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Molecular Genetics > Eukaryotic Transcription 4 > Flashcards

Eukaryotic Transcription 4 Flashcards

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1
Q

what is the role of the heptad repeats in the CTD of the largest subunit of RNA pol II?

A
  • Helps bind to DNA and is essential for proper functioning of RNA pol II
  • 2 and 5 are Serienes
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2
Q

Which large basal transcription factor could you capture with an affinity column comprised of a synthetic CTD (heptad repeats)?

A

TFIIH

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3
Q

Does Mediator bind hyperphosphorylated or hypophosphorylated CTD?

A

hypophosphorylated

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4
Q

Which protein (in which factor) responsible for phosphorylating Ser5 of the CTD? What happens regarding transcription as a consequence?

A
  • the Cdk7 of TFIIH
  • transcription is paused
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5
Q

What happens when RNA pol II pauses after initiation?

A

Capping complex, the splicing complex and the add poly(A) complex bind the CTD

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6
Q

How is the pause alleviated?

A

TEFb phosphorylates Ser2 of the CTD and the two negative factors, DSLIP and NELF

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7
Q

What removes Ser5 as elongation proceeds?

A

a phosphatase recruited by TFIIF

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8
Q

What keeps TFIIF from recruiting the phosphatase while bound to the promoter in the PIC?

A

contact with TFIIB

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9
Q

TFIIF

A
  • promoter targeting of RNA pol II by binding to TFIIB and reduced nonspecific DNA interactions of pol 2
  • involved in initiation and elongation; decreases pausing and protects elongation complex from arrest
  • stimulates phosphatase activity which removes phosphates from the CTD - prepares the CTD for the next round of initiation and binding to the mediator complex
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10
Q

TFIIF is usually bound to which enzyme?

A

RNA pol II

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11
Q

what is the role of TFIIB Zn-ribbon in recruitment of TFIIF/RNA pol II

A

in the N-terminus of TFIIB

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12
Q

Which basal factor decreases pausing once elongation is under way?

A

TFIIF

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13
Q

Which subunit of TFIIE (alpha or beta) can be traced back to Archaea?

A

alpha

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14
Q

Xerma pigmentosa

A

mutations in TFIIH (helicase) can result in xerma pigmentosa in humans

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15
Q

what are the components of TFIIH?

A

XPD, XPB, Mat1, cyclin H, cdk7

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16
Q

XPD

A
  • helicase in TFIIH
  • not active as a helicase during transcription but is required for NER
  • can be traced back to arachaea and contain RecA domains
17
Q

XPB

A
  • helicase in TFIIH
  • can be traced back to arachaea and contain RecA domains
18
Q

Mat1

A
  • TFIIH
  • components of the CAK
19
Q

cyclin H

A
  • regulated by the cdk8 module of mediator
  • apart of CAK
20
Q

cdk7

A
  • apart of CAK
21
Q

Which two subunits of TFIIH have domains obtained from the bacterial RecA protein?

A

the two helicases (XPB and XPD)

22
Q

Explain the ratchet mechanism for helicase action by XPB.

A
  • XPD helicase activity does not participate in transcription but is still needed structurally to properly align with the kinase domain
  • XPB helicase lobes 1 and 2 ratchet along the downstream DNA by binding and releasing the backbones of the minor groove
23
Q

Which component of TFIIH independently participates in the regulation of the cell cycle?

A

CAK

24
Q

Reinitiation Scaffold Complex: which 3 components leave each cycle of transcription?

A

TFIIB, TFIIF and RNA pol II

25
Q

what acts as the “trigger” that ends the initiation phase and begins elongation?

A

CTD phosphorylation

26
Q

what does hyperphosphorylated CTD dislodge from?

A

TBP and mediator

27
Q

when does RNA pol 2 initiate and clear the promoter?

A

when CTD is hyperphosphorylated

28
Q

what happens to the CTD in absence of TFIIB?

A

the CTD is dephosphorylated by phosphatase activity stimulated by TFIIF

29
Q

termination of the transcription cycle

A
  • RNA pol II/TFIIF complex leaves the template, forms complex with the mediator, reinitiates with the CTD in the underphosphorylated state
30
Q

what is the CTD?

A
  • carboxy-terminal domain
  • largest subunit and consists of an array in amino acid repeats (7)
  • tyr-ser-pro-thr-ser-pro-ser
  • 42 repeats in humans, 26 in yeast
31
Q

TFIIE

A
  • binds RNA pol 2 and recruits TFIIH
  • modulates TFIIH helicase, ATPase and kinase activity
  • assists TFIIH in promoter melting
32
Q

TFIIH

A
  • closely associated with TFIIE binding and regulation
  • promoter melting through helicase activity
  • promoter clearance by CTD kinase activity
  • functions in nucleotide excision repair
33
Q

TFIIH core

A
  • 2 helicases
  • DNA binding activity 6-7 subunits
34
Q

protein kinase complex

A
  • TFIIK in yeast, CAK everywhere else
  • 3 subunits
  • phosphorylates the CTD of RNA pol 2 large subunits and activates cyclin-dependent kinases
35
Q

what are the functions of TFIIE/H in transcription?

A
  • phosphorylates CTD which facilitates promoter clearance
  • together with TFIIE, metls the transcription start site using 3’ - 5’ helicase
  • required for formation of first phosphodiester bond in RNA synthesis
36
Q

Steps in formation of the open promoter complex

A

1-Promoter DNA is positioned above the cleft (DNA Channel) in the polymerase.
2-Cleft opens and the DNA swings into the cleft.
3-Clamp closes and distorts the DNA in the region just downstream from the TATAA in preparation for melting.

37
Q

what percentage of yeast RNA pol 2 promoters can melt without TFIIH?

A

18%

Molecular Genetics (28 decks)

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