DNA repair mechanisms

Question 1

Direct repair

Answer 1

• Cyclobutane dimers repaired by photo dependent DNA photolyase through process called photoreactivation
  (PHOTOREACTIVATION IS NOT DONE IN HUMANS)
• O6-methylguanine pairs with T instead of C. Methylguanine methyltransferase removes methyl from guanine to change it back

Question 2

Base-excision repair

Answer 2

Repairs small non distorting alterations; DNA glycolyase cleaves n-glycosyl linkages resulting in AP site, AP endonuclease recognizes AP site and removes base, DNA pol β resynthesizes strand and sealed by ligase

Question 3

Nucleotide-excision repair (NER)

Answer 3

completed NER complex made of XPA-XPG. repairs distorting, bulky damage (e.g. UV induced pyrimidine dimers, incorporation of benzopyrene by covalent bond to guanine); distortion recognized by XPC which recruits XPA, RPA, and TFIIH (contains XPB and XPD), unwinds (done by XPB and XPD), nicks both strands, and removes 29 nucleotide stretch that includes damage (XPF/ERCC1 dimer and XPG), DNA pol ε (pol I in e coli) fills gap and ligase seals. Xeroderma pigmentosum (XP) affected individuals have deficiencies in NER complex; show dry skin (xeroderma) and freckles (pigmentosum) in sun-exposed areas and are extremely sensitive to UV radiation

Question 4

Transcription coupled repair

Answer 4

type of NER in actively transcribed gene. RNA pol is stalled by damage and is recognized by CsB, which recruits CsA, XPA, RPA, and TFIIH (helicase activity done by TFIIH), XPG and XPF recruited and cut ends of damaged area and remove, gap filled by DNA pol and sealed by ligase. In eukaryotes, ERCC6 and ERCC8 recognize the stalled RNA pol and recruit repair enzymes. Cockayne syndrome is deficiency in ERCC6 and/or 8 (aka CsB and/or CsA); leads to photosensitivity (not to extent of XP), delayed neurological development, and premature aging.

Question 5

Mismatch repair

Answer 5

• Prokaryotes: A residues in GATC sequences are methylated in old strands (by Dam methylase) to differentiate. MutS recognizes error and binds to MutL which binds to MutH (endonuclease that cleaves at GATC sequences), polymerase fills gap, and ligase seals
• Eukaryotes: complex of MLH and MSH proteins involved in binding to mismatched DNA and distinguish old and new strands (new strand denoted by small nicks), endonuclease cut strand between nick and mismatch, helicase unwinds and exonuclease removes segment with error, and then replacement by DNA pol and ligase. People with inherited mutations are at higher risk for nonpolyposis colorectal cancers.

Question 6

Homologous recombination

Answer 6

repairs DNa after synthesis but before division. Broken ends are converted to 3’ overhangs by exonuclease, one of which hybridizes with homologous chromosome, displacing one strand. 3’ end of invading strand is extended, displacing mrore of other strand, which hybridizes with other strand and allows it to be extended. Both are extended and ligated to old strands, resulting in crossover structure called Holliday structure. These crossovers are cleaved and rejoined at crossover points and any mismatch is repaired by NER. BCRA1 and BCRA2 encode homologous recombination proteins

Question 7

Non-homologous end joining (NHEJ)

Answer 7

damaged segment not replaced, but joined by other free DNA end by ligase, but results in deletion of several bases at each end. Can occasionally ligate to other chromosomes, resulting in chromosomal translocations