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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
RNA polymerase 2
located in nucleoplasm synthesizes heterogeneous nuclear RNA (hnRNA) that become mRNA & small nuclear RNA (snRNA)
18
method for discovery of 3 RNA polymerases
ion-exchange chromatography from sea urchin embryos used in...?
19
DNA binding channel (x2)
located at base of the cleft lined with positively-charged basic residues that facilitate DNA binding (electrostatic positive charge)
21
Roger Kornberg et al. (x2)
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
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
1. rudder 2. lid 3. zipper
24
contain core promoter and upstream element - core promoter composed of...? - function=positions the polymerase to start transcription - sequence=PyPy**A**X(T/A)PyPy; function=required for transcription - help drive transcription and bind TFIID - binds TFIIB (which associates with RNA Pol2) - GC & CCAAT boxes
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
transcription initiation & DNA melting factor binds when...?
TFIIB -when polymerase is in form 2 (open)
27
_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
used to confrim polymerase compositions
29
RNA polymerase 3
located in nucleoplasm synthesizes transfer RNA (tRNA) precursors and the 5srRNA
31
Polymerase form 1
relatively closed, bringing DNA into close proximity with catalytic center
32
Class 1 promoters (x4) - core promoter region location & function? - upstream promoter element (UPE) location & function? - drive rRNA expression
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
RNA polymerase 1
located in nucleolus synthesizes ribosomal RNA (rRNA)
35
relatively closed, bringing DNA into close proximity with catalytic center
Polymerase form 1
37
5 switch regions -switch regions 1 & 2
shift into highly stable structure that closes the clamp during elongation -DNA is twisted and stabilized around these...?
38
have internal promoters + transcribe mostly snRNAs and tRNAs - distinguished by RNA types transcribed and promoter boxes - such as enhances/activators & silencers
Class 3 promoters (x2) - 3 types distinguished by...? - utilize elements outside promoter such as...?
39
used to confrim polymerase compositions
_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
Rbp3/5/6/10/12
required for transcription (may be targets of transcriptional activators)
41
TFIIB -when polymerase is in form 2 (open)
transcription initiation & DNA melting factor binds when...?
42
Rpb1 homologous to?
binds DNA directly, contains CDT homologous to B'/a subunits of *E. coli* polymerase
44
ion-exchange chromatography from sea urchin embryos
discovery of 3 RNA polymerases
45
roeder et al
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
RNA transcripts (aka?)
pre-mRNAs (aka?)
47
located at base of the cleft lined with positively-charged basic residues that facilitate DNA binding (electrostatic positive charge)
DNA binding channel
48
located in nucleoplasm synthesizes heterogeneous nuclear RNA (hnRNA) that become mRNA & small nuclear RNA (snRNA)
RNA polymerase 2

Molecular Biology (13 decks)

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