Nov 1

Question 1

When is 5’ cap put on RNA?

Answer 1

It is put on once the first few nucleotides are transcribed, so degradation doesn’t occur by 5’ to 3’ exonucleases

Question 2

What do elongation factors do for RNA Pol 2?

Answer 2

They limit the time that pol pauses, so increase elongation rate. They also can proofread the new transcript as RNA pol doesn’t as much as DNA pol

Question 3

When can RNA splicing occur?

Answer 3

It can happen during transcription as soon as the introns are available.

Question 4

What does a different combination of phosphorylations on different sites of CTD of RNA pol 2 do?

Answer 4

It gives diff results, like preinitiation, giving promotor escape, splicing etc.

Question 5

What are the steps in 5’ RNA cap formation?

Answer 5

1. RNA triphosphatase removes the y’ PO4 at the 5’ end of transcript
2. Guanylytransferase adds GMP (from GTP) do the terminal B-PO4 of the strand
3. Methyl transferase methylates C7 of guanine base

Question 6

What happens once the 5’ cap is on the RNA (2)?

Answer 6

1. The transcript is stabilized
2. Signal that the transcript is processed correctly

Question 7

What happens when RNA pol 2 encounters and transcribes the poly-A signal?

Answer 7

1. It will keep transcribing and recruit polyadenylation enzymes due to PO4’d state of the CTD.
   2.Cleavage polyadenylation specific factor (CPSF) and cleavage stimulatory factor (CstF) will cleave downstream of the poly A signal
2. The now released RNA strand will have poly -A polymerase (PAP) add about 200 adenines to the 3’end of the RNA strand
3. Poly -A binding proteins (PBP) will bind to the adenines.

Question 8

What 2 things does the poly A tail do?

Answer 8

Stabilizes mRNA and signals correct 3’ end processing

Question 9

Describe the torpedo model of termination

Answer 9

1. It starts with human Xrn2/Rat1 which is a 5’ to 3’ exonuclease, bound to RNA pol 2
2. Once RNA pol 2 reaches the Poly A signal sequence and the RNA strand is cut and Poly A tail added, the exonuclease will release and start degrading the rest of the strand still getting synthesized by Pol 2.
3. The torpedo is faster than Pol 2, catches up to it, and will cause RNA pol 2 to dissasociate from the template

Question 10

Describe the allosteric model of termination

Answer 10

RNA pol 2 is very processive, and once it reaches poly-A signal it will have conformational change and the processivity will decrease so it falls off

Question 11

How does Pol 1 get recruited to the strand? What does it transcribe?

Answer 11

Mainly transcribes rRNA precursor (non-protein coding). UBF (upstream binding factor) will bind to UCE upstream control element. Then SL1 (complex of TBP and other TAFs will bind and Pol 1 recruited.

Question 12

How does Pol 3 get recruited to the strand? What does it transcribe?

Answer 12

It transcribes tRNAs, some small ribosomal and other RNAs. The promotor is downstream of start site in this case.
2. TBP will bind, recruiting TF3C and then B, which will recruit Pol 3 which will displace TF3C and start transcription

Question 13

______________ is the primary point of gene regulation

Answer 13

Transcription initiation

Question 14

Nuclosomes and their modifieres have profound influence on ________

Answer 14

gene expression

Question 15

________ is controlled by activators and repressors

Answer 15

Transcription

Question 16

Definition of promotor

Answer 16

region of DNA involved in pre-initiation complex binding

Question 17

Definition of regulatory binding sites

Answer 17

binding sites for different
transcription factors

Question 18

Definition of regulatory sequences

Answer 18

The entire collection of regulator
binding sites for a given gene

Question 19

Definition of an enhancer

Answer 19

It is a tight cluster of regulatory binding sites that can affect long distances at either upstream or downstream of a gene

Question 20

Definition of an UAS (upstream activating sequence)

Answer 20

It is an “enhancer” inyeast, only found upstream of a gene and usually not a great
distance

Question 21

Definition of an insulator

Answer 21

blocks promoter activation by binding activators at the enhancer

Question 22

How do regulatory elements differ from bacteria to yeast to human?

Answer 22

Bacteria have like 1 regulatory sequence, and yeast have a few upstream of the promotor. Humans have multiple regulatory sequences up and downstream of the promotor

Question 23

What are the parts of Gal4, how does it come together to form a functional unit?

Answer 23

It has activation domain and DNA binding domain, it forms a dimer with itself.

Question 24

What is the gene that GAL4 will bind to. How test the effect of its binding. What repressor binds to what, and what happens if you do domain swap experiment?

Answer 24

GAL1 gene has UAS that has 4 sequences, each binding to the GAL4 dimer. When GAL4 binds, it can be used to activate gene lacZ and you will get colour change, so can tell if GAL4 binds. If the activating region taken off, and just DNA binding domain on the site, get no activation.

LexA repressor will bind to LexA site, and the DNA binding domain will also do nothing for lacZ. However, if you put GAL4 activating region on LexA DNA binding domain, you will turn on lacZ. It is a chimera (hybrid/recombinant)