Prokaryotic Transcription

Question 1

What are the three stages of prokaryotic transcription?

Answer 1

Initiation, elongation, termination

Question 2

Outline the process of prokaryotic transcription initiation.

Answer 2

1. Sigma factor recognizes -10 and -35; secures holoenzyme to promoter location
2. C-terminal of alpha subunit binds to UP element
3. DNA loaded onto holoenzyme
4. Sigma factor opens DNA, exposing template strand to the catalytic site.
5. Transcription begins by the addition of the first ribonucleotide by RNA polymerase.

Question 3

What is meant by the closed complex of RNA polymerase?

Answer 3

After loading DNA, DNA pol is in closed complex, meaning the dsDNA are yet to be separated.

Question 4

What is the open complex of RNA polymerase?

Answer 4

When the dsDNA has been separated.

Question 5

What is abortive initiation?

Answer 5

Sigma factor blocks RNA polymerase from moving further than about 10 nt of RNA transcription. The short RNA falls off and a new round of transcription begins. This repeats until the sigma factor falls off, allowing elongation to begin.

Question 6

What is required for elongation in prokaryotic transcription?

Answer 6

Only RNA polymerase core.

Question 7

Where does prokaryotic transcription termination occur?

Answer 7

in the 3’ UTR

Question 8

What are the two possible methods for prokaryotic transcription termination?

Answer 8

Intrinsic (Rho-independent) or Rho-dependent

Question 9

Explain intrinsic termination.

Answer 9

A highly GC rich followed by U rich segment where transcription is supposed to end. The GC region is complementary to each other, resulting in the RNA folding into a hairpin structure. The formation of the hairpin loop pulls on the RNA, causing the adjacent U-rich region (with weaker H bonds) to pull the RNA off of the template strand.

Question 10

Explain rho-dependent termination.

Answer 10

Rho recognizes the rho utilization site (RUT) and binds to the RNA. Each rho subunit hydrolyzes ATP, using this energy to move to the 3’ end of the RNA. As it is moving towards the core enzyme, a stem-loop structure forms on the RNA, slowing down the enzyme. Rho eventually catches up to the RNA polymerase core enzyme, causing the dissociation of RNA polymerase from DNA and RNA.