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CMB2001 Control of Eukaryotic Gene Expression > Lecture 1 - Eukaryotic promoters, RNA polymerases and the assembly of the PIC > Flashcards

Lecture 1 - Eukaryotic promoters, RNA polymerases and the assembly of the PIC Flashcards

1
Q

define transcription with regards to ds DNA and ss RNA

A

transcription is the transfer of genetic information from ds DNA to ss RNA (mRNA)

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2
Q

in prokaryotic transcription, the closed complex is made up of what?

A

sigma 70 + RNA polymerase (holoenzyme)

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3
Q

in the closed complex in prokaryotic transcription, at which numbers are the 3 sequence elements?

A

-35, -10, +1

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4
Q

what happens in the second stage of transcription in prokaryotes?

A

initiation - the open complex is formed

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5
Q

what is the third stage of prokaryotic transcription called? which direction does it occur in?

A

elongation from 5’ to 3’

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6
Q

what is the definition of promoter with regards to transcription? (hint- a DNA regulatory element)

A

a cis acting (DNA regulatory) element through which transcription is initiated and controlled

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7
Q

anything to the left (getting more minus) of the start site in promoters is termed as what?

A

upstream

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8
Q

anything to the right (getting more plus) of the start site in promoters is termed as what?

A

downstream

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9
Q

at which 2 positions are two hexamers in a prokaryotic promoter make up the consensus sequence?

A

-35 and -10

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10
Q

which 2 regions make up a EUKARYOTIC promoter?

A

regulatory and basal/core regions

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11
Q

name the 4 core/basal eukaryotic promoter elements

A

TATA box
Initiator
DPE
BRE

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12
Q

at which location is the TATA box found in eukaryotic promoters? (hint: downstream of start)

A

-30

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13
Q

at which location is the initiator found in eukaryotic promoters? think start/initiation

A

+1

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14
Q

at which location is the DPE found in eukaryotic promoters? (hint: upstream of start)

A

-30

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15
Q

at which location is the BRE found in eukaryotic promoters? (hint: more upstream from start than DRE)

A

-35

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16
Q

most mammals lack which two CORE promoter elements?

what does this mean for transcription?

A

TATA and initiator

transcription starts at multiple sites/ at a lower rate

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17
Q

CpG islands are associated with regions with a high frequency of what?

A

CG sequences

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18
Q

in mammals, C residues, followed by a G, are METHYLATED to what?

A

5-methyl-C

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19
Q

the methylation of CpG islands is associated with what in transcription?

A

silencing of transcription

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20
Q

UAS + enhancer is for which binding sites? activator or repressor?

A

activator

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21
Q

URS + silencer is for which binding sites? activator or repressor?

A

repressor

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22
Q

sequence comparison led to the identification of which core promoter element?

A

TATA box

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23
Q

the amount of reporter protein, encoded by reporter genes, provides a measure of what?

A

gene expression

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24
Q

name 3 reporter proteins, encoded for by reporter genes

A

GFP
LUCIFERASE
LAC Z

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25
Q

what is the reporter gene which encodes for the reporter protein Lac Z in mice?

A

URE2

26
Q

where in the cell is RNA pol 1 found?

A

nucleolus

27
Q

on which type of RNA are the target genes for RNA pol 1?

A

rRNA

28
Q

on which type of RNA are the target genes for RNA pol 2?

A

mRNA
snRNA
miRNA

29
Q

on which type of RNA are the target genes for RNA pol 3?

A

tRNA
5S RNA
U6 RNA
7S RNA

30
Q

in which part of the cell are eukaryotic RNA polymerases 2 and 3 located?

A

nucleus

31
Q

how many subunits make up eukaryotic RNA pol 2?

A

12

32
Q

how many subunits make up prokaryotic RNA pol?

A

5

33
Q

what are the 5 subunits which make up prokaryotic RNA pol?

A

beta
beta’
alpha x2
omega (w)

34
Q

what shape does eukaryotic RNA pol 2 take up?

A

crab claw

35
Q

which factor does bacterial RNA polymerase require to recognise promoter DNA?

A

sigma

36
Q

the general transcription factor (GTF) TFIIA is specific to which enzyme?

A

RNA polymerase - pol 2 especially

37
Q

TFIIA stabilises the binding of which other? GTF

A

TFIID

38
Q

TFIIA has anti…… function

A

repression

39
Q

TFIID binds to which core promoter element?

A

TATA box

40
Q

which other GTF is recruited by TFIID?

A

TFIIB

41
Q

which GTF is important for start site selection?

A

TFIIB

42
Q

which GTF recruits RNA pol 2 - TFIIF?

A

TFIIB

43
Q

which GTF stimulates elongation?

A

TFIIF

44
Q

which GTF recruits TFIIH and modulates its activity?

A

TFIIE

45
Q

which GTF controls promoter melting and clearance as well as DNA repair coupling?

A

TFIIH

46
Q

what happens at steps 1-5 of the PIC assembly? what is the order of assembly of GTFs?

A

1 - D and TATA box
2 - A joins
3 - B joins
4 - F and RNA pol 2 join
5 - H and E join

47
Q

the helicase activity of which GTF helps to separate the template strand?

which complex does this help to create?

A

TFIIH

Open complex

48
Q

after pol 2 is done transcribing which 2 GTFs may stay behind on the pre initiation complex?

A

D and A

49
Q

which 3 GTFs are released after RNA pol is done transcribing?

A

B, E, H

50
Q

which GTF moves down the template strand with RNA pol 2?

A

TFIIF

51
Q

write the number of subunits each GTF has:
A
B
D
E
F
H

A

A - 3
B - 1
D - 13
E - 2
F - 2
H - 9

52
Q

TFIIH is divided into which 2 parts?

A

CORE + CAK

53
Q

CAK in TFIIH contains kinases which phosphorylate what?

A

the C terminal domain of RNAP2

54
Q

TFIIH contains an ATPase called what?

what is this enzyme involved in with regards to promoters?

A

XPB

promoter melting

55
Q

TFIID is made up of which 2 elements?

A

TATA BP + TAFs

56
Q

what is the structure of TFIID described to be? (hint - lobes)

A

trilobular

57
Q

which shape can TATA BP be described as in TFIID?

A

a molecular saddle

58
Q

what must a promoter contain for a TATA BP to be able to direct the assembly of the PIC alone ?

A

TATA

59
Q

which type of transcription can the TATA BP not support?

A

activated

60
Q

TAFs promote the interaction of TFIID with what?

A

basal promoter

61
Q

what do TAFs interact with?

A

activators

62
Q

which 4 things can reporter genes be used for identifying?

A

when a gene is expressed
where it is expressed
which signals it responds to
which factors control its expression

when
where
signals
factors controlling

CMB2001 Control of Eukaryotic Gene Expression (9 decks)

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