The information content of genes is in the form of specific sequences of nucleotides along the
DNA strands. The DNA of an organism leads to specific traits by dictating the synthesis of proteins and of RNA molecules involved in protein synthesis (gene expression.)
Proteins are the link between genotype and phenotype.
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The study of metabolic defects provided evidence that genes specify proteins.
Garrod discovered that proteins (enzymes) are the link between genotype and phenotype.
He figured out that some inherited diseases are the inability to make enzymes
He noticed that the diaper of a baby was very brown.
He determined that the baby had alkaptonuria, which is a recessively inherited disorder where the urine is a brown color. This is due to homogentisic acid which cannot be broken down in the body, so it is excreted in the urine. The reason it cannot be broken down is because there is an absence of the enzyme needed in the biochemical pathway.
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Beadle and Tatum showed the relationship between genes and enzymes . They used the bread mold Neurospora and exposed it to X-rays to get mutants. They found 3 different classes of mutants. Each mutant was defective in a different gene. They exposed these mutants to different environments to see which ones allowed arginine to grow. They deduced that each mutant was unable to carry out one step in the arginine pathway – probably because it lacked the necessary enzyme
BEADLE
AND TATUM
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ONE GENE – ONE ENZYME HYPOTHESIS…AND
THE EVOLUTION OF THAT HYPOTHESIS
From Beadle and Tatums experiments, they came up with the one gene, one enzyme hypothesis.
However, not all proteins are enzymes, so it became the one gene- one protein hypothesis.
BUT…some genes have more than one polypeptide (THINK: quaternary structure of proteins), so it led to the one gene- one polypeptide hypothesis.
The newest discoveries have been taken into consideration and the scientific community have updated the definition of a gene as:
A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule.
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OVERVIEW: TRANSCRIPTION
TRANSLATION
DNA transcription Primary transcript (pre-mRNA) RNA processing mRNA translation protein
Genes provide the instructions for making specific proteins and getting from gene to protein needs two stages:
Transcription = DNA → RNA
Translation = RNA → Protein
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TRANSCRIPTION AND TRANSLATION IN
PROKARYOTES VS. EUKARYOTES
The basic mechanics of transcription and translation are similar in eukaryotes and bacteria.
Bacteria lack nuclei, and their DNA is not separated from ribosomes and other protein-synthesizing equipment.
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This allows the coupling of transcription and translation .
In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs at ribosomes in the cytoplasm.
The molecular chain of command in a cell has a directional flow of genetic information:
DNA  RNA  protein
Francis Crick dubbed this concept the central dogma in 1956.
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The message is carried in
RNA in the form of codons
(3 bases). It is read in the
5’ → 3’ direction.
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With a triplet code , three consecutive bases specify an amino acid, creating 4 3 (64) possible code words .
During transcription, one DNA strand, the template strand , provides a template for ordering the sequence of nucleotide bases in an mRNA transcript.
The mRNA base triplets are called codons .
Each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide chain.
The starting point establishes the reading frame ; subsequent codons are read in groups of three nucleotides.
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Marshall Nirenberg deciphered the code for the amino acids in 1961.
The genetic code must have evolved very early in the history of life  It is nearly universal, shared by organisms from the simplest bacteria to the most complex plants and animals.
Nirenberg determined the first match: UUU codes for the amino acid phenylalanine.
Sixty-one of 64 triplets code for amino acids.
The codon AUG not only codes for the amino acid methionine but also indicates the “ start ” or initiation of translation.
Three codons do not indicate amino acids but are “stop” signals marking the termination of translation.
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DNA → RNA
Promoter – DNA sequence where
RNA attaches and initiates transcription
Terminator – sequence that signals the end of transcription
Transcription Unit – sequence of
DNA that is transcribed into RNA
3 Steps of Transcription:
1. Initiation
2. Elongation
3. Termination
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The promoter determines which strand is the template and then transcription factors help RNA polymerase bind. The TATA box is an important part of the promoter that helps initiate transcription. The transcription complex consists of the promoter, transcription factors, and
RNA polymerase.
RNA polymerase separates the DNA strands at the appropriate point and joins RNA nucleotides complementary to the DNA template strand. Like DNA polymerases, RNA polymerases can assemble a polynucleotide only in its 5   3  direction ( therefore the template strand is 3’  5’ .)
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The RNA polymerase adds RNA nucleotides about 10-20 at a time to the growing 3’ end.
Several mRNA strands can be made at the same time….several different RNA polymerases can all be on the same DNA molecule and can all create mRNA. This helps the cell make the encoded protein in large amounts.
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In prokaryotes, termination stops at the termination signal (end of the gene)
In eukaryotes, transcription continues for 10-35 nucleotides past the stop signal. Later in the process, it gets cut down.
At this point, transcription has given us the primary transcripts or pre-mRNA
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RNA PROCESSING:
MODIFYING THE PRE-MRNA
- At the 5’ end , a 5’ cap is added (which is a modified guanine molecule)
- At the 3’ end , there is the poly-A tail (50-250 adenine nucleotides)  functions in helping to inhibit degradation and helps exportation from nucleus)
-- Both of these modifications have several important functions :
-Exporting mRNA from the nucleus
-Protecting mRNA from hydrolytic enzymes
-Helping the ribosome attach to the 5’ end of the mRNA
After both ends are modified, the introns
(non-coding portions) are spliced out.
