Regulation of Transcription

Question 1

What is the difference between anti-termination mechanisms of N and Q of lambda phage?

Answer 1

N acts at the ends of immediate early genes whereas Q acts on immediate late genes

Question 2

What is the function of cII gene in lambda phage?

Answer 2

cII promotes transcription from a leftward promoter (Panti-Q) within Q, promoting Q antisense RNA which blocks the production of Q. Q is required for late transcription in the lytic phase, so interfering with its synthesis favors lysogeny

Question 3

What is the function of cIII gene in lambda phage?

Answer 3

cIII protects cII from destruction by proteases in the cell. They work together to establish lysogeny by activating PRE and PI

Question 4

Explain the possible outcomes in the race between cro and cl

Answer 4

If cro wins, lytic cycle results

If cl wins, lysogeny results

Question 5

Which environmental conditions promote lysis and which conditions promote lysogeny?

Answer 5

Lysis requires more energy than lysogeny. So when glucose is abundant, lysis occurs

Question 6

What specific genes are transcribed by each of the 3 RNA polymerases?

Answer 6

I: pre-rRNA for 18, 5.8, and 28s rRNA
II: pre-mRNA, some snRNA
III: pre-tRNA, 5S rRNA, and some snRNA

Question 7

What is the function of the zipper within the clamp?

Answer 7

Initiates the dissociation of template DNA

Question 8

What is the function of the rudder within the clamp?

Answer 8

Initiates the dissociation of the RNA-DNA hybrid

Question 9

What is the function of the lid within the clamp?

Answer 9

Maintains dissociation

Question 10

How does the bridge helix mediate transcription within RNA polymerase II?

Answer 10

The bridge helix positions the template strand for decoding, oscillating between straight and bent conformations. When straight, the active site is open for nucleotide addition by polymerase, filling in the space between the 3’ end of RNA and straight bridge helix. During translocation, the bridge helix shifts to the bent space. When it straightens again, it reopens the active site at the 3’ end of RNA

Question 11

What is the order in which the general transcription factors are added to the preinitiation complex?

Answer 11

1. ) TFIID
2. ) TFIIA
3. ) TFIIB
4. ) TFIIF
5. ) TFIIE
6. ) TFIIH

Question 12

What is the function of TFIID?

Answer 12

Contains TATA-box-binding protein (TPB) and 8-10 TBP-associated factors. Interaction with promoter is the first step in formation of the pre-initiation complex.

Question 13

What is the function of TFIIA?

Answer 13

Stabilizes binding between TFIID and promoter to form the DA complex

Question 14

What is the function of TFIIB?

Answer 14

Positions polymerase at transcription start site, stabilizes TBP-TATA binding and interacts with transcription activators that bind to upstream elements.

Question 15

What is the function of TFIIF?

Answer 15

Binds polymerase and brings it to the DAB complex. Made up of 2 polypeptides: RAP30 and RAP70. Reduces nonspecific interactions between polymerase and the DNA.

Question 16

What is the function of TFIIE?

Answer 16

Increases TFIIH affinity

Question 17

What is the function of TFIIH?

Answer 17

Phosphorylates RNA polymerase II

Question 18

What are the 2 enzymatic activities of TAFII250?

Answer 18

1. ) Histone acetyltransferase (HAT) attaches acetyl groups to lysines on histones, usually activating transcription by opening up DNA
2. ) Protein kinase can phosphorylate itself, TFIIF, and to a lesser extent TFIIA and TFIIE

Question 19

How does phosphorylation modify activity of the pre-initiation complex?

Answer 19

Phosphorylation modifies efficiency of assembly of the pre-initiation complex

Question 20

What is the function of TBP?

Answer 20

Functions with RNA pol II promoters with a TATA box as well as RNA pol I, II, and III promoters without a TATA box. It is a universal transcription factor needed for transcription in eukaryotic cells

Question 21

What is the main role of TFIIF?

Answer 21

The main role of TFIIF is to bind the polymerase and direct it to promoters containing the DAB complex

Question 22

How is TFIIF similar to the prokaryotic sigma factor?

Answer 22

It reduces non-specific interactions between polymerases and DNA

Question 23

Which enzymatic form of TFIIH carries out RNA chain elongation?

Answer 23

IIo, the phosphorylated form

Question 24

Which general transcription factors are required for promoter clearance but not elongation?

Answer 24

TFIIE and TFIIH

Question 25

What are the 3 types of activation domains?

Answer 25

Acidic, Glutamine-rich, Proline-rich

Question 26

Give an example of an acidic activation domain

Answer 26

Gal4

Question 27

Give an example of a Glutamine-rich activation domain

Answer 27

Sp1

Question 28

Give an example of a Proline-rich activation domain

Answer 28

CTF