Chapters 16 and 17

 Before the end of the semester we will be covering…
 Historical DNA experiments
 Structure of DNA/RNA
 DNA Replication
 Protein Synthesis (Transcription and Translation)
 Mutations
 Gene Expression (if time)
 No more labs this semester!
 Your final will be comprehensive  Both multiple choice and short answer…more info to come!

 In the 1940s little was understood about inheritance and how it worked.
 It was believed the genetic material was either DNA or protein.
 It was understood that chromosomes are made of both DNA and protein
 Initial experiments suggested it was protein…little was understood about DNA’s structure or function (proteins were identified as being more complex)

 goal was to identify if inherited substance was either DNA, RNA, or protein
 used chemicals and bacteria that only allowed one of the above to be active at a time
 Results determined that the transforming agent was DNA
 Scientific community still skeptical

 used bacteriophages to confirm DNA is the genetic material
 bacteriophages were tagged with radioactive isotopes (DNA--P; protein--S)
 it was shown that the DNA was able to “infect” the bacteriophages, not the protein by tracking the radioactivity

 discovered the shape of DNA molecule was a double helix
 using pictures of the molecule, they built a model
 sugar/phosphate backbone
 nitrogen bases in the interior
 strands are antiparallel
 helix uniform in diameter
(base-pairing rules)

 Franklin used x-ray diffraction to photograph DNA (her pictures were used by Watson and Crick)
 Wilkins was working closely with
Franklin in her lab and allegedly showed
Watson and Crick the photograph that helped them build their model
 Watson, Wilkins, and Crick were awarded the Nobel Prize for science in
1962.
 Rosalind Franklin died in 1958 of cancer and was never given a Nobel Prize.

 Using the original papers published in Nature in
1953, identify the characteristics of a DNA molecule.
 What important characteristics did they (Watson,
Wilkins, Crick, and Franklin) discover?
List/highlight as many as you can.

 Classified as a nucleic acid
(biological molecule)
 Genetic material organisms inherit from their parents
 Copied prior to cell division
(mitosis/meiosis)
 Shape of a double helix
 Made up of nucleotides
(building blocks)
 5-carbon sugar (deoxyribose), phosphate, nitrogen base

 Base-Pairing Rules:


A  T
C  G
 Directionality


Complementary strands
Antiparallel: each strand runs in an opposite direction
 Designated 5’ and 3’ ends (carbon on sugar)
 Two types of bases


Purines: two carbon rings
 Guanine, Adenine
Pyrimidines: one carbon ring
 Cytosine, Thymine, Uracil

 mRNA (messenger RNA)—instructions (from
DNA) for making protein
 tRNA (transfer RNA)– carries amino acids
 rRNA(ribosomal RNA)—makes up ribosomes
 5-carbon sugar (ribose)
 Single stranded (one gene)
 Uracil instead of thymine
 A  U

 Have adenine, cytosine, and guanine
 Made of nucleotides
 Sugar and phosphate backbone
 Nitrogen bases perpendicular to backbone
 Held together by hydrogen bonds

 Occurs during S-phase of Interphase in the cell cycle
 Semi-conservative process. Each new strand of DNA produced is made of one parental and one new strand (described by Watson and
Crick)
 Each strand serves as a template for the new strand


In prokaryotes DNA is circular
In eukaryotes DNA is linear

 Begins at the origin of replication (specific sequences of
DNA nucleotides)
 Proteins recognize this sequence and attach to the DNA and separate the two strands creating a “bubble”
 At either end of this “bubble” is the replication fork
 Replication then proceeds in both directions from the origin until both strands are copied.
 In prokaryotes replication starts in one spot, in eukaryotes multiple spots

 Helicase: enzyme that unwinds and unzips the helix at the replication forks.
 Single-strand Binding Protein (SSBP’s): binds to unpaired DNA strand to keep them from re-pairing
 Topoisomerase: enzyme that relieves tension ahead of the replication fork (from untwisting of strand)
 Primase: enzyme that synthesizes the RNA primer for replication
 DNA Polymerase: several enzymes that catalyze the synthesis of new DNA (in eukaryotes there are 11 total); also checks for errors
 Ligase: links new fragmented DNA segments together

 Replication only occurs in the 5’ to 3’ direction
 Nucleotides added only to 3’ end of molecule…
 This is problematic for one side of the DNA molecule
 Leading strand: continuous strand
 Single RNA primer
 Lagging strand: discontinuous in fragments (Okazaki fragments)
 multiple RNA primers

