Repair Pathways

Question 1

MMR Pathway (5):

Answer 1

1. Mismatch/parent strand recognized (MSH2/3 inserts and deletes; MSH2/6 mismatches).
2. Endonuclease cleaves both sides of mismatch (MLH1/PMS2).
3. Helicase and exonuclease removes the mismatched nucelotide.
4. DNA Pol III (delta/epsilon + PCNA) fills gap.
5. DNA ligase seals.

Question 2

BER Pathway (6):

Answer 2

1. base-specific DNA-glycosylase recognizes damaged DNA base.
2. glycosylase cleaves N-gycosidic bond between base and deoxyribose.
3. apurinic apyrimidine (AP) endonuclease cleaves sugar-phosphate backbone.
4. deoxyribose phosphate lyase removes 5’ sugar-phosphate residue
5. DNA Pol I (beta) fills gap
6. DNA ligase seals

Question 3

GG-NER Pathway (6):

Answer 3

1. Repair proteins recognize the helix distortion (XPC, XPE)
2. Proteins nucleate assembly of repair complex (XPA)
3. Excinucleases (endonucleases) make incisions 5’ and 3’ of lesion (XPF/ERCC1, XPG)
4. Helicase unwinds DNA to release the damaged oligomer (XPB and XPD from TFIIH complex)
5. DNA Pol (δ/ε with PCNA) fills the gap
6. DNA ligase seals the DNA

Question 4

TC-NER Pathway (9):

Answer 4

1. RNA Pol II blocked by damage.
2. Proteins recognize and ubiquinate RNA Pol II (CSA and CSB).
3. RNA Pol II dissociates.
4. Other NER proteins recruited (XPA, XPC, TFIIH).
5. Helicase unwinds to create bubble.
6. Excinucleases make incisions on both ends of damaged oligomer. Oligomer released.
7. DNA Pol (delta/epsilon with PCNA) fills gap.
8. DNA ligase seals.
9. Transcription resumes.

Question 5

SSB Repair (5):

Answer 5

1. PARP1 recognizes single strand break.
2. XRCC1 recruited. Serves as molecular scaffold for other repair proteins.
3. Enzymes (like APTX) process 3’ and/or 5’ broken ends.
4. DNA Pol beta fills gap.
5. DNA ligase seals.

Question 6

NHEJ Pathway (6):

Answer 6

1. Ku70/Ku80 recognizes and binds to both broken DNA strand ends; facilitates strand alignment.
2. DNA-PKcs:Artemis recruited.
3. WRN helicase opens strands.
4. Endonuclease (FEN1) removes frayed ends if needed.
5. DNA Pol fills gaps.
6. DNA ligase joins ends.

Question 7

HR Pathway (5):

Answer 7

1. RAD52 recognizes and binds DNA strand ends.
2. RAD51 recombinase searches for and aligns homologous strands (BRCA1/2 mediate RAD51 recombinase).
3. Nuclease and helicase activities make nicks.
4. RAD51 promotes ATP-dependent single strand invasion of homologous strand.
5. Undamaged chromosome serves as template/no change in DNA sequence.