HRR: DNA repair

Question 1

what is direct reversal of DNA damage

Answer 1

specific enzymes repair DNA directly

Question 2

name the two main examples of direct reversal of DNA damage

Answer 2

• Repair of alkylated guanine by removing the ethyl or methyl at O6
• Joining of non-homologous ends of double strand breaks by DNA ligase

Question 3

define base-excision repair

Answer 3

Used to recognize and remove damaged or mutated bases; fixes C-U damage, hydroxylation of guanine, and damage from ionizing radiation

Question 4

describe base-excision repair

Answer 4

• DNA glycosylases look along the DNA for faulty base pairings and cleave N-glycosidic bonds to create an AP site
• AP endonuclease cleaves the backbone
• Deoxyribose phosphodiesterase removes the deoxyribose and forms a free 3’ and 5’
• DNA polymerase beta fills in the correct base
• DNA ligase reseals the strand

Question 5

define mismatch repair

Answer 5

Repairs mismatched base pairs or loops that occur during DNA replication

Question 6

describe mismatch repair in prokaryotes

Answer 6

• MutS scans the DNA and finds the mismatched base
• MutH binds to a hemi methylated site upstream near the mismatch.
• MutS binds to MutL, which then binds to MutH to form the mismatch repair complex. This bends the DNA.
• The endonuclease in MutH is activated, resulting in cleaving of the daughter strand
• Exonuclease is recruited and chews out the piece with the mismatch
• DNA polymerase III inserts the correct bases and ligase reseals the strand

Question 7

describe mismatch repair in eukaryotes

Answer 7

• MSH2 scans the DNA and finds the mismatched base
• Other mismatch proteins recognize the lagging strand via gaps between Okazaki fragments and recognizes the leading strand by the growing 3’.
• MSH2 binds to MLH1, which then binds to proteins at the okazaki fragments to form the mismatch repair complex. This bends the DNA.
• The endonuclease is activated, resulting in cleaving of the daughter strand
• Exonuclease is recruited and chews out the piece with the mismatch
• DNA polymerase beta inserts the correct bases and ligase reseals the strand

Question 8

define nucleotide excision repair

Answer 8

Recognizes and repairs lesions that cause distortions in the DNA helix

Question 9

describe nucleotide excision repair

Answer 9

• XP proteins control this process. The main one is XPC that recognizes and binds to the lesion in DNA.
• Helicases then unwind the DNA, allowing the section of DNA with the lesion is cut out
• DNA polymerase beta fills in the gap and ligase seals the strand

Question 10

define transcription coupled repair

Answer 10

repair occurring at the same time as transcription

Question 11

describe transcription coupled repair

Answer 11

• RNA polymerase encounters a thymine dimer and is stalled
• CSB recognizes that RNA polymerase has stalled
• CSB recruits XP proteins for nucleotide excision repair.

Question 12

define recombinatorial repair

Answer 12

Repairs double strand breaks by homologous recombination

Question 13

describe recombinatorial repair

Answer 13

• RAD51 binds to free 3’ ends, allowing them to invade non damaged DNA in the other chromosome via homologous recombination
• DNA polymerase beta fills in the base gaps, ligase rejoins the strands and forms holiday junctions

Question 14

describe the mutations in Lynch syndrome

Answer 14

mutations in genes involved in mismatch repair; 50% are due to defects in MSH2. This accounts for nearly 10% of cancers in the US

Question 15

describe the mutations in xeroderma pigmentosum

Answer 15

mutations in genes involved in nucleotide excision repair, normally XP proteins. Increase for risk of skin cancers and UV damage.

Question 16

describe the mutations in cockaynes syndrome

Answer 16

mutations in genes involved in transcription coupled repair, normally CSA or CSB. Impaired growth and neurological development, premature aging, sensitivity to sunlight.

Question 17

describe the mutations in hereditary breast cancer

Answer 17

mutations in BRCA1 or BRCA2 that code for recombinatorial repair of strand breaks.