of DNA binding proteins that fits into the <b>major</b> groove <br>Bonds to base pairs through hydrogen bonding and van der Waals interactions but these don’t stabilize enough – need chemical interactions between the DNA and protein</div><div> Predominant motif in prokaryotes for positioning the recognition helix is helix-turn-helix</div> <div><br>The 2nd helix is the recognition helix<br> This motif is seen in <span class=cloze>[...]</span> domain<br> Can be found in <b>both</b> prokaryotes (mainly) and eukaryotes </div> <div><br>Some DNA binding proteins are <span class=cloze>[...]</span><br> There will be a recognition helix on both subunits<br><span class=cloze>[...]</span> is recognized – read the same sequence on 5’ --&gt; 3’ on both strands <br>Dimers improve <span class=cloze>[...]</span> </div> <div><br>Molecular basis of specific DNA sequence recognition by a DNA binding protein are <b>chemical bonds</b> between the recognition helix amino acids and the DNA base pairs.&nbsp;</div> </div> </div></div><div> <div> <div> <div>The recognition helix&nbsp;is typically an a-helix of DNA binding proteins that fits into the <b>major</b> groove <br>Bonds to base pairs through hydrogen bonding and van der Waals interactions but these don’t stabilize enough – need chemical interactions between the DNA and protein</div><div> Predominant motif in prokaryotes for positioning the recognition helix is helix-turn-helix</div> <div><br>The 2nd helix is the recognition helix<br> This motif is seen in <span class=cloze>lacI DNA binding</span> domain<br> Can be found in <b>both</b> prokaryotes (mainly) and eukaryotes </div> <div><br>Some DNA binding proteins are <span class=cloze>dimeric</span><br> There will be a recognition helix on both subunits<br><span class=cloze>Palindromic sequence</span> is recognized – read the same sequence on 5’ --&gt; 3’ on both strands <br>Dimers improve <span class=cloze>specificity &amp; stability</span> </div> <div><br>Molecular basis of specific DNA sequence recognition by a DNA binding protein are <b>chemical bonds</b> between the recognition helix amino acids and the DNA base pairs.&nbsp;</div> </div> </div></div><br> <div> <div> <div> <div>The <span class=cloze>[...]</span>&nbsp;is typically an a-helix of DNA binding proteins that fits into the <b>major</b> groove <br>Bonds to base pairs through <span class=cloze>[...]</span> and <span class=cloze>[...]</span> interactions but these don’t stabilize enough – need chemical interactions between the DNA and protein</div><div> Predominant motif in prokaryotes for positioning the recognition helix is <span class=cloze>[...]</span></div> <div><br>The 2nd helix is the recognition helix<br> This motif is seen in lacI DNA binding domain<br> Can be found in <b>both</b> prokaryotes (mainly) and eukaryotes </div> <div><br>Some DNA binding proteins are dimeric<br> There will be a recognition helix on both subunits<br>Palindromic sequence is recognized – read the same sequence on 5’ --&gt; 3’ on both strands <br>Dimers improve specificity &amp; stability </div> <div><br>Molecular basis of specific DNA sequence recognition by a DNA binding protein are <b>chemical bonds</b> between the recognition helix amino acids and the DNA base pairs.&nbsp;</div> </div> </div></div><div> <div> <div> <div>The <span class=cloze>recognition helix</span>&nbsp;is typically an a-helix of DNA binding proteins that fits into the <b>major</b> groove <br>Bonds to base pairs through <span class=cloze>hydrogen bonding</span> and <span class=cloze>van der Waals</span> interactions but these don’t stabilize enough – need chemical interactions between the DNA and protein</div><div> Predominant motif in prokaryotes for positioning the recognition helix is <span class=cloze>helix-turn-helix</span></div> <div><br>The 2nd helix is the recognition helix<br> This motif is seen in lacI DNA binding domain<br> Can be found in <b>both</b> prokaryotes (mainly) and eukaryotes </div> <div><br>Some DNA binding proteins are dimeric<br> There will be a recognition helix on both subunits<br>Palindromic sequence is recognized – read the same sequence on 5’ --&gt; 3’ on both strands <br>Dimers improve specificity &amp; stability </div> <div><br>Molecular basis of specific DNA sequence recognition by a DNA binding protein are <b>chemical bonds</b> between the recognition helix amino acids and the DNA base pairs.&nbsp;</div> </div> </div></div><br> "<div> <div> <div> <div><span style=""font-weight: 700;"">Gene regulation </span></div> <div><br>Most of the gene regulation in prokaryotes is due to binding a protein to a site proximal to an inducible promoter. Initiation&nbsp;of transcription is the <b>most important step</b> in gene expression </div> <div><br>An inducible promoter is one that can be either activated or suppressed <br><br><b>Activators</b> and <b>repressors</b> are <span class=cloze>[...]</span><br><br><u>Activator</u> proteins bind a <span class=cloze>[...]</span> response element <span class=cloze>[...]</span> of a promoter </div> <div>Mediate positive gene regulation and <font color=""#547dfa"">recruits</font> RNA polymerase to a weak promoter <br><br><u>Repressors</u> bind an operator either <span class=cloze>[...]</span> of a promoter </div> <div>Can either <font color=""#547dfa"">block</font> RNA polymerase binding at a promoter or prevent RNA polymerase promoter clearage<br> Mediate <span class=cloze>[...]</span> gene regulation&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Gene regulation </span></div> <div><br>Most of the gene regulation in prokaryotes is due to binding a protein to a site proximal to an inducible promoter. Initiation&nbsp;of transcription is the <b>most important step</b> in gene expression </div> <div><br>An inducible promoter is one that can be either activated or suppressed <br><br><b>Activators</b> and <b>repressors</b> are <span class=cloze>transcription factors.</span><br><br><u>Activator</u> proteins bind a <span class=cloze>positive</span> response element <span class=cloze>upstream</span> of a promoter </div> <div>Mediate positive gene regulation and <font color=""#547dfa"">recruits</font> RNA polymerase to a weak promoter <br><br><u>Repressors</u> bind an operator either <span class=cloze>at or downstream</span> of a promoter </div> <div>Can either <font color=""#547dfa"">block</font> RNA polymerase binding at a promoter or prevent RNA polymerase promoter clearage<br> Mediate <span class=cloze>negative</span> gene regulation&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Gene regulation </span></div> <div><br>Most of the gene regulation in prokaryotes is due to binding a protein to a site proximal to an inducible promoter. <span class=cloze>[...]</span>&nbsp;of transcription is the <b>most important step</b> in gene expression </div> <div><br>An <span class=cloze>[...]</span> is one that can be either activated or suppressed <br><br><b>Activators</b> and <b>repressors</b> are transcription factors.<br><br><u>Activator</u> proteins bind a positive response element upstream of a promoter </div> <div>Mediate positive gene regulation and <font color=""#547dfa"">recruits</font> RNA polymerase to a weak promoter <br><br><u>Repressors</u> bind an operator either at or downstream of a promoter </div> <div>Can either <font color=""#547dfa"">block</font> RNA polymerase binding at a promoter or prevent RNA polymerase promoter clearage<br> Mediate negative gene regulation&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Gene regulation </span></div> <div><br>Most of the gene regulation in prokaryotes is due to binding a protein to a site proximal to an inducible promoter. <span class=cloze>Initiation</span>&nbsp;of transcription is the <b>most important step</b> in gene expression </div> <div><br>An <span class=cloze>inducible promoter</span> is one that can be either activated or suppressed <br><br><b>Activators</b> and <b>repressors</b> are transcription factors.<br><br><u>Activator</u> proteins bind a positive response element upstream of a promoter </div> <div>Mediate positive gene regulation and <font color=""#547dfa"">recruits</font> RNA polymerase to a weak promoter <br><br><u>Repressors</u> bind an operator either at or downstream of a promoter </div> <div>Can either <font color=""#547dfa"">block</font> RNA polymerase binding at a promoter or prevent RNA polymerase promoter clearage<br> Mediate negative gene regulation&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div><span class=cloze>[...]</span><span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div><span class=cloze>lacY</span><span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br><span class=cloze>[...]</span><span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br><span class=cloze>lacZ</span><span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as <span class=cloze>[...]</span> molecules&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as <span class=cloze>signaling</span> molecules&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in <span class=cloze>[...]</span> </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in <span class=cloze>prokaryotes</span> </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br>lacA<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br><span class=cloze>[...]</span><span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Lac Operon </span></div> <div>An operon is a single genetic unit containing an operator, a promoter, &amp; 1 or more structural genes <br>Mostly found in prokaryotes </div> <div><br>All 3 genes in the <span style=""font-style: italic;"">lac </span>operon (l<span style=""font-style: italic;"">ac<b>Z</b></span>, <span style=""font-style: italic;"">lac<b>Y</b></span>, &amp; <span style=""font-style: italic;"">lac<b>A</b></span>) are used in lactose metabolism <br>lacZ<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactosidase </div> <div>b-galactosidase catalyzes 2 reactions<br> 1 ̊ reaction lactose --&gt; galactose + glucose <br>2 ̊ reaction lactose --&gt; allolactose </div> <div>lacY<span style=""font-style: italic;"">&nbsp;:</span>&nbsp;lactose permease<br><span class=cloze>lacA</span><span style=""font-style: italic;"">&nbsp;:</span>&nbsp;b-galactoside transacetylase </div> <div><span style=""font-style: italic;""><br>E. coli </span>prefers glucose as its fuels source, so it will be consumed first<br>When glucose is absent, adenylate cyclase produces cAMP <br>cAMP and allolactose act as signaling molecules&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div>When lactose is absent...<br> <span style=""font-style: italic;"">Lac </span>repressor (encoded by <span style=""font-style: italic;"">lacI </span>) binds to the operator and inhibits RNA polymerase from binding </div> <div><br>When lactose is present...<br> Allolactose (or IPTG) binds to the repressor &amp; causes an <span class=cloze>[...]</span> change <br>The repressor can <span class=cloze>[...]</span> to the operator<br> Allows transcription of the operon by RNA polymerase </div> <div><br>When glucose levels are low...<br> cAMP levels will increase &amp; cAMP binds to cAMP receptor protein (CRP)<br> CRP binds to the CRP binding region in the lac promoter, which will recruit RNA polymerase&nbsp;<br></div> </div> </div>"" <div> <div> <div>When lactose is absent...<br> <span style=""font-style: italic;"">Lac </span>repressor (encoded by <span style=""font-style: italic;"">lacI </span>) binds to the operator and inhibits RNA polymerase from binding </div> <div><br>When lactose is present...<br> Allolactose (or IPTG) binds to the repressor &amp; causes an <span class=cloze>allosteric</span> change <br>The repressor can <span class=cloze>no longer bind</span> to the operator<br> Allows transcription of the operon by RNA polymerase </div> <div><br>When glucose levels are low...<br> cAMP levels will increase &amp; cAMP binds to cAMP receptor protein (CRP)<br> CRP binds to the CRP binding region in the lac promoter, which will recruit RNA polymerase&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div>When lactose is absent...<br> <span style=""font-style: italic;"">Lac </span>repressor (encoded by <span style=""font-style: italic;"">lacI </span>) binds to the operator and inhibits RNA polymerase from binding </div> <div><br>When lactose is present...<br> Allolactose (or IPTG) binds to the repressor &amp; causes an allosteric change <br>The repressor can no longer bind to the operator<br> Allows transcription of the operon by RNA polymerase </div> <div><br>When glucose levels are low...<br> cAMP levels will <span class=cloze>[...]</span> &amp; cAMP binds to cAMP receptor protein (CRP)<br> CRP binds to the CRP binding region in the lac promoter, which will recruit RNA polymerase&nbsp;<br></div> </div> </div>"" <div> <div> <div>When lactose is absent...<br> <span style=""font-style: italic;"">Lac </span>repressor (encoded by <span style=""font-style: italic;"">lacI </span>) binds to the operator and inhibits RNA polymerase from binding </div> <div><br>When lactose is present...<br> Allolactose (or IPTG) binds to the repressor &amp; causes an allosteric change <br>The repressor can no longer bind to the operator<br> Allows transcription of the operon by RNA polymerase </div> <div><br>When glucose levels are low...<br> cAMP levels will <span class=cloze>increase</span> &amp; cAMP binds to cAMP receptor protein (CRP)<br> CRP binds to the CRP binding region in the lac promoter, which will recruit RNA polymerase&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div>When lactose is absent...<br> <span style=""font-style: italic;"">Lac </span>repressor (encoded by <span style=""font-style: italic;"">lacI </span>) binds to the operator and <span class=cloze>[...]</span> RNA polymerase from binding </div> <div><br>When lactose is present...<br> Allolactose (or IPTG) binds to the repressor &amp; causes an allosteric change <br>The repressor can no longer bind to the operator<br> Allows transcription of the operon by RNA polymerase </div> <div><br>When glucose levels are low...<br> cAMP levels will increase &amp; cAMP binds to cAMP receptor protein (CRP)<br> CRP binds to the CRP binding region in the lac promoter, which will recruit RNA polymerase&nbsp;<br></div> </div> </div>"" <div> <div> <div>When lactose is absent...<br> <span style=""font-style: italic;"">Lac </span>repressor (encoded by <span style=""font-style: italic;"">lacI </span>) binds to the operator and <span class=cloze>inhibits</span> RNA polymerase from binding </div> <div><br>When lactose is present...<br> Allolactose (or IPTG) binds to the repressor &amp; causes an allosteric change <br>The repressor can no longer bind to the operator<br> Allows transcription of the operon by RNA polymerase </div> <div><br>When glucose levels are low...<br> cAMP levels will increase &amp; cAMP binds to cAMP receptor protein (CRP)<br> CRP binds to the CRP binding region in the lac promoter, which will recruit RNA polymerase&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><b style=""""><u style="""">Negative regulation</u></b><br><br><i>&nbsp;lacI </i>is located <span class=cloze>[...]</span> of the lac operon &amp; encodes the <span style=""font-style: italic;"">lac </span>repressor<br><br>The <span style=""font-style: italic;"">lac </span>repressor does not bind to DNA in the <span class=cloze>[...]</span> of allolactose or IPTG <br><br>The operator site is <b>located at the transcription start site&nbsp;</b></div> </div> </div></div>""<div> <div> <div> <div><b style=""""><u style="""">Negative regulation</u></b><br><br><i>&nbsp;lacI </i>is located <span class=cloze>upstream</span> of the lac operon &amp; encodes the <span style=""font-style: italic;"">lac </span>repressor<br><br>The <span style=""font-style: italic;"">lac </span>repressor does not bind to DNA in the <span class=cloze>presence</span> of allolactose or IPTG <br><br>The operator site is <b>located at the transcription start site&nbsp;</b></div> </div> </div></div><br> "
"<div> <div> <div> <div><u style=""""><b>Positive regulation </b></u></div> <div><br>cAMP receptor protein (CRP) binds to DNA in the presence of cAMP (its inducer) <br>The CRP binding site is <span class=cloze>[...]</span> of the lac promoter&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><u style=""""><b>Positive regulation </b></u></div> <div><br>cAMP receptor protein (CRP) binds to DNA in the presence of cAMP (its inducer) <br>The CRP binding site is <span class=cloze>upstream</span> of the lac promoter&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>The <span class=cloze>[...]</span>&nbsp;is a tetramer – a dimer or dimers/homotetramer<br><b> All</b> 4 subunits have the helix-turn-helix motif bonding at <b>2 palindromic operator sites&nbsp;</b></div> </div> </div></div>"<div> <div> <div> <div>The <span class=cloze><span style=""font-style: italic;"">lac </span>repressor</span>&nbsp;is a tetramer – a dimer or dimers/homotetramer<br><b> All</b> 4 subunits have the helix-turn-helix motif bonding at <b>2 palindromic operator sites&nbsp;</b></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-style: italic;"">lac </span>operon has 3 operator sites: O1, O2, &amp; O3<br> <br>O1 has the <span class=cloze>[...]</span> affinity binding site<br><br>The <span style=""font-style: italic;"">lac </span>repressor will bind to O1 and either O2 or O3<br> If O1 is destroyed in a mutation, regulation of the <span style=""font-style: italic;"">lac </span>promoter will be lost&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-style: italic;"">lac </span>operon has 3 operator sites: O1, O2, &amp; O3<br> <br>O1 has the <span class=cloze>highest</span> affinity binding site<br><br>The <span style=""font-style: italic;"">lac </span>repressor will bind to O1 and either O2 or O3<br> If O1 is destroyed in a mutation, regulation of the <span style=""font-style: italic;"">lac </span>promoter will be lost&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>CRP binds as a <span class=cloze>[...]</span> &amp; is a helix-turn-helix dimeric protein<br> Transcription activator and inducer cAMP present <span class=cloze>[...]</span> glucose<br> CRP when bound with cAMP will recruit RNA polymerase to the <span class=cloze>[...]</span></div> </div> </div></div>"<div> <div> <div> <div>CRP binds as a <span class=cloze>dimer</span> &amp; is a helix-turn-helix dimeric protein<br> Transcription activator and inducer cAMP present <span class=cloze>only at low</span> glucose<br> CRP when bound with cAMP will recruit RNA polymerase to the <span class=cloze><span style=""font-style: italic;"">lac </span>promoter&nbsp;</span></div> </div> </div></div><br> "
<div> <div> <div>EUKARYOTIC <br><br>Each cell type is able to express a <u>unique set of genes from the same DNA sequence</u> in the genome </div> <div>Gene regulation is what defines the properties of each cell <br>genes are the unit of heredity <br>Contains DNA to encode a functional RNA or protein along with the regulatory elements controlling expression</div> <div>Each gene has a <span class=cloze>[...]</span> on the genome&nbsp;<br></div> </div> </div> <div> <div> <div>EUKARYOTIC <br><br>Each cell type is able to express a <u>unique set of genes from the same DNA sequence</u> in the genome </div> <div>Gene regulation is what defines the properties of each cell <br>genes are the unit of heredity <br>Contains DNA to encode a functional RNA or protein along with the regulatory elements controlling expression</div> <div>Each gene has a <span class=cloze>specific location</span> on the genome&nbsp;<br></div> </div> </div><br> " <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Chromatin </span></div> <div>The <u>chromosomal material</u> within the cell <br>Chromatin consists of fibers containing DNA and bound proteins <br>Most abundant proteins are <span class=cloze>[...]</span>&nbsp;</div><div>Must be condensed (packaged) in order to fit into the cell nucleus <br>Naked DNA =&gt; 10 nm fiber =&gt; 30 nm fiber =&gt; loops =&gt; rosettes =&gt; coils =&gt; chromatids&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Chromatin </span></div> <div>The <u>chromosomal material</u> within the cell <br>Chromatin consists of fibers containing DNA and bound proteins <br>Most abundant proteins are <span class=cloze>histones</span>&nbsp;</div><div>Must be condensed (packaged) in order to fit into the cell nucleus <br>Naked DNA =&gt; 10 nm fiber =&gt; 30 nm fiber =&gt; loops =&gt; rosettes =&gt; coils =&gt; chromatids&nbsp;</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">2 Forms of Chromatin </span></div> <div><u>Heterochromatin </u></div> <div>Stains <span class=cloze>[...]</span> because more compact (closed), condensed chromatin <br>DNA contains fully inactivated (silenced) genes &amp; many types of repetitive DNA (centromeres &amp; telomeres)&nbsp;</div><div>Transcriptionally <span class=cloze>[...]</span></div><div><br><u>Euchromatin </u></div> <div>Stains lighter because less compact, more open chromatin <br>Transcriptionally active<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">2 Forms of Chromatin </span></div> <div><u>Heterochromatin </u></div> <div>Stains <span class=cloze>darker</span> because more compact (closed), condensed chromatin <br>DNA contains fully inactivated (silenced) genes &amp; many types of repetitive DNA (centromeres &amp; telomeres)&nbsp;</div><div>Transcriptionally <span class=cloze>inactive&nbsp;</span></div><div><br><u>Euchromatin </u></div> <div>Stains lighter because less compact, more open chromatin <br>Transcriptionally active<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">2 Forms of Chromatin </span></div> <div><u>Heterochromatin </u></div> <div>Stains darker because more compact (closed), condensed chromatin <br>DNA contains fully inactivated (silenced) genes &amp; many types of repetitive DNA (centromeres &amp; telomeres)&nbsp;</div><div>Transcriptionally inactive&nbsp;</div><div><br><u>Euchromatin </u></div> <div>Stains <span class=cloze>[...]</span> because less compact, more open chromatin <br>Transcriptionally <span class=cloze>[...]</span><br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">2 Forms of Chromatin </span></div> <div><u>Heterochromatin </u></div> <div>Stains darker because more compact (closed), condensed chromatin <br>DNA contains fully inactivated (silenced) genes &amp; many types of repetitive DNA (centromeres &amp; telomeres)&nbsp;</div><div>Transcriptionally inactive&nbsp;</div><div><br><u>Euchromatin </u></div> <div>Stains <span class=cloze>lighter</span> because less compact, more open chromatin <br>Transcriptionally <span class=cloze>active</span><br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Histones </span></div> <div>The basic unit of chromatin is the <span class=cloze>[...]</span>. Often referred to as “beads on a string”. <br>This is the <span class=cloze>[...]</span> fiber</div><div><br>&nbsp;Each nucleosome has a repeating unit of <span class=cloze>[...]</span> base pairs. <br>147 bp of DNA wraps around each histone core twice</div> <div>50 bp linker DNA connecting nucleosomes<br> The contact between the DNA and the histone are sequence-independent </div> <div><br>Electrostatic interactions between the <span class=cloze>[...]</span> charged histone and the <span class=cloze>[...]</span> charged DNA backbone. </div> <div>The histone core has 2 copies each of H2A, H2B, H3, and H4 (for a <b>total of 8 histones</b> per bead)<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Histones </span></div> <div>The basic unit of chromatin is the <span class=cloze>nucleosomes</span>. Often referred to as “beads on a string”. <br>This is the <span class=cloze>10 nm</span> fiber</div><div><br>&nbsp;Each nucleosome has a repeating unit of <span class=cloze>200</span> base pairs. <br>147 bp of DNA wraps around each histone core twice</div> <div>50 bp linker DNA connecting nucleosomes<br> The contact between the DNA and the histone are sequence-independent </div> <div><br>Electrostatic interactions between the <span class=cloze>positive</span> charged histone and the <span class=cloze>negative</span> charged DNA backbone. </div> <div>The histone core has 2 copies each of H2A, H2B, H3, and H4 (for a <b>total of 8 histones</b> per bead)<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;""><u>Eukaryotic Gene Expression </u></span></div> <div>Chromatin’s structure is a result of epigenetic markers and <span class=cloze>[...]</span> transcription factors <br><br><b>Epigenetics:</b> covalent modifications of the chromatin that don’t affect the DNA sequences.<br>Condensed chromatin is closed &amp; is accessible only by pioneering transcriptional factors&nbsp;</div><div>Open chromatin, like the 10nm fiber, allows for <span class=cloze>[...]</span> transcription </div> <div><br>Transcription factors (activators) bind to specific DNA sites to aid transcription&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;""><u>Eukaryotic Gene Expression </u></span></div> <div>Chromatin’s structure is a result of epigenetic markers and <span class=cloze>trans-acting</span> transcription factors <br><br><b>Epigenetics:</b> covalent modifications of the chromatin that don’t affect the DNA sequences.<br>Condensed chromatin is closed &amp; is accessible only by pioneering transcriptional factors&nbsp;</div><div>Open chromatin, like the 10nm fiber, allows for <span class=cloze>active</span> transcription </div> <div><br>Transcription factors (activators) bind to specific DNA sites to aid transcription&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div> <div> <div> <div><b>Histone Tail Modification<br></b><br>The <span class=cloze>[...]</span> allow for interactions between nucleosomes<br><font color=""#547dfa""> Include the N termini of H3 &amp; H4 and the N and C termini of H2A &amp; H2B</font><br><u> Modifications of the histone tails allow for the change between closed (heterochromatin) &amp; open chromatin </u></div> <div><br>Hypermethylation is associated with <span class=cloze>[...]</span> chromatin (with some exceptions) <br><br>Hyperacetylation is associated with <span class=cloze>[...]</span> chromatin<br><br>Done by the histone modifying enzymes HAT, HDAC, and HMT </div> <div><br>The <span class=cloze>[...]