DNA Repair Pathways 1

Question 1

What is the common pathway of DNA repair?

Answer 1

1. Lesion detection
2. DNA damage removal
3. Repair or resynthesis by Ligases or Polymerases
4. Stalling of replication or cell cycle to allow time for repair.

Question 2

What are the consequences of an accurate repair?

Answer 2

Survival

Question 3

What are the consequences of an inability to repair?

Answer 3

cell death

Question 4

What is the consequence of a mis-repair?

Answer 4

genome instability

Question 5

Direct Reversal Repair (DRR)

Answer 5

The repair of DNA damage caused by alkylation. This is a direct repair by methyl-guanine DNA methyltransferase (MGMT) and ALKBH alpha-ketoglutarate Fe(II) dioxygenases (FeKDGs).

Question 6

How do MGMTs work in DRR and why are they called suicide proteins?

Answer 6

These enzymes work by having the cysteine in its active site go and bind the methyl group to remove it in a single reaction. It’s called a suicide protein because removal of the cysteine from the active site causes the enzyme to be permanently deactivated.

Question 7

How do FeKGDs work in DRR?

Answer 7

These enzymes work by oxidative dealkylation via alpha-ketoglutarate and Fe(II).

Question 8

What are the advantages of DRR?

Answer 8

It is the simplest, most error-free and economical DNA repair mechanism.

Question 9

MisMatch Repair (MMR)

Answer 9

Repairs simple, non-DNA helix distorting base mismatches, insertions or deletions from replication errors.

Question 10

What is the MMR workflow?

Answer 10

MutS⍺ and MutSB recognise mismatch. Their interaction is mediated by MutL. MCM unwinds DNA. PCNA is loaded by RFC. RPA binds to avoid denaturation during repair. Exo1 removes a piece of ssDNA containing the mismatch. DNA polymerase delta fills the gap adding the correct nucleotide where the mismatch was. DNA Ligase seals the nick.

Question 11

Base Excision Repair (BER)

Answer 11

The resolution of pre-mutagenic minor base distortions like ROS induced damage or deamination.

Question 12

What is the workflow of BER?

Answer 12

1. DNA glycosylase enzymes recognize damaged base. Hydrolysis removes the base and leave an AP site.
2. AP endonuclease (APE1) hydrolyses the backbone immediate 5’ of the AP site to make a repair patch of a 5’-OH and 3’dRP (deoxyribose phosphate
3. DNA polymerase fills the gap.

Question 13

What happens at a small repair patch in BER?

Answer 13

1 nucleotide is replaced via non-displacing synthesis occurs where 5’dPR lyase removed 5’dPR and DNA polymerase fills the gap.

Question 14

What happens at a long repair patch in BER?

Answer 14

2 or more nucleotides are replaced via displacing synthesis where DNA polymerase fills the gap and displaces the 5’dPR side of DNA creating a flap. A flap endonuclease removed the flap and DNA ligase comes in to seal the nick.

Question 15

Nucleotide Excision Repair (NER)

Answer 15

Resolution of more complex, DNA helix distorting lesions.

Question 16

What are the two possible repair pathways in NER and what are their functions?

Answer 16

Transcription Coupled NER (TC-NER_ recognises lesions that disrupt RNA polymerase progression.

Global-genome NER (GG-NER) surveys the entire genome for helix disruptions.

Question 17

What is the workflow of NER?

Answer 17

1. XPA, RPA and XPC-hHR23B recognizes the lesion.
2. TFIIH acts as ahelicase loosening the DNA around lesion.
3. 22-33 base oligonucleotide is removed by XPG on 3’ end and ERCC1-XPF on 5’ end.
4. Depending on PCNA the gap is filled by either DNA polymerase delta or epsilon.

Question 18

What causes defects in NER?

Answer 18

1. UV hypersensitivity
2. xeroderma pigmentosum
3. Cockayne syndrome