4-1: Transcription

Question 1

What is the coding strand?

Answer 1

The strand that not used as the template by RNA pol, but will match the RNA transcript

Question 2

What is the template strand?

Answer 2

Used by RNA pol to make the RNA, complimentary to the RNA made

Question 3

What subunits make up RNA polymerase (core enzyme)

Answer 3

alpha subunit x2
Beta
Beta’
Omega

Question 4

What is the holoenzyme made up of, what does it do

Answer 4

Sigma factor (subunit) plus core enzyme
Recognize promoter sequences and will dissociated from the core enzyme

Question 5

What does the core enzyme do

Answer 5

Unwinds DNA, forms transcription bubble, Builds RNA using NTPs

Question 6

When is transcription terminated

Answer 6

When RNAp encounters a transcriptional terminator it dissociates

Question 7

What are the two transcriptional terminators

Answer 7

Intrinsic (rho-independent) terminators

Rho-dependent terminators

Question 8

What is the mechanism that intrinsic (rho independent) terminators use?

Answer 8

RNA hairpin forms, followed by string of ‘U’ residues (pause signal). Hairpin forces RNAp off

Question 9

What is the mechanism that rho dependent terminators use?

Answer 9

Protein called Rho binds RNA as it is transcribed, causes RNAp to dissociate after encountering certain sequence

Question 10

What do promoters do?

Answer 10

Guide transcriptional initiated

Question 11

What dictates whether or not a region acts as a promoter/if the promoter is active?

Answer 11

Sigma factors
Regulatory proteins

Question 12

What is the most common sigma factor

Answer 12

sigma^70 (RpoD)

Question 13

What two sequences does RpoD recognize

Answer 13

TTGACA and Pribnow box.

Question 14

Where is the TTGACA found?

Answer 14

35 bp upstream from the transcription start site (+)

Question 15

What is the sequence for the Pribnow box? Where is it found?

Answer 15

TATAAT. Found 10 bp upsteream from +1

Question 16

What is the transcriptional start site identified as?

Answer 16

+1

Question 17

What do negative numbers from the transcriptional start site mean?

Answer 17

Located upstream from the start site. Eg. Pribnow box is -10 upstream

Question 18

What do positive numbers from the transcriptional start site mean?

Answer 18

Downstream.

Question 19

What are the three major classes of RNAs

Answer 19

Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)

Question 20

What kind of RNA makes up ~95% of a growing cell

Answer 20

rRNA, tRNA

Question 21

what are the two regions of mRNA

Answer 21

Open reading frames (translated)
Untranslated regions (UTRs)

Question 22

What are polycistronic mRNAs

Answer 22

mRNA that encode multiple ORFs

Question 23

How are polycistronic mRNAs arranged. Why?

Answer 23

Into an operon. So they can be cotranscribed

Question 24

The ORF spans from…

Answer 24

The start codon (e.g. ATG) to the stop codon (e.g. TAA)

Question 25

The 5’UTR spans from which regions? What does it contain?

Answer 25

+1 to start codon. Contains ribosome binding site

Question 26

3’ UTR spans from which regions? What does it contain?

Answer 26

Stop codon to final transcribed residue. Contains transcriptional terminator sequences.

Question 27

How is transcription different in eukaryotes?

Answer 27

3 RNA polymerases
More complex RNAp (12+ subunits)
Euk RNA pol need TFs to recognize the promoters
No operons

Question 28

What is eukaryotic RNA pol II responsible for?

Answer 28

Producing mRNA that encodes proteins

Question 29

What is an example of a promoter sequence in euks?

Answer 29

TATA box, bound by TATA TFs

Question 30

How is Archaeal transcription similar to eukaryotes?

Answer 30

RNA pol resembles RNA pol II from euk that has 11-13 subunits
Uses Transcription factors
Also uses TATA boxes and TFs that bind TATA boxes

Question 31

How is archaeal transcription similar to bacteria?

Answer 31

No 5’ cap, no poly A tail, no introns
No nucleus
Use of operons