CH28: DNA replication, repair & recombination (2)

28.4

what are translesion or error-prone polymerases?

special DNA pol that can replicate DNA across many lesions & make draft seq of genome for further repair

what are mutagens? how can hydroxyl radicals and nitrous acid damage DNA?

• mutagens: chem/physical agents that can alter specific bases within DNA after replication is done

• hydroxyl radicals: oxidize guanine to 8-oxoguanine, which base pairs w A instead of C

• nitrous acid: deaminates A to form hypoxanthine, which bp w C intsead of T

what are the 3 steps to single-strand DNA repair system?

1. recognize offending bases

2. remove offending bases

3. repair gap w DNA pol & DNA ligase

what does the ε subunit of E.coli DNA pol III do for proofreading/repair?

• 3’—5’' exonuclease to remove mismatched nucleotides from 3’ end of DNA by hydrolysis

• if wrong base added, DNA synth slows, giving time to migrate newly synth strand from pol active site to exonuclease active site

define mismatch repair and the functions of MutS, MutL, and MutH

• mismatch repair: corrects errors made in replication that aren’t corrected by proofreading

• MutS: detects mismatch

• MutL: recruits restriction endonuclease that cleaves newly made DNA strand close to lesion to facilitate repair

• MutH: the endonuclease

what is base-excision repair? describe the steps and functions of what is involved (5)

base-excision repair: DNA repair for fixing small/dmg bases

1. dmg recognition (AlkA enz)

   1. AlkA binds to dmg base, flipping it out of DNA helix

   2. glycosidic bond is cut, base is removed

2. AP site formed

   1. AP site = DNA w/ no base

3. backbone nicking

   1. AP endonuclease recognize AP site

   2. cuts backbone near missing base

4. deoxyribose phosphodiesterase removes leftover sugar-phosphate

5. Repair gap by DNA pol and sealed by DNA ligase

what kind of DNA dmg does nucleotide-excision repair fix? how is it different from base-excision repair?

• it fixes bulky helix-distorting lesions by removing an entire nucleotide DNA segment, while base fixes single dmg bases

What does the UvrABC complex do in nucleotide-excision repair? After excision, how is DNA gap repaired?

• it is an excinuclease that detects DNA distortion and cuts the dmg strand on both sides, removing short oligonucleotide seg w/ lesion

  • 8 nuc away on 5’ side and 4 nuc away on 3’ side

after excision, DNA pol I fills missing nuc and DNA ligase seals backbone

why does DNA use thymine instead of uracil?

to let cells detect damaged cytosine (deamination to uracil would cause bp to change from C-G to U-A), and distinguish from normal DNA bases

• when C is deaminated to uracil, it would cause a mutation bp

what does uracil DNA glycosylase do in DNA repair?

• it removes uracil from DNA by hydrolyzing (breaking) bond between uracil and deoxyribose sugar to create AP site that then be repaired by cell to put correct C base in

what are tumor-suppressor genes?

genes that suppress tumor development when one copy is free of deleterious mutation onset (if both copies of a DNA repair enz are mutated, cancer is more likely)

what is the normal role of p53 in the cell? what happens if they are mutated?

• normal role: makes protein that detects DNA dmg and either activates DNA repair paths or triggers apoptosis (cell death) if dmg too severe

• mutated: cells lose ability to respond to dna dmg, so cells keep dividing to form tumors

  • most p53 mutations are somatic (acquired during life)

  • if smo inherits a copy, they have high risk of developing many cancers bc only one more mutation is needed to fully lose p53 function

what agents are cancer cells vulnerable to and why? what are 2 examples?

• they are vulnerable to agents that dmg DNA mc bc cancer cells

  • divide frequently, making their DNA rep path more active

  • often have defects in DNA-repair pathways

• examples: CYclophosphamide, cisplatin

for the following disease states, name their affected repair pathways

• xeroderma pigmentosum (skin)

• lynch syndrome (colorectal cancer)

• breast & ovarian cancer

• renal & lung cancer

• xeroderma pigmentosum (skin) — nucleotide excision repair

• lynch syndrome (colorectal cancer) —mismatch repair

• breast & ovarian cancer —double-strand break repair

• renal & lung cancer —base excision repair