Transcription (Bently)

Question 1

alpha - amanitin

Answer 1

Non-competitive inhibitor of Poll II
Binds bridge helix
halts trxn by blocking translocation and elongation

Question 2

Rifampicin

Answer 2

TB & broad spectrum antibiotic

Blocks exit channel to halt trxn

Question 3

What rxn does RNA polymerase catalyze?

Answer 3

3’-OH nuc. attack on 5’-phosphate

Question 4

What are the 5 steps in the trxn cycle? (both bact. and euk)

Answer 4

1. Binding –> closed complex
2. Open complex
3. Initial phosphodiester linkage
4. Elongation
5. Termination

Question 5

Where does RNA polymerase bind?

Answer 5

to the promoter (think tata box)

Question 6

How does the open complex form?

Answer 6

RNA polymerase “melts” the DNA to form a trxn bubble

Question 7

How does the initial linkage form?

Answer 7

polymerase catalyzes initial phosphodiester bond between the two initial rNTP’s

Question 8

In what direction does RNA pol. advance along the DNA?

Answer 8

3’ –> 5’

-so the complimentary new RNA is being built 5’ –> 3’

Question 9

Which steps in trxn are “heavily” regulated?

Answer 9

1. Initiation (and its 3 substeps)

2. Elongation (pauses allow for regulation)

Question 10

What are the 4 DNA dependent RNA polymerases?

Answer 10

1. Pol I
2. Pol II
3. Pol III
4. Mitrochondrial

Question 11

Function of RNA pol I ?

Answer 11

rRNA

Question 12

Function of RNA pol II?

Answer 12

mRNA
snRNA
miRNA
lncRNA

Question 13

Function of Pol III ?

Answer 13

tRNA, U6 snRNA

Question 14

Where does U6 snRNA function?

Answer 14

Is part of the splicing machinery

Question 15

What is special about mitochondrial RNA?

Answer 15

Is one small subunit and one small helper protein. Most others are multiprotein complexes.

Question 16

Define promoter

Answer 16

Specific sequence in the DNA that directs trxn of adjacent genes

• variable from gene to gene
• commonality is TATA box

Question 17

Where is the TATA box and why T’s and A’s?

Answer 17

10 - 30 bp upstream from start site

A-T easier to melt

Question 18

4 components of the RNA polymerase II pre-initiation complex.

Answer 18

1. TFIID - binds TATA box (guided by TBP = tata binding protein)
2. TFIIH - contains XPB, XPD = helicase activity
   - contains CD47 = phosphorylates C-term. domain of pol II
   - contains p44
3. Mediator - protein-protein contact during initiation
4. pol II holoenzyme

Question 19

What does TBP bind and where?

Answer 19

in the minor groove of the TATA box

signals assembly of the pre-initiation complex

Question 20

TFIIH has two major functions. What are they (broadly)?

Answer 20

1. trxn - initiation complex

2. DNA repair (helicase activity)

Question 21

Name 3 clinical syndromes caused by mutations in TFIIH subunits.

Answer 21

1. Xeroderma Pigmentosum
2. Cockaynes Syndrome
3. Trichothiodystrophy

Question 22

To help you remember Trichothiodystrophy, Tricho mean hair and (remember trichotelomania?)

What is a classic clinical presentation of TTD?

Answer 22

Brittle hair - lacks sulpher (thio)