Chiolo Lecture 1

Question 1

What are examples of replication error damages?

Answer 1

Mismatches and Insertions/Deletions

Question 2

What sources of DNA damage does mismatch repair solve?

Answer 2

1. replication errors
2. intercalating agents (EtBr)

Question 3

How were DNA repair genes identified?

Answer 3

by their sensitivity of mutations to DNA damaging agents

Question 4

What are “UVr” genes?

Answer 4

genes for nucleotide excision repair - loss leads to UV sensitivity

Question 5

What are “Rad” genes?

Answer 5

genes for double-stranded break repair - loss leads to radiation sensitivty

Question 5

What are “Mut” genes?

Answer 5

genes for mismatch repair - loss results in high mutation rate

Question 6

What is one health issue that results from mismatch repair mutation?

Answer 6

hereditary non-polyposis colorectal cancer (HNPCC)

Question 7

When do mismatches frequently occur?

Answer 7

during DNA replication

Question 8

When are mismatches permanent?

Answer 8

they are not repaired before a new round of replication

Question 9

What is the first protection against mismatches?

Answer 9

the proofreading activity of DNA polymerase

Question 10

What is the function of DNA polymerase?

Answer 10

contains a 3’-5’ exonuclease domain that facilitates the removal of mismatched nucleotides

Question 11

DNA polymerases raise the accuracy to:

Answer 11

10^-7 errors/bp

Question 12

Mismatch repair raises the accuracy to:

Answer 12

10^-9 errors/bp

Question 13

What components are needed for mismatch repair?

Answer 13

1. parental strand (template)
2. MutS
3. MutL
4. MutH

Question 14

What is the function of endo-nuclease?

Answer 14

(‘nickase’) = cleaves the DNA bonds within the DNA molecule

Question 15

What is the function of exo-nuclease?

Answer 15

cleaves the nucleotides at the end of a DNA molecule, require free 3’ or 5’ -OH, works with a helicase

Question 16

Which Mut recognizes the mismatch as a “distorsion” in the DNA molecule?

Answer 16

MutS, recognizes a kink at mismatch

Question 17

How is the parental strand recognized by Mut H?

Answer 17

by DNA methylation

Question 18

What is the function of MutH?

Answer 18

binds the nearest methylated sites and cuts only non-methylated DNA

Question 19

What is the function of Dam methylase?

Answer 19

adds methyl groups at 5’ -GATC sites (works before and after replication [before replication, Dam methylase methylates the parental strand. during replication, no methylation occurs. after methylation, Dam methylase methylates the replicate strand]) mismatch repair occurs before the methylation of newly synthesized DNA

Question 20

What exonuclease is used in the 5’-3’ position?

Answer 20

Exo VII or RecJ

Question 21

What exonuclease is used in the 3’-5’ position?

Answer 21

Exo VI

Question 22

What is the function of MutS?

Answer 22

recognizes the mismatch

Question 23

Does the nascent strand in eukaryotes need endonuclease?

Answer 23

No, no need for an endonuclease on lagging strand because Okazaki fragments

Question 24

What is the function of PCNA?

Answer 24

might provide a guide for strand recognition on the leading strand

Question 25

What is the function of specialized MutS variants?

Answer 25

recognize DNA loops and remove them

Question 26

What error is caused by defective MMR?

Answer 26

causes elongation or trimming of repeated DNAs

Question 27

What is microsatellite instability?

Answer 27

inconsistent DNA lengths in a typical marker of HNPCC

Question 28

What error is caused by intercalating agents?

Answer 28

cause the addition of base pairs by slipping between the bases in the template strands

Question 29

What are deletions caused by?

Answer 29

distortions and partial unwinding at the DNA polymerases; skipping or adding one or more bases