Biochemistry - Transcription

Question 1

What are the two steps of protein synhesis?

Answer 1

Transcription
Trnaslation

Question 2

RNA polymerase

Answer 2

This is the the primary gene expression enzyme transcribing DNA into RNA.

Question 3

What does RNAP II do?

Answer 3

Primary eukaryotic polymerase for all protein-coding genes and non=protein RN like nuclear RNA.

Question 4

What does RNAP III do?

Answer 4

Transcribes tRNA genes and the 5S component of rRNA.

Question 5

What is gene regulation mediated by?

Answer 5

Promoters like enhancers and silencers.

Question 6

Promoters

Answer 6

Regulatory regiosn where polymerases or TFs bind to initate gene transcription

Question 7

What region do RNAP bind?

Answer 7

The TATA box of the promoter.

Question 8

TATA box

Answer 8

This defines transcription direction and indicates the DNA strand to be read

Question 9

How do enhancers and silencers work?

Answer 9

Bind the TATA box and regulate their activity.

Question 10

What is required of the chromosome for transcription?

Answer 10

Chromatin remodelling complex opening of nucleosomes.

Question 11

What are the five TF mediating RNAPII function?

Answer 11

TFFIIB, E, D, F and H

Question 12

Why does so much cell variety exist in organisms?

Answer 12

Due to the variability by gene regulatory networks like enhancers and silencers.

Question 13

Gene Regulatory Networks

Answer 13

Molecular regulators interacting with TFs and genes to regulate mRNA expression

Question 14

Enhancers

Answer 14

Amplify gene expression, can be up to 1 million base pairs away, but on average 100-1000 bp.

Question 15

Intergenic

Answer 15

In between active genes

Question 16

Intronic

Answer 16

In between exons, on the introns.

Question 17

Where are enhancers, super-enhancers and silencers found?

Answer 17

Intergenic and intronic regions

Question 18

What happens in initaiton of PS?

Answer 18

TBP brings promoter DNA into contact with TFIIB of RNAPii, destabilising DNA to prepare elongation.

Question 19

What happens when RNAPII first contacts promoter region?

Answer 19

It folllows until 25-30bp from TATA, where transcription site near polymerase active site, where TFIIE and H is recruited.

Question 20

TFIIH

Answer 20

Destabilises DNA duplex to allow thermal unwinding forming transcription bubble.

Question 21

Transcription bubble

Answer 21

A complex formed when a limited portion of the DNA double helix is unwound.

Question 22

Template Strand

Answer 22

The strand copied to synthesise mRNA

Question 23

What happens after TFIIH destabilises DNA?

Answer 23

TFIIF binds non-template strand, whilst template strand follows through polymerase active site three NT deep, bending sharply and then clamped for elongation

Question 24

Elongation

Answer 24

This is the successive transcription of nucleotdies of the template strand from 5’s to 3’

Question 25

Which end are nucleotides transcribed from?

Answer 25

3' end.

Question 26

How does trigger loop permit hydrogen bond formation in the polymerase?

Answer 26

Trigger loop containing histidine residue alternates between clamping sites, promoting electron flow coupled with phosphodiester bond formation.

Question 27

What are the two trigger loop states?

Answer 27

One allows NTP to enter active centre, and a closed state holding NTP in the active centre

Question 28

When during PS can a second roundo of transcription occur?

Answer 28

After about 50-60NT are expressed.

Question 29

What are the processesing pathways primary transcript undergoes after formation?

Answer 29

7'methylguanosie cap addition 3' polyadenylation Splicing of introns

Question 30

Why is 7'MG cap addition important?

Answer 30

It allows ribosomal recognition for syntheses?

Question 31

What happens in 3' adenylation?

Answer 31

The 3' undergoes exonuclease digestion to a short sequence where a poly-a tail can be added.

Question 32

Why is it important transcription and RNA processing are coupled?

Answer 32

The occurence of one regulates the next, limiting diffusion required for progression.