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Trends in MB and BT > DNA Damage & Repair > Flashcards

DNA Damage & Repair Flashcards

1
Q

What is a mutation?

A

When DNA damage makes it into the next generation (has to be heritable)

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2
Q

How is uracil removed from DNA?

A

Base excision repair (BER)

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3
Q

Dam methylase

A

Methylates specific sequence, results in E. coli being able to discern between parent and daughter strand in mismatch repair

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4
Q

What is transcription coupled repair?

A

A form of NER

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5
Q

What is translesion DNA synthesis?

A

DNA synthesis “past” a lesion in the sequence; frequently results in mismatches. Also called SOS repair. Involves Pol IV and V

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6
Q

What are some harmful physical agents?

A

Heat, X-ray, UV

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7
Q

What are some harmful chemical agents?

A

Acrylamide (liquid), Monosodium glutamate

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8
Q

Base transition

A

Change to a base of similar shape (pyrimidine -> pyrimidine, purine -> purine)

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9
Q

Base transversions

A

Change to a base of dissimilar shape (pyrimidine <-> purine)

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10
Q

Depurination

A

Breakage of glycosidic bond results in AP site

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11
Q

Deamination

A

Detaches NH2 from bases (again w water). C -> U, for example

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12
Q

Pyrimidine dimers

A

UV radiation causing covalent linkage between T-T.

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13
Q

Direct repair

A

Ex: photolyase to directly repair pyrimidine dimers by using light to break covalent bonds between adjacent pyrimidines.

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14
Q

Nucleotide excision repair

A

Multi enzyme complex recognize bulky dimers (caused by UV) -> cut them out. UvrA-D, DNA pol I, ligase. Can also be done during transcription, RNA pol encounters lesion and falls off and NER is begun w same enzymes

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15
Q

UvrA

A

UvrAB in complex finds bulky dimers and binds to site of distortion

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16
Q

UvrB

A

UvrAB in complex finds bulky dimers and binds to site of distortion. Recruits UvrC

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17
Q

UvrC

A

Flanks UvrB, cleave

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18
Q

UvrD

A

Helicase! In both NER and mismatch repair

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19
Q

Base excision repair

A

Glycosylases specific for each base that is not allowed in DNA seq., removes them and creates AP site. Glycosylases, AP endo+exonucleases, DNA pol, ligase

20
Q

How is damaged bases found in the DNA? (BER)

A

Flips out (no hydrogen bonds), recognized by glycosylases

21
Q

How is strand directed mismatch repair done in eukaryotes?

A

New strand have unligated nicks on them (because of the removed RNA primers) -> works as distinction

22
Q

Mismatch repair in prokaryotes

A

Dam methylase, mut-proteins involved, UvrD helicase, DNA pol III and ligase

23
Q

MutS

A

ATPase. Scans for mismatches. When it stops, binds ATP, causes conformational change that recruits MutL and MutH

24
Q

MutL

A

Recognises methylated GATC sequence, directs MutH

25
Q

MutH

A

Creates nick at hemimethylated GATC when contacted by MutL. Exonuclease activity in 5’->3’ direction. Breaks down strand up until mismatch

26
Q

Pol IV & V

A

Can replicate past lesions (just adds something). Low processivity.

27
Q

Holliday model

A

A model of resolving SSB in two duplexes using homologous recombination, where there is only breaks on one strand?Involves strand invasion, branch migration, and resolution.

28
Q

Possible resolutions of Holliday model

A

Crossover product; all strands exchange information. The two uncut strands are also cut and recombined.
Non-crossover product; small patch of new DNA in each duplex. No crossover between parent strands.

29
Q

RecBCD pathway

A

Pathway to resolve double stranded break in a single duplex. Involves RecA, RuvA-C. 3’ ssDNA tail is generated and then ssDNA overhang. Strand invasion with this overhang.

30
Q

RecBCD

A

Exonuclease that recognize blunt ends, also helicase activity. Unwinds and breaks down. At chi-site, 5’ -> 3’ continues but 3’ -> 5’ stops.

31
Q

RecA

A

allosterically binds to ssDNA in RebBCD pathway. Two binding sites; primary for ssDNA and secondary for dsDNA that also searchs for homology in another duplex. Facilitates strand invasion

32
Q

RuvA

A

Binds to Holliday junction, recruits RuvB-duplex

33
Q

RuvB

A

ATPase, drive branch migration by hydrolysis

34
Q

RuvAB

A

catalyze branch migration

35
Q

RuvC

A

Endonuclease; resolves Holliday junctions in RecBCD pathway. Has some seq. specificity to ensure it doesnt just cleave Holliday junctions as soon as they form

36
Q

Possible resolution in RecBCD pathway

A

Patch; no crossover between duplexes, if both are cut in the same place
Splice; crossover between duplexes, if they are cut on different places

37
Q

DNA microsatellites

A

Mutation-prone sequences of di-tetranucleotide sequences, causing slippage of DNA machinery

38
Q

Deamination of cytosine

A

Happens spontaneously. Creates uracil

39
Q

Alkylation of guanine

A

Results in O6-methylguanine. Mispairs with thymine.

40
Q

Oxidation of guanine

A

Caused by radiation or free radicals. Generates oxoG. Can basepair with both A and C

41
Q

Recombinases

A

Uses side chains (serine/tyrosine) to attack and cleave phosphodiester bonds, cleave all 4 strands and exchange information between duplexes. Then seals nicks themselves.

42
Q

Eukaryotes homologs of RecA

A

Rad51 and Dmc1

43
Q

Which protein introduces DSB in prokaryotes and eukaryotes?

A

none in bacteria. Spo11 in eukaryotes

44
Q

RecB

A

Helicase, exonuclease. Also makes sure RecA and not SSB coats ssDNA.

45
Q

RecD

A

Helicase, exonuclease

46
Q

RecC

A

Recognition of Chi-site

Trends in MB and BT (5 decks)

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