DNA modification and repair

Question 1

What are the two normal modified bases in prokaryotic DNA?

Answer 1

N6-methyladenine and N4-methylcytosine

Question 2

What is the normal modified base in eukaryotic DNA and where are they primarily found?

Answer 2

5-methylcytosine found in CpG islands

Question 3

Does methylation occur on both strands simultaneously or one at a time?

Answer 3

One at a time

Question 4

What is the role of DNA methylation in prokaryotes versus eukaryotes?

Answer 4

Prokaryotes: protects DNA from own endonuclease and plays a role in mismatch repair
Eukaryotes: Plays a role in gene expression

Question 5

What is a transition mutation?

Answer 5

An AT to GC or GC to AT mutation i.e. purine to purine or pyrimidine to pyrimidine

Question 6

What is a transversion mutation?

Answer 6

An AT to TA or GC to CG mutation

Question 7

What is an intercalating agents, and what type of mutations are they often responsible for?

Answer 7

Molecules that insert themselves between base pairs and are often responsible for insertion/deletion mutations

Question 8

What normally causes inter/intra-strand cross-line and strand breaks?

Answer 8

UV or ionizing radiation. Also certain chemicals

Question 9

What is the general mechanism for all DNA repair systems?

Answer 9

1. Recognize the damage
2. Remove/repair the damaged DNA
3. Reseal the DNA

Question 10

Name two examples of enzymes that facilitate direct repair of damaged DNA bases

Answer 10

DNA photolyase–binds to UV damaged DNA containing pyrimidine dimers
O6 alkyl guanine alkyltransferase (MGMT)–fixes GC-AT transition mutations

Question 11

What are the steps of nucleotide excision repair?

Answer 11

1. ID damage with UvrAB (ATP)
2. UvrBC makes two endonucleocytic cuts 5’ and 3’ to lesion (ATP)
3. A helices unwinds and removes the excised piece
4. The gap is filled by DNA Pol I
5. The nick is sealed by DNA ligase

Question 12

What is nucleotide excision repair normally used for?

Answer 12

Repairing lesions that cause large structural changes eg. pyrimidine dimers

Question 13

What is base excision repair normally used for?

Answer 13

Specifically repairing singly mismatched base pairs

Question 14

What are the steps of prokaryotic base excision repair?

Answer 14

1. Mismatched bp ID’d by DNA N-glycosylase, which cleaves the base from the backbone
2. Endonuclease cleaves 5’ to empty backbone
3. DNA Pol I cleaves 5’ to damaged region
4. DNA Pol I fills the gap in a nick translation mechanism
5. DNA ligase seals the backbone

Question 15

What are the steps of mismatch repair?

Answer 15

1. MutS binds to DNA followed by MutL and MutH
2. MutS pulls DNA (uses ATP) until it finds a GATC sequence with a methylated A
3. MutH endonuclease cleaves the unmethylated strand 5’ to GATC
4. DNA helices II unwinds the DNA
5. Exonuclease removes the damaged DNA
6. DNA pol III and DNA ligase fill the gap and seal the nick

Question 16

How is eukaryotic base excision repair different?

Answer 16

Has two different pathways, short patch and long patch. Long batch pathway takes over if short patch doesn’t work completely.