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L3 Gene Regulation > Week 5 L3: DNA REPAIR > Flashcards

Week 5 L3: DNA REPAIR Flashcards

1
Q

WHAT TYPE OF REPAIR WILL BE FOCUSED ON HERE?

A

Nucleotide excision repair (NER)

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2
Q

What is the basic principle of NER?

A

Nucleotides on either side of the damage are excised (one 5’ direction and one 3’ direction) and DNA synthesis repairs

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3
Q

Why is this the most important method?

A

most general
recognise bulky components
doesn’t have to have a component predisposed to that damage
recognises anything wrong

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4
Q

What is the main enzyme in in E.coli for NER, cleaving fragment?

A

UvrABC

CLEAVES THE FRAGMENT FORM dna

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5
Q

What are the proteins in UvrABC?

A

Uvr, A, B,C

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6
Q

What enzymes are needed to process the gap which is left?

A

Helicase II (UvrD) and pol I required for catalytic turnover. ligase to seal it at the end

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7
Q

What proteins form the functional complex of UrvABC system?

A

B’s ATPase activity becomes activated by A.

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8
Q

What protein recognises damage in DNA?

A

UrvA

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9
Q

What are some features of UrvA?

A
  • 103 kDa ATPase that recognises damage
  • 2 Zn fingers
  • 2 ATP binding sites
  • binds damaged DNA Ks = 107 - 1011 M-
  • eg TT cyclobutane 2 x better than normal DNA, but
    6-4 photoproduct 1000 x tighter
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10
Q

What protein of UrvABC has nuclease activity?

A

C

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11
Q

Does UrvC bind to ss DNA specifically?

A

NO

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12
Q

Does C interact with A and B in solu?

A

NO

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13
Q

What protein has ATPase activity?

A

B

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14
Q

What is the first complex to bind to DNA?

A

UrvAB 2A 1 or 2 B

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15
Q

What does complex AB do when bound to DNA?

A

HYDROLYSES atp AND MAKES A BIG DISTORTION IN THE DNA,
DNA WRAPS AROUND URVB
giant kink in DNA

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16
Q

What binds once DNA wraps around UrvB?

A

C (nuclease)

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17
Q

How and where does C cleave DNA?

A

dual incisions
cuts 8 nt 5’
4 nt 3’ to damage

18
Q

What works on DNA after UrvC cleaves fragment?

A

UrvD/helicase ii

19
Q

How and where does UrvD

A

removes the fragment

12 nt fragment

20
Q

Is UrvB still present when helicase cleaves DNA?

A

YES

21
Q

What provides the E for helicase II activity?

A

ATP hydrolysis

22
Q

What is the role of Pol 1?

A

displaces UrvB and synthesise new strand. Ligase anneals the nick to existing DNA

23
Q

What sis the difference in NER between bacteria and humans (eukaryotes)?

A
  • similar just more proteins subunits involved.

- excised fragment excised is nearly 30 nt

24
Q

What are the effects if NER cannot be carried out in humans?

A

Xeroderma pigmentosum

25
Q

What are the effects of Xeroderma pigmentosum?

A

Hypermutability of cells on exposure to UV radiation

High frequency of light-induced skin cancer.

26
Q

What did Xeroderma pigmentosum allow us to discover?

A

identify important genes in the human NER

the genes are called XP…

27
Q

What human XP genes are involved in the recognition of the damage in the first place?

A

XPA, XPE

28
Q

What XP gene acts like UvrB?

A

XZPB and D

29
Q

What are the XP nucleases?

A

F and G

30
Q

In what regions are bulky lesions repaired more rapidly?

A

more rapidly in transcribed regions than in silent ones

31
Q

What strand has an enhanced rate of repair?

A

transcribed strand

32
Q

What blocks repair in transcribed strand?

A

RNA polymerase

33
Q

What is needed to overcome hinderance of RNA polymerase?

A

coupling factor

34
Q

What is the protein that deals with coupling in DNA?

A

TRCF

transcription-repair coupling factor

35
Q

What organisms is TRCF found in?

A

E.coli

36
Q

What motifs does TRCF contain?

A

Helicase

37
Q

What is the mechanism of TRCF?

A
  • TRCF recognises stalled RNAP
  • Binds to stalled complex, displacing RNAP
  • Binds UvrAB in A2B complex
  • Accelerates DNA repair
38
Q

What are the Transcription-repair coupling genes in humans and their proteins?

A

ERCC8 (CSA PROETIN)

ERCC6 (CSB PROTEIN)

39
Q

What XP proteins does CS protein enhance?

A

XPB XPD

40
Q

What does the CS come from?

A

Mutations lead to Cockayne’s syndrome.

syndrome with defects in transcription repair coupling/

41
Q

What are the symptoms of Cockayne’s syndrome?

A

moderate photosensitivity
serious developmental
neurological abnormalities

42
Q

What does CSB protein associate with and what does this result in?

A

RNA pol II. this is how the repair machinery couples to transcription of mRNA in EUK.

L3 Gene Regulation (14 decks)

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