Lec 50: Eukaryotic Gene Regulation

Question 1

Describe the organization of the Eukaryotic Promoter

Answer 1

Insulator - Distal Enhancer - Upstream Enhancer - Silencer - Proximal Promoting Elements (PPE) - TATA - Start Codon

Question 2

Important feature of histones that allows them to control DNA spatially

Answer 2

They are charged, + Tails - Heads

Question 3

What happens when we acetylate he histone tail?

Answer 3

DNA which is negatively charged wraps tightly around the positive tail of the histone. When you acetylate this, you take that positive charge away so the DNA will no longer pack on. You go from heterochromatin (tight chromatin) to euchromatin (spaced out, loose chromatin)

Question 4

What does methylation typically act on?

Answer 4

Lysine

Question 5

What is a chromodomain?

Answer 5

A protein structural domain associated with chromatin manipulation that binds to methylated histones to guide transcription processes at these sites. Activates transcription

Question 6

What is a bromodomain?

Answer 6

Homologue to chromodomain that associates with acetylated lysines of histones.

Question 7

Nuclear Receptors

Answer 7

1. Directly bind DNA = Transcription factors

2. Ligand needs to bind (so this means they have 2 binding domains, one for DNA and one for ligand)

Question 8

Nuclear Receptor Structure

Answer 8

Not letting me post a picture here for some reason, but the Structure is

A/B - C - D - E(huge) - F

A/B = N terminal domain
C = DNA binding domain
D = Hinge Region
E = Ligand Binding domain
F = C terminal domain

Question 9

Explain the sequence of steps by which steroid hormones increase/decrease the rate of transcription of hormonally responsive genes.

Answer 9

1. Ligand binds nuclear receptor, causing a conformational change that allows recruitment of coactivators
2. Ligand-Receptor complex binds directly to DNA to control expression of certain genes and enlists the coactivators to fulfill the effect designated by the ligand. Typically, these coactivators affect the state of the chromatin.

Question 10

What is a hormone response element?

Answer 10

Regulatory DNA binding proteins that are specifically activated by transcription factors binding them.

Question 11

Basal Transcription Complex

Answer 11

An RNA polymerase with general transcription factors and a promoter binding protein that binds the TATA Binding protein (core promoter)

Question 12

HAT

Answer 12

Histone Acetyltransferases - Acetylate lysine chains on histones. Reduces charge attraction between DNA and histones.

Question 13

HDAC

Answer 13

Histone Deacetylases- Remove acetate groups fro histones (opposite effect of HAT; it reassociates the DNA onto the histone)

Question 14

Euchromatin

Answer 14

Loose association of DNA and histones = transcriptionally active

Question 15

Heterochromatin

Answer 15

DNA locked down on histone = no activity

Question 16

Hey you’re awesome.

Answer 16

Keep on keepin’ on.

Question 17

Discuss the chromatin remodeling complex

Answer 17

Nucelosome displacement mechanism that allows for transcription tooccur. Bromodomains on the complex find the acetylated histones and displace them.

Question 18

Transcription Complex - Video

Answer 18

http://www.youtube.com/watch?v=ysxtZJUeTCE

Question 19

Transcription Complex Step wise written out

Answer 19

The process needs to begin with transcription factors binding straight to the DNA. Basal transcription proteins need to start this, so TBP (TATA binding protein) binds to the core promoting region (TATA) along with binding factors A and B (B on the side of the RNA Polymerase site). Then F binds to B, which allows RNA Polymerase to bind. With RNA Polymerase bound, you still can’t commence anything. You need factors E and H (H will unzip the DNA) to bind on top of the RNA polymerase attached to the F binding factor. Now we can proceed, but we need something o increase/decrease the rate of transcription. Coactivators, a second set of transcription factors, bind to the complex so that Activators can bind. These activators bind directly to the DNA enhancers and transcription ca begin, with the activators changing pace based on the signals they receive. If a repressor is bound to a silencing region, the activators can not bind, and transcription will not occur.

Question 20

Discuss the N terminal domain

Answer 20

Contains Activation Factor - 1 (AF-1) which does not need a ligand to activate transcription. Can work with (loosely synergize with) the AF-2 in the Ligand Binding domain to enhance transcription.

Question 21

Discuss the DNA binding domain

Answer 21

Highly conserved domain with two zinc fingers and binds directly to DNA sequences

Question 22

Discuss the Hinge Region

Answer 22

Flexible domain that influences intracellular trafficking

Question 23

Discuss the Ligand Binding Domain

Answer 23

Alpha helical complex. Binds coactivators and corepressors (ligands)

Question 24

Discuss the C terminal domain

Answer 24

Highly variable region between different nuclear receptors