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Molecular Biology > Chapter 10: Eukaryotic RNA Polymerases & Promoters > Flashcards

Chapter 10: Eukaryotic RNA Polymerases & Promoters Flashcards

1
Q

active site

-stabalizes growing nucleotide

A

lcoated at base of the cleft

binds Mg2+ ions (function?)

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1
Q

Pore 1 (x3)

A

facilitates immature RNA extrusion and binds transcriptional elongation factor TFIIS

-may also funcition as site for nucleotides to enter and for RNAs to be extruded during backtracking

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2
Q

Rpb2

homologous to?

A

contains catalytic site, is essential for elongation

homologous to B subunit

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2
Q

Polymerase form 2

A

clamp is open, allowing linear DNA to enter complex, contact Rpb1/2, and initiate transcription

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2
Q

contains catalytic site, is essential for elongation

homologous to B subunit

A

Rpb2

homologous to?

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3
Q
  1. crystallized yeast RNA Pol II structure
  2. determined RNA pol2 structure during elongation in which clamp is closed over both DNA template and RNA product
A

Roger Kornberg et al. (x2)

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3
Q

clamp is open, allowing linear DNA to enter complex, contact Rpb1/2, and initiate transcription

A

Polymerase form 2

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3
Q
  1. rudder
  2. lid
  3. zipper
A

3 loop regions that extend from the clamp

  1. initiates/facilitates dissociation of DNA-RNA hybrid
  2. guides RNA exit + maintains dissociation of DNA template
  3. helps stabilize transcription bubble + initiates dissociation of DNA template
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4
Q

located in nucleolus

synthesizes ribosomal RNA (rRNA)

A

RNA polymerase 1

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5
Q

Rpb4/9

A

non-essential but may help avoid nonspecific binding

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5
Q

binds DNA directly, contains CDT

homologous to B’/a subunits of E. coli polymerase

A

Rpb1

homologous to?

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6
Q

required for transcription (may be targets of transcriptional activators)

A

Rbp3/6/12/5/10

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7
Q

located in nucleoplasm

synthesizes transfer RNA (tRNA) precursors and the 5srRNA

A

RNA polymerase 3

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8
Q

locoated at base of the cleft

binds Mg2+ ions (function?)

A

active site

-stabalizes growing nucleotide

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9
Q

Class 3 promoters (x2)

  • 3 types distinguished by…?
  • utilize elements outside promoter such as…?
A

have internal promoters + transcribe mostly snRNAs and tRNAs

  • distinguished by RNA types transcribed and promoter boxes
  • such as enhances/activators & silencers
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10
Q

Eukaryotic features (x3)

A
  1. membrane-bound organelles
  2. distinct nucleus & nucleolus
  3. divide by mitosis
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10
Q

used alpha-amanitin to determine transcriptional activity and function of each polymerase

inhibitory concentrations:

  1. Polymerase III=20ug/ml
  2. Polymerase II=.02ug/ml
A

roeder et al

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11
Q

non-essential but may help avoid nonspecific binding

A

Rpb4/9

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11
Q

lack TATA box, usually contain AT-rich sequence, contain 2 major regions

  • located between positions -45 and +20; function=essential for transcription
  • located between positions -156 and -107; function=enhances transcription
A

Class 1 promoters (x3)

  • core promoter region location & function?
  • upstream promoter element (UPE) location & function?
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12
Q

shift into highly stable structure that closes the clamp during elongation

-DNA is twisted and stabilized around these…?

A

5 switch regions

-switch regions 1 & 2

13
Q

facilitates immature RNA extrusion and binds transcriptional elongation factor TFIIS

-may also funcition as site for nucleotides to enter and for RNAs to be extruded during backtracking

A

Pore 1 (x2)

14
Q
  1. membrane-bound organelles
  2. distinct nucleus & nucleolus
  3. divide by mitosis
A

Eukaryotic features (x3)

14
Q

pre-mRNAs (aka?)

A

immature RNA transcripts (aka?)

15
Q

Class 2 promoter

  • composed of TATA box, TFIIB recognition element (BRE), initiator (Inr) and downstream promoter element (DPE)
  • TATA box function?
  • initiator sequence (Inrs) & function?
  • DPE elements functions?
  • BRE elements function?
  • upsteam element?
A

contain core promoter and upstream element

  • core promoter composed of…?
  • function=positions the polymerase to start transcription
  • sequence=PyPyAX(T/A)PyPy; function=required for transcription
  • help drive transcription and bind TFIID
  • binds TFIIB (which associates with RNA Pol2)
  • GC & CCAAT boxes
16
Q

RNA polymerase 2

A

located in nucleoplasm

synthesizes heterogeneous nuclear RNA (hnRNA) that become mRNA & small nuclear RNA (snRNA)

18
Q

method for discovery of 3 RNA polymerases

A

ion-exchange chromatography from sea urchin embryos used in…?

