The Structure and Function of Activators

Question 1

what does PIC stand for

Answer 1

Pre-initiation complex

Question 2

name some common UAS/enhancer sequence elements

Answer 2

GC Box
Octamer
CAAT Box

Question 3

Common UAS/enhancers are located where and bind to what.

Answer 3

• located close to the core promoter
• Bind activators that are relatively abundant in the cell and constitutively active

Question 4

Other than common sequence elements what is the other enhancer element

Answer 4

response element

Question 5

what does SRE stands for

Answer 5

Serum response element

Question 6

what does SRE binds to and what does it induce

Answer 6

• binds to Serum response factor (SRF)
• Induces growth factors

Question 7

what does HSE stand for

Answer 7

heat shock element

Question 8

what does HSE binds to and what does it induce

Answer 8

Binds to heat shock factor which induces heat shock

Question 9

enhancer location has an effect on transcription activation T/F?

Answer 9

false

Question 10

eukaryotic activators are M_

Answer 10

Modular

Question 11

all eukaryotic activators have one _ and at least one _

Answer 11

1) DNA binding domain
2) Activation domain

Question 12

there are multiple types of DNA binding domain (4) name them

Answer 12

Zinc finger, leucine zipper, Homeodomain, Helix loop helix

Question 13

Activation domains are often characterised according to their

Answer 13

amino acid composition

Question 14

There are 3 types of activation domain -

Answer 14

Acidic patch (VP16), Glutamine rich (SP1), proline rich (Jun)

Question 15

describe the structure of an acidic patch

Answer 15

clusters of -ve charged residues (asp/glu)

Question 16

describe the structure of activation domain

Answer 16

• Lack of sequence conservation and structural information
• Unstructured
• Has multiple short segments that work together in an additive fashion
• interacts with other proteins in the transcriptional machinery (TAFs)

Question 17

3 in vitro approaches to analysis of activators

Answer 17

DNA foot-printing, Electrophoretic mobility shift assay, Transcription assay

Question 18

what are the two in vivo approaches to analyse activators

Answer 18

Reporter assays & Chromatin Immunoprecipitation

Question 19

How does chromatin immunoprecipitation

Answer 19

1) Cross link bound proteins to DNA
2) Isolate chromatin and shear DNA
3) Preciptate chromatin with protein specific antibody
4) Reverse cross link and digest protein
5) Analyse the DNA using eith PCR or sequencing (ChiP-Seq)

Question 20

How do activators work

Answer 20

1) promote binding of an additional activator
2) Stimulate complex assembly (Recruitment)
3) Release stalled RNA polymerase (Stimulate activity)
4) Modulation of Chromatin

Question 21

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

Answer 21

• TFIID via TAFs
• TFIIB
• Mediators

Question 22

what suggests that activators must require additional factors

Answer 22

many activators cannot activate transcription in minimal in vitro transcription systems

Question 23

describes the structure of mediators

Answer 23

• very large complex of approx 22 polypeptides
• can exist on it own or associated with RNA pol II
• 3 domains = head, middle and tail

Question 24

describe the mediator function

Answer 24

many interact with specific mediator subunits, provides a bridge between activator & RNA pol II which aids recruitment and enhances PIC formation

Question 25

in the absence of what, RNA pol II pauses after 50nts

Answer 25

heat shock, HS activates transcription factor which interacts with RNA pol II and releases it from the pause

Question 26

How does chromatin remodelling allow transcription

Answer 26

chromatin remodelling can cause TATA/UAS to be uncovered and allows complex formation