Transcription in Prokaryotes

Question 1

How many polymerases do Prokaryotes have?

Answer 1

just 1

Question 2

In what direction does the RNA polymerase work

Answer 2

5’-3’

Question 3

Is the RNA product base-paired to the template DNA?

Answer 3

No

Question 4

RNA sequence is analogous to which strand of DNA? (2 names)

What is the difference between them?

Answer 4

Coding strand/sense strand
DNA - Cytosine
RNA - Uracyl

Question 5

What is the name of transcription unit in prokaryotes?

Answer 5

Operon

Question 6

What are polycystronic transcripts ?

Answer 6

When multiple genes are under control of 1 operon and therefore are transcribed together

Question 7

What is the mechanism of the DNA polymerisation ?

Answer 7

rNTPs pair with their complementary bases and polymerase catalyses the formation of the phosphate bond between rNTs of the growing strand with the release of pyrophosphate.

Question 8

What is the structure of E.coli polymerase?

Answer 8

Core polymerase is sufficient for polimerisation, but no specificity for the promoter
	α subunit - scaffolding role
	β subunit - polymerase active site
	β’ subunit - DNA binding
	ω subunit – unkown role

Sigma factor
 σ subunit – promoter recognition sequence

Question 9

In transcription initiation what do σ4, σ2 and αCTD subunits bind to and what are their functions?
What is the net result of those 3 bindings?

Answer 9

o Sigma 4 -> -35 sequence (recognition site)
o Sigma 2 -> -10 sequence (start of DNA melting for transcription)
o Alpha CTD -> UP-element (promotes proper binding of polymerase to DNA)

Polymerase positions itself on the promoter region.

Question 10

How does RNA polymerase unwind DNA?

Answer 10

RNA polymerase undergoes isomerisation, which changes the shape of the complex and melts DNA

Question 11

Is the rate of RNA elongation constant?

Answer 11

No

Question 12

What is the terminator sequence?

Answer 12

A sequence that triggers the dissociation of RNA polymerasee from DNA and release of nascent RNA

Question 13

What is Rho factor? Where and what does it bind?

How does it terminate thetranscription?

Answer 13

Rho factor is a 6-ringed protein, which binds to the termination recognition site(rut site), only on ssRNA.

It terminates the transcription by pulling the RNA out of the polymerase, or inducing the confirmational change the that destabilises polymerisation complex.

Question 14

What are the intrinsic terminators and how does the rho-independent termination work?

Answer 14

Intrinsic terminators are the short inverted repeats + stretch of 8 A-T bp. This sequence is sufficient to destabilise the polymerisation complex and terminate transcription.

Question 15

What is the most important step in regulation of prokaryotic transcription?

Answer 15

Initiation of transcription.

Question 16

What are negative and positive regulators and what are their DNA binding sites?

Answer 16

Negative regulators - inhibit transcription by occupying the promoter.
Positive regulators - promote the transcription by binding to the activator binding-site and promoting RNA polymerase binding

Question 17

Describe Lactose operon example of prokaryotic transcription regulation.

Answer 17

glucose absent, lactose present ->CAP binds to the CAP site - transcription promoted
glucose present, lactose absent -> repressor binds to the promoter - transcription inhibited
both present -> no regulator bound - baseline transription

Question 18

What factor initiates the transcription in most bacterial genes?

Answer 18

sigma70 factor, but there are many other sigma factors recognising promoter sequences of genes with particular functions

Question 19

How is the tRNA processed?

Answer 19

1) RNAse P and other endonucleases cleave the primary transcript at 5’end
2) RNAse D cleaves the 3’end
3) tRNA nucleotidyl transferase adds CCA to the 3’end