</span> is a hypothesis that histone tail posttranslational modifications regulate the transcription of genetic information encoded in DNA (associated with closed or open chromatin). <br>A histone may have <span class=cloze>[...]</span> modification.&nbsp;</div> </div> </div></div> </div> </div>"" <div> <div> <div> <div> <div> <div><b>Histone Tail Modification<br></b><br>The <span class=cloze>histone tails</span> allow for interactions between nucleosomes<br><font color=""#547dfa""> Include the N termini of H3 &amp; H4 and the N and C termini of H2A &amp; H2B</font><br><u> Modifications of the histone tails allow for the change between closed (heterochromatin) &amp; open chromatin </u></div> <div><br>Hypermethylation is associated with <span class=cloze>closed</span> chromatin (with some exceptions) <br><br>Hyperacetylation is associated with <span class=cloze>open</span> chromatin<br><br>Done by the histone modifying enzymes HAT, HDAC, and HMT </div> <div><br>The <span class=cloze>histone code</span> is a hypothesis that histone tail posttranslational modifications regulate the transcription of genetic information encoded in DNA (associated with closed or open chromatin). <br>A histone may have <span class=cloze>more than one</span> modification.&nbsp;</div> </div> </div></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Histone Acetylation </span></div> <div>Histone acetyltransferase (HAT) – recruited by transcription factor to acetylate surrounding histones </div> <div><br>Acetylated histones open chromatin structure by weakening the electrostatic interactions between the nucleosomes &amp; DNA by neutralizing the positive lysine </div> </div> </div> <div> <div> <div><br>Acetylation <b>favors</b> chromatin remodeling complex recruitment&nbsp;<br><br>Lysine --&gt; Acetlysine<br><br><br><div> <div> <div> <div><span class=cloze>[...]</span> – removes acetyl groups from histone tails <br>Reverses the work of HAT – acetylation is easily reversed&nbsp;<br><br>Acetylsyine --&gt; Lysine</div> </div> </div></div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Histone Acetylation </span></div> <div>Histone acetyltransferase (HAT) – recruited by transcription factor to acetylate surrounding histones </div> <div><br>Acetylated histones open chromatin structure by weakening the electrostatic interactions between the nucleosomes &amp; DNA by neutralizing the positive lysine </div> </div> </div> <div> <div> <div><br>Acetylation <b>favors</b> chromatin remodeling complex recruitment&nbsp;<br><br>Lysine --&gt; Acetlysine<br><br><br><div> <div> <div> <div><span class=cloze>Histone deacetylase (HDAC)</span> – removes acetyl groups from histone tails <br>Reverses the work of HAT – acetylation is easily reversed&nbsp;<br><br>Acetylsyine --&gt; Lysine</div> </div> </div></div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Histone Acetylation </span></div> <div><span class=cloze>[...]</span> – recruited by transcription factor to acetylate surrounding histones </div> <div><br>Acetylated histones open chromatin structure by weakening the <span class=cloze>[...]</span> interactions between the nucleosomes &amp; DNA by neutralizing the <span class=cloze>[...]</span> lysine </div> </div> </div> <div> <div> <div><br>Acetylation <b>favors</b> chromatin remodeling complex recruitment&nbsp;<br><br>Lysine --&gt; Acetlysine<br><br><br><div> <div> <div> <div>Histone deacetylase (HDAC) – removes acetyl groups from histone tails <br>Reverses the work of HAT – acetylation is easily reversed&nbsp;<br><br>Acetylsyine --&gt; Lysine</div> </div> </div></div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Histone Acetylation </span></div> <div><span class=cloze>Histone acetyltransferase (HAT)</span> – recruited by transcription factor to acetylate surrounding histones </div> <div><br>Acetylated histones open chromatin structure by weakening the <span class=cloze>electrostatic</span> interactions between the nucleosomes &amp; DNA by neutralizing the <span class=cloze>positive</span> lysine </div> </div> </div> <div> <div> <div><br>Acetylation <b>favors</b> chromatin remodeling complex recruitment&nbsp;<br><br>Lysine --&gt; Acetlysine<br><br><br><div> <div> <div> <div>Histone deacetylase (HDAC) – removes acetyl groups from histone tails <br>Reverses the work of HAT – acetylation is easily reversed&nbsp;<br><br>Acetylsyine --&gt; Lysine</div> </div> </div></div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Chromatin Remodeling Complexes </span></div> <div><br>The combined actions of HATs and chromatin remodeling complexes (like <span class=cloze>[...]</span>) lead to the opening of chromatin </div> <div><br>Chromatin remodeling complexes alter the chromatin structure by <span class=cloze>[...]</span> from nucleosomes, repositioning nucleosomes, &amp; evicting nucleosomes </div> <div><br>SWI/SNF <b>binds to acetylated histones</b> or is recruited to the gene with a pioneering transcription factors. (brings on HATs)</div> <div><br>HATs bind near promoters, SWI/SNF complex binds to histone or is recruited to a gene to interact with transcriptions factors&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Chromatin Remodeling Complexes </span></div> <div><br>The combined actions of HATs and chromatin remodeling complexes (like <span class=cloze>SWI/SNF</span>) lead to the opening of chromatin </div> <div><br>Chromatin remodeling complexes alter the chromatin structure by <span class=cloze>unwrapping DNA</span> from nucleosomes, repositioning nucleosomes, &amp; evicting nucleosomes </div> <div><br>SWI/SNF <b>binds to acetylated histones</b> or is recruited to the gene with a pioneering transcription factors. (brings on HATs)</div> <div><br>HATs bind near promoters, SWI/SNF complex binds to histone or is recruited to a gene to interact with transcriptions factors&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Methylation </span></div> <div><span class=cloze>[...]</span> – methylates Lys &amp; Arg on histone tails<br><br>The promoter can be silenced by the <span class=cloze>[...]</span> of a CpG island near the promoter </div> <div>A cluster of CG sequences near the promoter proximal region is called CpG islands <br><br><span class=cloze>[...]</span> methylates the C in a CpG sequence.<br>methylates CPG islands.&nbsp;</div> <div><br>The added methyl group will protrude into the <span class=cloze>[...]</span> groove </div> <div>Methylation blocks some transcription factors is blocked by DNA methylation, some required it, and some others are indifferent to it&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Methylation </span></div> <div><span class=cloze>Histone methyltransferase (HMT)</span> – methylates Lys &amp; Arg on histone tails<br><br>The promoter can be silenced by the <span class=cloze>hypermethylation</span> of a CpG island near the promoter </div> <div>A cluster of CG sequences near the promoter proximal region is called CpG islands <br><br><span class=cloze>DNA methyltransferase (DNMT)</span> methylates the C in a CpG sequence.<br>methylates CPG islands.&nbsp;</div> <div><br>The added methyl group will protrude into the <span class=cloze>major</span> groove </div> <div>Methylation blocks some transcription factors is blocked by DNA methylation, some required it, and some others are indifferent to it&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Cis-acting Elements in Mammalian Genes </span></div> <div><br>Transcriptional activators will bind to <span class=cloze>[...]</span> in promoter proximal region &amp; enhancers </div> <div><br>The transcription start site is <span class=cloze>[...]</span> the promoter region (-200 to +100)<br><br>Promoter proximal elements –Typically located <span class=cloze>[...]</span> of the promoter (-40 to -200) </div> </div> </div> <div> <div> <div>Discreet sequence of ~8-25 bp<br><br>Enhancers – longer sequences (~200-500 bp) that are distal to the promoter </div> <div>Contain several different response elements <br>The human genome has ~400,000 enhancers&nbsp;<br><br>The TATA signals the promoter is coming</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Cis-acting Elements in Mammalian Genes </span></div> <div><br>Transcriptional activators will bind to <span class=cloze>cis-acting elements</span> in promoter proximal region &amp; enhancers </div> <div><br>The transcription start site is <span class=cloze>within</span> the promoter region (-200 to +100)<br><br>Promoter proximal elements –Typically located <span class=cloze>upstream</span> of the promoter (-40 to -200) </div> </div> </div> <div> <div> <div>Discreet sequence of ~8-25 bp<br><br>Enhancers – longer sequences (~200-500 bp) that are distal to the promoter </div> <div>Contain several different response elements <br>The human genome has ~400,000 enhancers&nbsp;<br><br>The TATA signals the promoter is coming</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Binding Domain Motifs </span></div> <div>Transcription factors will have a <font color=""#547dfa""><b>DNA binding domain</b> </font>(DBD) and an <b><font color=""#547dfa"">activation domain</font></b> (AD) </div> <div><br>The DNA binding domain (DBD) recognizes a specific DNA sequence and positions it in the <span class=cloze>[...]</span> groove to form a bond with the adjacent base pairs </div> <div><br>About <font color=""#547dfa""><i>80%</i> of eukaryotic</font> DNA binding proteins use one of several different DNA binding domain (DBD) motifs.&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">DNA Binding Domain Motifs </span></div> <div>Transcription factors will have a <font color=""#547dfa""><b>DNA binding domain</b> </font>(DBD) and an <b><font color=""#547dfa"">activation domain</font></b> (AD) </div> <div><br>The DNA binding domain (DBD) recognizes a specific DNA sequence and positions it in the <span class=cloze>major</span> groove to form a bond with the adjacent base pairs </div> <div><br>About <font color=""#547dfa""><i>80%</i> of eukaryotic</font> DNA binding proteins use one of several different DNA binding domain (DBD) motifs.&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Homeodomain </span></div> <div><br>Important in <b><font color=""#547dfa"">embryonic development</font></b> (found in homeotic proteins) <br>Motif looks similar to the helix-turn-helix, but it is not the same <br><br>Contains 3 a-helices&nbsp;– the 3rd is the recognition helix<br><br><span class=cloze>[...]</span> :&nbsp; The DNA sequence that encodes for the homeodomain&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Homeodomain </span></div> <div><br>Important in <b><font color=""#547dfa"">embryonic development</font></b> (found in homeotic proteins) <br>Motif looks similar to the helix-turn-helix, but it is not the same <br><br>Contains 3 a-helices&nbsp;– the 3rd is the recognition helix<br><br><span class=cloze>homeobox</span> :&nbsp; The DNA sequence that encodes for the homeodomain&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Homeodomain </span></div> <div><br>Important in <b><font color=""#547dfa"">embryonic development</font></b> (found in homeotic proteins) <br>Motif looks similar to the helix-turn-helix, but it is not the same <br><br>Contains <span class=cloze>[...]</span>&nbsp;– the 3rd is the <span class=cloze>[...]</span> helix<br><br>homeobox :&nbsp; The DNA sequence that encodes for the homeodomain&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Homeodomain </span></div> <div><br>Important in <b><font color=""#547dfa"">embryonic development</font></b> (found in homeotic proteins) <br>Motif looks similar to the helix-turn-helix, but it is not the same <br><br>Contains <span class=cloze>3 a-helices</span>&nbsp;– the 3rd is the <span class=cloze>recognition</span> helix<br><br>homeobox :&nbsp; The DNA sequence that encodes for the homeodomain&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Zinc Finger </span></div> <div><br>Major structural features:</div> <div>2 <span class=cloze>[...]</span>&nbsp;and 1 <span class=cloze>[...]</span><br> Zn is coordinated with 2 <span class=cloze>[...]</span> and 2 <span class=cloze>[...]</span><br>The conserved Phe/Tyr and Leu form a “strut” – positions the recognition helix </div> <div><br>The recognition helix is the AA that interact with the base pairs <br><br>Can be used to recognize many different DNA sequences </div> <div>Change the AA, change the recognized sequence </div> <div>AA’s on the recognition helix will be facing the major groove <br><br>It is normal to have multiple zinc fingers </div> <div>Each Zn finger can recognize a different sequence of bases.&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Zinc Finger </span></div> <div><br>Major structural features:</div> <div>2 <span class=cloze>b-strands</span>&nbsp;and 1 <span class=cloze>a-helix</span><br> Zn is coordinated with 2 <span class=cloze>Cys</span> and 2 <span class=cloze>His</span><br>The conserved Phe/Tyr and Leu form a “strut” – positions the recognition helix </div> <div><br>The recognition helix is the AA that interact with the base pairs <br><br>Can be used to recognize many different DNA sequences </div> <div>Change the AA, change the recognized sequence </div> <div>AA’s on the recognition helix will be facing the major groove <br><br>It is normal to have multiple zinc fingers </div> <div>Each Zn finger can recognize a different sequence of bases.&nbsp;</div> </div> </div></div><br> "
"<img src=""paste-dd5c819d6fc6d6224cb85e7c48b4fad28c85539c.jpg""><br><br><span class=cloze>[...]</span>""<img src=""paste-dd5c819d6fc6d6224cb85e7c48b4fad28c85539c.jpg""><br><br><span class=cloze>zinc finger</span><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Zinc Fingers in Nuclear Receptors </span></div> <div><br>Nuclear receptor TFs bind as DNA as dimers (homodimer or heterodimer) <br><br>Each subunit has 1 recognition helix - <span class=cloze>[...]</span> helices<br><br>&nbsp;2 zinc fingers on each subunit, but only the <span class=cloze>[...]</span>&nbsp;is recognition helix </div> <div><br>Other is structural – helps position recognition helix </div> <div><span class=cloze>[...]</span> coordinate the zinc on each finger<br><br>The <b>recognition helix</b> is perpendicular to the base pairs so it is here <u>for the structure</u>, NOT for the <i>reading</i> specific DNA sequence.<br><br></div> <div>Examples: Glucocorticoid receptor (GR) &amp; estrogen receptor (ER)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">Zinc Fingers in Nuclear Receptors </span></div> <div><br>Nuclear receptor TFs bind as DNA as dimers (homodimer or heterodimer) <br><br>Each subunit has 1 recognition helix - <span class=cloze>2 total recognition</span> helices<br><br>&nbsp;2 zinc fingers on each subunit, but only the <span class=cloze>1st</span>&nbsp;is recognition helix </div> <div><br>Other is structural – helps position recognition helix </div> <div><span class=cloze>4 Cys</span> coordinate the zinc on each finger<br><br>The <b>recognition helix</b> is perpendicular to the base pairs so it is here <u>for the structure</u>, NOT for the <i>reading</i> specific DNA sequence.<br><br></div> <div>Examples: Glucocorticoid receptor (GR) &amp; estrogen receptor (ER)&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span class=cloze>[...]</span><br></div> <div><br><img src=""paste-68b1967f7b167c61babba872b26bd4cd68e85526.jpg""><br><br>Series of Leu along an&nbsp;a-helix (every <span class=cloze>[...]</span>)&nbsp;<br><br>Protein-protein interaction of the leucines creates a dimer&nbsp;<br><br>Recognition helix is an <span class=cloze>[...]</span> of the Leu containing helix&nbsp;<br></div> </div> </div>"" <div> <div> <div><span class=cloze>Leucine Zipper</span><br></div> <div><br><img src=""paste-68b1967f7b167c61babba872b26bd4cd68e85526.jpg""><br><br>Series of Leu along an&nbsp;a-helix (every <span class=cloze>7th&nbsp;position</span>)&nbsp;<br><br>Protein-protein interaction of the leucines creates a dimer&nbsp;<br><br>Recognition helix is an <span class=cloze>extension</span> of the Leu containing helix&nbsp;<br></div> </div> </div><br> "
"<img src=""paste-28d2be5e0e282a4c187397375815a4278d5a706d.jpg""><br><br><div> <div> <div> <span class=cloze>[...]</span><br><br>2 α-helices linked by α loop of variable length&nbsp;<div><br><span class=cloze>[...]</span> domain<br><br>Recognition helix is an extension of the α -helices <br><br>Different from helix-turn-helix&nbsp;</div> </div> </div></div>""<img src=""paste-28d2be5e0e282a4c187397375815a4278d5a706d.jpg""><br><br><div> <div> <div> <span class=cloze>&nbsp;<span style=""font-style: italic; font-weight: 700;"">Helix-loop-helix</span></span><br><br>2 α-helices linked by α loop of variable length&nbsp;<div><br><span class=cloze>Dimerization</span> domain<br><br>Recognition helix is an extension of the α -helices <br><br>Different from helix-turn-helix&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><span class=cloze>[...]</span> =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><span class=cloze>siRNA = small interfering RNA</span> =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br><span class=cloze>[...]</span> = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br><span class=cloze>rRNA = ribosomal RNA</span> = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br><span class=cloze>[...]</span> = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br><span class=cloze>snRNA = small nuclear RNA</span> = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br><span class=cloze>[...]</span> = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br><span class=cloze>mRNA = messenger RNA</span> = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br><span class=cloze>[...]</span> = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br><span class=cloze>tRNA = transfer RNA</span> = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br>miRNA = microRNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br><span class=cloze>[...]</span> =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Vocab: RNAs in Eukaryotic Cells </span></div> <div><br>mRNA = messenger RNA = carries genetic information from DNA for encoding an amino acid sequence to form a protein. The 1 ̊ transcript is processed to generate mature mRNA which is used by the ribosome </div> <div><br>tRNA = transfer RNA = carries an amino acid to the catalytic site of a ribosome. Receives the amino acid codon from mRNA </div> <div><br>rRNA = ribosomal RNA = structural components of the ribosome that catalyze protein synthesis </div> <div><br>snRNA = small nuclear RNA = components of the spliceosome </div> <div>The spliceosome is the enzyme that catalyzes the removal of introns during RNA processing </div> <div><br><span class=cloze>miRNA = microRNA</span> =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br>siRNA = small interfering RNA =acts on mature RNA in the cytoplasm to block translation &amp; mediate turnover </div> <div><br><b>snoRNA</b> = small nucleolar RNA = guide posttranslational base modifications in tRNAs, rRNAs, &amp; snRNAs </div> <div><b>lncRNA</b> = long non-coding RNA = RNA molecules with more than 200 bp that don’t encode a protein but may affect gene expression&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Gene Organization </span></div> <div>Eukaryotic genes stand alone in a single transcription unit and have their own promoter(s) and terminator(s) </div> <div><br>Unlike in bacteria, the primary transcript produced is not a fully functional mRNA <br>Eukaryotes will require additional processing. </div> <div><br>The transcription unit will include both introns and exons since RNA polymerase is not able to distinguish between them. </div> <div><br><span class=cloze>[...]</span> code sequences that will be in mature RNA (~100-200 bp) <br><span class=cloze>[...]</span> will be <b>removed</b> during RNA processing to give mRNA&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Gene Organization </span></div> <div>Eukaryotic genes stand alone in a single transcription unit and have their own promoter(s) and terminator(s) </div> <div><br>Unlike in bacteria, the primary transcript produced is not a fully functional mRNA <br>Eukaryotes will require additional processing. </div> <div><br>The transcription unit will include both introns and exons since RNA polymerase is not able to distinguish between them. </div> <div><br><span class=cloze>exons</span> code sequences that will be in mature RNA (~100-200 bp) <br><span class=cloze>introns</span> will be <b>removed</b> during RNA processing to give mRNA&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div>Simple eukaryotes and prokaryotes have little, if any, intron sequences <br><br>Introns are only present in 3% of yeast </div> <div><br>The <b>primary transcripts in mammals</b> typically have <span class=cloze>[...]</span> intron sequences than exon sequences. </div> <div><br><i>92%</i> of human genes have an intron, with an average of 8 introns per gene </div> </div> </div> <div> <div> <div><br>The number and length of the introns and exons will vary in different genes <br><br>Introns are, on average, <span class=cloze>[...]</span> than exons<br><br>&nbsp;Average exon length is about 170bp<br><br>Intron lengths range widely </div> <div>Most are from 100 – 5,000 bp <br>10% are over 11,000 bp&nbsp;</div> </div> </div></div><div> <div> <div> <div>Simple eukaryotes and prokaryotes have little, if any, intron sequences <br><br>Introns are only present in 3% of yeast </div> <div><br>The <b>primary transcripts in mammals</b> typically have <span class=cloze>more</span> intron sequences than exon sequences. </div> <div><br><i>92%</i> of human genes have an intron, with an average of 8 introns per gene </div> </div> </div> <div> <div> <div><br>The number and length of the introns and exons will vary in different genes <br><br>Introns are, on average, <span class=cloze>longer</span> than exons<br><br>&nbsp;Average exon length is about 170bp<br><br>Intron lengths range widely </div> <div>Most are from 100 – 5,000 bp <br>10% are over 11,000 bp&nbsp;</div> </div> </div></div><br> " <div> <div> <div><span style=""font-weight: 700;"">Organization of Mammalian Genomes </span></div> <div>Humans have <span class=cloze>[...]</span> copies each of ~29,000 genes <br>~ 21,000 genes encode proteins </div> <div>1.5% of human DNA is exons <br><br>Introns make up 25.9% <br></div> <div>The other things are not junk. <br>They have regulatory rolls or function as non-coding RNA&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Organization of Mammalian Genomes </span></div> <div>Humans have <span class=cloze>2</span> copies each of ~29,000 genes <br>~ 21,000 genes encode proteins </div> <div>1.5% of human DNA is exons <br><br>Introns make up 25.9% <br></div> <div>The other things are not junk. <br>They have regulatory rolls or function as non-coding RNA&nbsp;</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Organization of Mammalian Genomes </span></div> <div>Humans have 2 copies each of ~29,000 genes <br>~ 21,000 genes encode proteins </div> <div>1.5% of human DNA is exons <br><br>Introns make up 25.9% <br></div> <div>The other things are not junk. <br>They have regulatory rolls or function as <span class=cloze>[...]</span> RNA&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Organization of Mammalian Genomes </span></div> <div>Humans have 2 copies each of ~29,000 genes <br>~ 21,000 genes encode proteins </div> <div>1.5% of human DNA is exons <br><br>Introns make up 25.9% <br></div> <div>The other things are not junk. <br>They have regulatory rolls or function as <span class=cloze>non-coding</span> RNA&nbsp;</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerases in Eukaryotic Cells </span></div> <div><br>RNA Polymerase is an enzyme that <b>produces</b> RNA<br> There are 3 types of RNA polymerases in eukaryotic cells<br><br><u>RNA polymerase I</u> synthesizes ribosomal <span class=cloze>[...]</span><br><u> RNA polymerase II</u> synthesizes <span class=cloze>[...]</span> and some small RNAs </div> <div>Large, multi-subunit enzyme </div> <div>Catalytic mechanism is the same as in prokaryotes except cannot recognize the promoter (no <span class=cloze>[...]</span> subunit), so it must be recruited to the promoter by activators (transcription factors) </div> <div><br>Major subunits of prokaryotic RNA polymerase <span class=cloze>[...]</span> enzyme are preserved <br>Subunits 1 and 2 are homologous to b and b’<br> 2 a subunit homologs (but not identical like in bacteria)<br> One <b>omega</b> subunit </div> <div>There are additional subunits, but you aren’t responsible for knowing them<br>C-terminal domain (CTD) on subunit 1 (b’-like) is unique to RNA pol II </div> <div><br>RNA pol III synthesizes <span class=cloze>[...]</span> and some small RNAs&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Polymerases in Eukaryotic Cells </span></div> <div><br>RNA Polymerase is an enzyme that <b>produces</b> RNA<br> There are 3 types of RNA polymerases in eukaryotic cells<br><br><u>RNA polymerase I</u> synthesizes ribosomal <span class=cloze>rRNA</span><br><u> RNA polymerase II</u> synthesizes <span class=cloze>mRNA</span> and some small RNAs </div> <div>Large, multi-subunit enzyme </div> <div>Catalytic mechanism is the same as in prokaryotes except cannot recognize the promoter (no <span class=cloze>sigma</span> subunit), so it must be recruited to the promoter by activators (transcription factors) </div> <div><br>Major subunits of prokaryotic RNA polymerase <span class=cloze>core</span> enzyme are preserved <br>Subunits 1 and 2 are homologous to b and b’<br> 2 a subunit homologs (but not identical like in bacteria)<br> One <b>omega</b> subunit </div> <div>There are additional subunits, but you aren’t responsible for knowing them<br>C-terminal domain (CTD) on subunit 1 (b’-like) is unique to RNA pol II </div> <div><br>RNA pol III synthesizes <span class=cloze>tRNA</span> and some small RNAs&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Gene Expression </span></div> <div><br>For a gene to be activated, there must be both open euchromatin &amp; trans-acting factors to recruit RNA polymerase II </div> <div><br><img src=""paste-2b6c87bdf35119ef99e65ee4ebce9702e05455cd.jpg"">&nbsp;<br><br>Most regulation is <span class=cloze>[...]