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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
How many sigma factors does e coli have
4
26
How many sigma factors does Bacillus obscillus have?
approx 20
27
How do conformational changes affect sigma factor binding?
- oxidative stress - phosphorylation - increase or decrease affinity
28
closed TI complex
dsDNA, no downstream-RNAP
29
intermediate TI complex
- sigma region 1.1 moves out of main channel - downstream dna moves in
30
open TI complex
- dna strands separate - template strand bps with first NTP
31
scrunching
production of >10nt oligos
32
Ds/ss DNA-sigma interactions
A-11 and T-7 flip, resulting in dsDNA separation via melting
33
supercoils
torsional tension
34
high DNA-DNA interaction
transcriptional quiescence
35
low DNA-DNA interaction
heavy transcription
36
RNAPI
18s/28s rRNA
37
RNAPII
- mRNA - some sRNAs
38
RNAPIII
- tRNAs - 5S rRNAs - other sRNAs
39
RNAPIV
inverted dna repeat transcription in RNAi-mediated DNA methylation; transcribes ONSEN
40
eukaryotic initiation
requires basal TFs to generate docking sites
41
RNAPI initiation
1. UBF binds upstream promotor 2. SL1 binds AT-rich core promotor
42
SL1
basal TF
43
RNAPII initiation
1. TATA BP binds 2. DNA bends up to 80degrees 3. TFTA, TFTB associate 4. RNAP recruitment 5. TF2E, TF2F, TF2H
44
TF2F
catalytic and general TF
45
TF23, H
- separate strands - energy consumptive
46
RNAPIII initiation
- 3 different promotors; conserved elements in alternative configurations
47
Elongation
- TF2H kinase phosphorylate catalytic subunit C-terminal domains - factor release and recycling
48
Termination
- CstF and CpsF bind to catalytic subunit C-terminal domain - CstF cuts terminator - CpsF recruits alternative polymerases for poly-A - RNAP dissociates
49
CstF
- capping specification termination factor - endonuclease
50
CpsF
capping and polyadenylation specification factor
51
polyA
100-250bps
52
Two end-termination hypotheses
- catalytic subunit confirmation change causes loss of affinity - catalytic subunit displaced by uncapped exonuclease action
53
moderate transcription
transient H2A/B loss/exchange
54
active transcription
transient octamer loss/exchange
55
NAC - the specifics
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
What is NAC?
phosphor transfer reaction

Exam Prep 2.0 (33 decks)

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