Lecture 25 - Replication fidelity, DNA repair and recombination (pt 1)

Question 1

Why DNA replication fidelity is extremely high

Answer 1

DNAP -> proofreading. Checks previous nt added and removes it with 3’ exonuclease activiy if mismatched

Question 2

DNAP delta and epsilon 4 domains

Answer 2

1) Polymerase activity finger
2) Exonuclease activity finger
3) Thumb
4) Palm

Question 3

Error rate of RNAP and DNAP and final error rate of DNAP after repair mechanisms

Answer 3

1 error in 10^4 nts.

final error rate of DNAP after repair mechanisms : 1 error in 10^9 nts.

Question 4

What proofreading mechanism explains

Answer 4

Explains the need for a primer

Question 5

Name of a single base change in DNA (which possibly affects protein)

Answer 5

Point mutation

Question 6

Name of point mutation changing amino acid encoded

Answer 6

Missense mutation

Question 7

Name of point mutation where codon becomes stop codon

Answer 7

Nonsense mutation

Question 8

Name of point mutation where codon becomes start codon and what happens

Answer 8

Missense mutation. Met is added w/ a regular tRNA-Met

Question 9

Consequence of missense and nonsense mutations

Answer 9

Impact on protein function

Question 10

Name of point mutation that changes codon into a SYNONYMOUS codon

Answer 10

Silence mutation

Question 11

3 possible consequences of silence mutations

Answer 11

1) May alter splicing -> indirect effect on protein stability
2) May affect RNA stability so amount of protein produced
3) May have no effect

Question 12

Why a lot of mutations is not good even though mutations allow evolution

Answer 12

Higher rate of mutation is bad. Affects all cellular functions, including growth

Question 13

Cause of many human genetic cancer syndromes

Answer 13

DNA repair diseases

Question 14

How uracil can arise in the genome and to what extent it is a problem

Answer 14

Deamination of a cytosine, not a problem, uracil easily removed

Question 15

How T in T-G bases can arise in the genome

Answer 15

Deamination of 5-methylcytosine

Question 16

What happens after replication of a dsDNA containing a TG mismatch (how are daughter strands affected)

Answer 16

One mutant daughter strand with a T-A pair

One wild-type daughter strand with a C-G pair

Question 17

How 5-methylcytosine occurs and rate of cytosine and 5-methylcytosine deamination

Answer 17

DNA methylase. C and 5-methylC low rate deamination at normal conditions

Question 18

3 DNA repair mechanisms and what they target

Answer 18

1) Base excision-repair
2) Mismatch excision-repair
3) Nucleotide excision-repair
Target damaged bases/mismatched base-pairs

Question 19

Base excision-repair : What errors recognized (3)

Answer 19

1) T in T-G pairs
2) 8 oxyguanine
3) alkylated bases (alkylating agents in cell)

Question 20

Base excision-repair : First step (3 things happen)

Answer 20

1) DNA glycosylase removes base
2) APEI endonuclease cuts at ribose 5’ end
3) AP lyase cuts at ribose 3’ end

Question 21

Base excision-repair : Important thing about lyase

Answer 21

Is part of DNA Pol beta

Question 22

Base excision-repair : Second step (2 things happen)

Answer 22

1) DNA Pol beta adds correct base (C)

2) DNA ligase seals DNA:DNA joints

Question 23

Mismatch excision repair : What errors recognized (2)

Answer 23

1) Most single-base mismatches (except T-G mismatch)

2) Short (1 to several nucleotides) insertions/deletions errors

Question 24

Mismatch excision repair : First step (2 proteins involved)

Answer 24

MSH2 and MSH6 bind mismatch site

Question 25

Mismatch excision repair : Second step (4 proteins involved)

Answer 25

MLH1 endonuclease, PMS2, DNA exonuclease and DNA helicase : Remove many nts on mismatch side

Question 26

Mismatch excision repair : Third step

Answer 26

DNA Pol fills gaps and DNA ligase seals DNA:DNA joints

Question 27

What can cause a high incidence of colorectal cancer in a family

Answer 27

Nonfunctional copy of MSH2 or MLH1 genes