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CHEM 350 > Lecutre 27 - DNA Replication and Repair > Flashcards

Lecutre 27 - DNA Replication and Repair Flashcards

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1
Q

where does DNA replication initiate?

A

at replication origins

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2
Q

what are the 3 stages of DNA replication?

A
  1. initiation
  2. elongation
  3. termination
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3
Q

what are the 6 basic steps of DNA replication?

A
  1. origin unwinding + helicase recruitmen
  2. primase loading
  3. loading of sliding clamp
  4. loading of replicative polymerase
  5. bidirectional fork movement
  6. completion of replication
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4
Q

what does the structure of DNA polymerase resemble?

A

a right hand

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5
Q

what is exonuclease activity?

A

associated with proofreading

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6
Q

polymerase ensures ___ by _____

A

fidelity by proofreading

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7
Q

what does helicase do?

A

undwinds DNA base pairs

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8
Q

what are two types of replicative helicases?

A
  1. bacterial

2. eukaryotic

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9
Q

what is the helicase called in eukaryotes?

A

MCM

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10
Q

what are single-stranded binding proteins?

A

-they can adopt many secondary structures that would make copying by polymerase difficult

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11
Q

what is the single stranded binding protein called in eukaryotes? in bacteria?

A

RPA

SSB

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12
Q

what does topoisomerase do?

A

relieves supercoiling strains

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13
Q

where does DNA supercoil?

A

ahead of the replication fork

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14
Q

what does the sliding clamp and loader do?

A
  • clamp loader is an ATPase

- helps to load the clamp onto the template DNA

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15
Q

what is the clam in eukaryotes? in bacteria?

A
  • PCNA

- beta protein

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16
Q

what do initiator proteins do?

A

help recognize replication origin

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17
Q

what is the initiator protein in eukaryotes? in bacteria?

A
  • ORC

- DnaA

18
Q

what does primase do?

A

synthesizes short 10-30 nt RNA primer

19
Q

how does the polymerase/primase complex switch?

A

it switches form primer synthesis to replicative elongation

20
Q

where is the lagging strand synthesized?

A

in Okazaki fragments

21
Q

what happens to the ends of linear chromosomes during replication?

A

ends of linear chromosomes are truncated

22
Q

what is the solution to truncated ends?

A

-telomeric sequences are added

23
Q

what is a cause of truncated ends?

A

-inability to fill the gap left after the removal of the last RNA primer

24
Q

besides the typical DNA replication error rate, what is another cause of DNA damage?

A

exposure to radiation or chemical agents

25
Q

what are 2 main types of DNA damages?

A
  1. point mutations

2. insertions/deletions

26
Q

what are 2 types of point mutations?

A
  1. transitions (purine/ pyrimidine replaced by another purine/pyrimidine)
  2. transversion (purine replaced by a pyrimidine or vice versa)
27
Q

what is insertion/deletion?

A

-one or more nucleotide pairs missing or added

28
Q

how are DNA damage repairs mediated?

A

by enzymes

29
Q

distortions in ______ causes replication errors

A

dsDNA

30
Q

bases are subject to ______

A

natural/unnatural modifications

31
Q

what is the most common type of base damage?

A
  • hydrolytic breakage of the glycosidic bond between a purine and the sugar-phosphate backbone of DNA
  • leaves a gap which causes substitutions or deletions when the DNA is replicated
32
Q

what are the 4 mechanisms for DNA repair?

A
  1. Mismatch repair (MMR)
  2. Base excision repair (BER)
  3. Nucleotide excision repair (NER)
  4. Translesion synthesie (TLS)
33
Q

what does MMR do?

A
  1. fixes single base errors

2. fix splipped-strand replication errors

34
Q

what does BER do?

A

-abasic sites cleaved by AP endonucleases

-

35
Q

what does NER do?

A
  • short stretches of damaged DNA with bulky lesions are removed by NER
  • followed by resynthesis
36
Q

what can NER be coupled with?

A

transcription

37
Q

what is TCR?

A
  • transcription coupled repair

- used to repair damaged DNAs that have stalled transcription

38
Q

what is TLS?

A
  • follow the sliding clamp

- switched between normal replication to TLS when a lesion is found

39
Q

how are double-strand breaks (DSB) fixed?

A
  1. homology directed repair

2. homologous recombination

40
Q

what is homology directed repair

A
  • uses homologous chromosome

- conversion of info in the region of the break to info from the homolog

41
Q

what is homologous recombination?

A

-exchange large segments of DNA

CHEM 350 (22 decks)

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