g. Lecture 5 Slide Deck (January 23rd)

Question 1

Describe the following
a) promoters
b) promoter-proximal elements and enhancers
c) transcription activators and repressors

Answer 1

a) the direct binding site for RNA poll I to initiate transcription
b) gene and cell-type-specific regulatory elements on DNA that regulate transcription
c) modulator proteins that contain a DNA-binding domains and one or more effector domains

Question 2

ANS the following w/ regards to hormones used to regulate transaction factor activity
a) lipophilic or lipophobic?
b) What types of proteins do they bind to?
c) where do they bind; cytoplasm, membrane, extracellular space, nucleus
d) what element does the complex bind to in order to regulate gene expression?

Answer 2

a) lipophilic
b) lipid-hormone receptors/transcription activators
c) cytoplasm or sometimes in the nucleus
d) HRE = hormones response element

Question 3

Provide an example for each scenario
a) transcription factor activates being directly regulated
b) transcription factor activities being indirectly regulated

Answer 3

a) lipid-hormones diffusing into the cell and binding directly to the receptor to form a receptor/hormone complex which acts as a transcription factor that can directly regulate gene expression
b) peptide hormone binds to a membrane imbedded receptor and initiation a signal transduction cascade which activates a transcription factor via phosphorylation. Resulting in that transcription factor regulating gene expression

Question 4

When indirectly regulating genes through cell-surface receptors nd intracellular signal transduction cascades what type of enzymes activate the near by transcription factors w/in the recipient cell and what type of modification occurs?

Answer 4

a) kinases
b) phosphorylation - change in confirmation due to addiction of phosphate

Question 5

Name the 3 lipid-soluble hormones that bind to nuclear or cytoplasmic receptors

Answer 5

1. cortisol
2. retinoic acid
3. thyroxine

Question 6

Describe the following domains of a hormone nuclear receptor
a) variable region
b) DBD
c) LBD

Answer 6

1. the region that differentiates the different types of hormone nuclear receptors
2. DNA-binding domain - domain that binds the protein to the specific DNA sequence
3. ligand-binding domain - domain that binds the protein to the specific receptor that recognizes it

Question 7

All of the following are hormone nuclear receptors except
a) thyroxine receptor (TR)
b) androgen receptor (AR)
c) estrogen receptor (ER)
d) glucocorticoid receptor (GR)

Answer 7

b

Question 8

According to this image ANS the following (Dex is present)
a) What does the Dex represent?
b) is the ligand binding domain present? How do you know?

Answer 8

a) Dexamethasone which is a type of glucocorticoid thus will bind to a glucocorticoid receptor
b) no, b/c despite Dex being present the receptor is still in the cytoplasm (spread of light shown)

Question 9

According to this image ANS the following (Dex is present)
a) What does the Dex represent?
b) is the ligand binding domain present? How do you know?

Answer 9

a) Dexamethasone which is a type of glucocorticoid thus will bind to a glucocorticoid receptor
b) yes, b/c the receptors are now relieved of their chaperones allowing for a concise glow

Question 10

The glucocorticoid receptor (GR) is already found in the cytoplasm and it contains the DNA-binding Domain. Furthermore, it is lipophilic thus it can diffuse through the nuclear mem. So does it need a hormone to bind to it in order to allow it to translocate into the nuclease. Where does the hormone bind?

Answer 10

The ligand binding domain contain chaperones which prevent it from entering the nucleus. Once the hormone binds to this domain its conformation changes causing the chaperones to disassociate from the receptor. Thus allowing translocation to occur

Question 11

P-TEFb is a ______, which inactivates the factors _____ causing a pause at the beginning of transcriptional elongation

Answer 11

kinase, NELF/DSIF

Question 12

Which of the following remains bound to the RNA pol II during elongation after the pause?
a) CDk9
b) CycT
c) NELF
d) DSIF

Answer 12

d

Question 13

Which of the following is a kinase
a) P-TEFb
b) CycT
c) CDk9
d) b and c
e) all of the above

Answer 13

e

Question 14

Describe the difference b/w activator/repressors and co-activator/co-repressor complexes

Answer 14

1. activators/repressor bind directly to DNA (contain a DNA-binding domain)
2. co-activator/co-repressor complexes bind directly to proteins (contain a protein-binding domain)

Question 15

a) how do activators stimulate transcriptions? - 2
b) how do repressors inhibit transcription?

Answer 15

a) they help w/ the assembly of the PIC and move nucleosomes away (open up DNA)
b) build up repressive chromatin structures such as nucleosomes (wind up DNA)

Question 16

a) Where on the histone does post-translational modification (PTM) take place?
b) What is the purpose of PTMs
c) the variety of PTMs are referred to as what?

Answer 16

a) the N-terminal tail
b) to dictate the fxn of the DNA that is wrapped around the nucleosome
c) histone codes

Question 17

What are the 4 post-translational modification (PTM) that take place on histone tails?

Answer 17

1. phosphorylation
2. methylation
3. acetylation
4. ubiquitinylation