Euk Promoters And PIC

Question 1

What is the core basal promoter

Answer 1

It’s the area around start site for example Tata box and inr (initiator)

Question 2

Where is tata box and initiator on the basal promoter

Answer 2

-30 - -25)

+2-4

Question 3

Do all promoters have a tata box

Answer 3

No

Question 4

What bases are in the inr

Answer 4

Pyrimidine c and t

Question 5

What is the element called + 30 from the start site

Answer 5

Downstream promoter element dpe

Question 6

Which element of the basal promoter is recognised by tf 2 B

Answer 6

BRE (-37)

Question 7

What makes up the regulatory region

Answer 7

UAS/ URS

Enhancers or silencers

(Upstream activator/repressor sequences)

Question 8

What is the UAS / enhancers

Answer 8

UAS makes up enhancers. This is where activators will bind proximal or distal ly from start site

Question 9

What binds to URS/ silencers proximally or distal ly

Answer 9

Repressors

Question 10

What makes up the basal transcription machinery (PIC)

Answer 10

General Tfs and rna pol II

Question 11

What is the CTD

Answer 11

Carboxy terminal domain of rna pol - on the largest subunit of rna pol

Question 12

What does CTD do

Answer 12

Binds to mediator and also is phosphorylated via tf d

Question 13

What other promoter element are present if the tata and inr are lacking ( in 70% of genes)

Answer 13

Cpg islands

Question 14

What causes silencing in cpg islands

Answer 14

When c residues followed by g are methylated this causes silencing

Originally the cpg islands are hypomethylated

Question 15

Which 2 ways were promoter elements identified

Answer 15

Sequence comparisons (similar means promoter area)

Reporter analysis

Question 16

Explain reporter analysis

Answer 16

The regulatory sequence was introduced into a plasmid before a reporter genes. These are genes which encode for localisation proteins Eg gfp

The level of expression and thus promotion is then recognised via the translation of these

Question 17

What does rna pol 1 transcribe (and where)

Answer 17

rRNA for ribosome production in the nucleolus

28s and 18s

Question 18

What does rna pol II transcribe and where

Answer 18

Mrna , snrna and mirna

In nucleus

Question 19

What does rna pol III transcribe

Answer 19

tRNA and Other translation rna (5s,7SA,U6)

In nucleolus

Question 20

What are the differences between pro rna pol and eukaryotic

Answer 20

Prokaryotic has 5 subunits (aabb’w)

Eukaryotic has 12 subunits

Question 21

Which subunit of euk rna pol II is largest (where CTD is) and what is it homologous to

Answer 21

Rpb1

Homologous to b’ subunit in prokaryotes

Question 22

What are the 6 general TFs which make the basal transcription machinery

Answer 22

II A,b,d,e,f,h

Question 23

All gtfs are multi component except which one

Answer 23

II b

Question 24

Which gtf binds first and how

Answer 24

Binds to the tata box

Question 25

What does II d recruit and in which order

Answer 25

A and B second

Question 26

What is the importance of II a

Answer 26

Stabilises d on the tata box Anti repression

Question 27

What is the importance of II b

Answer 27

Recruits polymerase II and F with it

Question 28

What does II f stimulate

Answer 28

Elongation (stays attached to pol)

Question 29

Which gtf recruits H at the end

Answer 29

E

Question 30

What is the pic/ basal transcription machinery equivalent to

Answer 30

Closed complex

Question 31

What is the first role of TF II h

Answer 31

Helicase activity via ATPase hydrolysis Opens dna on the start site

Question 32

What is helicase activity of II h called

Answer 32

Promoter melting

Question 33

Which ATPase is in the helicase core region of II h

Answer 33

Xpb

Question 34

What is it called when pol II begins transcription after promoter melting

Answer 34

Promoter clearance

Question 35

What happens and how when promoter clearance occurs

Answer 35

CTD phosphorylation via the kinase activity of II h

Question 36

What domain in the II h phosphorylsted ctd

Answer 36

Cak domain

Question 37

Which factor is the only one that stays during elongation

Answer 37

II f

Question 38

Which domain of tf II d binds to the tata box

Answer 38

Tata binding protein TBP

Question 39

What is associated with tbp on the II d

Answer 39

TBP associated factors (TAFs)

Question 40

Can TBP initiate the pic production on its own

Answer 40

Yes

Question 41

Why are tafs needed

Answer 41

For activated basal transcription via activator interaction

Question 42

Other than interacting with the activators what do tafs do

Answer 42

Interact with basal promoter elements to increase II d binding

Question 43

Where do taf 1 and 2 vine

Answer 43

To the inr

Question 44

Which taf binds to the dpe to increase II d interaction with basal promoter

Answer 44

Taf 6