</span> because&nbsp;activators are required for RNA pol II binding to promoters</div> <div><br>Let’s recall how we get to the point of open chromatin...<br> Condensed chromatin is closed &amp; is accessible only by pioneering transcriptional factors<br>Open chromatin, like the 10nm fiber, allows for active transcription <br>Modifications of the histone tails allow for the change between closed &amp; open chromatin </div> <div><font color=""#547dfa"">Hypermethylation</font> is associated with <font color=""#547dfa"">closed</font> chromatin (with some exceptions) </div> <div><font color=""#f879ba"">Hyperacetylation</font> is associated with <font color=""#f879ba"">open</font> chromatin (along with chromatin remodeling complexes)&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Gene Expression </span></div> <div><br>For a gene to be activated, there must be both open euchromatin &amp; trans-acting factors to recruit RNA polymerase II </div> <div><br><img src=""paste-2b6c87bdf35119ef99e65ee4ebce9702e05455cd.jpg"">&nbsp;<br><br>Most regulation is <span class=cloze>positive</span> because&nbsp;activators are required for RNA pol II binding to promoters</div> <div><br>Let’s recall how we get to the point of open chromatin...<br> Condensed chromatin is closed &amp; is accessible only by pioneering transcriptional factors<br>Open chromatin, like the 10nm fiber, allows for active transcription <br>Modifications of the histone tails allow for the change between closed &amp; open chromatin </div> <div><font color=""#547dfa"">Hypermethylation</font> is associated with <font color=""#547dfa"">closed</font> chromatin (with some exceptions) </div> <div><font color=""#f879ba"">Hyperacetylation</font> is associated with <font color=""#f879ba"">open</font> chromatin (along with chromatin remodeling complexes)&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Activation of Transcription </span></div> <div><br>In order for transcription to begin we must... <br>Have <span class=cloze>[...]</span> chromatin </div> <div>Bind transcription factors (activator) to promoter <span class=cloze>[...]</span> site or to enhancers </div> <div>Recruit <span class=cloze>[...]</span> proteins (transcription factors, HAT, chromatin remodeling complex) and a <i>mediator </i></div> <div>Form a large protein complex (<u>the transcription pre-initiation complex</u>) on the <span class=cloze>[...]</span> elements (can occur before or after mediator is recruited) </div> <div><br>Activators have a sequence-specific DNA binding domain (DBD) and activation domain (AD) that will interact with other proteins (coactivators, HAT, chromatin remodeling complexes, mediators, preinitiation complex)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Activation of Transcription </span></div> <div><br>In order for transcription to begin we must... <br>Have <span class=cloze>open</span> chromatin </div> <div>Bind transcription factors (activator) to promoter <span class=cloze>proximal</span> site or to enhancers </div> <div>Recruit <span class=cloze>coactivator</span> proteins (transcription factors, HAT, chromatin remodeling complex) and a <i>mediator </i></div> <div>Form a large protein complex (<u>the transcription pre-initiation complex</u>) on the <span class=cloze>cis-acting</span> elements (can occur before or after mediator is recruited) </div> <div><br>Activators have a sequence-specific DNA binding domain (DBD) and activation domain (AD) that will interact with other proteins (coactivators, HAT, chromatin remodeling complexes, mediators, preinitiation complex)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Gene Activation by Glucocorticoid Receptor (GR) </span></div> <div>GR is a nuclear zinc finger TF that acts as an activator <br>Binds as a <span class=cloze>[...]</span> with 2 zinc fingers per subunit </div> <div>GR is involved in increasing <span class=cloze>[...]</span> &amp; metabolic rate while <span class=cloze>[...]</span> immune responses </div> <div><br>GR binds to a hormone response element (HRE) in the cytosol and moves into the nucleus <br>The HRE may be located on either the promoter proximal sites or enhancers </div> <div><br>GR <span class=cloze>[...]</span> a coactivator to form the GR-coactivator complex which recruits a coactivator with HAT activity, a mediator (MED1), and the preinitiation complex (including RNA pol II) </div> <div><br><b>Cortisol</b> (hydrocortisone) <u>binds</u> GR&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Gene Activation by Glucocorticoid Receptor (GR) </span></div> <div>GR is a nuclear zinc finger TF that acts as an activator <br>Binds as a <span class=cloze>dimer</span> with 2 zinc fingers per subunit </div> <div>GR is involved in increasing <span class=cloze>gluconeogenesis</span> &amp; metabolic rate while <span class=cloze>suppressing</span> immune responses </div> <div><br>GR binds to a hormone response element (HRE) in the cytosol and moves into the nucleus <br>The HRE may be located on either the promoter proximal sites or enhancers </div> <div><br>GR <span class=cloze>recruits</span> a coactivator to form the GR-coactivator complex which recruits a coactivator with HAT activity, a mediator (MED1), and the preinitiation complex (including RNA pol II) </div> <div><br><b>Cortisol</b> (hydrocortisone) <u>binds</u> GR&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Enhancers </span></div> <div><br>Clusters of recognition sequences (each for a different TF) within an enhancer <br><br>Enhancers are found <span class=cloze>[...]</span> from the transcription start site</div> <div><br>Specific example:<br>The human interferon b gene enhancer has TF binding sites for IRF-3 and IRF- 7 (helix-turn helix motif), Jun/ATF2 (leucine-zipper motif), and p50/p65 (aka NFKB) </div> <div><br>HMG (<span class=cloze>[...]</span>) proteins <u>bends</u> the DNA to allow for interaction between mediator and PIC – <b><font color=""#5374fb"">important for enhancer region functionality </font></b></div> <div><br>Human <span class=cloze>[...]</span><span style=""font-style: italic;"">&nbsp;</span>gene has 3 promoters for development-dependent regulation<br>Defects are associated with aniridia (absense of iris)</div> <div><br>Expressed during early and late development </div> <div><br>Transcription factors complements bind to enhancers to activate specific transcription in different tissues </div> <div><br>Multiple enhancers <span class=cloze>[...]</span> from <u>promoters</u> in eye, brain, spine and pancreas cells. </div> <div><br>The gene also contains 3 different possible promoters, meaning 3 different genes could be made depending on which promoter transcription begins at. Which <b>promoter is used</b> in each tissue <b>is regulated by the enhancers</b>.&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Enhancers </span></div> <div><br>Clusters of recognition sequences (each for a different TF) within an enhancer <br><br>Enhancers are found <span class=cloze>further away</span> from the transcription start site</div> <div><br>Specific example:<br>The human interferon b gene enhancer has TF binding sites for IRF-3 and IRF- 7 (helix-turn helix motif), Jun/ATF2 (leucine-zipper motif), and p50/p65 (aka NFKB) </div> <div><br>HMG (<span class=cloze>high mobility group</span>) proteins <u>bends</u> the DNA to allow for interaction between mediator and PIC – <b><font color=""#5374fb"">important for enhancer region functionality </font></b></div> <div><br>Human <span class=cloze>Pax6</span><span style=""font-style: italic;"">&nbsp;</span>gene has 3 promoters for development-dependent regulation<br>Defects are associated with aniridia (absense of iris)</div> <div><br>Expressed during early and late development </div> <div><br>Transcription factors complements bind to enhancers to activate specific transcription in different tissues </div> <div><br>Multiple enhancers <span class=cloze>control expression</span> from <u>promoters</u> in eye, brain, spine and pancreas cells. </div> <div><br>The gene also contains 3 different possible promoters, meaning 3 different genes could be made depending on which promoter transcription begins at. Which <b>promoter is used</b> in each tissue <b>is regulated by the enhancers</b>.&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Mediator </span></div> <div>Allow for communication between <span class=cloze>[...]</span> and the <span class=cloze>[...]</span> via protein-protein interactions. <br>Large protein complex with ≤ 26 subunits</div> <div>Opportunities to interact with many different activators bound to enhancers and the promoter proximal region of a gene. </div> <div><br>Specific Example: GR interacts with MED1 subunit<br><br>&nbsp;Makes protein-protein contacts with general transcription factors of PIC<br>While most activators work through mediator, some interact with PIC directly&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Mediator </span></div> <div>Allow for communication between <span class=cloze>activators</span> and the <span class=cloze>preinitiation complex</span> via protein-protein interactions. <br>Large protein complex with ≤ 26 subunits</div> <div>Opportunities to interact with many different activators bound to enhancers and the promoter proximal region of a gene. </div> <div><br>Specific Example: GR interacts with MED1 subunit<br><br>&nbsp;Makes protein-protein contacts with general transcription factors of PIC<br>While most activators work through mediator, some interact with PIC directly&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Transcription Preinitiation Complex </span></div> <div>The preinitiation complex (PIC) is needed for <span class=cloze>[...]</span> to start<br> Can be <span class=cloze>[...]</span> on to the <b>promoter</b> either before or after <b>mediator</b> is recruited <br>The PIC is formed in a <span class=cloze>[...]</span> sequence </div> <div>There are several general transcription factors that make up the preinitiation complex Same TFs are used for all genes that are transcribed using RNA <span class=cloze>[...]</span> </div> <div><br>(1) Identify the promotor<br> TFIID is the one that finds and binds to the promoter <br>Made up of <u>TATA binding protein (TBP)</u> and 13 TBP associated factors (TAFs) <br>TBP is the first to find and bind to the TATA box</div> <div>Binds in the minor groove of DNA and bends the DNA </div> <div>TATA boxes are only present in a minority of promoters (10-12%) <br>TAFs can look for an another sequence element if the TATA box is not present </div> <div>Examples: initiation sequence (at +1), DRE (at +40) </div> <div>There is not one single consensus sequence like in bacteria <br><br>(2) <u>TFIIA</u> may or may not join the complex </div> <div><br>(3) <u>TFIIB</u> binds DNA to to TBP and recruits RNA pol II<br><br>(4) <u>TFIIF/RNA pol II</u> binds to TFIIB and TFIID to join the complex <br><br>(5) <u>TFIIE</u> joins the complex followed by TFIIH </div> <div><br>TFIIH is a DNA helicase &amp; protein kinase that initiates transcription by phosphorylating RNA pol II CTD (stimulated by interactions with mediator) *creates transcription bubble*<br></div> <div>RNA pol II CTD will not be phosphorylated until after the PIC is formed and mediator is recruited </div> <div>Phosphorylation of CTD is the signal to start transcription – allows for promoter clearance and transcription elongation </div> <div><br>Transcription will occur at a rate of 200-700 nucleotides per second<br> Specific example: The Dystrophin gene DMD has over 2 million base pairs, with 79 exons </div> <div>Takes <b>16 hours</b> to transcribe<br>Located on the <span class=cloze>[...]</span> <br>Mutations cause <b><font color=""#5374fb"">muscular dystrophy</font></b>&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Transcription Preinitiation Complex </span></div> <div>The preinitiation complex (PIC) is needed for <span class=cloze>transcription</span> to start<br> Can be <span class=cloze>loaded</span> on to the <b>promoter</b> either before or after <b>mediator</b> is recruited <br>The PIC is formed in a <span class=cloze>specific</span> sequence </div> <div>There are several general transcription factors that make up the preinitiation complex Same TFs are used for all genes that are transcribed using RNA <span class=cloze>pol II</span> </div> <div><br>(1) Identify the promotor<br> TFIID is the one that finds and binds to the promoter <br>Made up of <u>TATA binding protein (TBP)</u> and 13 TBP associated factors (TAFs) <br>TBP is the first to find and bind to the TATA box</div> <div>Binds in the minor groove of DNA and bends the DNA </div> <div>TATA boxes are only present in a minority of promoters (10-12%) <br>TAFs can look for an another sequence element if the TATA box is not present </div> <div>Examples: initiation sequence (at +1), DRE (at +40) </div> <div>There is not one single consensus sequence like in bacteria <br><br>(2) <u>TFIIA</u> may or may not join the complex </div> <div><br>(3) <u>TFIIB</u> binds DNA to to TBP and recruits RNA pol II<br><br>(4) <u>TFIIF/RNA pol II</u> binds to TFIIB and TFIID to join the complex <br><br>(5) <u>TFIIE</u> joins the complex followed by TFIIH </div> <div><br>TFIIH is a DNA helicase &amp; protein kinase that initiates transcription by phosphorylating RNA pol II CTD (stimulated by interactions with mediator) *creates transcription bubble*<br></div> <div>RNA pol II CTD will not be phosphorylated until after the PIC is formed and mediator is recruited </div> <div>Phosphorylation of CTD is the signal to start transcription – allows for promoter clearance and transcription elongation </div> <div><br>Transcription will occur at a rate of 200-700 nucleotides per second<br> Specific example: The Dystrophin gene DMD has over 2 million base pairs, with 79 exons </div> <div>Takes <b>16 hours</b> to transcribe<br>Located on the <span class=cloze>X-chromosome</span> <br>Mutations cause <b><font color=""#5374fb"">muscular dystrophy</font></b>&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Transcription Preinitiation Complex </span></div> <div>The preinitiation complex (PIC) is needed for transcription to start<br> Can be loaded on to the <b>promoter</b> either before or after <b>mediator</b> is recruited <br>The PIC is formed in a specific sequence </div> <div>There are several general transcription factors that make up the preinitiation complex Same TFs are used for all genes that are transcribed using RNA pol II </div> <div><br>(1) Identify the promotor<br> <span class=cloze>[...]</span> is the one that finds and binds to the promoter <br>Made up of <u>TATA binding protein (TBP)</u> and 13 TBP associated factors (TAFs) <br>TBP is the first to find and bind to the TATA box</div> <div>Binds in the <span class=cloze>[...]</span> groove of DNA and bends the DNA </div> <div>TATA boxes are only present in a minority of promoters (10-12%) <br>TAFs can look for an another sequence element if the TATA box is not present </div> <div>Examples: initiation sequence (at +1), DRE (at +40) </div> <div>There is not one single consensus sequence like in bacteria <br><br>(2) <u>TFIIA</u> may or may not join the complex </div> <div><br>(3) <u>TFIIB</u> binds DNA to to TBP and recruits RNA pol II<br><br>(4) <u>TFIIF/RNA pol II</u> binds to TFIIB and TFIID to join the complex <br><br>(5) <u>TFIIE</u> joins the complex followed by TFIIH </div> <div><br>TFIIH is a DNA helicase &amp; protein kinase that initiates transcription by phosphorylating RNA pol II CTD (stimulated by interactions with mediator) *creates transcription bubble*<br></div> <div>RNA pol II CTD will not be phosphorylated until after the PIC is formed and mediator is recruited </div> <div><span class=cloze>[...]</span> of CTD is the signal to start transcription – allows for promoter clearance and transcription elongation </div> <div><br>Transcription will occur at a rate of 200-700 nucleotides per second<br> Specific example: The Dystrophin gene DMD has over 2 million base pairs, with 79 exons </div> <div>Takes <b>16 hours</b> to transcribe<br>Located on the X-chromosome <br>Mutations cause <b><font color=""#5374fb"">muscular dystrophy</font></b>&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Transcription Preinitiation Complex </span></div> <div>The preinitiation complex (PIC) is needed for transcription to start<br> Can be loaded on to the <b>promoter</b> either before or after <b>mediator</b> is recruited <br>The PIC is formed in a specific sequence </div> <div>There are several general transcription factors that make up the preinitiation complex Same TFs are used for all genes that are transcribed using RNA pol II </div> <div><br>(1) Identify the promotor<br> <span class=cloze>TFIID</span> is the one that finds and binds to the promoter <br>Made up of <u>TATA binding protein (TBP)</u> and 13 TBP associated factors (TAFs) <br>TBP is the first to find and bind to the TATA box</div> <div>Binds in the <span class=cloze>minor</span> groove of DNA and bends the DNA </div> <div>TATA boxes are only present in a minority of promoters (10-12%) <br>TAFs can look for an another sequence element if the TATA box is not present </div> <div>Examples: initiation sequence (at +1), DRE (at +40) </div> <div>There is not one single consensus sequence like in bacteria <br><br>(2) <u>TFIIA</u> may or may not join the complex </div> <div><br>(3) <u>TFIIB</u> binds DNA to to TBP and recruits RNA pol II<br><br>(4) <u>TFIIF/RNA pol II</u> binds to TFIIB and TFIID to join the complex <br><br>(5) <u>TFIIE</u> joins the complex followed by TFIIH </div> <div><br>TFIIH is a DNA helicase &amp; protein kinase that initiates transcription by phosphorylating RNA pol II CTD (stimulated by interactions with mediator) *creates transcription bubble*<br></div> <div>RNA pol II CTD will not be phosphorylated until after the PIC is formed and mediator is recruited </div> <div><span class=cloze>Phosphorylation</span> of CTD is the signal to start transcription – allows for promoter clearance and transcription elongation </div> <div><br>Transcription will occur at a rate of 200-700 nucleotides per second<br> Specific example: The Dystrophin gene DMD has over 2 million base pairs, with 79 exons </div> <div>Takes <b>16 hours</b> to transcribe<br>Located on the X-chromosome <br>Mutations cause <b><font color=""#5374fb"">muscular dystrophy</font></b>&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">HO </span><span style=""font-weight: 700;"">Gene Activation in Yeast </span></div> </div> </div> <div> <div> <ol> <li> <div>1) &nbsp;Condensed chromatin is accessed by pioneering transcription factor <span class=cloze>[...]</span>, activator binds to an <span class=cloze>[...]</span> enhancer </div> </li> <li> <div>2) &nbsp;Recruitment of chromatin remodeling complex SWI/SNF to expose histone tails </div> </li> <li> <div>3) &nbsp;GCN5 complex (HAT) acetylates histones to continue the chromatin opening </div> </li> <li> <div>4) &nbsp;SBF activator binds at promoter proximal regulatory region </div> </li> <li> <div>5) &nbsp;SBF recruitment of mediator </div> </li> <li> <div>6) &nbsp;Preinitiation complex assembly (including RNA pol II) </div> </li> <li> <div>7) &nbsp;The CTD is phosphorylated and transcription begins&nbsp;</div> </li> </ol> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">HO </span><span style=""font-weight: 700;"">Gene Activation in Yeast </span></div> </div> </div> <div> <div> <ol> <li> <div>1) &nbsp;Condensed chromatin is accessed by pioneering transcription factor <span class=cloze>SWI5</span>, activator binds to an <span class=cloze>upstream</span> enhancer </div> </li> <li> <div>2) &nbsp;Recruitment of chromatin remodeling complex SWI/SNF to expose histone tails </div> </li> <li> <div>3) &nbsp;GCN5 complex (HAT) acetylates histones to continue the chromatin opening </div> </li> <li> <div>4) &nbsp;SBF activator binds at promoter proximal regulatory region </div> </li> <li> <div>5) &nbsp;SBF recruitment of mediator </div> </li> <li> <div>6) &nbsp;Preinitiation complex assembly (including RNA pol II) </div> </li> <li> <div>7) &nbsp;The CTD is phosphorylated and transcription begins&nbsp;</div> </li> </ol> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Combinatorial Control </span></div> <div>Gene regulation depends on the cis-acting <span class=cloze>[...]</span> being occupied by <span class=cloze>[...]</span> that can function as either activators or repressors </div> <div><br>All cells have the same genetic material to work with but what is actually expressed will vary across cell types. A stimulus to one cell may have no effect on another. </div> <div><br>There are 29,000 genes in humans but only 2-3,000 transcription factors. </div> <div>Regulatory regions with similar functions often <span class=cloze>[...]</span> cis-acting elements but each gene has a unique combination </div> <div><br>Eukaryotic genes normally have at least 6 regulatory sites, and many have dozen or more&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Combinatorial Control </span></div> <div>Gene regulation depends on the cis-acting <span class=cloze>elements</span> being occupied by <span class=cloze>trans-acting factors</span> that can function as either activators or repressors </div> <div><br>All cells have the same genetic material to work with but what is actually expressed will vary across cell types. A stimulus to one cell may have no effect on another. </div> <div><br>There are 29,000 genes in humans but only 2-3,000 transcription factors. </div> <div>Regulatory regions with similar functions often <span class=cloze>share</span> cis-acting elements but each gene has a unique combination </div> <div><br>Eukaryotic genes normally have at least 6 regulatory sites, and many have dozen or more&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Changes in Kitl Expression </span></div> <div>Looking for genome difference between individuals with light hair vs dark hair </div> <div><br>Single nucleotide polymorphism (SNP) at -335 kbp of human kit ligand (KITLG) where some blondes will have a G in place of A <br>Not a mutation – normal expression</div> <div><br>SNP is more commonly seen in Northern Europeans (Iceland and Netherlands) and rarely seen in Africans and Asians </div> <div><br>Most likely located at an <span class=cloze>[...]</span> site of the KITLG </div> <div><br>In mice a broken chromosome mutation at SIpan upstream of Kitl<br>No mutation, dark coat </div> <div>Heterozygous mutation, lighter coat<br>Homozygous mutation, white coat </div> <div>There is a consensus sequence around SNP site for activator LEF <br>A --&gt; G SNP <span class=cloze>[...]</span> LEF binding to an enhancer&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Changes in Kitl Expression </span></div> <div>Looking for genome difference between individuals with light hair vs dark hair </div> <div><br>Single nucleotide polymorphism (SNP) at -335 kbp of human kit ligand (KITLG) where some blondes will have a G in place of A <br>Not a mutation – normal expression</div> <div><br>SNP is more commonly seen in Northern Europeans (Iceland and Netherlands) and rarely seen in Africans and Asians </div> <div><br>Most likely located at an <span class=cloze>enhancer</span> site of the KITLG </div> <div><br>In mice a broken chromosome mutation at SIpan upstream of Kitl<br>No mutation, dark coat </div> <div>Heterozygous mutation, lighter coat<br>Homozygous mutation, white coat </div> <div>There is a consensus sequence around SNP site for activator LEF <br>A --&gt; G SNP <span class=cloze>inhibits</span> LEF binding to an enhancer&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Negative Regulation in Eukaryotes </span></div> <div>Gene expression is largely based on activators (<span class=cloze>[...]</span>), but repressors also play a role </div> <div><br>Ways that <u>repressors inhibit transcription</u>:<br> Displacing an activator by <b>binding to cis-acting elements</b><br> Preventing interaction between the activator and the mediator – <span class=cloze>[...]</span> action&nbsp; &nbsp;<u>Altering the assembly of the preinitiation complex</u><br> Repression domain (RD) recruits and binds HDAC </div> <div>Repressors have DBDs that bind to <span class=cloze>[...]</span> regulatory elements<br><br>Specific example: H4K16ac </div> <div>HDAC targets H4K16ac </div> <div>Deacetylation of H4K16ac gives Lys a positive charge, which favors the conversion of the <span class=cloze>[...]</span> nm fiber to the <span class=cloze>[...]</span> nm fiber </div> <div>Allows for electrostatic interactions between histone 4 and histones H2A and H2B on adjacent nucleosomes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Negative Regulation in Eukaryotes </span></div> <div>Gene expression is largely based on activators (<span class=cloze>positive regulation</span>), but repressors also play a role </div> <div><br>Ways that <u>repressors inhibit transcription</u>:<br> Displacing an activator by <b>binding to cis-acting elements</b><br> Preventing interaction between the activator and the mediator – <span class=cloze>corepressor</span> action&nbsp; &nbsp;<u>Altering the assembly of the preinitiation complex</u><br> Repression domain (RD) recruits and binds HDAC </div> <div>Repressors have DBDs that bind to <span class=cloze>negative</span> regulatory elements<br><br>Specific example: H4K16ac </div> <div>HDAC targets H4K16ac </div> <div>Deacetylation of H4K16ac gives Lys a positive charge, which favors the conversion of the <span class=cloze>10</span> nm fiber to the <span class=cloze>30</span> nm fiber </div> <div>Allows for electrostatic interactions between histone 4 and histones H2A and H2B on adjacent nucleosomes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Gene Silencing in Heterochromatin </span></div> <div><span class=cloze>[...]</span> of chromatin can permanently <span class=cloze>[...]</span> genes<br> The compact heterochromatin form does <span class=cloze>[...]</span> for gene transcription </div> <div>Condensation to heterochromatin depends on HMTs, DNMTs, &amp; chromatin associated proteins <br><br><u>Specific example:</u> HMT = histone H3K9 methyltransferase </div> <div>Methylates H3K9 --&gt; H3K9me3 *methylated 3 times*<br>Methylation of lysine stabilizes the charge and interaction between DNA, histones, and </div> <div>nucleosomes <br>H3K9me3 gives a docking site for heterochromatin protein (HP1) on histone tail <br>HP1 protein-protein interactions compact the chromatin&nbsp;</div><div>HP1 recruits more HMT, which recruits more HP1... to create more heterochromatin&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Gene Silencing in Heterochromatin </span></div> <div><span class=cloze>Condensation</span> of chromatin can permanently <span class=cloze>silence</span> genes<br> The compact heterochromatin form does <span class=cloze>not allow</span> for gene transcription </div> <div>Condensation to heterochromatin depends on HMTs, DNMTs, &amp; chromatin associated proteins <br><br><u>Specific example:</u> HMT = histone H3K9 methyltransferase </div> <div>Methylates H3K9 --&gt; H3K9me3 *methylated 3 times*<br>Methylation of lysine stabilizes the charge and interaction between DNA, histones, and </div> <div>nucleosomes <br>H3K9me3 gives a docking site for heterochromatin protein (HP1) on histone tail <br>HP1 protein-protein interactions compact the chromatin&nbsp;</div><div>HP1 recruits more HMT, which recruits more HP1... to create more heterochromatin&nbsp;</div> </div> </div></div><br> "