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The introns are cut out using splicesomes. Therefore, the mRNA that leaves the nucleus
(exons only) is the abridged version that only carries genes – not “filler” DNA.
Introns = noncoding segments
Exons = coding segments
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There are short sequences at the end of introns that signal to the snRNP’s (small nuclear ribonucleoproteins). The snRNP’s recognize these sites and the splicesomes then cut out the introns and reattach the exons.
Ribozyme → RNA molecules that act like enzymes; in some organsisms RNA splicing can occur without additional proteins because the introns can catalyze their own excision
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Humans can get along with a small number of genes because we can “shuffle” our DNA; different polypeptides can be made depending on which segments we consider introns and which are considered exons.
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BUILDING A
POLYPEPTIDE!
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-The cell is always stocked with all 20 AA’s (from diet)
-The tRNA is folded like a cloverleaf; on one side it has an anticodon that matches up with the codon from the mRNA; on the other side it carries a specific AA
-The tRNA’s are used over and over; they drop off their AA’s and then go get another to be used again
Wobble → relaxation of 3 rd base pairing; sometimes the 3 rd base of the ANTICODON has an
“I” (inosine), which is an altered adenine; this can match up with U, C, or A; If each anticodon had to be a perfect match to each codon, we would expect to find 61 types of tRNA, but the actual number is about 45, because the anticodons of some tRNAs recognize more than one codon (the wobble!!)
CCI anticodon can match up with GGU, GGC and GGA (codons)
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This enzyme attaches each AA to its appropriate tRNA.
This process uses 1 ATP
There are 20 different aminoacyl-tRNA synthetases (one for each AA)
Process:
1. The active site of the aminoacyl tRNA synthetase binds to the AA and ATP
2. The ATP loses 2 P groups to become
AMP and binds with the AA
3. Then the right tRNA binds to the AA and displaces the AMP
4. The enzyme then releases the “activated
AA”
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RIBOSOMES:
SITES OF TRANSLATION
Ribosomes consist of 2 subunits, large and small; they are composed of rRNA and proteins
They have 3 binding sites for tRNA:
E = about to exit
P = holds the AA chain
A = “on-deck” AA
The ribosomes itself catalyzes the peptide bond between amino acids.
Like transcription, translation can be divided into 3 stages:
initiation
- elongation
- termination
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GTP (guanosine triphosphate ) → energy source for translation; this is very similar to
ATP and releases energy by breaking off phosphates
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Steps :
1. Small ribosomal subunit binds to mRNA leader (5’ end)
2. Initiator tRNA (methionine) binds to “start” codon –
AUG
3. Next the large ribosomal subunit binds
4. All of these components (small unit, mRNA, tRNA, large subunit) are brought together by initiation factors and form the translation initiation complex
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3 step process for each AA:
1. Codon recognition
2. Peptide bond formation
3. Translocation
This process uses elongation factors (proteins)
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TRANSLATION - TERMINATION
When a stop codon (mRNA) gets to get the A-site and instead of a tRNA binding, a release factor binds.
This adds a water molecule to the AA chain, and then releases the chain from the ribosome.
After the chain is released, all the factors dissociate from one another.
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POLYRIBOSOMES
OR
POLYSOMES
This is when many ribosomes trail along the same mRNA molecule. They can translate many proteins simultaneously and therefore are much more efficient.
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During and after synthesis, a polypeptide spontaneously coils and folds to its three-dimensional shape.
In addition, proteins may require post-translational modifications before doing their particular job.
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These modifications may require additions such as sugars, lipids, or phosphate groups to amino acids.
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In other cases, a polypeptide may be cleaved in two or more pieces OR two or more polypeptides may join to form a protein with quaternary structure.
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SIGNAL PEPTIDES – DETERMINE WHETHER
RIBOSOME WILL BE ATTACHED OR FREE
All ribosomes start as free (in the cytosol ); however, the polypeptide can cue the ribosome to go attach to the ER and become bound. The signal peptide is a sequence of about 20 AA’s near the front of the strand that tells the ribosome to go attach. This is the case for proteins/ enzymes that are going to be secreted from the cell . The signal recognition particle (SRP) sees this signal peptide and brings the ribosome to the ER to attach.
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Mutations are changes in the genetic material of a cell
(or virus). They are the ultimate source of new genes
(and genetic diversity!)
A point mutation (also called a substitution ) is a change in one base pair . It can have huge effects ( sickle cell ) or no affect at all (silent mutation), depending on which base is affected and where the AA is located in the protein.
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MISSENSE AND
NONSENSE MUTATIONS
Missense = codes for a different AA
Nonsense = changes into a stop codon, so it leads to a nonfunctional protein
Silent = changes the nucleotide but it codes for the same AA
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A frameshift mutation is when there is an insertion or deletion that causes the reading frame to change. This means that all of the AA’s after the mutation will be wrong. It has disastrous effects.
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Errors during DNA replication or recombination can lead to nucleotide-pair substitutions, insertions, or deletions.
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Mutagens are chemical or physical agents that interact with DNA to cause mutations.
Physical agents include high-energy radiation like X-rays and ultraviolet light.
Chemical mutagens cause mutations in different ways.
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