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Molecular Biology > Chapter 11: General Transcription Factors in Eukaryotes > Flashcards

Chapter 11: General Transcription Factors in Eukaryotes Flashcards

1
Q

TFIIIC

A

600kD protein w/ 6 subunits and “linker” region (dumbell shaped) that can contact 2 internal promoters simultaneously and can stretch to span large distances (required for all class III transcription)

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2
Q

GC-rich box/region

A

located in genes lacking TATA box upstream of transcription start site

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3
Q

determined by Reinberg et al to be important elongation factor using radio-labelled nucleotides in vitro

-prevents RNA polymerase from sustained pausing at specific pause sites in DNA & triggers proofreading by stimulatig RNase enzyme to remove RNA & resume transcription

A

TFIIS (x2)

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4
Q

TAF250 & TAF150 (x3)

-other functions=acetyltransferase or protein kindase enzyme that phosphorylates other proteins

A

essential for TFIID binding to promoter; can bind initiators and DPEs without binding TATA box: can function as coactivators b/c can stimulate transcription in TATA box/TBP absence (recruit TBP and other TAFs to complex)

-other functions?

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5
Q

UBF (upstream binding factor) (x3)

-binds to upstream promoter element (UPE)

A

bends the DNA to help SL1 bind to the core promoter element by functioning as an assembly factor (coactivator)

  • composed of 2 polypeptides, sufficient to stimulate rRNA transcription
  • binds to?
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6
Q

pre-initiation complex

A

promoter with RNA Pol & trxn factors assembled there

-tightly bound, initiates open promoter complex (DNA melted)

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6
Q

TFIIIB (x3)

A

orients polymerase at start site and tightly binds DNA at upstream promoter, promoting several rounds of transcription

-required for all classIII gene expression

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6
Q

Sentenac et al

A

observed TFIIIC attachment to different sizes of tRNA genes using SEM

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6
Q

zinc finger protein with 2 cysteines/histidines that binds the 5S rRNA internal promoter with TFIIIC, triggering TFIIIB binding to upstream promoter; essential for 5S rRNA transcription

A

TFIIIA

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7
Q

observed TFIIIC attachment to different sizes of tRNA genes using SEM

A

Sentenac et al

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8
Q

bends the DNA to help SL1 bind to the core promoter element by functioning as an assembly factor (coactivator)

  • composed of 2 polypeptides, sufficient to stimulate rRNA transcription
  • binds to?
A

UBF (upstream binding factor)

-binds to upstream promoter element (UPE)

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9
Q

composed of 30 and 70kD peptides that tightly/specifically bind RNA polymerase and prevents nonspecific DNA binding by polymerase

-other function?

A

TFIIF

-can prevent short pausing at pause sites

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10
Q

TFIIE

A

enhances TFIIH kinase activity

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11
Q

TFIIIA (x4)

A

zinc finger protein with 2 cysteines/histidines that binds the 5S rRNA internal promoter with TFIIIC, triggering TFIIIB binding to upstream promoter; essential for 5S rRNA transcription

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11
Q

promoter with RNA Pol & trxn factors assembled there

-tightly bound, initiates open promoter complex (DNA melted)

A

pre-initiation complex

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13
Q

TAFs (TBP-associated proteins)

A

14 ID’d by precipitating TBP and western blotting (8 in Drosophila, 12 in yeasts)

-function=interact with promoter initiator, downstream promoter element (DPE), and gene-specific transcription factors

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14
Q

TBP (universal transcription factor) (x4)

-structure=saddle-shaped; function=opens up DNA and bends TATA box

A

38/43kD protein rich in basic amino acids (giving positive charge) which binds to the minor groove within the TATA box by mutating nucleotides in both major and minor grooves; recruits TAFs to assemble preinitiation complex

-structure/function?

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15
Q

binds to GC domains and recruits TAF-110 (130 human) which functions as bridge for TAF250-150. These then recruit TBP to form preinitiation complex and begin transcription

A

Sp1 (an activator)

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16
Q

TFIIS (x3)

A

determined by Reinberg et al to be important elongation factor using radio-labelled nucleotides in vitro

-prevents RNA polymerase from sustained pausing at specific pause sites in DNA & triggers proofreading by stimulatig RNase enzyme to remove RNA & resume transcription

How well did you know this?
1
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17
Q

located in genes lacking TATA box upstream of transcription start site

A

GC-rich box/region

How well did you know this?
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18
Q

TFIIF (x2)

-can prevent short pausing at pause sites

A

composed of 30 and 70kD peptides that tightly/specifically bind RNA polymerase and prevents nonspecific DNA binding by polymerase

-other function?

19
Q

contains TATA-Box binding protein (TBP) and TBP-associated proteins/factors (TAFs)

19
Q

found evidence of pre-formed preinitiation comlex: RNA polymerase holoenzyme

-contains?

A

Kornberg & Young

-contains TFIIB, A, F, & H

20
Q

essential for TFIID binding to promoter; can bind initiators and DPEs without binding TATA box: can function as coactivators b/c can stimulate transcription in TATA box/TBP absence (recruit TBP and other TAFs to complex)

-other functions?

A

TAF250 & TAF150

-other functions=acetyltransferase or protein kindase enzyme that phosphorylates other proteins

21
Q

complete preinitiation complex; TFIIE then TFIIH bind DABPolF complex

A

DABPolFEH complex

22
Q

DA complex recruits TFIIB

-function=recruits TFIIF & RNA pol2 which join complex upstream of start site

A

DAB complex

-function?

