Transcription 1

Question 1

What are the 5 major functions of RNA polymerases?

Answer 1

1) They search for promoters
2) They unwind a short piece of DNA to produce single stranded DNA templates
3) They select the right nucleoside triphosphate
4) They detect transcription termination signals
5) Interact with activators and repressors to determine rate of transcription

Question 2

Describe 4 major differences between transcription in prokaryotes and eukaryotes

Answer 2

1) Transcription occurs in the nucleus in eukaryotes, therefore you cannot have co-transcriptional translation. In eukaryotes you can regulate the translation of a gene by altering the stability of the mRNA
2) Chromatin is more compacted in eukaryotes. DNA must be unwound from histones before it can be transcribed
3) Gene regulation is more complex. several cis acting and trans-acting factors
4) mRNA is extensively modified after transcription in eukaryotes

Question 3

Describe the structure of bacterial RNAP

Answer 3

α2ββ’ω core enzyme

addition of σ subunit helps find promoter regions

structure resembles a crab claw.
two identical alpha subunits in the back, two beta subunits making claws, omega in back (small grey) and then sigma overlaying the whole thing

Question 4

Describe the assembly of bacterial RNAP

Answer 4

1) core enzyme forms away from DNA α2ββ’ω
2) this then receives a sigma factor forming a holoenzyme
3) closed complex
4) open complex
5) initiation complex
6) loss of sigma factor
7) elongation complex
8) sigma factor joins another core enzyme

Question 5

Describe the Ratchetable and Ratcheted forms of RNAP

Answer 5

Transcription is unidirectional

Mismatching can cause a small backtrack = ratchetable form

Long backtracking = ratcheted form, this opens up a secondary channel on the RNAP to accomodate the backtracked RNA

in the backtracked form the RNAP elongation function is lost and a hydrolytic function takes over to remove incorrect RNA

Question 6

Describe the structure of the bridge helix

Answer 6

It is an alpha helix.

It is a flexible, hinge like structure, proposed to act in a ratchet like mechanism pulling the DNA through the polymerase

Question 7

Rudder, Lid and Fork loop, what binds to what

Answer 7

Rudder binds DNA, Lid binds RNA, fork loop holds them both

Question 8

Describe eukaryotic RNAP biogenesis

Answer 8

You start off with the free floating subunits that have been transcribed on their own

they then bind together with the help of assembly factors, which then dissociate and then other things bind that are import factors

import factors take them through the nuclear pore, import factors are released and exported back through the pore.