10 - Transcription Control

Question 1

What is the direction in which, you:
read DNA? make an RNA?

Answer 1

Read: 3’ -> 5’
Make: 5’ -> 3’

Question 2

What is a “transcription bubble”?

Answer 2

A piece of DNA, opened up for the RNA to transcribe from.

Question 3

The functions of which enzymes are included in RNA polymerase?

Answer 3

Helicase: can split open the DNA
3’ exonuclease: can correct errors.

Question 4

Compare the error rate of DNA and RNA polymerases?
Why this difference is OK?

Answer 4

RNA polymerase: 1/10^5-10^6
DNA polymerase: 1 in 10^7-10^8

RNA polymerase is 10-1000X less accurate that DNA polymerase. You can get away with an error in your mRNA, because of their shorter life. It can be a big deal if an error is made in DNA, because they are more permanent, and probably transferrable to the next generation.

Question 5

What are transcription factors?

Answer 5

Proteins during the transcription which activate or repress it.

Question 6

Which processes are envolved in controling transcription?

Answer 6

1. Promoters and enhancers
2. chromatin remodeling
3. 5’ capping
4. 3’ polyadenylation
5. Splicing

Question 7

What promoters and enhancers do during transcription?

Answer 7

They make a mature mRNA which is ready to leave the nucleus from pre mRNA

Question 8

What happens during chromatin remodeling? Which one promotes and which one reduce transcription?

Answer 8

DNA: methylation of cytosine,
stablizes the DNA -> downregulates transcription
Histone: modification
reduces the positive charge of histones
destablizes the DNA -> upregulates transcription

Question 9

Which amino acids are involved in chromatin remodeling?

Answer 9

Histone modification: Arginine/lysine
become the amide (not charged)
DNA methylation: cytosine

Question 10

What happens during 5’ capping?

Answer 10

cap added to 5’ end of RNA. Protects from exonuclease.

Question 11

What happens during 3’ polyadenylation?

Answer 11

Multiple adenines (As) added to the 3’ end of RNA. Something that exonuclease can chew on, until it gets to the main message. Some kind of a timer for mRNA.

Question 12

What threats mRNAs the most?

Answer 12

exonucleases

Question 13

How do you characterize transcriptome? What is its advantage vs genome?

Answer 13

It’s much shorter that genome -> easier to process
We add beads with polyT on them to catch polyadenylation of the 3’ ends.

Question 14

What is splicing?

Answer 14

Removing introns. 3’ and 5’ ends are not changed. The only change is removing introns from in between exons.