11.3 - The activity of positive regulatory transcription factors: repressors

Question 1

What are ways that repressors can control transcription?

Answer 1

1. sequester activator in the cytoplasm - repressor binds to domain that allows protein to transport through nuclear membrane
2. repressor binds to
   an activator that is already bound to an enhancer and masks its activation domain
3. can be masked and held in cytoplasm until needed
4. can compete with activator for an enhancer

Question 2

Are the DNA-binding domain and activation domains dependent of e/o?

Answer 2

• No, the activation domain interacts with the basal apparatus irrespective of DNA location
• As long as DNA is present, the activation domain can be brough to the basal apparatus

Question 3

What is the two-hybrid assay?

Answer 3

• Works by testing the ability of two proteins to interact where one has a DNA-binding domain and the other has a transcription-activation
  domain.

Question 4

What is the result of this test?

Answer 4

• If the tested proteins can interact, then the hybrid proteins will interact

Question 5

How does activation occur in this test?

Answer 5

• Protein w/ DNA-binding domains binds to reporter gene but does not activate gene
• Activation occurs only if second hybrid binds to first hybrid to bring activation domain to promoter

Question 6

How do activators interact w/ basal apparatus?

Answer 6

• Through the use of DNA-binding domain which searches for an activation domain that it covalently attaches to and is close to the basal apparatus
• Activators should have a DNA-binding and a activation domain

Question 7

What role does the activation domain play?

Answer 7

• contacts w/ transcriptional factors that promote basal apparatus assembly

Question 8

What happens when an activator does not have an activation domain?

Answer 8

• A coactivator is then needed to bind the activator to the basal apparatus

Question 9

What are some basal factors that activators contact with?

Answer 9

• TF D, TF B, or TF A
• TF D is the most common ana it may contact on of several TAFs (TAFs provide connection between activators and basal apparatus)

Question 10

What is another component that may be required for activators to stimulate transcription?

Answer 10

• RNA polymerase may be associated with various
  alternative sets of transcription factors in the form of a holoenzyme complex
• Mediator complexes associate with RNA polymerase and replace activators/co-activators
  and basal factor

Question 11

What are the types of DNA-binding domains?

Answer 11

1. Zinc finger
2. Steroid receptor
3. Helix-turn-helix
4. Homeodomain
5. Helix-loop-helix
6. Leucine zipper
7. bZIP (“basic zipper”)

Question 12

What is the zinc finger?

Answer 12

DNA-binding motif that typifies transcription factors
- made up of Cys and His residues

Question 13

What is the steroid receptor?

Answer 13

• transcription factors that are activated by binding of a steroid ligand

Question 14

What is the helix-turn-helix?

Answer 14

• the motif that describes an arrangement of two α-helices that form a site that binds to DNA, one fitting into the major groove (C-terminal) of DNA and the other in the minor groove (N-terminal)

Question 15

What is the homeodomain?

Answer 15

• DNA-binding motif that typifies a class of transcription factors
• can be activators or repressors

Question 16

What is the helix-loop-helix?

Answer 16

• hydrophobic residues on one side and charged residues on the other side
• motif enables proteins to dimerize, either homodimers or
  heterodimers, and a basic region near this motif contacts DNA
• Not all of the HLH proteins contain a DNA-binding domain, but rather rely on their partner for sequence specificity.

Question 17

What is the leucine zipper?

Answer 17

• A dimerization motif that is
  found in a class of transcription factor

Question 18

What is the bZIP (basic zipper)?

Answer 18

• a bZIP protein has a basic
  DNA-binding region adjacent to a leucine zipper dimerization motif

Question 19

What is chromatin remodeling?

Answer 19

• Inducing charges in chromatin structure
• the energy-dependent displacement or reorganization of nucleosomes that occurs
  in conjunction with activation of genes for transcription

Question 20

What type of energy is used in chromatin remodeling?

Answer 20

• energy provided by ATP hydrolysis

Question 21

How are remodeling complexes categorized and how does it take form? (COME BACK)

Answer 21

• grouped into ATPase catalytic subunit
• Remodeling complexes can alter, slide, or displace nucleosomes
• displacing histones