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Exam Prep 2.0 > RNA transcription > Flashcards

RNA transcription Flashcards

1
Q

NAC - the basics

A
  1. translocation
  2. NTP binding and release
  3. Mg2+ catalysis
  4. PPi binding and release
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2
Q

NAC - the basics

A

1) translocation
2) NTP binding and release
3) Mg2+ catalysis
4) PPi binding and release

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3
Q

translocation

A

transcription machinery positions dna template against mrna

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4
Q

catalytic phosphoryl transfer occurs by

A

nucleotide addition

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5
Q

reverse reaction

A

phosphorolysis

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6
Q

proofreading

A
  • recovery from backtrack arrest
  • exo/endonuclease hydrolysis
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7
Q

transcription

A

information to function

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8
Q

RNAP topology

A
  1. DNA enters pore in jaw region
  2. slides bridge -> wall
  3. 90degree reorientation
  4. escape channel directing
  5. dsDNA rudder insertion; opens
  6. Mg2+ catalysis
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9
Q

RNAP components:

A

stalk, clamp, jaw, duplex DNA-binding channel, catalytic centre, wall, assembly platform, rudder

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10
Q

upstream dna

A

between clamp and rudder

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11
Q

rna exit

A

rudder

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12
Q

RNAPs

A
  • common accessory elongation factors (elongation-first hypothesis)
  • domain-specific initiation factors
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13
Q

T7

A
  • single-subunit phage RNAP
  • transcribed without additional factors
  • regulates bacterial expression
  • co-opted for PCR
  • specific promotor
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14
Q

Bacterial RNAP

A
  • AT initiator affinity
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15
Q

beta

A

downstream

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16
Q

beta prime

A

central

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17
Q

sigma

A

-35, -10 regions
- transiently regulated

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18
Q

finding a promotor

A

experimental and modelling approaches

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19
Q

intersegmental transfer occurs when

A

contact is indirect

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20
Q

if a promotor is occupied by sigma but not RNAP

A
  • delay/inhibition to transcription
  • full contact necessary for specific binding
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21
Q

protection assay

A
  1. incubate RNAP w DNA
  2. add endo+ exo nucleases
  3. sequence associated with RNAP
  4. electrophorese for non-fragmented regions
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22
Q

How do sigma factors work?

A
  • alpha-helices expose necessary aas at intervals of 3s
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23
Q

sigma factor

A
  • variable, high no
24
Q

FecI

A

don’t yet know the sequence for

25
Q

How many sigma factors does e coli have

A

4

26
Q

How many sigma factors does Bacillus obscillus have?

A

approx 20

27
Q

How do conformational changes affect sigma factor binding?

A
  • oxidative stress
  • phosphorylation
  • increase or decrease affinity
28
Q

closed TI complex

A

dsDNA, no downstream-RNAP

29
Q

intermediate TI complex

A
  • sigma region 1.1 moves out of main channel
  • downstream dna moves in
30
Q

open TI complex

A
  • dna strands separate
  • template strand bps with first NTP
31
Q

scrunching

A

production of >10nt oligos

32
Q

Ds/ss DNA-sigma interactions

A

A-11 and T-7 flip, resulting in dsDNA separation via melting

33
Q

supercoils

A

torsional tension

34
Q

high DNA-DNA interaction

A

transcriptional quiescence

35
Q

low DNA-DNA interaction

A

heavy transcription

36
Q

RNAPI

A

18s/28s rRNA

37
Q

RNAPII

A
  • mRNA
  • some sRNAs
38
Q

RNAPIII

A
  • tRNAs
  • 5S rRNAs
  • other sRNAs
39
Q

RNAPIV

A

inverted dna repeat transcription in RNAi-mediated DNA methylation; transcribes ONSEN

40
Q

eukaryotic initiation

A

requires basal TFs to generate docking sites

41
Q

RNAPI initiation

A
  1. UBF binds upstream promotor
  2. SL1 binds AT-rich core promotor
42
Q

SL1

A

basal TF

43
Q

RNAPII initiation

A
  1. TATA BP binds
  2. DNA bends up to 80degrees
  3. TFTA, TFTB associate
  4. RNAP recruitment
  5. TF2E, TF2F, TF2H
44
Q

TF2F

A

catalytic and general TF

45
Q

TF23, H

A
  • separate strands
  • energy consumptive
46
Q

RNAPIII initiation

A
  • 3 different promotors; conserved elements in alternative configurations
47
Q

Elongation

A
  • TF2H kinase phosphorylate catalytic subunit C-terminal domains
  • factor release and recycling
48
Q

Termination

A
  • CstF and CpsF bind to catalytic subunit C-terminal domain
  • CstF cuts terminator
  • CpsF recruits alternative polymerases for poly-A
  • RNAP dissociates
49
Q

CstF

A
  • capping specification termination factor
  • endonuclease
50
Q

CpsF

A

capping and polyadenylation specification factor

51
Q

polyA

A

100-250bps

52
Q

Two end-termination hypotheses

A
  • catalytic subunit confirmation change causes loss of affinity
  • catalytic subunit displaced by uncapped exonuclease action
53
Q

moderate transcription

A

transient H2A/B loss/exchange

54
Q

active transcription

A

transient octamer loss/exchange

55
Q

NAC - the specifics

A
  1. nucleophilic free hydroxide attacks and captures 1st nucleotide C3 OH proton
  2. cascade
  3. C2O links covalently to C5PO43-
  4. associates w/ proton acceptor
  5. free to diffuse
56
Q

What is NAC?

A

phosphor transfer reaction

Exam Prep 2.0 (33 decks)

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