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CMB2001 Control of Eukaryotic Gene Expression > Lecture 2 - Mechanisms of activation, enhancers, activators, activator targets (mediator complex) > Flashcards

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

1
Q

basal transcription means that levels of transcription are what?

A

low or inactive

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2
Q

activated transcription means that levels of transcription are what?

A

high

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3
Q

name the 3 common sequence enhancer elements?

A

GC box
octamer
CAAT box

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4
Q

where are common sequence enhancer elements often located?

A

close to the core promoter

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5
Q

what do common sequence enhancer elements bind?

A

activators which are constantly active

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6
Q

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

what factor is associated with it?

A

GGGCGG

Sp1

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7
Q

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

what factor is associated with it?

A

ATTTGCAT

Oct-1

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8
Q

what is the factor associated with a CAAT box?

A

NFY

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9
Q

what are the 2 response elements?

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

A

SRE, HSE

inducers e.g heat shock

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10
Q

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

A

growth factors

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11
Q

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

A

heat shock

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12
Q

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

A

tracking and looping

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13
Q

give 4 examples of DNA binding domains

A

leucine zipper, zinc finger, homeodomain, helix loop helix

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14
Q

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

A

negatively

asp
glu

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15
Q

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

A

glutamine

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16
Q

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

A

TAFs

17
Q

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

A

DNA footprinting, electrophoretic mobility shift assays, transcription assays

18
Q

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

A

non-denaturing acrylamide gel

19
Q

which 4 components are needed for a transcription assay?

A

RNA pol 2, GTFs, DNA template, radiolabelled rNTPs

20
Q

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

A

DNA binding domain and an activation domain

21
Q

give examples of an IN VIVO method for analysing activators

A

reporter assays, chromatin immunoprecipitation

22
Q

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

A

true

23
Q

true or false, activators decrease RNA pol 2 recruitment?

A

false, they increase it

24
Q

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

A

false. they do stimulate it

25
Q

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

A

TFIID, TFIIB, Mediator

26
Q

how many polypeptides approximately make up a mediator?

A

22

27
Q

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

A

C terminal domain

28
Q

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

A

3 - head, middle, tail

29
Q

what do mediators provide a bridge between?

what does this therefore enhance the function of?

A

activators and RNA pol 2

enhances PIC formation and transcription initiation therefore

30
Q

what can activators help to release?

A

stalled RNA polymerase

31
Q

give an example of an active activator protein gene which releases stalled RNA pol 2

what does this gene control - which physiological response?

A

hsp70 (heat shock genes)

32
Q

which transcription factor does hsp70 activate?

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

A

HSF

interacts with RNA pol 2

33
Q

what can activators modulate, allowing the PIC formation?

A

chromatin

34
Q

list the 4 ways in which activators work

A

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

CMB2001 Control of Eukaryotic Gene Expression (9 decks)

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