<div> <div> <div> <div><b>Gene Expression Regulation</b><br><br>In prokaryotes, the primary transcript is ready to <span class=cloze>[...]</span> proteins </div> </div> </div> <div> <div> <div><br>In eukaryotes, the primary transcript is just an RNA copy of the DNA coding strand and is not yet ready to encode proteins.&nbsp;</div> </div> </div></div><div> <div> <div> <div><b>Gene Expression Regulation</b><br><br>In prokaryotes, the primary transcript is ready to <span class=cloze>encode</span> proteins </div> </div> </div> <div> <div> <div><br>In eukaryotes, the primary transcript is just an RNA copy of the DNA coding strand and is not yet ready to encode proteins.&nbsp;</div> </div> </div></div><br> <div> <div> <div> <div><b>Gene Expression Regulation</b><br><br>In prokaryotes, the primary transcript is ready to encode proteins </div> </div> </div> <div> <div> <div><br>In eukaryotes, the primary transcript is just an <span class=cloze>[...]</span> of the DNA coding strand and is not <span class=cloze>[...]</span> to encode proteins.&nbsp;</div> </div> </div></div><div> <div> <div> <div><b>Gene Expression Regulation</b><br><br>In prokaryotes, the primary transcript is ready to encode proteins </div> </div> </div> <div> <div> <div><br>In eukaryotes, the primary transcript is just an <span class=cloze>RNA copy</span> of the DNA coding strand and is not <span class=cloze>yet ready</span> to encode proteins.&nbsp;</div> </div> </div></div><br> "<img src=""paste-0c0fba65f51e9b77c4639fb7a89cdf6e654c6cd0.jpg"">"
" <div> <div> <div><span style=""font-weight: 700;"">Maturation of Eukaryotic mRNA </span></div> <div>The RNA primary transcript must undergo RNA processing before it is translation-ready mRNA <br>The <font color=""#5374fb"">primary transcript</font> will contain <span style=""font-style: italic;"">both </span><font color=""#5374fb"">introns &amp; exons</font> because RNA polymerase II cannot </div> <div>distinguish between them </div> <div><br>Processing occurs in the <span class=cloze>[...]</span>&nbsp; *transcription*<br>The mature mRNA is exported to the <span class=cloze>[...]</span> after processing *translated by ribosomes*<br>Transcription &amp; translation are <b>segregated</b> in eukaryotes<br></div> <div><br>During processing the RNA will have a 5’ and a 3’ untranslated region (<span class=cloze>[...]</span>) along with a 5’ <span class=cloze>[...]</span> &amp; 3’ poly-A <span class=cloze>[...]</span> added to the ends of the coding sequence </div> <div><br>Both UTRs and the poly-A tail are not translated into the protein </div> <div><br>The coding sequence / <b>open reading frame (ORF)</b> is the region between the UTRs that <span class=cloze>[...]</span> into the protein </div> <div><br>A specific sequence can be seen in short transcripts: <br>(1) Transcription 5’ capping<br> (2) Cleavage at poly A site<br> (3) Polyadenylation </div> <div>(4) Splicing<br> For larger transcripts (over 8,000 – 10,000 bp) the order is not fixed </div> <div>Splicing might occur before the 5’ capping&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Maturation of Eukaryotic mRNA </span></div> <div>The RNA primary transcript must undergo RNA processing before it is translation-ready mRNA <br>The <font color=""#5374fb"">primary transcript</font> will contain <span style=""font-style: italic;"">both </span><font color=""#5374fb"">introns &amp; exons</font> because RNA polymerase II cannot </div> <div>distinguish between them </div> <div><br>Processing occurs in the <span class=cloze>nucleus</span>&nbsp; *transcription*<br>The mature mRNA is exported to the <span class=cloze>cytoplasm</span> after processing *translated by ribosomes*<br>Transcription &amp; translation are <b>segregated</b> in eukaryotes<br></div> <div><br>During processing the RNA will have a 5’ and a 3’ untranslated region (<span class=cloze>UTR</span>) along with a 5’ <span class=cloze>cap</span> &amp; 3’ poly-A <span class=cloze>tail</span> added to the ends of the coding sequence </div> <div><br>Both UTRs and the poly-A tail are not translated into the protein </div> <div><br>The coding sequence / <b>open reading frame (ORF)</b> is the region between the UTRs that <span class=cloze>will be translated</span> into the protein </div> <div><br>A specific sequence can be seen in short transcripts: <br>(1) Transcription 5’ capping<br> (2) Cleavage at poly A site<br> (3) Polyadenylation </div> <div>(4) Splicing<br> For larger transcripts (over 8,000 – 10,000 bp) the order is not fixed </div> <div>Splicing might occur before the 5’ capping&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription Factory </span></div> <div>Within the nucleus of mammalian cells, transcription and translation both occur at <br>approximately 5000-10000 discrete sites (factory) </div> <div><br>Each transcription factory has 6-8 RNA pol II<br> Same <span class=cloze>[...]</span> is transcribed by the group of RNA pol II </div> <div><br><span class=cloze>[...]</span> occurs at transcription factories as well <br>These two processes are linked by <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription Factory </span></div> <div>Within the nucleus of mammalian cells, transcription and translation both occur at <br>approximately 5000-10000 discrete sites (factory) </div> <div><br>Each transcription factory has 6-8 RNA pol II<br> Same <span class=cloze>gene</span> is transcribed by the group of RNA pol II </div> <div><br><span class=cloze>RNA processing</span> occurs at transcription factories as well <br>These two processes are linked by <span class=cloze>the CTD</span>&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">CTD of RNA Polymerase II </span></div> <div><span class=cloze>[...]</span> = C-terminal domain<br> CTD has a repeating YSPTSPS sequence </div> <div><b>27 repeats</b> in yeast vs <b>52 repeats</b> in humans </div> <div><br>The <span class=cloze>[...]</span> residues in the repeat sequence will be phosphorylated by protein kinases </div> <div><br>Phosphorylation is needed for promoter escape, to act as a docking site for capping enzyme, cap binding complex (CBC), cleavage/termination complexes, and RNA splicing factors&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">CTD of RNA Polymerase II </span></div> <div><span class=cloze>CTD</span> = C-terminal domain<br> CTD has a repeating YSPTSPS sequence </div> <div><b>27 repeats</b> in yeast vs <b>52 repeats</b> in humans </div> <div><br>The <span class=cloze>serine</span> residues in the repeat sequence will be phosphorylated by protein kinases </div> <div><br>Phosphorylation is needed for promoter escape, to act as a docking site for capping enzyme, cap binding complex (CBC), cleavage/termination complexes, and RNA splicing factors&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Adding the 5’ Cap </span></div> <div>Synthesis of the cap occurs at the CTD of RNA Pol II </div> <div><span class=cloze>[...]</span> gives protection from 5’ --&gt;3’ <span class=cloze>[...]</span> &amp; is <b>recognized</b> by <u>ribosomes</u> to start translation </div> <div><br>The capping process: <br>(1) Capping enzyme acts as a phosphohydrolase </div> <div>Removes one of the phosphate groups from the 5’ end<br><br>(2) Capping enzyme acts as a guanyltransferase </div> <div>Uses GTP to add GMP and remove a pyrophosphate group </div> <div>The new linkage is a 5’, 5’ triphosphate linkage<br><br>&nbsp;(3) Guanine-7-methyltransferase methylates the added guanine at N-7 to give Cap 0 <br>Cap 0 is what is seen in lower eukaryotes (like yeast)</div> <div><br><font color=""#5374fb"">(4)</font> 2’-O-methyltransferase adds a methyl group to the 2’ hydroxyl group of the 1st base in the primary transcript to give Cap 1 <br>This is what is typically seen in humans</div> <div><br>(5) 2’-O-methyltransferase <span style=""font-style: italic;"">may </span>add another methyl group to the 2’ hydroxyl group of the 2nd base in the primary transcript to give Cap 2 </div> <div><br>After the <u>cap is formed</u>, it will be <u>replaced by cap binding complex</u> (CBC)&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Adding the 5’ Cap </span></div> <div>Synthesis of the cap occurs at the CTD of RNA Pol II </div> <div><span class=cloze>Capping</span> gives protection from 5’ --&gt;3’ <span class=cloze>exonucleases</span> &amp; is <b>recognized</b> by <u>ribosomes</u> to start translation </div> <div><br>The capping process: <br>(1) Capping enzyme acts as a phosphohydrolase </div> <div>Removes one of the phosphate groups from the 5’ end<br><br>(2) Capping enzyme acts as a guanyltransferase </div> <div>Uses GTP to add GMP and remove a pyrophosphate group </div> <div>The new linkage is a 5’, 5’ triphosphate linkage<br><br>&nbsp;(3) Guanine-7-methyltransferase methylates the added guanine at N-7 to give Cap 0 <br>Cap 0 is what is seen in lower eukaryotes (like yeast)</div> <div><br><font color=""#5374fb"">(4)</font> 2’-O-methyltransferase adds a methyl group to the 2’ hydroxyl group of the 1st base in the primary transcript to give Cap 1 <br>This is what is typically seen in humans</div> <div><br>(5) 2’-O-methyltransferase <span style=""font-style: italic;"">may </span>add another methyl group to the 2’ hydroxyl group of the 2nd base in the primary transcript to give Cap 2 </div> <div><br>After the <u>cap is formed</u>, it will be <u>replaced by cap binding complex</u> (CBC)&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription Termination </span></div> <div>The sequence AAUAAA signals for termination but the transcript will be extended past the termination region (cleavage usually happens 10-20 bp downstream) </div> <div><br>The termination sequence is found in the <span class=cloze>[...]</span></div> <div><br>The cleavage sequence is recognized by <span class=cloze>[...]</span> that are bound at <span class=cloze>[...]</span>, which signals for endonucleases to cleave the chain </div> <div><br><u>After cleavage</u>, polyadenylation (via poly-A polymerase) occurs to add the poly-A tail (~100-250 nucleotides long) </div> <div><br>The poly-A tail <span class=cloze>[...]</span> for export into the <b>cytoplasm</b>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription Termination </span></div> <div>The sequence AAUAAA signals for termination but the transcript will be extended past the termination region (cleavage usually happens 10-20 bp downstream) </div> <div><br>The termination sequence is found in the <span class=cloze>RNA</span></div> <div><br>The cleavage sequence is recognized by <span class=cloze>termination factors</span> that are bound at <span class=cloze>CTD</span>, which signals for endonucleases to cleave the chain </div> <div><br><u>After cleavage</u>, polyadenylation (via poly-A polymerase) occurs to add the poly-A tail (~100-250 nucleotides long) </div> <div><br>The poly-A tail <span class=cloze>must be present</span> for export into the <b>cytoplasm</b>&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Splicing </span></div> <div><br>May occur before or after termination (<span class=cloze>[...]</span>)<br><b><br>&nbsp;Removes introns</b> and <b>links (ligates) exons</b></div> <div><br>The sequence of the exons will remain the same from 3’ --&gt; 5’ along the gene<br>Seen in most <span class=cloze>[...]</span> in mammals <br>92% or human transcripts undergo splicing&nbsp;</div><div><br>Must be precise to minimize errors&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Splicing </span></div> <div><br>May occur before or after termination (<span class=cloze>size-dependent</span>)<br><b><br>&nbsp;Removes introns</b> and <b>links (ligates) exons</b></div> <div><br>The sequence of the exons will remain the same from 3’ --&gt; 5’ along the gene<br>Seen in most <span class=cloze>mRNA</span> in mammals <br>92% or human transcripts undergo splicing&nbsp;</div><div><br>Must be precise to minimize errors&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> <span class=cloze>[...]</span>: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> <span class=cloze>U1 snRNP</span>: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br><span class=cloze>[...]</span>: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br><span class=cloze>U4 snRNP</span>: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> <span class=cloze>[...]</span>: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> <span class=cloze>U2 snRNP</span>: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> <span class=cloze>[...]</span>: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> <span class=cloze>U5 snRNP</span>: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into <span class=cloze>[...]</span> <br>Each has a unique 100-200 nt sequence </div> <div>Named for their <span class=cloze>[...]</span> molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into <span class=cloze>snRNPs (small nuclear ribonuclear proteins)</span> <br>Each has a unique 100-200 nt sequence </div> <div>Named for their <span class=cloze>snRNA</span> molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> U6 snRNP: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> <span class=cloze>[...]</span>: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Spliceosomes </span></div> <div><br>The complex responsible for splicing<br><b> Very large</b> - made up of more than <u>100 proteins</u> and RNA molecules </div> <div>Organize into snRNPs (small nuclear ribonuclear proteins) <br>Each has a unique 100-200 nt sequence </div> <div>Named for their snRNA molecule </div> <div>Each has about 10-12 proteins – some proteins are present in all but each has unique ones too </div> <div><br><br>The 5 snRNP functions:<br> U1 snRNP: Identifies the 5’ splice site in hnRNA<br> U2 snRNP: Binds branch site and aligns for 1st splicing reaction <br>U4 snRNP: Binds to snRNP6 &amp; sequesters *bends*<br> U5 snRNP: Aligns hnRNA for the 2nd splicing reaction<br> <span class=cloze>U6 snRNP</span>: Promotes catalysis of RNA splicing reaction&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Basic Principles of Splicing </span></div> <div><br>The <b><font color=""#478828"">GU/AG rule</font></b> and governs RNA splicing<br> The GU is at the <span class=cloze>[...]</span> of an intron – the <span class=cloze>[...]</span> splice site is immediately upstream <br>The AG is at the <span class=cloze>[...]</span> of an intron – the <span class=cloze>[...]</span> splice site is immediately <span class=cloze>[...]</span> </div> <div><br>Branch point A within the intron<br> Upstream of the 3’ splice site, but relatively close </div> <div><br>There is a pyrimidine-rich region between the branch point and the 3’ splice site<br>The <span class=cloze>[...]</span> is where the 5’ exon and 3’ exon are linked&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Basic Principles of Splicing </span></div> <div><br>The <b><font color=""#478828"">GU/AG rule</font></b> and governs RNA splicing<br> The GU is at the <span class=cloze>5' end</span> of an intron – the <span class=cloze>5'</span> splice site is immediately upstream <br>The AG is at the <span class=cloze>3' end</span> of an intron – the <span class=cloze>3'</span> splice site is immediately <span class=cloze>downstream</span> </div> <div><br>Branch point A within the intron<br> Upstream of the 3’ splice site, but relatively close </div> <div><br>There is a pyrimidine-rich region between the branch point and the 3’ splice site<br>The <span class=cloze>splice junction</span> is where the 5’ exon and 3’ exon are linked&nbsp;</div> </div> </div></div><br> "
"<img src=""paste-e2f47dc6124f862cd2d7a3b30d032f9345910a1f.jpg"">"
"<div> <div> <div> <div><span style=""font-weight: 700;"">Splicing Mechanism </span></div> <div><br>SR proteins bind at exonic splice enhancers and recruit snRNPs needed for splicing<br>Found in <b>exons </b></div> <div><br>The snRNPs know where to bind because their RNA will look to match the correct bp sequence<br>Recall that snRNPs contain both proteins and RNA </div> <div><br>U1 snRNP binds at the <span class=cloze>[...]</span> splice site<br> There can’t be a sequence-specific U1 for every gene, but post-transcriptional modification </div> <div>to pseudouridine (y) allows for a range of recognition sequences <br><br>U2 snRNP binds at branch <span class=cloze>[...]</span> and the branch site bulges out</div><div>U2 binds with the bps surrounding A, but not actually to it </div> <div>The 2’ OH of the bulge is needed for splicing<br><br>&nbsp;U5 snRNP along with the U4 snRNP/U6 snRNP complex bind to complete <b>inactive</b> spliceosome </div> <div><br>Spliceosome undergoes dynamic rearrangement (U1 snRNP &amp; U4 snRNP leave) to become <b>catalytically</b> active </div> <div>Once in the catalytic conformation, U2 snRNP &amp; U6 snRNP base pair to each other to align the branch site with the 5’ splice site for the 1st reaction (2’ OH attacks 5’ P of intron) </div> <div>U2 snRNP, U6 snRNP base, &amp; U5 snRNP base pair to each other to align the 5’ &amp; 3’ splice sites for the 2nd reaction (3’ OH of exon attacks 5’ P of downstream exon) </div> <div><br>Both reaction1 &amp; 2 are <u>two-step transesterifications </u></div> <div><br>Intron product is a “lariat” structure, this formation requires an unusual <span class=cloze>[...]</span> bond </div> <div><br>Recall that this process is happening in the transcription factories<br>The SR proteins and snRNPs are docked on RNA pol II <span class=cloze>[...]</span></div> <div><br>They are available as soon as needed:<br> <span class=cloze>[...]</span> transcript: splicing at the same time of transcription <br><span class=cloze>[...]</span> transcript: splicing after transcription termination&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Splicing Mechanism </span></div> <div><br>SR proteins bind at exonic splice enhancers and recruit snRNPs needed for splicing<br>Found in <b>exons </b></div> <div><br>The snRNPs know where to bind because their RNA will look to match the correct bp sequence<br>Recall that snRNPs contain both proteins and RNA </div> <div><br>U1 snRNP binds at the <span class=cloze>5'</span> splice site<br> There can’t be a sequence-specific U1 for every gene, but post-transcriptional modification </div> <div>to pseudouridine (y) allows for a range of recognition sequences <br><br>U2 snRNP binds at branch <span class=cloze>site A</span> and the branch site bulges out</div><div>U2 binds with the bps surrounding A, but not actually to it </div> <div>The 2’ OH of the bulge is needed for splicing<br><br>&nbsp;U5 snRNP along with the U4 snRNP/U6 snRNP complex bind to complete <b>inactive</b> spliceosome </div> <div><br>Spliceosome undergoes dynamic rearrangement (U1 snRNP &amp; U4 snRNP leave) to become <b>catalytically</b> active </div> <div>Once in the catalytic conformation, U2 snRNP &amp; U6 snRNP base pair to each other to align the branch site with the 5’ splice site for the 1st reaction (2’ OH attacks 5’ P of intron) </div> <div>U2 snRNP, U6 snRNP base, &amp; U5 snRNP base pair to each other to align the 5’ &amp; 3’ splice sites for the 2nd reaction (3’ OH of exon attacks 5’ P of downstream exon) </div> <div><br>Both reaction1 &amp; 2 are <u>two-step transesterifications </u></div> <div><br>Intron product is a “lariat” structure, this formation requires an unusual <span class=cloze>2’-5’ phosphodiester</span> bond </div> <div><br>Recall that this process is happening in the transcription factories<br>The SR proteins and snRNPs are docked on RNA pol II <span class=cloze>CTD</span></div> <div><br>They are available as soon as needed:<br> <span class=cloze>Long</span> transcript: splicing at the same time of transcription <br><span class=cloze>Short</span> transcript: splicing after transcription termination&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing </span></div> <div>Seen in about 60% of mammalian primary transcripts <br><span class=cloze>[...]</span> is the mechanism that allows for tissue-specific development from a <b>single</b> gene <br><br>Exons can also be removed in splicing to for developmental or tissue-specific production&nbsp; <br><br>Expands the coding capacity of a genome - 1 gene can lead to several mRNAs, which can lead to several proteins</div> <br> <div><br><u>Mechanisms for alternative splicing vary <br></u><br>Selection of exons is depending on the proteins binding to sequences of a primary RNA molecule&nbsp;<br><br>SR proteins binding to exonic splicing enhancers (ESE) <span class=cloze>[...]</span> splicing at nearby sites</div> <div><br>Heterogeneous nuclear ribonuclearproteins (hnRNP) binding to exonic splicing silencers (ESS) <span class=cloze>[...]</span> splicing at nearby sites </div> <div><br>Other factors binding to intronic splicing enhancers and intronic splicing silencers (ISS) affects whether splicing occurs, but they’re not a focus in this class&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing </span></div> <div>Seen in about 60% of mammalian primary transcripts <br><span class=cloze>Alternative splicing</span> is the mechanism that allows for tissue-specific development from a <b>single</b> gene <br><br>Exons can also be removed in splicing to for developmental or tissue-specific production&nbsp; <br><br>Expands the coding capacity of a genome - 1 gene can lead to several mRNAs, which can lead to several proteins</div> <br> <div><br><u>Mechanisms for alternative splicing vary <br></u><br>Selection of exons is depending on the proteins binding to sequences of a primary RNA molecule&nbsp;<br><br>SR proteins binding to exonic splicing enhancers (ESE) <span class=cloze>favors</span> splicing at nearby sites</div> <div><br>Heterogeneous nuclear ribonuclearproteins (hnRNP) binding to exonic splicing silencers (ESS) <span class=cloze>inhibits</span> splicing at nearby sites </div> <div><br>Other factors binding to intronic splicing enhancers and intronic splicing silencers (ISS) affects whether splicing occurs, but they’re not a focus in this class&nbsp;</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br><span class=cloze>[...]</span> <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br><span class=cloze>Alternative exon (exon skipping)</span> <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div><span class=cloze>[...]</span><br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div><span class=cloze>Intron retention</span><br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span class=cloze>[...]</span><br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span class=cloze>Alternative 3’ splice sites</span><br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div><span class=cloze>[...]</span></div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div><span class=cloze>Mutually exclusive alternative exon</span></div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br><span class=cloze>[...]</span><br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br><span class=cloze>Alternative promoter and first exon</span><br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div><span class=cloze>[...]</span><br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div><span class=cloze>Alternative 5’ splice sites</span><br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div>Alternative poly(A) site and terminal exon </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div><span class=cloze>[...]</span> </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Alternative Splicing Mechanisms </span></div> <div>There are 9 different genes that encode for SR proteins exist <br><br>The primary transcript produced by the SR protein can also be alternatively spliced <br><br>Different cell types have different SR protein composition <br>Allows for tissue-specific expression :</div> <div><br>Alternative exon (exon skipping) <br>One exon in the sequence is skipped </div> <br></div></div><div> <div>Alternative 5’ splice sites<br> Changes the 3’ boundary of the upstream exon </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div>Alternative 3’ splice sites<br> Changes the 5’ boundary of the downstream exon </div> <br></div></div><div><div> <div>Intron retention<br> An intron piece is retained in the splicing </div> </div> <div> <br></div></div><div><div> <div>Mutually exclusive alternative exon</div></div></div><div><div> </div> </div> <div> <div> <div>Two different exons are chosen at a particular position </div> <div>If one copy has exon 2, the other cannot have exon 2 and must have a different exon in its place </div> </div></div></div><div><div><div><br>Alternative promoter and first exon<br> Different starting point, different exons included <b><span style=""font-style: italic;"">Pax</span>6 is an example</b> of this </div> <br> <div><span class=cloze>Alternative poly(A) site and terminal exon</span> </div> <div>Inclusion of a particular exon gives an early termination signal while skipping it allows for a longer mRNA&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription and RNA Processing are Segregated from Translation </span></div> <div>Once the mature RNA is exported through the <span class=cloze>[...]