Bio Lecture 20/21

Question 1

What are positive and negative control?

Answer 1

Positive control increases transcription when activators bind to DNA.
Negative control decreases transcription when repressors are bound to DNA.

Question 2

What is an operon?

Answer 2

In prokaryotes, it is the section of DNA that includes all the gens necessary for a given metabolic pathway.

Question 3

What are the six ways that eukaryote gene expression can be controlled?

Answer 3

1. Transcription
2. RNA processing
3. mRNA transportation
4. Translation (rate of protein production)
5. Post processing of proteins to activate/inactivate proteins
6. Degradation of mRNA ( has to do with the poly A tail)

Question 4

What are cis-elements?

Answer 4

Specific DNA sequences where transcription factors bind. These help to control transcription.

Question 5

What are trans-elements?

Answer 5

Gene regulatory proteins that recognize the cis-elements and bind to DNA.

Question 6

What are GTFs?

Answer 6

General transcription factors: these are required for transcription initiation. They bind to promotor regions of a gene.

Question 7

What are specific transcription factors?

Answer 7

Also called activators. These increase transcription in response to certain signals and in certain cells. They bind to enhancers.

Question 8

What is meant by the rate of transcription/translation?

Answer 8

The rate is not how fast a given RNApol advances, but how fast and how often RNApol drops off the end and restarts.

Question 9

How are enhancers affected by their location and orientation?

Answer 9

The efficiency of the enhancers is not affected by the position or the orientation of the enhancer.

Question 10

Explain how the lac operon works.

Answer 10

When glucose is low, this causes adenylyl cyclase activity increases. This converts ATP to cAMP. cAMP binds to CAP which then binds to the CAP promotor binding site which allows transcription to take place.
When lactose is high, it is converted to allolactose which binds to lac repressor proteins and remove them from the operator.

Question 11

What is the difference between a promotor and an operator?

Answer 11

Promotors are binding sites for RNA pol, operators are binding sites for other proteins that control transcription.

Question 12

What are the two domains of trans-acting factors?

Answer 12

DNA-binding domain: very specific to DNA sequence

Activation domain:

Question 13

What are the structural motifs of the DNA binding domain?

Answer 13

Zinc Finger: (zinc ions form loops of the protein)
Leucine Zipper: (two alpha helices bind with leucines to dimerize)
Helix-Loop-Helix:
Helix-Turn-Helix:

Question 14

What are HATs?

Answer 14

Histone AcetylTransferases: these acetylate histones and loosen the wrapping of DNA so that transcription can happen.

Question 15

What are HDACs?

Answer 15

Histone DeAcetylasess: these deacetylate histones and cause the DNA to wrap more tightly around the histones.

Question 16

What are the 4 modes of gene repression?

Answer 16

1. Competition: repressors compete with activators for the same DNA regulatory sequences
2. Inhibition: repressors bind DNA and inhibit transcription through protein-protein interaction, the repressor interacts with the activation domain of the activator
3. Direct Repression: prevent other transcription factors directly from working
4. Indirect: they recruit other subunits that inhibit transcription (example is recruiting deacetylases to the histones)

Question 17

What is RNAi?

Answer 17

RNA interference: double stranded RNA prevents translation from occurring, miRNA and siRNA bind to the mRNA and block translation or cause premature breaking of the strand.