Control of Gene Expression

Question 1

What does beta-galactosidase do?

Answer 1

Hyrolyzes lactose into glucose and galactose

Question 2

What does galactoside permease do?

Answer 2

Moves lactose into the cell

Question 3

What food source do bacteria prefer?

Answer 3

Glucose

Question 4

How does the lac operon behave when glucose is present?

Answer 4

A repressor binds to the operator because the cell is happy with glucose is around and eating lactose is unnecessary.

Question 5

How does the lac operon behave when lactose is present?

Answer 5

B-gal converts lactose to glu and galac

and also converted into a lactose isomer, allolactose

Allolactose then binds to the operon repressor to allow a teensy bit of gene expression continue

Question 6

How are cAMP levels affected by glucose levels?

Answer 6

High levels of glucose keep cAMP levels low. When glucose drops, cAMP levels increase

Question 7

How does cAMP affect lac operon transcription?

Answer 7

cAMP will bind to CRP, binding to the DNA and acting as a lac operon enhancer (high level of transcription)

Question 8

On a high level, what is the purpose of the lac operon?

Answer 8

To allow the bacteria to mobilize lactose as a food source when glucose availability is low

Question 9

What motif of CRP interacts with DNA?

Answer 9

Helix-turn-Helix binds to the major groove via H bonds.

Specifically: recognition helix-turn-stabilization helix

Question 10

How do transcription factors interact with DNA?

Are they specific?

Answer 10

Common motifs that interact with the major groove of DNA. Often are dimers

Very specific!

Question 11

What are 4 common transcription factor motifs?

Answer 11

1. Helix-turn-helix
2. Zn finger
3. Leucine zipper/bZIP
4. Helix-loop-helix

Question 12

Describe the Zn finger motif

Answer 12

Repetitive motif of 2 cystine and 2 histidine residues

Question 13

Describe the leucine zipper motif

Answer 13

35 AA stretch with a leucine every 7 + basic alpha helices that interact with the DNA

Question 14

Describe bZIP

Answer 14

“Leucine” zipper motifs with arginine or histidine in place of leucine

Question 15

Describe the basic helix-loop-helix motif

Answer 15

Like other motifs, many + charges in the BASIC alpha helix binds DNA

Question 16

In transcription factor motifs many _____ interactions amount to ____ and _____ binding overall.

Answer 16

Weak, strong, specific

Question 17

What are the 7 ways in which transcription factors can be regulated?

Answer 17

1. Protein synthesis
2. Ligand binding
3. Protein phosphorylation
4. Addition of subunit
5. Unmasking
6. Stimulation of nuclear entry
7. Release from membrane

Question 18

Generally speaking, will a methylated promoter be active?

Answer 18

No! Methylation will stop transcription

Question 19

How can cancer co-opt methylation for its own ends?

Answer 19

Methylating tumor suppressor genes turns them off

Question 20

How does methylation block gene expression?

Answer 20

1. Methylated CpG islands inhibit transcription by physically precluding TF recruitment

OR

2. Methyl CpG binding protein 2 (MeCP2) binds to methyl groups and recruits chromatin remodeling factors

Question 21

What causes Rett Syndrome?

Answer 21

Mutations in MeCP2 on the X chromosome

Question 22

How is Igf2 an example of how methylation can actually lead to activation?

Answer 22

Methylation prevents binding of a repressor

Question 23

What is ATP-chromatin remodeling?

Answer 23

Chromatin remodeling factors interact with C-terminal of large subunit of RNA Pol II and ATP to “open up” nucleosomes

Question 24

What ways in which histone tails can be covalently modified?

Answer 24

Methylation (HMT and PRMT)
Phosphorylation (kinase)
Acetylation (HAT)

Question 25

Which AAs are often modified via methylation to control histones?

Answer 25

Lysine and/or arginine

Question 26

Which AAs can be modified via acetylation to control histones?

Answer 26

Lysine

Question 27

Which AAs can be modified via phosphorylation to control histones?

Answer 27

Serine

Question 28

Histone acetyl transferase (HAT) can acetylate histones…what enzyme removes them?

Answer 28

Histone Deacetylase (HDAC)

Question 29

Acetylation will _____ chromatin with the exception of _____.

Answer 29

Open

Sometimes methylation of lysine can cause repression.