</span> to the cytoplasm, most of the binding proteins are replaced by cytoplasmatic binding proteins&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Transcription and RNA Processing are Segregated from Translation </span></div> <div>Once the mature RNA is exported through the <span class=cloze>nuclear pore complex</span> to the cytoplasm, most of the binding proteins are replaced by cytoplasmatic binding proteins&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">mRNA Turnover </span></div> <div><br>Options for degredation:<br> Deadenylation by <span class=cloze>[...]</span> (<u>most common</u>) <br>Decapping by decapping enzyme (some mRNA) <br>mRNA transcript cleavage by endonuclease </div> <div><br>Once degradation begins, most of the mRNA will be <b>reduced</b> to nucleotides by an <span class=cloze>[...]</span>&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">mRNA Turnover </span></div> <div><br>Options for degredation:<br> Deadenylation by <span class=cloze>exonucleases</span> (<u>most common</u>) <br>Decapping by decapping enzyme (some mRNA) <br>mRNA transcript cleavage by endonuclease </div> <div><br>Once degradation begins, most of the mRNA will be <b>reduced</b> to nucleotides by an <span class=cloze>exosome</span>&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Hemophilia </span></div> <div>A <u>X-linked</u> hereditary disorder that impairs blood clotting </div> <div><br>XY Chromosomes: If the X-chromosome has the mutation, hemophilia will be expressed </div> <div><br>XX Chromosones: As long as only one damage X is inherited, the individual will be a carrier of hemophilia, but will not be a hemophiliac </div> <div><br>Result of a splicing error in selection of 3’ splice site, it <b>changes the ORF </b><br><br>Normal individuals: AAAG&nbsp;*AU<br> Hemophiliacs: AG&nbsp;*AGAU<br> &nbsp;*= splicing end signal </div> <div><br>Mutation results in loss of factor IX activity (<span class=cloze>[...]</span>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Hemophilia </span></div> <div>A <u>X-linked</u> hereditary disorder that impairs blood clotting </div> <div><br>XY Chromosomes: If the X-chromosome has the mutation, hemophilia will be expressed </div> <div><br>XX Chromosones: As long as only one damage X is inherited, the individual will be a carrier of hemophilia, but will not be a hemophiliac </div> <div><br>Result of a splicing error in selection of 3’ splice site, it <b>changes the ORF </b><br><br>Normal individuals: AAAG&nbsp;*AU<br> Hemophiliacs: AG&nbsp;*AGAU<br> &nbsp;*= splicing end signal </div> <div><br>Mutation results in loss of factor IX activity (<span class=cloze>Coagulation pathway</span>)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Hemophilia </span></div> <div>A <u>X-linked</u> hereditary disorder that <span class=cloze>[...]</span> </div> <div><br>XY Chromosomes: If the X-chromosome has the mutation, hemophilia will be expressed </div> <div><br>XX Chromosones: As long as only one damage X is inherited, the individual will be a carrier of hemophilia, but will not be a hemophiliac </div> <div><br>Result of a splicing error in selection of 3’ splice site, it <b>changes the ORF </b><br><br>Normal individuals: AAAG&nbsp;*AU<br> Hemophiliacs: AG&nbsp;*AGAU<br> &nbsp;*= splicing end signal </div> <div><br>Mutation results in loss of factor IX activity (Coagulation pathway)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Hemophilia </span></div> <div>A <u>X-linked</u> hereditary disorder that <span class=cloze>impairs blood clotting</span> </div> <div><br>XY Chromosomes: If the X-chromosome has the mutation, hemophilia will be expressed </div> <div><br>XX Chromosones: As long as only one damage X is inherited, the individual will be a carrier of hemophilia, but will not be a hemophiliac </div> <div><br>Result of a splicing error in selection of 3’ splice site, it <b>changes the ORF </b><br><br>Normal individuals: AAAG&nbsp;*AU<br> Hemophiliacs: AG&nbsp;*AGAU<br> &nbsp;*= splicing end signal </div> <div><br>Mutation results in loss of factor IX activity (Coagulation pathway)&nbsp;</div> </div> </div></div><br> "
"<img src=""paste-d1b30e6d2558d90a77e5b7a1736ac55ade212252.jpg"">"
<div> <div> <div>Translation is making <span class=cloze>[...]</span> from RNA&nbsp;<br><br></div></div></div> <div> <div> <div>The <b>coding sequence</b> needed for a protein’s <b>primary sequence</b> is carried in the <span class=cloze>[...]</span> <br><br>The reading of this sequence and the production of the protein is translation<br>Translation occurs at a <span class=cloze>[...]</span> (enzyme complex)&nbsp;<br></div> </div> </div> <div> <div> <div>Translation is making <span class=cloze>proteins</span> from RNA&nbsp;<br><br></div></div></div> <div> <div> <div>The <b>coding sequence</b> needed for a protein’s <b>primary sequence</b> is carried in the <span class=cloze>mRNA</span> <br><br>The reading of this sequence and the production of the protein is translation<br>Translation occurs at a <span class=cloze>ribosome</span> (enzyme complex)&nbsp;<br></div> </div> </div><br> " <div> <div> <div><span style=""font-weight: 700;"">Principles of the Genetic Code </span></div> <div><br>The mRNA is read in nucleotide triplets called <span class=cloze>[...]</span><br> Each codon codes for a specific amino acid, which will be used to form a protein </div> <div><br>1 codon --&gt; 1 amino acid<br> The coding sequence (or <span class=cloze>[...]</span>) is read from <span class=cloze>[...]</span> and the protein is synthesized from the <span class=cloze>[...]</span>-terminus to the <span class=cloze>[...]</span>-terminus</div> <div><br>The genetic code is non-overlapping, so 1 codon does not affect the next </div> <div>Reading will begin with the start codon (AUG) and end with the stop codon <br>From the start codon, the sequence will be read as a continuous series of 3 nucleotides at a time with no gaps or overlaps until the stop codon is reached</div> <div><br>A non-overlapping sequence gives the <b>most flexibility</b> since any AA can be followed by any other AA.&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Principles of the Genetic Code </span></div> <div><br>The mRNA is read in nucleotide triplets called <span class=cloze>codons</span><br> Each codon codes for a specific amino acid, which will be used to form a protein </div> <div><br>1 codon --&gt; 1 amino acid<br> The coding sequence (or <span class=cloze>ORF</span>) is read from <span class=cloze>5' to 3'</span> and the protein is synthesized from the <span class=cloze>N</span>-terminus to the <span class=cloze>C</span>-terminus</div> <div><br>The genetic code is non-overlapping, so 1 codon does not affect the next </div> <div>Reading will begin with the start codon (AUG) and end with the stop codon <br>From the start codon, the sequence will be read as a continuous series of 3 nucleotides at a time with no gaps or overlaps until the stop codon is reached</div> <div><br>A non-overlapping sequence gives the <b>most flexibility</b> since any AA can be followed by any other AA.&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Principles of the Genetic Code </span></div> <div><br>The mRNA is read in nucleotide triplets called codons<br> Each codon codes for a specific amino acid, which will be used to form a protein </div> <div><br>1 codon --&gt; 1 amino acid<br> The coding sequence (or ORF) is read from 5' to 3' and the protein is synthesized from the N-terminus to the C-terminus</div> <div><br>The genetic code is <span class=cloze>[...]</span>, so 1 codon does not affect the next </div> <div>Reading will begin with the start codon (<span class=cloze>[...]</span>) and end with the stop codon <br>From the start codon, the sequence will be read as a continuous series of 3 nucleotides at a time with no gaps or overlaps until the stop codon is reached</div> <div><br>A non-overlapping sequence gives the <b>most flexibility</b> since any AA can be followed by any other AA.&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Principles of the Genetic Code </span></div> <div><br>The mRNA is read in nucleotide triplets called codons<br> Each codon codes for a specific amino acid, which will be used to form a protein </div> <div><br>1 codon --&gt; 1 amino acid<br> The coding sequence (or ORF) is read from 5' to 3' and the protein is synthesized from the N-terminus to the C-terminus</div> <div><br>The genetic code is <span class=cloze>non-overlapping</span>, so 1 codon does not affect the next </div> <div>Reading will begin with the start codon (<span class=cloze>AUG</span>) and end with the stop codon <br>From the start codon, the sequence will be read as a continuous series of 3 nucleotides at a time with no gaps or overlaps until the stop codon is reached</div> <div><br>A non-overlapping sequence gives the <b>most flexibility</b> since any AA can be followed by any other AA.&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">The Universal Genetic Code </span></div> <div>The genetic code is <font color=""#478828"">the same in prokaryotes and eukaryotes</font><br><br>There are 64 possible codons (43)<br> The code is <span class=cloze>[...]</span> meaning that most amino acids can be coded by more than 1 codon </div> <div>Exceptions: Met &amp; Trp only have 1 corresponding codon </div> <div><br>Even though an AA may go with more than 1 codon, each codon goes with only 1 AA <br><br>The initiation codon is <span class=cloze>[...]</span></div> <div>Codes for <span class=cloze>[...]</span><br> The 3 stop codons are <b><font color=""#478828"">UAA , UGA, &amp; UAG</font></b></div> <div>Stop codons <span class=cloze>[...]</span> encode for any amino acids</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">The Universal Genetic Code </span></div> <div>The genetic code is <font color=""#478828"">the same in prokaryotes and eukaryotes</font><br><br>There are 64 possible codons (43)<br> The code is <span class=cloze>degenerate</span> meaning that most amino acids can be coded by more than 1 codon </div> <div>Exceptions: Met &amp; Trp only have 1 corresponding codon </div> <div><br>Even though an AA may go with more than 1 codon, each codon goes with only 1 AA <br><br>The initiation codon is <span class=cloze>AUG</span></div> <div>Codes for <span class=cloze>Met</span><br> The 3 stop codons are <b><font color=""#478828"">UAA , UGA, &amp; UAG</font></b></div> <div>Stop codons <span class=cloze>do not</span> encode for any amino acids</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a <span class=cloze>[...]</span> sequence (in the <b>genome</b>), which is <span class=cloze>[...]</span> to the RNA, which is <span class=cloze>[...]</span> to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) nonsense mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) missense mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) silent mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a <span class=cloze>DNA</span> sequence (in the <b>genome</b>), which is <span class=cloze>transcribed</span> to the RNA, which is <span class=cloze>translated</span> to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) nonsense mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) missense mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) silent mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a DNA sequence (in the <b>genome</b>), which is transcribed to the RNA, which is translated to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) <span class=cloze>[...]</span> mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) missense mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) silent mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a DNA sequence (in the <b>genome</b>), which is transcribed to the RNA, which is translated to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) <span class=cloze>nonsense</span> mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) missense mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) silent mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a DNA sequence (in the <b>genome</b>), which is transcribed to the RNA, which is translated to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) nonsense mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) <span class=cloze>[...]</span> mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) silent mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a DNA sequence (in the <b>genome</b>), which is transcribed to the RNA, which is translated to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) nonsense mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) <span class=cloze>missense</span> mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) silent mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a DNA sequence (in the <b>genome</b>), which is transcribed to the RNA, which is translated to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) nonsense mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) missense mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) <span class=cloze>[...]</span> mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Mutations in the Genetic Code </span></div> <div><br>Mutations are changes in a DNA sequence (in the <b>genome</b>), which is transcribed to the RNA, which is translated to a potentially mutated protein<br><br></div> <div><span style=""font-style: italic;""><u>Single base substitutions </u></span></div> <div>(1) nonsense mutation <br>Introduces a stop codon </div> <div>Example: UAC --&gt; UAA<br> Protein will be <b>shorter</b> and typically <b>inactive </b></div> <div><br>(2) missense mutation<br> Replaces 1 amino acid codon for another </div> <div>Example: UAC --&gt; UCC<br> it’s difficult to predict the effect of these changes </div> <div><br>(3) <span class=cloze>silent</span> mutation<br> The codon is altered, but still encodes for the same amino acid <br>Example: UAC --&gt; UAU , both encode for Tyr</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-style: italic;""><b>Frameshift Mutations </b></span></div> <div><br>Occur with insertions or deletions that are not in a multiple of 3 bases Typically <font color=""#478828""><b>destroys the functionality</b></font> of the protein<br> Frameshifts often lead to an <u>early termination</u> (due to an early stop codon) Mutations in <span class=cloze>[...]</span> often lead to frameshifts </div> <div><br>(1) Insertion<br> One or two AAs are added to the sequence, shifting the reading frame <u>Hemophilia</u> is caused by a frameshift due to insertion </div> <div><br><br>(2) Deletion<br> One or two AAs are removed from the sequence, shifting the reading frame </div> <div><br>Inframe deletions </div> <div>Deletions of 3 bases or a multiple of 3 </div> <div>If you <b>add 3 bases</b> it usually isn’t a frameshift, it’s a <b>new codon </b></div> <div><br>Example: <i><b>Deletion of UUC</b></i> in CFTR (cystic fibrosis transmembrane conductance regulator) is the most common mutation associated with cystic fibrosis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-style: italic;""><b>Frameshift Mutations </b></span></div> <div><br>Occur with insertions or deletions that are not in a multiple of 3 bases Typically <font color=""#478828""><b>destroys the functionality</b></font> of the protein<br> Frameshifts often lead to an <u>early termination</u> (due to an early stop codon) Mutations in <span class=cloze>RNA splicing</span> often lead to frameshifts </div> <div><br>(1) Insertion<br> One or two AAs are added to the sequence, shifting the reading frame <u>Hemophilia</u> is caused by a frameshift due to insertion </div> <div><br><br>(2) Deletion<br> One or two AAs are removed from the sequence, shifting the reading frame </div> <div><br>Inframe deletions </div> <div>Deletions of 3 bases or a multiple of 3 </div> <div>If you <b>add 3 bases</b> it usually isn’t a frameshift, it’s a <b>new codon </b></div> <div><br>Example: <i><b>Deletion of UUC</b></i> in CFTR (cystic fibrosis transmembrane conductance regulator) is the most common mutation associated with cystic fibrosis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-style: italic;""><b>Frameshift Mutations </b></span></div> <div><br>Occur with insertions or deletions that are not in a multiple of 3 bases Typically <font color=""#478828""><b>destroys the functionality</b></font> of the protein<br> Frameshifts often lead to an <u>early termination</u> (due to an early stop codon) Mutations in RNA splicing often lead to frameshifts </div> <div><br>(1) Insertion<br> One or two AAs are added to the sequence, shifting the reading frame <u>Hemophilia</u> is caused by a frameshift due to insertion </div> <div><br><br>(2) <span class=cloze>[...]</span><br> One or two AAs are removed from the sequence, shifting the reading frame </div> <div><br><span class=cloze>[...]</span> deletions </div> <div>Deletions of 3 bases or a multiple of 3 </div> <div>If you <b>add 3 bases</b> it usually isn’t a frameshift, it’s a <b>new codon </b></div> <div><br>Example: <i><b>Deletion of UUC</b></i> in CFTR (cystic fibrosis transmembrane conductance regulator) is the most common mutation associated with cystic fibrosis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-style: italic;""><b>Frameshift Mutations </b></span></div> <div><br>Occur with insertions or deletions that are not in a multiple of 3 bases Typically <font color=""#478828""><b>destroys the functionality</b></font> of the protein<br> Frameshifts often lead to an <u>early termination</u> (due to an early stop codon) Mutations in RNA splicing often lead to frameshifts </div> <div><br>(1) Insertion<br> One or two AAs are added to the sequence, shifting the reading frame <u>Hemophilia</u> is caused by a frameshift due to insertion </div> <div><br><br>(2) <span class=cloze>Deletion</span><br> One or two AAs are removed from the sequence, shifting the reading frame </div> <div><br><span class=cloze>Inframe</span> deletions </div> <div>Deletions of 3 bases or a multiple of 3 </div> <div>If you <b>add 3 bases</b> it usually isn’t a frameshift, it’s a <b>new codon </b></div> <div><br>Example: <i><b>Deletion of UUC</b></i> in CFTR (cystic fibrosis transmembrane conductance regulator) is the most common mutation associated with cystic fibrosis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-style: italic;""><b>Frameshift Mutations </b></span></div> <div><br>Occur with insertions or deletions that are not in a multiple of 3 bases Typically <font color=""#478828""><b>destroys the functionality</b></font> of the protein<br> Frameshifts often lead to an <u>early termination</u> (due to an early stop codon) Mutations in RNA splicing often lead to frameshifts </div> <div><br>(1) <span class=cloze>[...]</span><br> One or two <span class=cloze>[...]</span> are added to the sequence, shifting the reading frame <u>Hemophilia</u> is caused by a frameshift due to insertion </div> <div><br><br>(2) Deletion<br> One or two AAs are removed from the sequence, shifting the reading frame </div> <div><br>Inframe deletions </div> <div>Deletions of 3 bases or a multiple of 3 </div> <div>If you <b>add 3 bases</b> it usually isn’t a frameshift, it’s a <b>new codon </b></div> <div><br>Example: <i><b>Deletion of UUC</b></i> in CFTR (cystic fibrosis transmembrane conductance regulator) is the most common mutation associated with cystic fibrosis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-style: italic;""><b>Frameshift Mutations </b></span></div> <div><br>Occur with insertions or deletions that are not in a multiple of 3 bases Typically <font color=""#478828""><b>destroys the functionality</b></font> of the protein<br> Frameshifts often lead to an <u>early termination</u> (due to an early stop codon) Mutations in RNA splicing often lead to frameshifts </div> <div><br>(1) <span class=cloze>Insertion</span><br> One or two <span class=cloze>AAs</span> are added to the sequence, shifting the reading frame <u>Hemophilia</u> is caused by a frameshift due to insertion </div> <div><br><br>(2) Deletion<br> One or two AAs are removed from the sequence, shifting the reading frame </div> <div><br>Inframe deletions </div> <div>Deletions of 3 bases or a multiple of 3 </div> <div>If you <b>add 3 bases</b> it usually isn’t a frameshift, it’s a <b>new codon </b></div> <div><br>Example: <i><b>Deletion of UUC</b></i> in CFTR (cystic fibrosis transmembrane conductance regulator) is the most common mutation associated with cystic fibrosis&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Cracking the Genetic Code </span></div> <div>Experiment by <b>Marshall Nirenberg</b> – Nobel prize winner &amp; UF grad </div> <div><br>Synthesized a <u>RNA</u> code that <b>only had Uracil</b> – Poly-U RNA </div> <div><br>Poly-U incubated with an <span style=""font-style: italic;"">E.Coli </span>extract, GTP, ATP in 20 different test tubes. Each of test tubes contains an amino acid dissolved in a buffer </div> <div>Since only U was present, the polypeptide that formed should go along with the codon UUU. <br>Only polyphenylalanine was formed, therefore UUU --&gt; phenylalanine </div> <div><br>Process was repeated with poly-C to give polyproline, therefore CCC --&gt; proline <br>Process was repeated with poly-A to give polylysine, therefore AAA --&gt; lysine <br><br>Poly-G didn’t work because Guanine will spontaneously form a <span class=cloze>[...]</span> that is unable to bind to the ribosome <span style=""font-style: italic;"">(he eventually figured out how to do it later on)</span></div> <div><br>The experiment should have failed because it didn’t have a start codon, but the buffer he used didn’t match a living cell conditions, so it allowed the start of transcription with a wrong codon&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Cracking the Genetic Code </span></div> <div>Experiment by <b>Marshall Nirenberg</b> – Nobel prize winner &amp; UF grad </div> <div><br>Synthesized a <u>RNA</u> code that <b>only had Uracil</b> – Poly-U RNA </div> <div><br>Poly-U incubated with an <span style=""font-style: italic;"">E.Coli </span>extract, GTP, ATP in 20 different test tubes. Each of test tubes contains an amino acid dissolved in a buffer </div> <div>Since only U was present, the polypeptide that formed should go along with the codon UUU. <br>Only polyphenylalanine was formed, therefore UUU --&gt; phenylalanine </div> <div><br>Process was repeated with poly-C to give polyproline, therefore CCC --&gt; proline <br>Process was repeated with poly-A to give polylysine, therefore AAA --&gt; lysine <br><br>Poly-G didn’t work because Guanine will spontaneously form a <span class=cloze>tetraplex</span> that is unable to bind to the ribosome <span style=""font-style: italic;"">(he eventually figured out how to do it later on)</span></div> <div><br>The experiment should have failed because it didn’t have a start codon, but the buffer he used didn’t match a living cell conditions, so it allowed the start of transcription with a wrong codon&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the ribosome <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The anticodon of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary determinants for the amino acid <br>The 3rd base is known as the <span class=cloze>[...]</span> base&nbsp;</div> </div> </div></div></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the ribosome <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The anticodon of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary determinants for the amino acid <br>The 3rd base is known as the <span class=cloze>wobble</span> base&nbsp;</div> </div> </div></div></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the ribosome <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The anticodon of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary <span class=cloze>[...]</span> for the amino acid <br>The 3rd base is known as the wobble base&nbsp;</div> </div> </div></div></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the ribosome <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The anticodon of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary <span class=cloze>determinants</span> for the amino acid <br>The 3rd base is known as the wobble base&nbsp;</div> </div> </div></div></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the <span class=cloze>[...]</span> <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The anticodon of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary determinants for the amino acid <br>The 3rd base is known as the wobble base&nbsp;</div> </div> </div></div></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the <span class=cloze>ribosome</span> <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The anticodon of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary determinants for the amino acid <br>The 3rd base is known as the wobble base&nbsp;</div> </div> </div></div></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the ribosome <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The <span class=cloze>[...]</span> of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary determinants for the amino acid <br>The 3rd base is known as the wobble base&nbsp;</div> </div> </div></div></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">tRNA (transfer RNA) </span></div> <div>tRNA is needed for the translation of RNA into proteins <br>Brings amino acids to the ribosome <br>74-93 nucleotides in length <br><br>Cloverleaf secondary structure </div> <div><br>(1) Amino acid arm/ Acceptor Arm<br>5’ and 3’ ends of tRNA will base pair with each other here<br>The 3’ end is site for amino acid attachment </div> <div><br>(2) D arm<br><br>(3) TYC arm<br><br>(4) Anti-codon arm <br><br>(5) Extra arm&nbsp;<br><br><br><br><div> <div> <div> <div>The <span class=cloze>anticodon</span> of the tRNA binds antiparallel to the codon <br><br><b>Essential</b> for the tRNA to be positioned in the <u>ribosome’s catalytic site </u><br><br>The 1st base of the codon pairs with the <b>3rd of the anticodon </b><br>The first 2 bases of the codon are the primary determinants for the amino acid <br>The 3rd base is known as the wobble base&nbsp;</div> </div> </div></div></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the 1st base of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with <span class=cloze>[...]</span> </div> <div>A pairs with <span class=cloze>[...]</span><br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with A or G </div> <div>G pairs with C or U<br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; NEVER G&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the 1st base of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with <span class=cloze>G</span> </div> <div>A pairs with <span class=cloze>U</span><br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with A or G </div> <div>G pairs with C or U<br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; NEVER G&nbsp;</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the 1st base of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with G </div> <div>A pairs with U<br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with A or G </div> <div>G pairs with C or U<br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; <span class=cloze>[...]</span></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the 1st base of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with G </div> <div>A pairs with U<br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with A or G </div> <div>G pairs with C or U<br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; <span class=cloze>NEVER G&nbsp;</span></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the 1st base of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with G </div> <div>A pairs with U<br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with <span class=cloze>[...]</span> or <span class=cloze>[...]</span> </div> <div>G pairs with <span class=cloze>[...]</span> or <span class=cloze>[...]</span><br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; NEVER G&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the 1st base of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with G </div> <div>A pairs with U<br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with <span class=cloze>A</span> or <span class=cloze>G</span> </div> <div>G pairs with <span class=cloze>C</span> or <span class=cloze>U</span><br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; NEVER G&nbsp;</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the <span class=cloze>[...]</span> of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with G </div> <div>A pairs with U<br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with A or G </div> <div>G pairs with C or U<br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; NEVER G&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Wobble Bases </span></div> <div><br>The <u>1st &amp; 2nd base</u> in the codon form Watson-Crick base pairs to the <u>3rd &amp; 2nd bases</u> of the anticodon </div> <div><br>The 3rd base in the codon is referred to as the <u>wobble base </u>and can have non-Watson-Crick base pairs – Remember that this will be pairing to the <span class=cloze>1st base</span> of the anticodon </div> <div>This means that you don’t need a tRNA for each of the 64 possible codons </div> <div><br>If the 1st base of the anticodon is C or A, the base pairing is specific to 1 codon<br>C pairs with G </div> <div>A pairs with U<br><br>&nbsp;If the 1st base of the anticodon is U or G, 2 different codons can be read </div> <div>U pairs with A or G </div> <div>G pairs with C or U<br><br>If the 1st base of the anticodon is I, 3 different codons can be read <br>I = <b>inosine</b> = purine base seen in some tRNAs <br>I pairs with <b>A</b> or <b>C</b> or <b>U</b>.&nbsp; NEVER G&nbsp;</div> </div> </div><br> "
