Lecture 2 - Mechanisms of activation, enhancers, activators, activator targets (mediator complex)

Question 1

basal transcription means that levels of transcription are what?

Answer 1

low or inactive

Question 2

activated transcription means that levels of transcription are what?

Answer 2

high

Question 3

name the 3 common sequence enhancer elements?

Answer 3

GC box
octamer
CAAT box

Question 4

where are common sequence enhancer elements often located?

Answer 4

close to the core promoter

Question 5

what do common sequence enhancer elements bind?

Answer 5

activators which are constantly active

Question 6

what is the exact sequence of a GC box? (6 NUCLEOTIDES)

what factor is associated with it?

Answer 6

GGGCGG

Sp1

Question 7

what is the exact sequence of an octamer? (7 nucleotides)

what factor is associated with it?

Answer 7

ATTTGCAT

Oct-1

Question 8

what is the factor associated with a CAAT box?

Answer 8

NFY

Question 9

what are the 2 response elements?

what do they bind to which help the body to respond to specific stimuli?

Answer 9

SRE, HSE

inducers e.g heat shock

Question 10

what does the response element SRE elicit a response from in the body?

Answer 10

growth factors

Question 11

what does the response element HSE control the physiological response to? (think temp)

Answer 11

heat shock

Question 12

via which two models/mechanisms do activators CONTACT the basal transcription machinery?

Answer 12

tracking and looping

Question 13

give 4 examples of DNA binding domains

Answer 13

leucine zipper, zinc finger, homeodomain, helix loop helix

Question 14

an activation domain with an acidic patch will have clusters of ……… charged amino acids such as ………. and ……….

Answer 14

negatively

asp
glu

Question 15

an activation domain which is glutamine rich will have a high …….. content

Answer 15

glutamine

Question 16

activation domains interact with other proteins in the transcriptional machinery such as ……

Answer 16

TAFs

Question 17

give examples of IN VITRO approaches towards the analysis of activators (think assays)

Answer 17

DNA footprinting, electrophoretic mobility shift assays, transcription assays

Question 18

on which type of gel is an electrophoretic mobility shift assay run on?

Answer 18

non-denaturing acrylamide gel

Question 19

which 4 components are needed for a transcription assay?

Answer 19

RNA pol 2, GTFs, DNA template, radiolabelled rNTPs

Question 20

in a transcription assay, the activator being used is required to have which 2 domains?

Answer 20

DNA binding domain and an activation domain

Question 21

give examples of an IN VIVO method for analysing activators

Answer 21

reporter assays, chromatin immunoprecipitation

Question 22

activators can promote the binding of an additional activator. true or false?

Answer 22

true

Question 23

true or false, activators decrease RNA pol 2 recruitment?

Answer 23

false, they increase it

Question 24

true or false, activators do not stimulate the assembly of the PIC complex?

Answer 24

false. they do stimulate it

Question 25

What components of the PIC complex do activators interact with to promote assembly?

Answer 25

TFIID, TFIIB, Mediator

Question 26

how many polypeptides approximately make up a mediator?

Answer 26

22

Question 27

through which terminal domain does a mediator associate with RNA pol 2?

Answer 27

C terminal domain

Question 28

how many domains are mediators composed of? what are they?

Answer 28

3 - head, middle, tail

Question 29

what do mediators provide a bridge between? what does this therefore enhance the function of?

Answer 29

activators and RNA pol 2 enhances PIC formation and transcription initiation therefore

Question 30

what can activators help to release?

Answer 30

stalled RNA polymerase

Question 31

give an example of an active activator protein gene which releases stalled RNA pol 2 what does this gene control - which physiological response?

Answer 31

hsp70 (heat shock genes)

Question 32

which transcription factor does hsp70 activate? what does this transcription factor interact with, releasing it from a pause?

Answer 32

HSF interacts with RNA pol 2

Question 33

what can activators modulate, allowing the PIC formation?

Answer 33

chromatin

Question 34

list the 4 ways in which activators work

Answer 34

1 - promote binding of additional activators 2 - stimulate PIC assembly by recruiting RNA pol 2 and GTFs 3 - promote release of stalled RNA pol 2 4 - modulate chromatin