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1
Q

Components in E coli RNAP

A

Five
Two alpha, one beta, one beta prime and one sigma70

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2
Q

Direction of RNA synthesis

A

5’ to 3’

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3
Q

What metal ions are needed in Ecoli RNAP?

A

Two Mg2+

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4
Q

How to identify promoter sequence in RNAP through experiment?

A
  • Add RNAP to radiolabelled DNA strand
  • Induce DNA cuts across the strand with DNase
  • lots of fragments formed of different sizes
  • conduct gel electrophoresis to determine binding site (without bands in sample with RNAP)
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5
Q

Location of initiation site in numbers

A

+1

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6
Q

Sequence of Pribnow box

A

TATAAT from 5’ to 3’

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7
Q

Terminology for Template strand

A

Non-coding strand or antisense

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8
Q

Terminology for non-template strand

A

Coding strand or sense

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9
Q

What binds to UP Elements?

A

C terminus of alpha subunit on RNAP

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10
Q

Where is Pribnow box located

A

-10

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11
Q

What binds to Pribnow box

A

Sigma subunit on RNAP thorugh recognition helix

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12
Q

Difference between genes with strong promoter and those with weak promoters

A

Strong: more transcription
Weak: lots of substitutions

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13
Q

Characteristics of UP Elements

A

AT rich

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14
Q

Components in promoter sequence of prokaryotes

A

-35 sequence
Pribnow box (-10)
UP Element

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15
Q

Which is the last step where transcription is reversible in prokaryotes

A

Complex formed between RNA polymerase and promoter

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16
Q

When is transcription in prokaryotes irreversible

A

Once DNA is unwounded in promoter region

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17
Q

What is holoenzyme in prokaryotic transcription

A

Sigma subunit plus core enzyme of RNAP

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18
Q

Structures important for nucleotide insertion in transcription of prokaryotes

A

Bridge helix and trigger loop

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19
Q

Intrinsic termination site in prokaryotic transcription

A
  1. GC rich inverted repeats —> forming a stem loop
  2. Non repeating segment between inverted repeats
  3. 6-8 U in transcript
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20
Q

Characteristics of Rho termination factor

A

Only in prokaryotes

ATP dependent helicase

Hexamer

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21
Q

How does Rho stop transcription in prokaryotes?

A

move along RNA transcript, unwind DNA:RNA hybrid and release DNA chain

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22
Q

Where does Rho bind to?

A

Rho utilization site (rut)
-C-rich

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23
Q

What happens when ribosome is on transcript of prokaryotes?

A

Rho factor cannot bind to transcript

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24
Q

How does rifampicin inhibits bacterial transcription?

A

binds to DNA RNA hybrid helix channel
—> blocks helix from forming

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25
Q

How does actinomycin inhibit bacterial transcription?

A

act to intercalate within double helical DNA

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26
Q

How is 16S rRNA formed after transcription in prokaryotes?

A

cleaved by both RNase III and M16 to remove stem loop

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27
Q

How is 23S rRNA formed after prokaryotic transcription?

A

RNase III, M23

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28
Q

How is 5S rRNA formed after prokaryotic transcription?

A

M5 (only for cleaving 5S rRNA)

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29
Q

How is tRNA cleaved after prokaryotic transcription?

A

5’ of tRNA —> RNase P
3’ of tRNA —> RNase D

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30
Q

Function of RNase P

A

cleave 5’ of tRNA from primary transcript in prokaryotes

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31
Q

Function of RNase D

A

cleave 3’ of tRNA from primary transcript in prokaryotes

32
Q

What happens after primary transcript formed for rRNA or tRNA in prokaryotes?

A

cleave spacer regions
Process them (e.g. tRNA add CCA to end)
Modification

33
Q

Rank their steady state level from highest to lowest (tRNA, rRNA, mRNA)

A

rRNA»tRNA»mRNA

34
Q

Effects of alpha amanitin to RNAP II

A

Strongly inhibited

35
Q

A domain only found in RNAP II

A

C terminal domain with YSPTSPS repeats

36
Q

Prokaryotic homolog of RPB4 in yeast RNAP II

A

sigma subunit —> promoter recognition

37
Q

Prokaryotic homolog for RPB1

A

Beta prime

38
Q

Feature of RPB 1 in RNAPII

A

YSPTSPS CTD

39
Q

Feature of RPB4 in yeast RNAP II

A

Recognize promoter

40
Q

In which steps of transcription does alpha amanitin act on?