"<img src=""paste-d6bd22090a22f5fa6bb3523165c2d91c9e8f69c9.jpg"">"
" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) <span class=cloze>[...]</span><br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) <span class=cloze>Elongation and translocation</span><br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) <span class=cloze>[...]</span> (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) <span class=cloze>Activation of Amino Acids</span> (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) <span class=cloze>[...]</span> <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) <span class=cloze>Termination and ribose recycling</span> <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) <span class=cloze>[...]</span><br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) <span class=cloze>Initiation</span><br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) Posttranslational processing and folding</div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) <span class=cloze>[...]</span></div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Protein Synthesis Overview </span></div> <div><br>There are 5 stages in translation<br><br>&nbsp;(1) Activation of Amino Acids (Charging tRNA) </div> <div>Done by attaching the amino acid to the 3’ end of the anticodon on tRNA using aminoacyl-tRNA synthetases </div> <div><br>(2) Initiation<br> Binding mRNA and an initiator tRNA-fmet <br>The ribosome is assembled </div> <div><br>(3) Elongation and translocation<br> A ribosome is a peptidyl transferase </div> <div><br>(4) Termination and ribose recycling <br>The protein is completed </div> <div><br>(5) <span class=cloze>Posttranslational processing and folding</span></div><div><br>The stages of translation are similar between prokaryotes and eukaryotes, but there will be some differences&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">tRNA Tertiary Structure </span></div> <div>The invariant bases generate the rigid <span class=cloze>[...]</span> conformation, due to the base pairing between D and TYC arms </div> <div><br>This conformation is essential for <span class=cloze>[...]</span> the amino acid into the ribosome catalytic site&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">tRNA Tertiary Structure </span></div> <div>The invariant bases generate the rigid <span class=cloze>L</span> conformation, due to the base pairing between D and TYC arms </div> <div><br>This conformation is essential for <span class=cloze>adding</span> the amino acid into the ribosome catalytic site&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Aminoacyl-tRNA Synthetases </span></div> <div>The “second genetic code”<br><br><u>Aminoacyl-tRNA synthetases</u> (AARS) are responsible for selecting the correct tRNA to be <span class=cloze>[...]</span> with a particular amino acid based on <span style=""font-style: italic;"">variant </span>sequence elements</div><div><br>The location of the determinants recognized by aminoacyl-tRNA synthetases is variable </div> <div>Anticodons &amp; other sites (like the extra arm) contribute to amino acid selection<br>Example: Ala-tRNA synthetase recognizes a G=U in the amino acid arm </div> <br> <div>Each amino acid needs its own AARS<br> The tRNA attached to its appropriate amino acid is known as <span class=cloze>[...]</span><br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Aminoacyl-tRNA Synthetases </span></div> <div>The “second genetic code”<br><br><u>Aminoacyl-tRNA synthetases</u> (AARS) are responsible for selecting the correct tRNA to be <span class=cloze>charged</span> with a particular amino acid based on <span style=""font-style: italic;"">variant </span>sequence elements</div><div><br>The location of the determinants recognized by aminoacyl-tRNA synthetases is variable </div> <div>Anticodons &amp; other sites (like the extra arm) contribute to amino acid selection<br>Example: Ala-tRNA synthetase recognizes a G=U in the amino acid arm </div> <br> <div>Each amino acid needs its own AARS<br> The tRNA attached to its appropriate amino acid is known as <span class=cloze>charged tRNA</span><br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (70s ribosome)<br> Large subunit = 50s (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = 30s (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are 80s ribosomes<br> Large subunit = 60s (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = 40s (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~<span class=cloze>[...]</span> % rRNA &amp; ~<span class=cloze>[...]</span> % protein by weight<br> The rRNA lines the <span class=cloze>[...]</span> site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has 1 RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has 2 RNA in prokaryotes &amp; 3 in eukaryotes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (70s ribosome)<br> Large subunit = 50s (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = 30s (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are 80s ribosomes<br> Large subunit = 60s (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = 40s (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~<span class=cloze>65</span> % rRNA &amp; ~<span class=cloze>35</span> % protein by weight<br> The rRNA lines the <span class=cloze>catalytic</span> site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has 1 RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has 2 RNA in prokaryotes &amp; 3 in eukaryotes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (70s ribosome)<br> Large subunit = 50s (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = 30s (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are 80s ribosomes<br> Large subunit = 60s (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = 40s (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~65 % rRNA &amp; ~35 % protein by weight<br> The rRNA lines the catalytic site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has <span class=cloze>[...]</span> RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has <span class=cloze>[...]</span> RNA in prokaryotes &amp; <span class=cloze>[...]</span> in eukaryotes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (70s ribosome)<br> Large subunit = 50s (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = 30s (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are 80s ribosomes<br> Large subunit = 60s (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = 40s (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~65 % rRNA &amp; ~35 % protein by weight<br> The rRNA lines the catalytic site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has <span class=cloze>1</span> RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has <span class=cloze>2</span> RNA in prokaryotes &amp; <span class=cloze>3</span> in eukaryotes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (<span class=cloze>[...]</span> ribosome)<br> Large subunit = <span class=cloze>[...]</span> (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = <span class=cloze>[...]</span> (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are 80s ribosomes<br> Large subunit = 60s (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = 40s (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~65 % rRNA &amp; ~35 % protein by weight<br> The rRNA lines the catalytic site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has 1 RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has 2 RNA in prokaryotes &amp; 3 in eukaryotes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (<span class=cloze>70s</span> ribosome)<br> Large subunit = <span class=cloze>50s</span> (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = <span class=cloze>30s</span> (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are 80s ribosomes<br> Large subunit = 60s (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = 40s (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~65 % rRNA &amp; ~35 % protein by weight<br> The rRNA lines the catalytic site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has 1 RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has 2 RNA in prokaryotes &amp; 3 in eukaryotes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (70s ribosome)<br> Large subunit = 50s (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = 30s (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are <span class=cloze>[...]</span> ribosomes<br> Large subunit = <span class=cloze>[...]</span> (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = <span class=cloze>[...]</span> (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~65 % rRNA &amp; ~35 % protein by weight<br> The rRNA lines the catalytic site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has 1 RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has 2 RNA in prokaryotes &amp; 3 in eukaryotes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Ribosomes </span></div> <div><br>Prokaryotes: Single ribosome (70s ribosome)<br> Large subunit = 50s (5S rRNA, 23S rRNA + 36 proteins) <br>Small subunit = 30s (16S rRNA + 21 proteins) </div> <div><br>Eukaryotes: Cytosolic &amp; membrane are <span class=cloze>80s</span> ribosomes<br> Large subunit = <span class=cloze>60s</span> (5S rRNA, 18S rRNA, 5.8S rRNA, + 47 proteins) <br>Small subunit = <span class=cloze>40s</span> (18S rRNA + 33 proteins)<br> There are other types of ribosomes in eukaryotes... </div> <div><br>Ribosomes are comprised of rRNA and proteins<br> ~65 % rRNA &amp; ~35 % protein by weight<br> The rRNA lines the catalytic site<br> The proteins are found on the <u><b>surface</b></u> &amp; provide <u>stability </u></div> <div><br>Protein polymerases with a small and a large subunit<br> The small subunit has 1 RNA in both prokaryotes &amp; eukaryotes <br>The large subunit has 2 RNA in prokaryotes &amp; 3 in eukaryotes&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Organization of Bacterial Genomes </span></div> <div><span class=cloze>[...]</span> are gene clusters simultaneously regulated <br>ORFs are arranged 5’ --&gt; 3’ </div> <div><br><span class=cloze>[...]</span> = use of a single promoter and terminator to encode for several proteins <br>Example: The atp synthase operon encodes for nine proteins </div> <br> <div><span class=cloze>[...]</span> are multiple ribosomes bound to a single mRNA </div> <div>Allows for efficient utilization of mRNA as multiple ribosomes are synthesizing the same protein at once&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Organization of Bacterial Genomes </span></div> <div><span class=cloze>Operons</span> are gene clusters simultaneously regulated <br>ORFs are arranged 5’ --&gt; 3’ </div> <div><br><span class=cloze>Polycistronic mRNA</span> = use of a single promoter and terminator to encode for several proteins <br>Example: The atp synthase operon encodes for nine proteins </div> <br> <div><span class=cloze>Polysomes</span> are multiple ribosomes bound to a single mRNA </div> <div>Allows for efficient utilization of mRNA as multiple ribosomes are synthesizing the same protein at once&nbsp;</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic 70S Ribosome </span></div> <div>Bacterial ribosomes have a large (50S) and a small (30S) subunit and <u>3 tRNA binding sites </u><br><br>There is a cleft between the two subunits, which the mRNA passes through </div> <div>The catalytic site is found in the cleft <br><br>The 3 binding sites: </div> <div><span class=cloze>[...]</span>: aminoacyl tRNA site<br><span class=cloze>[...]</span>: peptidyl tRNA site<br><span class=cloze>[...]</span>: empty site&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic 70S Ribosome </span></div> <div>Bacterial ribosomes have a large (50S) and a small (30S) subunit and <u>3 tRNA binding sites </u><br><br>There is a cleft between the two subunits, which the mRNA passes through </div> <div>The catalytic site is found in the cleft <br><br>The 3 binding sites: </div> <div><span class=cloze>A</span>: aminoacyl tRNA site<br><span class=cloze>P</span>: peptidyl tRNA site<br><span class=cloze>E</span>: empty site&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">The Shine-Dalgarno Sequence </span></div> <div>The Shine-Dalgarno sequence is the mRNA site where the ribosome binds<br><br>Also called the <span class=cloze>[...]</span> (RBS)<br> Found in the 5’ UTR of mRNA<br> 8-13 nucleotides in length </div> <div><br>RBS is purine-rich, so base pairs with a pyrimidine rich sequence at the 3’ end of the 16S rRNA&nbsp; <br>The 16S rRNA is in the <span class=cloze>[...]</span> ribosomal subunit </div> <div><br>The start codon will be located a couple of nucleotides downstream from the RBS<br>Positioned in the <span class=cloze>[...]</span> site </div> <div>While <span class=cloze>[...]</span> is the start codon, it can be in other positions as well and code for <span class=cloze>[...]</span>&nbsp;<br>There are actually 2 different methionine tRNAs in bacteria </div> <div>One is for translation initiation while the other is the standard <br><span class=cloze>[...]</span> (N-formyl methionine) is the translation initiation </div> <div><br>Takeaway: The Shine-Dalgarno sequence helps to <b>recruit</b> the ribosome to the mRNA to <b>initiate</b> <b>translation</b> by <b>aligning</b> the <b>ribosome</b> with the start codon&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">The Shine-Dalgarno Sequence </span></div> <div>The Shine-Dalgarno sequence is the mRNA site where the ribosome binds<br><br>Also called the <span class=cloze>ribose binding sequence</span> (RBS)<br> Found in the 5’ UTR of mRNA<br> 8-13 nucleotides in length </div> <div><br>RBS is purine-rich, so base pairs with a pyrimidine rich sequence at the 3’ end of the 16S rRNA&nbsp; <br>The 16S rRNA is in the <span class=cloze>30s</span> ribosomal subunit </div> <div><br>The start codon will be located a couple of nucleotides downstream from the RBS<br>Positioned in the <span class=cloze>P</span> site </div> <div>While <span class=cloze>AUG</span> is the start codon, it can be in other positions as well and code for <span class=cloze>Met</span>&nbsp;<br>There are actually 2 different methionine tRNAs in bacteria </div> <div>One is for translation initiation while the other is the standard <br><span class=cloze>Fmet</span> (N-formyl methionine) is the translation initiation </div> <div><br>Takeaway: The Shine-Dalgarno sequence helps to <b>recruit</b> the ribosome to the mRNA to <b>initiate</b> <b>translation</b> by <b>aligning</b> the <b>ribosome</b> with the start codon&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the <span class=cloze>[...]</span> ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the <span class=cloze>[...]</span> site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <span class=cloze>[...]</span></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the A site attacks the fMet-tRNAfMet at the P site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the A&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is VACANT<br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div>""<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the <span class=cloze>70s</span> ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the <span class=cloze>A</span> site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <span class=cloze><b><font color=""#478828"">vacant</font></b></span></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the A site attacks the fMet-tRNAfMet at the P site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the A&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is VACANT<br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div><br> "
"<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the 70s ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the A site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <b><font color=""#478828"">vacant</font></b></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the A site attacks the fMet-tRNAfMet at the P site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the <span class=cloze>[...]</span>&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is VACANT<br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div>""<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the 70s ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the A site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <b><font color=""#478828"">vacant</font></b></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the A site attacks the fMet-tRNAfMet at the P site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the <span class=cloze>A</span>&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is VACANT<br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div><br> "
"<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the 70s ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the A site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <b><font color=""#478828"">vacant</font></b></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the A site attacks the fMet-tRNAfMet at the P site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the A&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is <span class=cloze>[...]</span><br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div>""<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the 70s ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the A site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <b><font color=""#478828"">vacant</font></b></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the A site attacks the fMet-tRNAfMet at the P site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the A&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is <span class=cloze>VACANT</span><br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div><br> "
"<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the 70s ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the A site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <b><font color=""#478828"">vacant</font></b></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the <span class=cloze>[...]</span> site attacks the fMet-tRNAfMet at the <span class=cloze>[...]</span> site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the A&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is VACANT<br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div>""<div> <div> <div> <div> <div><span style=""font-weight: 700;"">Translation Elongation </span></div> <div>Goal: Form peptide bonds to produce a peptide<br> Elongation factors (EFs) act on the 70s ribosomal subunit<br> The <font color=""#478828"">first amino acid will always be <b>fMet</b></font>, but the 2nd and following could be any of the 20 <br><b>Elongation</b> is looking to add amino acid #2, and all subsequent ones as well </div> <div><span style=""font-weight: 700;""><br>Step 1: </span>Binding of aminoacyl-tRNA to A site<br><u><b> EF-Tu-GTP</b></u> binds to aminoacyl-tRNA and the charged-tRNA complex binds to the A site on the ribosome</div><div> The aminoacyl-tRNA anticodon must base pair with the codon of the mRNA GTP is hydrolyzed and EF-Tu-GDP leaves &amp; is recycled to EF-Tu-GTP by EF-Ts<br><br>At the end of step 1... </div> </div> </div> <div> <div> <div>The A site has <b><font color=""#478828"">amino acyl-tRNA</font></b><br>&nbsp;The P site has <font color=""#478828""><b>fmet-tRNA fmet</b></font><br>The E site is <b><font color=""#478828"">vacant</font></b></div> <br></div></div><div> <br></div></div><div><div><div> </div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 2: </span>Peptide bond formation (amide bond)<br> The ribosome is a peptidyl transferase </div> <div>Catalyzes peptide bond formation (23S rRNA)<br> The free amino group at the <span class=cloze>A</span> site attacks the fMet-tRNAfMet at the <span class=cloze>P</span> site<br> fMet is transferred to the growing (nascent) chain at the A site -- the peptide bond is formed <br>The uncharged tRNAfMet is left at the P site </div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div> <div><span style=""font-weight: 700;"">Step 3: </span>Translocation<br><u> EF-G-GTP translocase</u> binds near the A&nbsp;site<br> GTP hydrolysis to GDP shifts the ribosome one codon over on the mRNA The A site is VACANT<br> The P site has dipeptidyl-tRNA<br> The E site has the uncharged tRNA that will dissociate soon </div> <div><br>Keep repeating the process to continue to grow the nascent protein one amino acid at a time at a rate of about 20 nucleotides per second </div> </div> </div> <div> <div> <div><br>EF-Tu brings next aminoacyl-tRNA into the A site<br> New peptide bond is formed<br> EF-G translocase relocates the next codon into the A site</div></div></div></div></div><div><div><div><div> </div> </div> </div></div><br> "
