Transcription in Prokaryotes part 2

Question 1

Define the promoter

Answer 1

A sequence of nucleotides prior to the gene of interest to which the transcriptional machinery binds

Question 2

What two factors control the formation rate of the DNA-RNA pol. complex?

Answer 2

1. Two consensus sequences in the promoter region

2. Proteins that modify the affinity of the RNA pol. for the promoter

Question 3

What are the positions of the two consensus sequences in the promoter region?

Answer 3

position -10 and -35

Question 4

What is the consensus sequence at position -10

Answer 4

TATAAT

Question 5

What is the consensus sequence at position -35

Answer 5

TTGACA

Question 6

Proteins that increase the affinity of the RNA pol. for the promoter are called…

Answer 6

activators

Question 7

Proteins that decrease the affinity of the RNA pol. for the promoter are called…

Answer 7

repressors

Question 8

Define a “down” mutation

Answer 8

decreases transcription efficiency by shifting the sequence further away from the consensus sequence

Question 9

Define an “up” mutation

Answer 9

Increases transcription efficiency by shifting the sequence closer to the consensus sequence

Question 10

What is the general sigma factor?

Answer 10

Sigma 70

Question 11

Sigma factors control promoter recognition for the RNA pol. How?

Answer 11

Sigma factors are responsible for recognizing the DNA sequence the RNA pol binds to. Thus, substitution of a sigma factor causes the RNA pol to recognize a different set of promoters

Question 12

How many different sigma factors did he show us? What was the takeaway from that?

Answer 12

Five.

• Each sigma factor recognizes different sequences at the -10 and -35 positions
• One general sigma factor (sigma 70) used most of the time

Question 13

What are the two types of promoters

Answer 13

1. Typical promoter
   - holoenzyme is bound to DNA @ sequences -10 and -35
2. Promoter with activator site
   - An activator site, usually upstream (sometimes between -35 and -10), contains a sequence where an activator protein can bind.
   - This activator, once bound, interacts with the sigma factor

Question 14

What are the two types of supercoiling?

Answer 14

1. Negative supercoiling (behind site of transcription)
   - helix opening facilitated
2. Positive supercoiling (in front of site of transcription
   - helix opening hindered

Question 15

Define the role of gyrase with regards to supercoiling

Answer 15

Helps task of RNA pol be creating overall NEGATIVE supercoiling on the DNA strand

Question 16

Define the role of topoisomerase with regards to supercoiling

Answer 16

Returns excessive negative levels of supercoiling to normal coiling levels

Question 17

What are the three types of terminators?

Answer 17

1. Intrinsic terminator
2. Rho-dependent terminator
3. Antitermination

Question 18

List three characteristics of an intrinsic terminator

Answer 18

1. part of the strand being synthesized
2. Two major structural features: hairpin structure and 6 Us near hairpin
3. Once hairpin is formed, it bends around and interacts with RNA pol, halting transcription

Question 19

List some characteristics of Rho-dependent terminators

Answer 19

1. Rho protein is a hexamer, binding to RUT site on freshly synthesized RNA
2. The RUT site they bind to is C-rich, G-poor
3. Rho uses helicase to separate DNA from RNA

Question 20

How does Rho terminate transcription

Answer 20

• while RNA pol is paused at a hairpin, Rho catches up by moving up mRNA.
• Rho then unwinds DNA-RNA hybrid

Question 21

What is antitermination?

Answer 21

A property of RNA pol that allows it to ignore a termination sequence and continue synthesis.
- certain proteins need to bind in order for this result to occur.