Symes DNA Repair

Question 1

Normal methylation sites in prokaryotes

Answer 1

A and C

Question 2

What function does 5-azacytidine have, and how does it work?

Answer 2

Nucleoside analogue
- contains an N instead of a CH2 to prevent methylation

Question 3

What is a transition mutation and how does it occur?

Answer 3

GC -> AT
Pu-Pyr to Pu-Pyr

Deamination of a 5-methylcytosine leads to a conversion to Thymine

Question 4

Transversion mutation

Answer 4

AT -> TA
Pu-Pyr to Pyr-Pu
- can’t be repaired

Happens by radiation or other bad stuff

Question 5

Can photodimerization occur with purines and pyrimidines?

Answer 5

No, it can only occur with pyrimidines

via UV light
- creates Thymine dimers

Question 6

What causes the creation of 8-oxoguanine, and what does it end up being paired with?

Answer 6

ROS, Adenine

Question 7

3 methods of single-strand repair

Answer 7

1) Direct repair of a base
2) Excision repair (NER, BER)
3) Mismatch repair

Question 8

What is an example of Direct Base Repair?

Answer 8

Repair of O6-alkylguanine
- similar in prokaryotes and eukaryotes
- MGMT alkylates itself to restore the guanine

Question 9

Mechanism Nucleotide Excision Repair in Prokaryotes

Answer 9

1) UvrAB scans (ATP) recognizes damage and bends DNA (ATP)
2) UvrA leaves, UvrC joins
3) 3’ cut, 5’ cut, UvrB helicase removes damaged piece
4) DNA Pol I replaces excised DNA, ligase seals nick

Prokaryotes

Question 10

Mechanism of Base Excision Repair

Answer 10

1) Uracil-DNA N-glycosylase recognizes and removes damaged base from backbone
2) Endonuclease creates 5’ nick
3) Backbone removed and replaced with new base by DNA Pol I 5’ endonuclease
4) DNA ligase reseals gap

Prokaryotes

Question 11

Mechanism of Prokaryotic Mismatch Repair

Answer 11

DNA Pol III epsilon subunit scans for mistakes during replication
1) MutS scans for damage
2) MutHLS created (ATP), scans for GATC sequence closest to damage
3) MutL cuts backbone 5’ to G in GATC
4) Helicase unwinds DNA, random exonuclease removes DNA
5) DNA Pol III fills the gap
6) DNA Ligase

Prokaryotes

Question 12

In mismatch repair, why is DNA Pol III used instead of DNA Pol I to reseal the gap

Answer 12

The gap is big, so DNA Pol I is not used

Question 13

Normal methylation sites in eukaryotes

Answer 13

C

Question 14

Maintenance methylase function

Answer 14

Methylates DNA after replication

Question 15

When are methylation sites chosen

Answer 15

Gametogenesis and Embryogenesis

Question 16

Are all C’s methylated in terms of heritability?

Answer 16

Nahh

Question 17

Which enzymes are involved in Prokaryotic BER?

Answer 17

Uracil-DNA N-glycosylase, DNA Pol I 5’ endonuclease, some other endonuclease

Question 18

Which enzymes are involved in Prokaryotic NER?

Answer 18

UvrABC, DNA Pol I

Question 19

Which enzymes are involved in Prokaryotic Mismatch Repair?

Answer 19

MutHLS, Exonuclease, DNA Pol III

Question 20

Enzyme involved in Direct Base Repair?

Answer 20

MGMT

Question 21

Difference between NER and BER

Answer 21

NER removes bigger chunks of DNA to repair things like Thymine dimers, while BER removes single bases to repair things like deamination of Cytosine that produces a Uracil

Question 22

When does single-strand repair occur?

Answer 22

Before translation