"<div><div><div><span style=""font-weight: 700;"">Translation Termination</span></div><div>As the chain grows, it exits the large ribosomal subunit through a tunnel Termination occurs at a stop codon</div><div>Recall the 3 stop codons: <b><font color=""#478828"">UAA, UGA, &amp; UAG</font></b></div><div><br>At stop codon, the ribosome is waiting for the next aminoacyl-tRNA, but a release factor (RF) binds instead at <span class=cloze>[...]</span> site</div><div><span class=cloze>[...]</span> recognizes UAA &amp; UAG</div><div><span class=cloze>[...]</span> recognizes UAA &amp; UGA<br>Release factors activate peptidyl transferase activity of the ribosome</div><div>But, since there is not a peptide to transfer, this will <span class=cloze>[...]</span> the peptidyl-tRNA bond</div><div><br>This terminates translation &amp; the RF dissociates (this is the official end of translations)</div></div></div><div><div><div>EF-G-GTP binds to the <span class=cloze>[...]</span> (RRF) EF-G-GTP will hydrolyze its GTP to GDP<br><font color=""#478828""><b>EFG</b></font> and <b><font color=""#478828"">RRF</font></b> both dissociate the complex</div><div>IF-3 binds again to the <span class=cloze>[...]</span> subunit&nbsp;</div></div></div>""<div><div><div><span style=""font-weight: 700;"">Translation Termination</span></div><div>As the chain grows, it exits the large ribosomal subunit through a tunnel Termination occurs at a stop codon</div><div>Recall the 3 stop codons: <b><font color=""#478828"">UAA, UGA, &amp; UAG</font></b></div><div><br>At stop codon, the ribosome is waiting for the next aminoacyl-tRNA, but a release factor (RF) binds instead at <span class=cloze>A</span> site</div><div><span class=cloze>RF-1</span> recognizes UAA &amp; UAG</div><div><span class=cloze>RF-2</span> recognizes UAA &amp; UGA<br>Release factors activate peptidyl transferase activity of the ribosome</div><div>But, since there is not a peptide to transfer, this will <span class=cloze>hydrolyze</span> the peptidyl-tRNA bond</div><div><br>This terminates translation &amp; the RF dissociates (this is the official end of translations)</div></div></div><div><div><div>EF-G-GTP binds to the <span class=cloze>ribosome recycling factor</span> (RRF) EF-G-GTP will hydrolyze its GTP to GDP<br><font color=""#478828""><b>EFG</b></font> and <b><font color=""#478828"">RRF</font></b> both dissociate the complex</div><div>IF-3 binds again to the <span class=cloze>30s</span> subunit&nbsp;</div></div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><span class=cloze>[...]</span><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><span class=cloze><b><u>Erythromycin</u></b></span><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><span class=cloze>[...]</span> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><span class=cloze><b><u>Tetracyclines</u></b></span> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><span class=cloze>[...]</span> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><span class=cloze><b><u>Puromycin</u></b></span> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><span class=cloze>[...]</span> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><span class=cloze><b><u>Streptomycin</u></b></span> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><span class=cloze>[...]</span> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><span class=cloze><b><u>Chloramphenicol</u></b></span> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><span class=cloze>[...]</span></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><span class=cloze><b><u>Oxazolidinones</u></b></span></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><b><u>Streptogramins</u></b><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><span class=cloze>[...]</span><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Antibiotics </span></div> <div>Some antibiotics work by inhibiting translation in bacteria </div> <div><br><b><u>Puromycin</u></b> </div> <div>Translation inhibitor (very effective) </div> <div>Not used clinically because it affects both prokaryotic &amp; eukaryotic ribosomes (so it would kill the bacteria, but it would also kill the person, so obviously that’s not a really useful drug design) </div> <div>Produced by streptomyces bacteria<br> Mimics charged tRNA and binds to the A site<br> Peptidyl transferase activity adds to the polypeptide, which ends translation </div> <div><br><b><u>Chloramphenicol</u></b> *transferase*</div> <div>Binds 23S rRNA and blocks peptidyl </div> <div>Not often used clinically in developed countries because of serious side effects (blindness) but it is effective and cheap </div> <div><br><b><u>Erythromycin</u></b><br> Bind to 50S subunit and blocks the EF-G binding site<br> Blocks translocation<br> Example of a macrolide (Other examples: Roxithromycin, Azithromycin) </div> <div><br><b><u>Tetracyclines</u></b> </div> <div>Binds to 30S subunit </div> <div>Blocks aminoacyl-tRNA from entering the A site (so EF-tu is not going to be able to bring in the next charged tRNA to the A site) </div> <div><br><b><u>Streptomycin</u></b> </div> <div>Binds 16S rRNA affecting 30S-50S interaction </div> <div>Genetic code will be misread and the wrong amino acids will be added, which will lead to a non- functional protein (similar effect as a frameshift mutation) </div> <div>Example of an aminoglycosides (Other examples: Amikacin, Abrekacin, Kanamycin)<br><br><b><u>Oxazolidinones</u></b></div><div> <div> <div> <div> Example: Linezolid </div> <div>Binds 23S rRNA<br> Blocks initiation complex assembly </div> <div><br><span class=cloze><b><u>Streptogramins</u></b></span><br> Bind 23S rRNA </div> <div>Blocks peptidyl transferase &amp; releases incomplete polypeptides&nbsp;</div> </div> </div></div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Location </span></div> <div>Very similar to Prokaryotes but important differences </div> <div><br>mRNAs synthesis and RNA processing occur in the <span class=cloze>[...]</span></div> <div><br>mRNA is moved to <span class=cloze>[...]</span> for translation and may be intercepted by miRNA- RISC (if it isn’t intercepted then it can undergo translation) </div> <div><br>Translation is carried out by the <span class=cloze>[...]</span> ribosome&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Location </span></div> <div>Very similar to Prokaryotes but important differences </div> <div><br>mRNAs synthesis and RNA processing occur in the <span class=cloze>nucleus</span></div> <div><br>mRNA is moved to <span class=cloze>cytoplasm</span> for translation and may be intercepted by miRNA- RISC (if it isn’t intercepted then it can undergo translation) </div> <div><br>Translation is carried out by the <span class=cloze>80S</span> ribosome&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span><span class=cloze>[...]</span><span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span><span class=cloze>siRNA</span><span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br><span class=cloze>[...]</span><br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br><span class=cloze>siRNA action:</span><br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span><span class=cloze>[...]</span><span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span><span class=cloze>miRNA synthesis:</span><span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span><span class=cloze>[...]</span><span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span><span class=cloze>miRNA</span><span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div>miRNA action:<br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span class=cloze>[...]</span><br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">RNA Interference (RNAi) </span></div> <div>RNA interference is a group of mechanisms in eukaryotes involving small RNAs that impair expression of certain genes <br><u><font color=""#478828"">MicroRNA (miRNA)</font></u> &amp;<font color=""#478828""><u> small interfering RNA (SiRNA)</u></font> act on <font color=""#478828""><b>mature RNA</b></font> in the cytoplasm <br>Action of both <u><font color=""#478828"">relies on the RISC complex</font></u></div> <div><span style=""font-style: italic;""><br></span>miRNA<span style=""font-style: italic;""><br></span></div> <div>Regulates translation &amp; mRNA stability &gt; 2000 miRNA in human genome Regulates 30-50% of mammalian mRNA <br>More <b>common in animals than plants </b></div> <div><span style=""font-style: italic;""><br></span>siRNA<span style=""font-style: italic;""><br></span></div> </div> </div> <div> <div> <div>Regulates mRNA levels by endonuclease cleavage<br> More <font color=""#478828""><b>common in plants than animals</b></font><br> Useful in labs for “knockdown experiments”<br> SiRNA/RISC uses <font color=""#478828"">endonuclease</font> activity to <b>cleave</b> target mRNA </div> <div>Need <u>perfect pairing</u> between SiRNA and target mRNA </div> </div> </div> <div> <div> <div><span style=""font-style: italic;""><br></span>miRNA synthesis:<span style=""font-style: italic;""><br></span></div> <div>The miRNA gene is transcribed by RNA <b>polymerase II </b>and will end up with a stem-loop secondary structure where each of the stem-loops will be a functional miRNA </div> <div>pri-miRNA stem-loop structure is removed from the transcript by the Drosha-DGCR8 complex and brought to Exportin-5 (XPO5) </div> <div>The pre-miRNA is exported to the cytoplasm by XPO5 &amp; undergoes a 2nd cleavage by Dicer (22-25 bp) to cut off the loop of the stem-loop structure to leave a double-stranded RNA </div> <div>The two strands are separated and the mature miRNA (or siRNA) is loaded into the RNA Induced Silencing Complex (RISC) </div> <div><br>siRNA action:<br> Perfect base pair alignment with the target mRNA will follow the siRNA pathway<br><b>RISC</b> acts as an <font color=""#478828"">endonuclease</font> on the mRNA so it will not be translated<br> Target site is usually in the coding sequence of the mRNA </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span class=cloze>miRNA action:</span><br></div> <div>miRNA action happens when there is an imperfect base pairing between miRNA &amp; the non- coding region of the target mRNA. <br>mRNA turnover is still signaled but it <font color=""#478828""><b>takes longer</b></font> than with siRNA </div> <div>miRNA/RISC represses translation and increases turnover of the target mRNAs by the presence of RISC </div> <div>The target site is usually in the 3’ UTR of the mRNA (<u>non-coding region</u>)&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Therapeutics – Onpattro Treatment of hATTR </span></div> <div>hATTR: Hereditary amyloid transthyretin<br> Late onset disease – <span class=cloze>[...]</span><br> Progressive, <b><font color=""#478828"">fatal</font></b> disease<br> <span class=cloze>[...]</span> generates a TTR protein that won’t be able to fold properly </div> <div><br>The drug Patisaran (OnpattroTM) is a <span class=cloze>[...]</span> that will act in <b>liver cells blocking the translation </b>of the misfolded TTR </div> <div>Onpattro was the first FDA approved <span class=cloze>[...]</span>-based drug in August 2018&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Therapeutics – Onpattro Treatment of hATTR </span></div> <div>hATTR: Hereditary amyloid transthyretin<br> Late onset disease – <span class=cloze>doesn’t present until adulthood</span><br> Progressive, <b><font color=""#478828"">fatal</font></b> disease<br> <span class=cloze>Missense mutation</span> generates a TTR protein that won’t be able to fold properly </div> <div><br>The drug Patisaran (OnpattroTM) is a <span class=cloze>siRNA</span> that will act in <b>liver cells blocking the translation </b>of the misfolded TTR </div> <div>Onpattro was the first FDA approved <span class=cloze>siRNA</span>-based drug in August 2018&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the A site<br> eIF-3 binds to the 40s subunit to prevent the 60s subunit from binding <br>eIF-1 binds to the E site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the <span class=cloze>[...]</span> site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the start codon (AUG) <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The 60s subunit binds to form the 80s ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the A site<br> eIF-3 binds to the 40s subunit to prevent the 60s subunit from binding <br>eIF-1 binds to the E site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the <span class=cloze>P</span> site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the start codon (AUG) <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The 60s subunit binds to form the 80s ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the A site<br> eIF-3 binds to the 40s subunit to prevent the 60s subunit from binding <br>eIF-1 binds to the E site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the P site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the start codon (AUG) <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The <span class=cloze>[...]</span> subunit binds to form the <span class=cloze>[...]</span> ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the A site<br> eIF-3 binds to the 40s subunit to prevent the 60s subunit from binding <br>eIF-1 binds to the E site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the P site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the start codon (AUG) <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The <span class=cloze>60s</span> subunit binds to form the <span class=cloze>80s</span> ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the A site<br> eIF-3 binds to the 40s subunit to prevent the 60s subunit from binding <br>eIF-1 binds to the E site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the P site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the <span class=cloze>[...]</span> <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The 60s subunit binds to form the 80s ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the A site<br> eIF-3 binds to the 40s subunit to prevent the 60s subunit from binding <br>eIF-1 binds to the E site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the P site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the <span class=cloze>start codon (AUG)</span> <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The 60s subunit binds to form the 80s ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the <span class=cloze>[...]</span> site<br> eIF-3 binds to the <span class=cloze>[...]</span> subunit to prevent the <span class=cloze>[...]</span> subunit from binding <br>eIF-1 binds to the <span class=cloze>[...]</span> site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the P site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the start codon (AUG) <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The 60s subunit binds to form the 80s ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation Initiation Complex </span></div> <div><br>Step 1:<br> eIF-A binds to the <span class=cloze>A</span> site<br> eIF-3 binds to the <span class=cloze>40s</span> subunit to prevent the <span class=cloze>60s</span> subunit from binding <br>eIF-1 binds to the <span class=cloze>E</span> site </div> <div><br>Step 2:<br> eIF-2-GTP binds to Met-tRNAMet and brings it to the P site </div> <div><br>Step 3:<br> eIF-4 binds to the 5’ cap </div> <div>mRNA enters<br> The ribosome scans the mRNA from 5’ to 3’ to look for the start codon (AUG) <br>Translation initiates at a <b><u>Kozak sequence </u></b></div> </div> </div> <div> <div> <div>Example: ACCAUGG </div> <div><br>Step 4:<br> The eIFs exit </div> <div>The 60s subunit binds to form the 80s ribosome <br>The initiation complex is now complete&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">SARS-CoV-2 Inhibits Translation </span></div> <div><br>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus that causes COVID-19 <br><br>Produces Nsp1, which binds near <span class=cloze>[...]</span> and acts like a <b><u>translation initiation inhibitor</u></b> by <font color=""#478828"">blocking</font> the mRNA from binding with the ribosome <br><br>The <font color=""#478828"">availability of ribosomes</font> that can be used for translation is <font color=""#478828"">reduced</font> and, at some point, the <font color=""#478828"">viral translation will be favored&nbsp;</font></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">SARS-CoV-2 Inhibits Translation </span></div> <div><br>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus that causes COVID-19 <br><br>Produces Nsp1, which binds near <span class=cloze>40S mRNA site</span> and acts like a <b><u>translation initiation inhibitor</u></b> by <font color=""#478828"">blocking</font> the mRNA from binding with the ribosome <br><br>The <font color=""#478828"">availability of ribosomes</font> that can be used for translation is <font color=""#478828"">reduced</font> and, at some point, the <font color=""#478828"">viral translation will be favored&nbsp;</font></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation, Elongation, and Termination </span></div> <div><br>Translation, elongation and termination are the same as in prokaryotes <br><br>Eukaryote difference: The 5' and 3' ends are held together by protein interactions between the <span class=cloze>[...]</span> and the <span class=cloze>[...]</span></div> <div><br>Elongation factors:<br> Function the same, just with different names <br>eEF-1a = <font color=""#478828"">EF-Tu</font><br> eEF-1bg = <font color=""#478828"">EF-Ts</font><br> eEF-2 = <font color=""#478828"">EF-G <br></font></div> <div>The <font color=""#478828"">green</font> is prokaryotic names but most used in exams!<br><br>Termination factors:<br> eRF recognizes all stop codons </div> <div><br>Translation initiates as each new <span class=cloze>[...]</span> sequence <br>Each ribosome is making a copy of the same protein <br><span class=cloze>[...]</span>&nbsp;is a group of ribosomes on a single mRNA&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Eukaryotic Translation, Elongation, and Termination </span></div> <div><br>Translation, elongation and termination are the same as in prokaryotes <br><br>Eukaryote difference: The 5' and 3' ends are held together by protein interactions between the <span class=cloze>cap binding complex</span> and the <span class=cloze>PABP1</span></div> <div><br>Elongation factors:<br> Function the same, just with different names <br>eEF-1a = <font color=""#478828"">EF-Tu</font><br> eEF-1bg = <font color=""#478828"">EF-Ts</font><br> eEF-2 = <font color=""#478828"">EF-G <br></font></div> <div>The <font color=""#478828"">green</font> is prokaryotic names but most used in exams!<br><br>Termination factors:<br> eRF recognizes all stop codons </div> <div><br>Translation initiates as each new <span class=cloze>ribosome reads the Kozak</span> sequence <br>Each ribosome is making a copy of the same protein <br><span class=cloze>Polysome</span>&nbsp;is a group of ribosomes on a single mRNA&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Ricin Toxin </span></div> <div>Ricin is one of the most <span class=cloze>[...]</span> substances LD50 ~ 22μg/kg (~ 1.76 mg for an adult) <br><br>Enters the cell as a two-subunit protein linked by a disulfide bridge and is cleaved into ricin toxin A &amp; B by a protease inside cell <br><br><b><font color=""#478828"">Depurinates</font></b> 28S rRNA at A4324, which <span class=cloze>[...]</span> factor binding site <br>“RTA” is the glycoside hydrolase that depurinates <br><br>Can <span class=cloze>[...]</span> all the ribosomes in the cell to <b>shutdown translation</b> and <b>inhibit protein synthesis&nbsp;</b> <br><br>Ricin’s efficacy comes from its action as an enzyme&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Ricin Toxin </span></div> <div>Ricin is one of the most <span class=cloze>toxic known natural</span> substances LD50 ~ 22μg/kg (~ 1.76 mg for an adult) <br><br>Enters the cell as a two-subunit protein linked by a disulfide bridge and is cleaved into ricin toxin A &amp; B by a protease inside cell <br><br><b><font color=""#478828"">Depurinates</font></b> 28S rRNA at A4324, which <span class=cloze>destroys an elongation</span> factor binding site <br>“RTA” is the glycoside hydrolase that depurinates <br><br>Can <span class=cloze>inactivate</span> all the ribosomes in the cell to <b>shutdown translation</b> and <b>inhibit protein synthesis&nbsp;</b> <br><br>Ricin’s efficacy comes from its action as an enzyme&nbsp;</div> </div> </div><br> "
" <div> <div> <div>Almost all proteins formed in eukaryotic cells must undergo posttranslational modification to <font color=""#478828""><b><u>become fully functional proteins&nbsp;<br></u></b></font><span style=""font-weight: 700;""><br>Processing the N-Terminus</span></div> <div>Proteolytic processing is a very common posttranslational modification <br><br>Occurs in both prokaryotes and eukaryotes </div> <div><br><span class=cloze>[...]</span> is the first residue<br><br></div><div>In prokaryotes: peptide deformylase (PDF) removes the formal group of fMet </div> <div><u><font color=""#478828""><br>Methionine aminopeptidease </font></u>is responsible for the cleavage of methionine in both prokaryotes &amp; eukaryotes </div> <div><br>Typically occurs if the 2nd amino acid has a small, uncharged side chain N-terminus is very often acetylated in eukaryotes </div> <div><span style=""font-weight: 700;""><br>Proteolysis </span></div> <div>Common modification<br> Recall that <u><b><font color=""#478828"">zymogen</font></b></u> cleavage gives the active enzyme </div> <div>Trypsinogen cleaved by enteropeptidase to give trypsin <br>Chymotrypsinogen cleaved by trypsin to give chymotrypsin&nbsp;<br></div> </div> </div>"" <div> <div> <div>Almost all proteins formed in eukaryotic cells must undergo posttranslational modification to <font color=""#478828""><b><u>become fully functional proteins&nbsp;<br></u></b></font><span style=""font-weight: 700;""><br>Processing the N-Terminus</span></div> <div>Proteolytic processing is a very common posttranslational modification <br><br>Occurs in both prokaryotes and eukaryotes </div> <div><br><span class=cloze>Methionine</span> is the first residue<br><br></div><div>In prokaryotes: peptide deformylase (PDF) removes the formal group of fMet </div> <div><u><font color=""#478828""><br>Methionine aminopeptidease </font></u>is responsible for the cleavage of methionine in both prokaryotes &amp; eukaryotes </div> <div><br>Typically occurs if the 2nd amino acid has a small, uncharged side chain N-terminus is very often acetylated in eukaryotes </div> <div><span style=""font-weight: 700;""><br>Proteolysis </span></div> <div>Common modification<br> Recall that <u><b><font color=""#478828"">zymogen</font></b></u> cleavage gives the active enzyme </div> <div>Trypsinogen cleaved by enteropeptidase to give trypsin <br>Chymotrypsinogen cleaved by trypsin to give chymotrypsin&nbsp;<br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Amino Acid Modifications in Proteins </span></div> <div>Covalent chemical modifications of amino acids often alter or stabilize a charge </div> <div><br><u>Phosphorylation</u><br> Adding a phosphate group will add a <span class=cloze>[...]</span>&nbsp;charge<br> The hydroxyl groups of serine, threonine, &amp; tyrosine can be phosphorylated using ATP </div> <div><br><u>Carboxylation&nbsp;<br></u>The addition of a carboxyl group to glutamate activates prothrombin for <span class=cloze>[...]</span><br><span style=""font-style: italic;""><font color=""#478828""><b>This is specific for gamma-carboxylation</b></font></span></div> <div><br><u>Methylation &amp; acetylation&nbsp;<br></u>Lysine can receive 1-3 methyl groups<br> Glutamate can be methylated to give an <span class=cloze>[...]</span><br> Lysine can be acetylated to give an <span class=cloze>[...]</span> on the side chain <br><br><font color=""#478828"">Methylation &amp; acetylation of histones regulate <b>chromatin </b></font></div> <div>&gt; 80% of human proteins are N-acetylated on the N-terminus by <span class=cloze>[...]</span><br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Amino Acid Modifications in Proteins </span></div> <div>Covalent chemical modifications of amino acids often alter or stabilize a charge </div> <div><br><u>Phosphorylation</u><br> Adding a phosphate group will add a <span class=cloze>negative</span>&nbsp;charge<br> The hydroxyl groups of serine, threonine, &amp; tyrosine can be phosphorylated using ATP </div> <div><br><u>Carboxylation&nbsp;<br></u>The addition of a carboxyl group to glutamate activates prothrombin for <span class=cloze>Ca2+ binding&nbsp;</span><br><span style=""font-style: italic;""><font color=""#478828""><b>This is specific for gamma-carboxylation</b></font></span></div> <div><br><u>Methylation &amp; acetylation&nbsp;<br></u>Lysine can receive 1-3 methyl groups<br> Glutamate can be methylated to give an <span class=cloze>ester</span><br> Lysine can be acetylated to give an <span class=cloze>amide</span> on the side chain <br><br><font color=""#478828"">Methylation &amp; acetylation of histones regulate <b>chromatin </b></font></div> <div>&gt; 80% of human proteins are N-acetylated on the N-terminus by <span class=cloze>N-terminal acetyltransferase&nbsp;</span><br></div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Protein Kinases </span></div> <div>Protein kinases are enzymes that phosphorylate other proteins, in many cases altering the <span class=cloze>[...]</span>&nbsp;of the target <span class=cloze>[...]</span> </div> <div><br>Example: PKA phosphorylates enzymes, ion channels, chromosomal proteins, transcription factors </div> <div><br>The two classes are: ser-thr kinases and tyr kinases<br> Proteins must contain a <u>primary</u> sequence motif to be phosphorylated <br>A kinase may have <font color=""#478828""><b>several targets</b></font>, so it can <b><font color=""#478828"">regulate several pathways</font></b> <br><br>Protein phosphatases oppose kinase action (remove phosphates)&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Protein Kinases </span></div> <div>Protein kinases are enzymes that phosphorylate other proteins, in many cases altering the <span class=cloze>activity</span>&nbsp;of the target <span class=cloze>proteins</span> </div> <div><br>Example: PKA phosphorylates enzymes, ion channels, chromosomal proteins, transcription factors </div> <div><br>The two classes are: ser-thr kinases and tyr kinases<br> Proteins must contain a <u>primary</u> sequence motif to be phosphorylated <br>A kinase may have <font color=""#478828""><b>several targets</b></font>, so it can <b><font color=""#478828"">regulate several pathways</font></b> <br><br>Protein phosphatases oppose kinase action (remove phosphates)&nbsp;</div> </div> </div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Protein Kinases </span></div> <div>Protein kinases are enzymes that phosphorylate other proteins, in many cases altering the activity&nbsp;of the target proteins </div> <div><br>Example: PKA phosphorylates enzymes, ion channels, chromosomal proteins, transcription factors </div> <div><br>The two classes are: <span class=cloze>[...]</span> and <span class=cloze>[...]</span><br> Proteins must contain a <u>primary</u> sequence motif to be phosphorylated <br>A kinase may have <font color=""#478828""><b>several targets</b></font>, so it can <b><font color=""#478828"">regulate several pathways</font></b> <br><br><span class=cloze>[...]</span> oppose kinase action (remove phosphates)&nbsp;</div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Protein Kinases </span></div> <div>Protein kinases are enzymes that phosphorylate other proteins, in many cases altering the activity&nbsp;of the target proteins </div> <div><br>Example: PKA phosphorylates enzymes, ion channels, chromosomal proteins, transcription factors </div> <div><br>The two classes are: <span class=cloze>ser-thr kinases</span> and <span class=cloze>tyr kinases</span><br> Proteins must contain a <u>primary</u> sequence motif to be phosphorylated <br>A kinase may have <font color=""#478828""><b>several targets</b></font>, so it can <b><font color=""#478828"">regulate several pathways</font></b> <br><br><span class=cloze>Protein phosphatases</span> oppose kinase action (remove phosphates)&nbsp;</div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Biological Membranes </span></div> <div><br>Membranes serve as <span class=cloze>[...]</span> for both the <font color=""#478828"">boundaries</font> of the cell and the <font color=""#478828"">compartments</font> within the cell </div> <div><br>The protein content is unique and specialized for each membrane &amp; cellular compartment </div> <div><br>It is common for membrane proteins to undergo <span class=cloze>[...]</span> posttranslational modifications </div> <div><br>Synthesis of integral membrane and secreted proteins occurs on ribosomes of endoplasmicreticulum. Golgi apparatus <span class=cloze>[...]</span> and <span class=cloze>[...]</span>&nbsp;proteins made in ER.&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Biological Membranes </span></div> <div><br>Membranes serve as <span class=cloze>permeability barriers</span> for both the <font color=""#478828"">boundaries</font> of the cell and the <font color=""#478828"">compartments</font> within the cell </div> <div><br>The protein content is unique and specialized for each membrane &amp; cellular compartment </div> <div><br>It is common for membrane proteins to undergo <span class=cloze>multiple</span> posttranslational modifications </div> <div><br>Synthesis of integral membrane and secreted proteins occurs on ribosomes of endoplasmicreticulum. Golgi apparatus <span class=cloze>sorts</span> and <span class=cloze>distributes</span>&nbsp;proteins made in ER.&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Biological Membranes </span></div> <div><br>Membranes serve as permeability barriers for both the <font color=""#478828"">boundaries</font> of the cell and the <font color=""#478828"">compartments</font> within the cell </div> <div><br>The protein content is unique and specialized for each membrane &amp; cellular compartment </div> <div><br>It is common for membrane proteins to undergo multiple posttranslational modifications </div> <div><br>Synthesis of integral membrane and secreted proteins occurs on <span class=cloze>[...]</span>. Golgi apparatus sorts and distributes&nbsp;proteins made in ER.&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Biological Membranes </span></div> <div><br>Membranes serve as permeability barriers for both the <font color=""#478828"">boundaries</font> of the cell and the <font color=""#478828"">compartments</font> within the cell </div> <div><br>The protein content is unique and specialized for each membrane &amp; cellular compartment </div> <div><br>It is common for membrane proteins to undergo multiple posttranslational modifications </div> <div><br>Synthesis of integral membrane and secreted proteins occurs on <span class=cloze>ribosomes of endoplasmicreticulum</span>. Golgi apparatus sorts and distributes&nbsp;proteins made in ER.&nbsp;</div> </div> </div></div><br> "
