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

Question 1

define transcription with regards to ds DNA and ss RNA

Answer 1

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

Question 2

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

Answer 2

sigma 70 + RNA polymerase (holoenzyme)

Question 3

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

Answer 3

-35, -10, +1

Question 4

what happens in the second stage of transcription in prokaryotes?

Answer 4

initiation - the open complex is formed

Question 5

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

Answer 5

elongation from 5’ to 3’

Question 6

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

Answer 6

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

Question 7

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

Answer 7

upstream

Question 8

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

Answer 8

downstream

Question 9

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

Answer 9

-35 and -10

Question 10

which 2 regions make up a EUKARYOTIC promoter?

Answer 10

regulatory and basal/core regions

Question 11

name the 4 core/basal eukaryotic promoter elements

Answer 11

TATA box
Initiator
DPE
BRE

Question 12

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

Answer 12

-30

Question 13

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

Answer 13

+1

Question 14

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

Answer 14

-30

Question 15

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

Answer 15

-35

Question 16

most mammals lack which two CORE promoter elements?

what does this mean for transcription?

Answer 16

TATA and initiator

transcription starts at multiple sites/ at a lower rate

Question 17

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

Answer 17

CG sequences

Question 18

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

Answer 18

5-methyl-C

Question 19

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

Answer 19

silencing of transcription

Question 20

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

Answer 20

activator

Question 21

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

Answer 21

repressor

Question 22

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

Answer 22

TATA box

Question 23

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

Answer 23

gene expression

Question 24

name 3 reporter proteins, encoded for by reporter genes

Answer 24

GFP
LUCIFERASE
LAC Z

Question 25

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

Answer 25

URE2

Question 26

where in the cell is RNA pol 1 found?

Answer 26

nucleolus

Question 27

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

Answer 27

rRNA

Question 28

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

Answer 28

mRNA snRNA miRNA

Question 29

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

Answer 29

tRNA 5S RNA U6 RNA 7S RNA

Question 30

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

Answer 30

nucleus

Question 31

how many subunits make up eukaryotic RNA pol 2?

Answer 31

12

Question 32

how many subunits make up prokaryotic RNA pol?

Answer 32

5

Question 33

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

Answer 33

beta beta' alpha x2 omega (w)

Question 34

what shape does eukaryotic RNA pol 2 take up?

Answer 34

crab claw

Question 35

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

Answer 35

sigma

Question 36

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

Answer 36

RNA polymerase - pol 2 especially

Question 37

TFIIA stabilises the binding of which other? GTF

Answer 37

TFIID

Question 38

TFIIA has anti...... function

Answer 38

repression

Question 39

TFIID binds to which core promoter element?

Answer 39

TATA box

Question 40

which other GTF is recruited by TFIID?

Answer 40

TFIIB

Question 41

which GTF is important for start site selection?

Answer 41

TFIIB

Question 42

which GTF recruits RNA pol 2 - TFIIF?

Answer 42

TFIIB

Question 43

which GTF stimulates elongation?

Answer 43

TFIIF

Question 44

which GTF recruits TFIIH and modulates its activity?

Answer 44

TFIIE

Question 45

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

Answer 45

TFIIH

Question 46

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

Answer 46

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

Question 47

the helicase activity of which GTF helps to separate the template strand? which complex does this help to create?

Answer 47

TFIIH Open complex

Question 48

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

Answer 48

D and A

Question 49

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

Answer 49

B, E, H

Question 50

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

Answer 50

TFIIF

Question 51

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

Answer 51

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

Question 52

TFIIH is divided into which 2 parts?

Answer 52

CORE + CAK

Question 53

CAK in TFIIH contains kinases which phosphorylate what?

Answer 53

the C terminal domain of RNAP2

Question 54

TFIIH contains an ATPase called what? what is this enzyme involved in with regards to promoters?

Answer 54

XPB promoter melting

Question 55

TFIID is made up of which 2 elements?

Answer 55

TATA BP + TAFs

Question 56

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

Answer 56

trilobular

Question 57

which shape can TATA BP be described as in TFIID?

Answer 57

a molecular saddle

Question 58

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

Answer 58

TATA

Question 59

which type of transcription can the TATA BP not support?

Answer 59

activated

Question 60

TAFs promote the interaction of TFIID with what?

Answer 60

basal promoter

Question 61

what do TAFs interact with?

Answer 61

activators

Question 62

which 4 things can reporter genes be used for identifying?

Answer 62

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