1. Origin of replication is located
2. Bubble forms in DNA helix by Helicase
3. Primase synthesizes primer to begin replication
 Need RNA primer to have something to add nucleotides to.
4. DNA Nucleotides are added by DNA polymerase to primer to begin new strand
5. Replication proceeds in the 5’ to 3’ direction on both sides of the molecule
 Leading and lagging strands
6. Replication continues until the entire molecule is copied http://highered.mheducation.com/sites/0035456775/student_view0/chapter12/dna_replication.html
http://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html

 After every round of replication some of the DNA molecule is lost due to polymerase not being able to replicate it.
 To avoid excess loss of DNA, the ends of eukaryotic chromosomes have telomeres (long repeating sequences)


Excess DNA nucleotides (no genetic info)
Acts as a buffer to actual genes (does shorten over time— thought to be evidence of aging)

Chapter 18

 Gene Expression: process by which
DNA directs the synthesis of proteins
 occurs in two parts: Transcription and Translation
 this process dictates the presence of specific traits (genotype/phenotype)
 occurs in all organisms
 Watson and Crick describes this as the “central dogma”
(DNA  RNA  Protein)

 synthesis of RNA (mRNA) using DNA as a template (protein instructions)
 occurs in nucleus (eukaryotes) or cytoplasm
(prokaryotes)
 Prokaryotes can begin translation before transcription is finished
 Eukaryotes have an extra step during transcription before translation can begin

 DNA is a template strand, which is used to produce mRNA instructions (for protein)
 mRNA is complementary to DNA
 uses different nucleotides (uracil)
 RNA polymerase unzips DNA and joins complementary RNA nucleotides to copy instructions
 reads 5’ to 3’ , no primer needed
 promoter: DNA sequence where RNA polymerase attaches and initiates transcription http://www.dnalc.org/resources/3d/13transcription-advanced.html




Initiation


RNA polymerase joins to the promoter and begins to unwind helix helped by transcription factors (proteins), creates a
“transcription-initiation complex”
Elongation


RNA polymerase unwinds/untwist 10-20 nucleotides at a time nucleotides added to 3’ end
 as mRNA is built, the molecule peels away from DNA and the double helix reforms
Termination

 in prokaryotes there is a terminator sequence (stop signal) eukaryotes transcribe a specific sequence to stop transcription (creates pre-mRNA)

 RNA processing: enzymes in the nucleus modify pre-mRNA
 To help protect from degradation
 5’ cap (modified G sequence)
 3’ (poly-A tail)
 RNA splicing: removal of large portions of the RNA molecule (cut and paste)
 eukaryotes have long stretches of non-coding DNA interspersed with coding segments
 introns: non-coding segments
 exons: coding segments eventually expressed

RNA Splicing…
 introns are removed and exons are joined together
 snRNPs: join together to form a spliceosome
 Once finished, completed mRNA leaves nucleus to begin translation

 synthesis of a polypeptide using mRNA as instructions
 occurs on ribosomes
(rRNA) in cytoplasm
 tRNA: transfers amino acids to growing protein
 each associated with a particular amino acid
 anticodon: complementary RNA sequence to mRNA

 instructions for producing a protein uses three letters on mRNA (triplet code)
 codon: mRNA triplet (3 nucleotides)

 methionine is “start”
“stop” codons UAA, UAG, UGA

http://www.dnalc.org/resources/3d/16translation-advanced.html
 Initiation

 mRNA, tRNA, and ribosome start with amino acid methionine (initiator tRNA)
“translation initiation complex”
 Elongation
 amino acid added to chain via sites on ribosome (A-P-E)


“elongation factors” help process; reads 5-3’ requires energy
 Termination
 stop codons end synthesis, codes for “release factor”

 release factors bind and protein is released via hydrolysis
Protein is then folded into appropriate shape with help of chaperonin proteins

 http://www.bozemanscience.com/mutations/
Mutation: change to genetic information
 Ultimate source of new genes
 May be spontaneous or result from mutagens
 Point mutations: change in single nucleotide (substitution)


 silent: change doesn’t alter amino acid sequence missense: changes one amino acid into another (minor changes) nonsense: change codon for amino acid into a stop codon
(premature end to translation)
 Frameshift mutation: add/lose nucleotides resulting in change to reading frame of codons (not multiples of 3)
 Insertion or Deletion