19
Q

DNA binding channel (x2)

A

located at base of the cleft

lined with positively-charged basic residues that facilitate DNA binding (electrostatic positive charge)

21
Q

Roger Kornberg et al. (x2)

A
  1. crystallized yeast RNA Pol II structure
  2. determined RNA pol2 structure during elongation in which clamp is closed over both DNA template and RNA product
23
Q

3 loop regions that extend from the clamp

  1. initiates/facilitates dissociation of DNA-RNA hybrid
  2. guides RNA exit + maintains dissociation of DNA template
  3. helps stabilize transcription bubble + initiates dissociation of DNA template
A
  1. rudder
  2. lid
  3. zipper
24
Q

contain core promoter and upstream element

  • core promoter composed of…?
  • function=positions the polymerase to start transcription
  • sequence=PyPyAX(T/A)PyPy; function=required for transcription
  • help drive transcription and bind TFIID
  • binds TFIIB (which associates with RNA Pol2)
  • GC & CCAAT boxes
A

Class 2 promoter

  • composed of TATA box, TFIIB recognition element (BRE), initiator (Inr) and downstream promoter element (DPE)
  • TATA box function?
  • initiator sequence (Inrs) & function?
  • DPE elements functions?
  • BRE elements function?
  • upsteam element?
25
Q

transcription initiation & DNA melting factor

binds when…?

A

TFIIB

-when polymerase is in form 2 (open)

27
Q

epitope tagging:

expressing “tagged” protein in cells that is specifically precipitated from mixture of celluar contents. Tagged proteins + associated molecules are extracted, washed, & run on PAGE to analyze proteins in complex

A

used to confrim polymerase compositions

29
Q

RNA polymerase 3

A

located in nucleoplasm

synthesizes transfer RNA (tRNA) precursors and the 5srRNA

31
Q

Polymerase form 1

A

relatively closed, bringing DNA into close proximity with catalytic center

32
Q

Class 1 promoters (x4)

  • core promoter region location & function?
  • upstream promoter element (UPE) location & function?
  • drive rRNA expression
A

lack TATA box, usually contain AT-rich sequence, contain 2 major regions

  • located between positions -45 and +20; function=essential for transcription
  • located between positions -156 and -107; function=enhances transcription
  • drive?
34
Q

RNA polymerase 1

A

located in nucleolus

synthesizes ribosomal RNA (rRNA)

35
Q

relatively closed, bringing DNA into close proximity with catalytic center

A

Polymerase form 1

37
Q

5 switch regions

-switch regions 1 & 2

A

shift into highly stable structure that closes the clamp during elongation

-DNA is twisted and stabilized around these…?

38
Q

have internal promoters + transcribe mostly snRNAs and tRNAs

  • distinguished by RNA types transcribed and promoter boxes
  • such as enhances/activators & silencers
A

Class 3 promoters (x2)

  • 3 types distinguished by…?
  • utilize elements outside promoter such as…?
39
Q

used to confrim polymerase compositions

A

epitope tagging:

expressing “tagged” protein in cells that is specifically precipitated from mixture of celluar contents. Tagged proteins + associated molecules are extracted, washed, & run on PAGE to analyze proteins in complex

40
Q

Rbp3/5/6/10/12

A

required for transcription (may be targets of transcriptional activators)

41
Q

TFIIB

-when polymerase is in form 2 (open)

A

transcription initiation & DNA melting factor

binds when…?

42
Q

Rpb1

homologous to?

A

binds DNA directly, contains CDT

homologous to B’/a subunits of E. coli polymerase

44
Q

ion-exchange chromatography from sea urchin embryos

A

discovery of 3 RNA polymerases

45
Q

roeder et al

A

used alpha-amanitin to determine transcriptional activity and function of each polymerase

inhibitory concentrations:

  1. Polymerase III=20ug/ml
  2. Polymerase II=.02ug/ml
46
Q

RNA transcripts (aka?)

A

pre-mRNAs (aka?)

47
Q

located at base of the cleft

lined with positively-charged basic residues that facilitate DNA binding (electrostatic positive charge)

A

DNA binding channel

48
Q

located in nucleoplasm

synthesizes heterogeneous nuclear RNA (hnRNA) that become mRNA & small nuclear RNA (snRNA)

A

RNA polymerase 2

Molecular Biology (13 decks)

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