RNA Metobolism

Question 1

Functions of the RNA subunits [Beta, sigma, alpha]

Answer 1

Beta: carries active site
Sigma: part of the enzyme that binds to the promoter sequence
Alpha: promote assembly and bind to upstream elements

Question 2

What is a promoter sequence?

Answer 2

Specific sequences in the genome where RNA polymerase binds

Question 3

What are consensus sequences?

Answer 3

These are promoter sequences shared by many different transcripts. One base change can affect binding by several orders of magnitude

Question 4

RNA Polymerase Initiation

Answer 4

1) RNA polymerase binds (through sigma) to DNA at a promoter sequence forming the closed complex
2) Open complex forms as base pairing at -10 region are disrupted. Two strands of DNA are then unwound.
3) Transcription begins

Protein NusG links RNA polymerase and ribosome
A protein NusA binds competitively with sigma to the polymerase and remains bound until transcription is complete, at which time it dissociates and is replaced once again by sigma.

Question 5

Protein Dependent Termination

Answer 5

Depends on a rho protein. The termination sequence for protein dependent termination is a stem loop that causes the RNA polymerase to pause briefly. During this time the rho protein catches up and dissociates the RNA-DNA hybrid.

The protein dependent termination requires a rho protein because the termination sequence lacks AAA therefore the RNA and DNA are more tightly associated with each other. This causes the help of a rho protein to dissociate the RNA-DNA hybrid.

Question 6

Protein Independent Termination

Answer 6

RNA Forms hairpin followed by poly (U) sequence.

There are self-complementary sequences in the termination sequence that form a hairpin and weak A/U base pairs in the termination sequence cause the RNA to dissociate from DNA. This causes the RNA Polymerase to dissociate from RNA and transcription terminates.

Question 7

Activator proteins [How do they work?]

Answer 7

1) Bind to proper sequences that facilitate opening of DNA
2) Help RNA polymerase favor open conformation by inducing allosteric changes
3) Increase affinity of polymerase for promoter by binding to RNA polymerase and DNA at site next to promoter

Question 8

Repressor Proteins [How do they work?]

Answer 8

1) Bind to repressor sequences that overlap promoter causing steric block which prevents RNA polymerase from binding (prevents opening of DNA)

Question 9

TAFS function (Tata box associated factors)

Answer 9

Recruit TBP (tata box binding protein) and bring them to other promoters in the absence of a tata box

Question 10

What are enhancers?

Answer 10

Enhancers bind to regulatory sites and transcription factors protomote transcription

Question 11

What are insulators?

Answer 11

Insulators regulate DNA’s ability to loop to maintain some form of control.