A
  1. After NTP inserted with open trigger loop
    —> prevent closure of loop

2.after intermediate formed in translocation steps
—> prevent wedged trigger loop to open up

41
Q

Promoters for RNAP II

A
  1. TATA box
  2. CAAT box (around -150 to -40)
  3. GC box
42
Q

Role of TFIID in transcription initiation

A

Has TBP component that recognizes TATA box
—> then recruits TFIIA

43
Q

Role of TFIIA in transcription initiation

A

stabilize TBP in TFIID after being recruited

44
Q

Role of TFIIF in transcription initiation

A

bind to RNAP II —> bringing RNAP to promoter

45
Q

TFIIH function in transcription initiation

A

Phosphorylate CTD in RNAP
Unwind promoter with helicase activity

46
Q

Two types of positive transcriptional regulation

A
  1. Bind of ligand —> activator bind to transcript —> increase transcription efficiency
  2. Bind of ligand —> dissociates activator from transcript —> inhibit transcription
47
Q

Two types of negative transcriptional regulation

A
  1. Ligand causes repressor to leave transcript —> allow transcription
  2. Ligand causes repressor to bind transcript —> inhibit transcription
48
Q

What does lac z code for?

A

beta galactosidase

49
Q

what does lac y code for?

A

Gal permease

50
Q

What does lac a code for?

A

Gal transacetylase

51
Q

Function of beta galactosidase

A

i) breakdown lactose to galactose + glucose

ii) change glycosidic linkage from 1-4 in lactose to 1-6 in allolactose (Side rxn)

52
Q

Function of permease

A

Transporter of lactose

53
Q

Function of Gal transacetylase

A

acetylates any unhydrolyzed lactose –> eliminate

54
Q

What does lac i codes for?

55
Q

Amino residue important for DNA adn Lac repressor interaction

A

Arginine, forming H bond with guanine

56
Q

Function of allolactose

A

an inducer to repressor protein formed
–> when bound, prevent repressor from binding to operator region

57
Q

Function of repressor

A

form dimer
–> bind to operator region to inhibit transcription

58
Q

Structure of recognition helix in lac repressor

A

helix turn helix

59
Q

How is catabolite activator protein (CAP) activated)?

A

low glucose level –> cAMP increase
–> bind to N-term of CAP –>CAP activates

60
Q

What happens after CAP is activated?

A

goes to binding region with AT rich inverted repeats
(axis of symmetry)

61
Q

What happens when there is low glucose levels + high lactose levels?

A

i) CAP activated (attached to cAMP)
ii) lack lac repressor (as lactose is present)
–> allolactose formed that bind to repressor

– increase transcription rate

62
Q

What happens with High glucose + Low lactose?

A

i) CAP not activated (low amount of cAMP present)
ii) lac repressor present (as lactose is absent)

–> inhibit transcription

63
Q

What happens with low levels of glucose and lactose?

A

i) CAP activated (high cAMP)
ii) lac repressor present

–> inhibit transcription

64
Q

What happens with high levels of glucose and lactose?

A

i) CAP not activated (little cAMP)
ii) lac repressor absent (allolactose bind to repressor)

–> increase transcription

65
Q

What does CAP bind to?

A

cAMP on N-term
DNA on C-Term

66
Q

How does CAP usually appear as?

67
Q

Three classes of DNA binding proteins

A

i) helix-turn-helix (HTH) motif
ii) zinc-finger motif
iii) Leucine zipper-basic region (bZIP)

68
Q

Where does helix-turn helix (HTH) bind to DNA?

A

Major groove

69
Q

What residues do zinc in zinc finger binds to?

A

Only Cys
Half Cys, Half His

70
Q

Characteristics of leucine zipper (bZIP)

A

i) DNA binding region (lot of basic aa like lysine and arginine)
ii) Zipper region (Leu found in every 7 aa)
–> Leu from both ends join tgt –> form coiled coil structure

71
Q

How doese hormone receptor interact with DNA?

A

Zinc finger motif

72
Q

What part of hormone receptor contributes most to conformation change during ligand binding?

73
Q

Effect of conformational change in hormone receptor to transcription

A

i) doesn’t change receptor’s affinity to DNA
ii) allow recruitment of coactivator by increasing affinity to coactivator
–> increase transcription

74
Q

How does tamoxifen target hormone receptors?

A

act as antagonist of receptor
–> helix 12 doesn’t pack properly
–> coactivator not recruited

75
Q

Structure of hormone receptors

BCH311 (4 decks)

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