" <div> <div> <div><span style=""font-weight: 700;"">Membrane Protein Signal Sequences </span></div> <div><br>The signal sequence is responsible for identifying if a protein needs to be synthesized at an ER ribosome <br><br>Features of the signal sequence <br><br>Located near the <span class=cloze>[...]</span> of the protein</div><div> 10-15 hydrophobic AA residues along with a few basic AA residues </div> <div><br>The signal sequence is typically removed by signal peptidase in the ER Cleavage site after an <span class=cloze>[...]</span> or <span class=cloze>[...]</span> residue </div> <div>Cytoplasmic signal recognition particle (<font color=""#478828""><b>SRP</b></font>) <u>recognizes</u> and binds to the signal sequence. </div> <div><br><br>How it works<br> (1) Protein synthesis begins on a <font color=""#478828"">free ribosome</font><br><br>&nbsp;(2) The signal sequence is formed early in translation<br><br>(3) The signal sequence and the ribosome bind to a signal recognition particle (SRP) <br>The <font color=""#478828"">signal sequence is what’s telling the SRP that this is a protein</font> that needs to be synthesized at the endoplasmic reticulum</div> <div>SRP binds to GTP and stops translation at ~70 AA<br><br>(4) SRP-GTP directs mRNA &amp; the ribosome to SRP-GTP receptor on the cytosolic face of ER </div> <div>Growing chain joins the peptide translocation complex (5) GTP <b><font color=""#478828"">hydrolyzes</font></b>, SRP dissociates<br><br>(6) Translation resumes </div> <div>The ATP-driven peptide translocation complex feeds the growing chain into the ER lumen until the protein is full synthesized </div> <div><br>(7) Signal peptidase within the ER lumen removes the signal sequence (8) The ribosome dissociates and is recycled&nbsp;<br></div> </div> </div>"" <div> <div> <div><span style=""font-weight: 700;"">Membrane Protein Signal Sequences </span></div> <div><br>The signal sequence is responsible for identifying if a protein needs to be synthesized at an ER ribosome <br><br>Features of the signal sequence <br><br>Located near the <span class=cloze>N-terminus</span> of the protein</div><div> 10-15 hydrophobic AA residues along with a few basic AA residues </div> <div><br>The signal sequence is typically removed by signal peptidase in the ER Cleavage site after an <span class=cloze>Ala</span> or <span class=cloze>Gly</span> residue </div> <div>Cytoplasmic signal recognition particle (<font color=""#478828""><b>SRP</b></font>) <u>recognizes</u> and binds to the signal sequence. </div> <div><br><br>How it works<br> (1) Protein synthesis begins on a <font color=""#478828"">free ribosome</font><br><br>&nbsp;(2) The signal sequence is formed early in translation<br><br>(3) The signal sequence and the ribosome bind to a signal recognition particle (SRP) <br>The <font color=""#478828"">signal sequence is what’s telling the SRP that this is a protein</font> that needs to be synthesized at the endoplasmic reticulum</div> <div>SRP binds to GTP and stops translation at ~70 AA<br><br>(4) SRP-GTP directs mRNA &amp; the ribosome to SRP-GTP receptor on the cytosolic face of ER </div> <div>Growing chain joins the peptide translocation complex (5) GTP <b><font color=""#478828"">hydrolyzes</font></b>, SRP dissociates<br><br>(6) Translation resumes </div> <div>The ATP-driven peptide translocation complex feeds the growing chain into the ER lumen until the protein is full synthesized </div> <div><br>(7) Signal peptidase within the ER lumen removes the signal sequence (8) The ribosome dissociates and is recycled&nbsp;<br></div> </div> </div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Ubiquitin </span></div> <div>A small, conserved, 76 AA protein </div> <div><br>Ubiquitin is attached at its <span class=cloze>[...]</span> to a <span class=cloze>[...]</span> residue in the target protein by a 3-enzyme system </div> <div><br>E1 – Ubiquitin <span class=cloze>[...]</span> enzyme<br> Ubiquitin attaches to the cysteine of E1, using ATP </div> <div><br>E2 – Ubiquitin <span class=cloze>[...]</span> enzyme<br> Ubiquitin is passed to the cysteine of E2 </div> <div><br>E3 – Ubiquitin <span class=cloze>[...]</span><br> Catalyzes the transfer of ubiquitin is passed to the lysine of the target protein <br>Different ubiquitin ligases target different proteins </div> <div><br>Repeating the process on the lysines in ubiquitin gives polyubiquitin <br><br><span class=cloze>[...]</span> is a marker for protein degradation by proteasomes&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Ubiquitin </span></div> <div>A small, conserved, 76 AA protein </div> <div><br>Ubiquitin is attached at its <span class=cloze>C-terminus</span> to a <span class=cloze>Lys</span> residue in the target protein by a 3-enzyme system </div> <div><br>E1 – Ubiquitin <span class=cloze>activating</span> enzyme<br> Ubiquitin attaches to the cysteine of E1, using ATP </div> <div><br>E2 – Ubiquitin <span class=cloze>conjugating</span> enzyme<br> Ubiquitin is passed to the cysteine of E2 </div> <div><br>E3 – Ubiquitin <span class=cloze>ligase</span><br> Catalyzes the transfer of ubiquitin is passed to the lysine of the target protein <br>Different ubiquitin ligases target different proteins </div> <div><br>Repeating the process on the lysines in ubiquitin gives polyubiquitin <br><br><span class=cloze>Polyubiquitination</span> is a marker for protein degradation by proteasomes&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (<span class=cloze>[...]</span>) or a <span class=cloze>[...]</span> break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the <span class=cloze>[...]</span>&nbsp;so you will lose a chunk of DNA is replication </div> <div><span class=cloze>[...]</span> strands are not easily re-ligated&nbsp;</div> </div> </div></div>""<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (<span class=cloze>nick</span>) or a <span class=cloze>double strand</span> break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the <span class=cloze>chromosome</span>&nbsp;so you will lose a chunk of DNA is replication </div> <div><span class=cloze>Highly oxidized</span> strands are not easily re-ligated&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by <span class=cloze>[...]</span> agents <br>Can be monofunctional, <span class=cloze>[...]</span></div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div>""<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by <span class=cloze>alkylating</span> agents <br>Can be monofunctional, <span class=cloze>bifunctional</span></div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of <span class=cloze>[...]</span> to <span class=cloze>[...]</span><br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs <span class=cloze>[...]</span>, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can <span class=cloze>[...]</span>&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div>""<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of <span class=cloze>cytosine</span> to <span class=cloze>uracil</span><br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs <span class=cloze>Spontaneous</span>, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can <span class=cloze>accelerate</span>&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span><span class=cloze>[...]</span> site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div>""<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span><span class=cloze>(AP)</span> site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate <span class=cloze>[...]</span>&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br><span class=cloze>[...]</span> levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div>""<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate <span class=cloze>reactive oxygen species (ROS)</span>&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br><span class=cloze>High</span> levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; thymine dimer&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks transcription &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; <span class=cloze>[...]</span>&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks <span class=cloze>[...]</span> &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div>""<div> <div> <div><div>If a mutation is not repaired, it will be passed on to daughter cells (become permanent), so it must be fixed! <br><br>Types of <b>damage</b>: Deamination, thymine dimer, alkylation, depurination, strand breaks</div></div></div><div> <br> <div><span style=""font-weight: 700;"">Deamination </span></div> <div>Most common is the deamination of cytosine to uracil<br>Occurs spontaneously in human cells (about 100/day)<br>5-meC --&gt; T is also spontaneous <br>Deamination of adenine to guanine occurs Spontaneous, but less often (10-9)</div> <div>Sodium <font color=""#478828"">nitrites</font> and sodium <font color=""#478828"">nitrates</font> can accelerate&nbsp;deamination </div> <br></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Oxidation </span></div> <div>Respiration and inflammation generate reactive oxygen species (ROS)&nbsp;&nbsp;<br>Hydroxide free radicals act as nucleophiles to attack <font color=""#478828""><b>Guanine or Thymine</b></font> <br>&nbsp;Cytosine and Adenine are less likely to be oxidized <br>High levels of ROS can lead to DNA strand breaks</div> </div> </div> <div> <div> <br></div></div><div><div> </div> </div> <div> <div> <div><span style=""font-weight: 700;"">Depurination </span></div> </div> </div> <div> <div> <div>Hydrolysis of the N-b-glycosyl bond between a purine base and the sugar-phosphate backbone <br>Occurs <font color=""#478828""><b>spontaneously</b></font> in humans<br> Creates <span style=""font-weight: 700; font-style: italic;"">a basic&nbsp;</span>(AP) site</div> <br></div></div><div><div> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Alkylation </span></div> <div>Covalent modification of the DNA bases by alkylating agents <br>Can be monofunctional, bifunctional</div> <div><font color=""#478828""><b>Nitrogen mustard</b></font> = bifunctional </div> <div><span style=""font-weight: 700;""><br>UV-Induced Damage </span></div> <div>2 adjacent pyrimidines form a cyclobutane ring<br> Most common with thymine --&gt; <span class=cloze>thymine dimer</span>&nbsp;<br>Causes a kink in the DNA helical axis&nbsp;</div><div>Blocks <span class=cloze>transcription</span> &amp; replication </div> <br> <div><span style=""font-weight: 700;"">Ionizing Radiation-Induced Damage </span></div> <div>Ionization of water can cause DNA damage<br> IR exposure can cause either single strand break (nick) or a double strand break </div> <div>Single strand breaks (SSB) are easily repaired by ligases <br>Double strand breaks (DSB) break the chromosome&nbsp;so you will lose a chunk of DNA is replication </div> <div>Highly oxidized strands are not easily re-ligated&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in <span class=cloze>[...]</span>-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br><span class=cloze>[...]</span>&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in <span class=cloze>transcription</span>-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br><span class=cloze>DNA Pol e</span>&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br><span class=cloze>[...]</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br><span class=cloze>High-fidelity DSB repair</span><span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div><span class=cloze>[...]</span> finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH <span class=cloze>[...]</span> activity <b>nicks</b> the unmethylated strand </div> <div>The <span class=cloze>[...]</span> strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA <span class=cloze>[...]</span> fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div><span class=cloze>MutL-MutS</span> finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH <span class=cloze>endonuclease</span> activity <b>nicks</b> the unmethylated strand </div> <div>The <span class=cloze>nascent</span> strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA <span class=cloze>Pol III</span> fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br><span class=cloze>[...]</span> repair&nbsp;</div><div><span class=cloze>[...]</span> binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which <span class=cloze>[...]</span></div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br><span class=cloze>Error prone</span> repair&nbsp;</div><div><span class=cloze>Ku70/80 complex</span> binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which <span class=cloze>results in DNA loss</span></div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited <span class=cloze>[...]</span> in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited <span class=cloze>recessive mutations</span> in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in <span class=cloze>[...]</span><br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br><span class=cloze>[...]</span> direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in <span class=cloze>eukaryotes</span><br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br><span class=cloze>Prokaryote</span> direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) <span class=cloze>[...]</span> makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) <span class=cloze>[...]</span> helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) <span class=cloze>[...]</span> fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) <span class=cloze>UvrABC excinuclease</span> makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) <span class=cloze>UvrD</span> helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) <span class=cloze>DNA Pol I</span> fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is <span class=cloze>[...]</span><br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) <span class=cloze>[...]</span>&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An abasic site (AP site) is formed </div> <div>(2) AP endonuclease cleaves the sugar-phosphate backbone at the abasic site <br>(3) DNA Pol I goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is <span class=cloze>eliminated</span><br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) <span class=cloze>ERCC1/XPF endonuclease</span>&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An <span class=cloze>[...]</span> is formed </div> <div>(2) AP <span class=cloze>[...]</span> cleaves the sugar-phosphate backbone at the abasic site <br>(3) <span class=cloze>[...]</span> goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700; font-style: italic;"">DNA REPAIR </span></div> <div>Overlap across repair systems is common between prokaryotes and higher organisms<br><br></div><div><span style=""font-weight: 700;"">Mismatch Repair </span></div> <div>MMR repairs incorrect base pairs and <u>small gaps</u> formed during replication In prokaryotes (you don’t need to know process for eukaryotes): </div> <div>MutL-MutS finds the mismatch and recruits MutH<br> MutH recognizes the GAmeTC strand<br> MutH endonuclease activity <b>nicks</b> the unmethylated strand </div> <div>The nascent strand will be unmethylated<br> An exonuclease creates a gap at the nick in the unmethylated strand DNA Pol III fills in the gap<br> DNA ligase seals the nick </div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Base Excision Repair </span></div> <div>BER repairs mismatched base pairs and <u>oxidized bases</u> formed due to damage <br>Eukaryotes have different glycosylases for different mismatches<br><br>How it works:</div> </div> </div> <div> <div> <div>(1) A DNA glycosylase cleaves the N--glycosyl bond <br>An <span class=cloze>abasic site (AP site)</span> is formed </div> <div>(2) AP <span class=cloze>endonuclease</span> cleaves the sugar-phosphate backbone at the abasic site <br>(3) <span class=cloze>DNA Pol I</span> goes from 5’ --&gt;&nbsp;3’ removing old bases and adding new ones – leaves a nick where it finishes<br>&nbsp;Exonuclease and synthesis activities <br>(4) DNA ligase seals the nick finishes</div></div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Prokaryotic Nucleotide Excision Repair </span></div> <div>NER repairs <u>helix-distorting legions</u> <br>Like <b><font color=""#478828"">thymine dimers</font></b> &amp; <b><font color=""#478828"">DNA alkylation </font></b></div> <div><br>How it works:<br>(1) UvrABC excinuclease makes 2 nicks </div> <div>1 on either site of the lesion <br>(2) UvrD helicase removes the damaged DNA <br>Leaves a gap&nbsp;</div><div>(3) DNA Pol I fills the gap<br>(4) DNA ligase seals the nick</div> <div><span style=""font-weight: 700;""><br>Eukaryotic Nucleotide Excision Repair </span></div> <div>NER repairs helix-distorting legions, especially in transcription-coupled repair <br>The excinuclease is a large complex <br>Contains: TFIIH helicase and XP-A through XP-G <br>DNA Pol e&nbsp;fills the gap <br>DNA ligase seals the nick</div> </div> </div> <div> <div> <br> </div> </div> </div> <div> <div> <div> <div><span style=""font-weight: 700;"">Xeroderma pigmentosum </span></div> <div>Inherited recessive mutations in XP protein (<b>homozygous</b>) <br><font color=""#478828"">Unable to repair damage cause by UV light </font></div> <div>Very high rate of skin cancers <br>Affects 1:250,00 births </div> <div>Presentation: Solar keratosis, squamous cell carcinoma, &amp; <b><u>melanoma </u></b></div> <div><span style=""font-weight: 700;""><br>Direct Repair Mechanisms </span></div> <div>For <u>guanine alkylation</u> in eukaryotes<br> Guanine’s tautomer can be methylated to give O6-methylguanine </div> <div>This will form an unfavorable G=T pair&nbsp;<br>Repaired by O6-methylguanine-DNA methyltransferase </div> <div>O6-meG is highly mutagenic </div> <div><br>Prokaryote direct repair mechanisms:<br> DNA photolyase breaks cyclobutane ring of the thymine dimer<br>AlkB demethylates 1-methyladenine and 3-methylcytosine </div> </div> </div> <div> <div> <div><span style=""font-weight: 700;""><br>Non-Homologous End Joining </span></div> <div>NHEJ repairs <u>double-strand breaks</u> <br>Main mechanism in higher organisms<br>Error prone repair&nbsp;</div><div>Ku70/80 complex binds the free DNA ends <br>Processing involves activation of Artemis exonuclease, which results in DNA loss</div></div></div><div><div><div> Artemis endonuclease clean up the ends by removing overhanging flaps DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Single-Strand Annealing Repair</span></div></div></div> </div> <div> <div> <div> <div>SSA repairs double-strand breaks<br> Found in <font color=""#478828""><b>both prokaryotes and eukaryotes</b></font><br> Error prone because DNA is eliminated<br> Must have homologous sequence on flanking the damage </div> <div><br>How it works:<br>(1) A 5’ --&gt; 3’ exonuclease cleans up the damaged ends </div> <div>(2) Single strand annealing protein (SSAP, Rad52) binds to the repeat sequences &amp; aligns the homologous sequences </div> <div>(3) ERCC1/XPF endonuclease&nbsp;removes the overhanging flaps <br>DNA ligase seals the nick </div> <div><span style=""font-weight: 700;""><br>Homologous Recombination DNA Repair </span></div> <div>HR repairs double=strand breaks<br>High-fidelity DSB repair<span style=""font-weight: 700; font-style: italic;"">&nbsp;</span>– undamaged sister chromatid used as a template for DNA resynthesis&nbsp;</div> </div> </div></div><br> "
"<div> <div> <div> <div><span style=""font-weight: 700;"">Gene Editing (CRISPR) </span></div> <div>Modeled after <span class=cloze>[...]</span> (in prokaryote)<br> The CRISPR locus contains the genes needed for protein encoding (<span style=""font-weight: 700; font-style: italic;"">Cas</span>) &amp; CRISPR sequences<br><br><b><font color=""#478828"">Cas </font></b>= CRISPR associated protein</div><div><font color=""#478828""><b> CRISPR</b></font> = Clustered Regularly Interspaced Short Palindromic Repeats </div> <div>23-47 bp sequences that match up with host pathogen <br><br>There can be <b><font color=""#478828""><u>1+ CRIPSR loci</u></font></b> in a genome </div> <div>Can make up a significant part of bacterial genome </div> <div><br>How the CRISPR complex is formed:<br> CRISPR loci is transcribed into primary transcript<br> The CRISPR sequence is complimentary to the tracker RNA (trRNA) Endonucleases process to give CRISPR-RNA duplexes<br> crRNA/trRNA duplex joins with Cas endonuclease to form the CRISPR complex </div> <div><br>Site-specific DNA cleavage by CRISPR:<br> trRNA and crRNA transcripts are fused into single-guide RNA (sgRNA) transcript <br><br>A Protospacer-Adjacent Motif (PAM) is needed in target DNA for CRISPR to cut </div> <div>3 nucleotide sequence </div> <div>Not present in CRISPR locus<br><br>Cas9 creates a DSB in target DNA between sgRNA and target </div> <div>Cas9 is most commonly used <span class=cloze>[...]</span> (<span style=""font-style: italic;"">S. pyrogenes</span>) <br>DSB typically repaired with NHEJ </div> <div>Gives a +/- 5 bp insertion or deletion (Indel) within the target – <font color=""#478828""><i>frameshift mutation&nbsp;</i></font></div> </div> </div></div>""<div> <div> <div> <div><span style=""font-weight: 700;"">Gene Editing (CRISPR) </span></div> <div>Modeled after <span class=cloze>bacteriophages</span> (in prokaryote)<br> The CRISPR locus contains the genes needed for protein encoding (<span style=""font-weight: 700; font-style: italic;"">Cas</span>) &amp; CRISPR sequences<br><br><b><font color=""#478828"">Cas </font></b>= CRISPR associated protein</div><div><font color=""#478828""><b> CRISPR</b></font> = Clustered Regularly Interspaced Short Palindromic Repeats </div> <div>23-47 bp sequences that match up with host pathogen <br><br>There can be <b><font color=""#478828""><u>1+ CRIPSR loci</u></font></b> in a genome </div> <div>Can make up a significant part of bacterial genome </div> <div><br>How the CRISPR complex is formed:<br> CRISPR loci is transcribed into primary transcript<br> The CRISPR sequence is complimentary to the tracker RNA (trRNA) Endonucleases process to give CRISPR-RNA duplexes<br> crRNA/trRNA duplex joins with Cas endonuclease to form the CRISPR complex </div> <div><br>Site-specific DNA cleavage by CRISPR:<br> trRNA and crRNA transcripts are fused into single-guide RNA (sgRNA) transcript <br><br>A Protospacer-Adjacent Motif (PAM) is needed in target DNA for CRISPR to cut </div> <div>3 nucleotide sequence </div> <div>Not present in CRISPR locus<br><br>Cas9 creates a DSB in target DNA between sgRNA and target </div> <div>Cas9 is most commonly used <span class=cloze>endonuclease in labs</span> (<span style=""font-style: italic;"">S. pyrogenes</span>) <br>DSB typically repaired with NHEJ </div> <div>Gives a +/- 5 bp insertion or deletion (Indel) within the target – <font color=""#478828""><i>frameshift mutation&nbsp;</i></font></div> </div> </div></div><br> "