Transcription

Question 1

Explain the initiation of prokaryotic transcription. Include terms like -10 region, -35 region, etc.

Answer 1

The sigma factor binds to RNA polymerase and the DNA promoter sequence. The -10 region of the promoter is called the pribnow box, and has the sequence TATAAT. The -35 region contains the sequence ACA. The +1 initiation site is where transcription begins.

Question 2

Formation of pre-initiation complex and elongation in eukaryotes for RNA pol II. Be specific on what TFIIH does. What type of energy does TFIIH use?

Answer 2

For order: Do bad friends eat hair?

1. TFIID binds to TATA box via the subunit TBP. (also contains TAFs)
2. TFIIB is recruited, and interacts with TBP and DNA, while assisting the polymerase in melting DNA strands at start site.
3. TFIIF comes and forms a complex w/polymerase and positions over the start site, which creates space for TFIIE to bind.
4. TFIIH binds, which has helicase activity, and phosphorylates the polymerase CTD on serine residues which releases the initiation complex so that elongation can happen. uses ATP.

Question 3

Initiation complex for RNA pol I consists of?

Answer 3

Upstream binding factor (UBF), SL1 containing TBP/Pol I specific TAFs

Question 4

What transcription factors are in the initiation complex for RNA pol III? Where are the promoters for these genes? What do they use to recruit the polymerase III?

Answer 4

TFIIIA, TFIIIB, TFIIIC. Promoters for the tRNA and 5S-rRNA are within the transcribed region (examples of internal control region).
U6 snRNA genes use upstream PSE and TATA sites to recruit RNA III to the promoter .

Question 5

Explain Rho independent termination of transcription.

- What forms the structures?

Answer 5

Hairpin structures are formed in the RNA by GC rich sequences. U residues are transcribed after the pin. These Us only bind weakly to the As in the template DNA, so the polymerase falls off.

Question 6

Explain Rho dependent termination in prokaryotes

Answer 6

Hairpin structure forms in RNA due to GC rich sequences, but there is not a strand of Us after. The polymerase slows down when it hits the hairpin, the Rho protein associates with the polymerase/mRNA (not the DNA), and transcription is terminated.

Question 7

how is transcription terminated in eukaryotes with RNA pol I?
Pol II?
Pol III?

Answer 7

Pol I- Similar to rho dependent
Pol II- More complex, 3’ cleavage
Pol III- similar to rho independent

Question 8

In the lac operon, what happens if glucose is present and there is no lactose?
Glucose and lactose available?
Just lactose?

Answer 8

Glucose, no lactose- Operon is repressed, and polymerase can’t bind. Lac z thus not expressed.
Both available- Lac repressor inhibited by lactose, polymerase binds and Lac z expressed in LOW LEVELS
no glucose, yes lactose- CAP binds cAMP, allowing it to bind at CAP site, repressor is inhibited by lactose, and polymerase can bind. High level of Lac z expressed.

Question 9

What does RNA Pol I transcribe in euk?

Answer 9

5.8, 18, 28S rRNA genes

Question 10

What does RNA Pol II transcribe in euk?

Answer 10

All protein-coding genes, snoRNA genes, miRNA genes, siRNA genes, and most snRNA genes,

Question 11

What does RNA Pol III transcribe in euk?

Answer 11

tRNA genes, 5S rRNA genes, some snRNA genes, and genes for other small RNAs.

Question 12

Why are TBP important even in promoters lacking a TATA box?

Answer 12

Because it interacts with DNA and recruits other pre-initiation transcription factors to appropriate location, even for promoters lacking a TATA box.

Question 13

How does the repressor work in the Trp operon?

Answer 13

tryptophan binds to repressor allows it to associate with operator sequence of the operon, which makes it so polymerase can’t attach