The Mutiblity and Repair of Dna

Question 0

Transition mutation

Answer 0

Pyrimidine to pyrimidine or purine to purine

(T –> C) (A –> G)

Question 1

Substitution

Answer 1

Are mutations with simple base switches
There are two types:
1. Transitions
2. Transversions

Question 2

Transversions mutation

Answer 2

Pyrimidine to purine or purine to pyrimidine

(T or C –> A or G) (A or G –> T or C)

Question 3

Silent mutations

Answer 3

Mutations that does not alter protein function

Question 4

Missense mutation

Answer 4

Different amino acid; resulting protein may have partial function

Question 5

Nonsense mutation

Answer 5

Specifies stop codon; truncated, non functional protein

Question 6

Insertions and deletions, of numbers not divisible by 3, cause a ______________________.

Answer 6

Frameshift mutation

Question 7

Alternative forms of insertion and deletion?

Answer 7

1. Inversions - piece of DNA sequence separates, inverted and reattaches itself
2. Transpositions - DNA segments from different chromosome switch

Question 8

MutS

Answer 8

Protein that repairs DNA

• can go up or down stream
• look for bump out caused by mismatch

Question 9

MutS mismatch repair in E. Coli (10 + 1)

Answer 9

1. A homodimer of MutS recognizes a mismatch-induced distortion in the DNA
   2 conformational change occurs to MutS homodimer and ATP binds to each
2. Causes further kink
3. Complex recruits MutL which activates MutH in E. coli
4. In eukaryotes and most bacteria, MutL is the endonuclease and it’s homologues nick one strand of DNA near the mismatch
5. In E. Coli, MutH is the endonuclease that nicks the strand
6. The nick creates and excision entry point for exonuclease activity
7. Exonuclease chews strand with kink
8. Removes error
9. DNA pol fills gap
10. Ligase reseals

Question 10

How does MutS know which nucleotide to replace? (6)

Answer 10

1. Dam methylase (E. coli enzyme) methylates A residues in th 5-GATC-3 sequence
2. Occurs every 246 bp
3. Following replication and before Dam methylase activity, the daughter DNA duplexes are hemimethylated
4. In E. Coli, MutH recognizes the the hemimethylated sites,
5. but MutH is inactive unless activated by MutL.
6. Thus, only areas of mismatch and hemimethylation are repaired by the MutS system

Question 11

Mutagens

Answer 11

1. Alkylation
2. Oxidation
3. Radiation

Question 12

Alkylation

Answer 12

Transfer of a methyl or ethyl group to bases and phosphate groups in DNA

Eg. O6-methylguanine, which mispairs with thymine

Question 13

Oxidation

Answer 13

Reactive oxygen species (ROS)

Eg oxoG which base pairs with A and C

Question 14

Radiation

Answer 14

260nm wavelength absorbed by bases causes dimerization or adducts

Causes DNA pol to stop during replication

Question 15

Dimerization

Answer 15

1) Creates bond between two thymine side by side (on same backbone)
2) does not bond to opposite - creates bulge
3) more likely to happen to thymine but also occurs with cytosine

Question 16

Intercalating Agents

Answer 16

1. Flat like DNA bases
2. Can do coaxial stacking
3. Induce Frameshift mutation

Question 17

Photoreactivation

Answer 17

1. Simple reversal of damage
2. After dimerization occurs, whiles in the dark, DNA photolyase binds to dimer and waits for sunlight
3. Using same wavelength (260nm) photolyase breaks dimer and restores DNA

Question 18

Chromosome repair: NHEJ

Answer 18

• A method to repair double stranded DNA breaks (DSB)

- Loss of sequence - mutagenic consequence but allows DNA to be replicated to pass on

Question 19

Chromosome repair: NHEJ process (6)

Answer 19

1. Ku 70/80 heterodimer binds the broken ends of DNA
2. And recruits kinase DNA-PKcs
3. DNA-PKcs recruits Artimis
4. Artimis processes the broken end via exo and endonuclease activity (cleans end - wants blunt ends)
5. Ligase binds back together
6. Non-hemologous end joining

Question 20

Translesion synthesis

Answer 20

1. Mechanism for bypassing a lesion in DNA
2. Allows replication to continue
3. Avoids incomplete replicated DNA

Question 21

Prokaryote Translesion repair

Answer 21

1. DNA pol III reaches bulge and dissociated from DNA
2. Pol IV or V binds on and can read through lession/bulge
3. Pol III binds again and continues after bulge with newly synthesized strand complete

Question 22

Eukaryote translesion repair - polymerase-switching model

Answer 22

1. DNA pol stalls at site of lesion
2. Ubiquitination of PCNA occurs
3. Causes the recruiting of translesion pol
4. Reads through lesion.
5. Replication pol replaces the translesion pol and replication continues

Question 23

Eukaryote translesion repair - gap-filling model

Answer 23

1. DNA pol does not stall at site of lesion but skips over leaving a gap
2. Translesion polymerase follows behind and fills in the gap