22
Q

ID’d essential class III transcription factors (TFIIIA, B, and C)

A

Roeder et al

23
Q

discovered SL1 requirement by incubating in increasing concentration with rRNA promoters and measuring transcription levels

  • also demoed that UBF greatly enhances transcription w/ rRNA upstream promoter element
  • analyzed SL1 protein complex with immunoprecipitation
A

R. Tijan et al (x3)

24
Q

35kD protein w/ 2 key domains: one interacts with TBP (of TFIID), the other with RNA polymerase/TFIIF near transcription start site

25
Q

Key featuers:

  1. class I genes
  2. class II genes
  3. class III genes
A
  1. utilize UBF as key assembly factor (lack TATA box)
  2. may use Sp1 or TAF250-150
  3. utilize TFIIIC to bind TFIIIB and help assemble preinitiation complex
26
Q

14 ID’d by precipitating TBP and western blotting (8 in Drosophila, 12 in yeasts)

-function=interact with promoter initiator, downstream promoter element (DPE), and gene-specific transcription factors

A

TAFs (TBP-associated proteins)

28
Q

developed specific binding sequence of class II proteins and enzymes

A

Reinberg et al

30
Q

TFIID

A

contains TATA-Box binding protein (TBP) and TBP-associated proteins/factors (TAFs)

31
Q

600kD protein w/ 6 subunits and “linker” region (dumbell shaped) that can contact 2 internal promoters simultaneously and can stretch to span large distances (required for all class III transcription)

32
Q

core biding protein that recruits polymerase1

  • complex composed of TATA-box binding protein (TBP) and 3 unique TAFs: TAF110, 63, & 48
  • binds?
A

SL1

-binds core promoter element

34
Q

Kornberg & Young

-contains TFIIB, A, F, & H

A

found evidence of pre-formed preinitiation comlex: RNA polymerase holoenzyme

-contains?

35
Q
  1. utilize UBF as key assembly factor (lack TATA box)
  2. may use Sp1 or TAF250-150
  3. utilize TFIIIC to bind TFIIIB and help assemble preinitiation complex
A

Key featuers:

  1. class I genes
  2. class II genes
  3. class III genes
36
Q

orients polymerase at start site and tightly binds DNA, promoting several rounds of transcription

37
Q

SL1 (x2)

-binds core promoter element

A

core biding protein that recruits polymerase1

  • complex composed of TATA-box binding protein (TBP) and 3 unique TAFs: TAF110, 63, & 48
  • binds?
39
Q

R. Tijan et al (x3)

A

discovered SL1 requirement by incubating in increasing concentration with rRNA promoters and measuring transcription levels

  • also demoed that UBF greatly enhances transcription w/ rRNA upstream promoter element
  • analyzed SL1 protein complex with immunoprecipitation
40
Q

DAB complex

-function?

A

DA complex recruits TFIIB

-function=recruits TFIIF & RNA pol2 which join complex upstream of start site

41
Q

38/43kD protein rich in basic amino acids (giving positive charge) which binds to the minor groove within the TATA box by mutating nucleotides in both major and minor grooves; recruits TAFs to assemble preinitiation complex

-structure/function?

A

TBP (universal transcription factor)

-structure=saddle-shaped; function=opens up DNA and bends TATA box

42
Q

TFIIB (x2)

A

35kD protein w/ 2 key domains: one interacts with TBP (of TFIID), the other with RNA polymerase/TFIIF near transcription start site

43
Q

TFIIH (x3)

  • function=enhance DNA melting and moving polymerase across target gene promoter
  • demoed by ability to separate 41 base strand from phage M13 DNA
A

large complex protein w/ 9 subunits; functions as protein kinase b/c can phosphorylate RNA Pol2 w/in its CTD while it’s bound to DNA (requires ATP)

  • function?
  • also contains protein helicase activity (capable of unwinding DNA) required for transcription b/c allows polymerase to clear promoter and elongate new RNA strand (requires ATP)

demoed by?

44
Q

large complex protein w/ 9 subunits; functions as protein kinase b/c can phosphorylate RNA Pol2 w/in its CTD while it’s bound to DNA (requires ATP)

  • function?
  • also contains protein helicase activity (capable of unwinding DNA) required for transcription b/c allows polymerase to clear promoter and elongate new RNA strand (requires ATP)

demoed by?

A

TFIIH (x2)

  • function=enhance DNA melting and moving polymerase across target gene promoter
  • demoed by ability to separate 41 base strand from phage M13 DNA
45
Q

Reinberg et al

A

developed specific binding sequence of class II proteins and enzymes

47
Q

Sp1 (an activator)

A

binds to GC domains and recruits TAF-110 (130 human) which functions as bridge for TAF250-150. These then recruit TBP to form preinitiation complex and begin transcription

48
Q

first one formed in preinitiation complex; TFIID and TFIIA bind TATA box

A

DA complex

49
Q

DA complex

A

first one formed in preinitiation complex; TFIID and TFIIA bind TATA box

50
Q

enhances TFIIH kinase activity

51
Q

DABPolFEH complex

A

complete preinitiation complex; TFIIE then TFIIH bind DABPolF complex

52
Q

Roeder et al

A

ID’d essential class III transcription factors (TFIIIA, B, and C)

Molecular Biology (13 decks)

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