Control of Gene Expression 1: Transcriptional Controls

Question 1

What does gene regulation require?

Answer 1

1. short stretches of DNA of defined sequence- recognition sites for DNA binding proteins
2. Gene regulatory proteins- transcription factors that will bind and activate gene

Question 2

What are the steps to DNA motif recognition?

Answer 2

1. association of regulatory proteins with major groove
2. proteins recognize and bind to bases in major groove
3. major groove presents a specific face for each of the specific base pairs
4. gene regulatory protein recognizes a specific DNA sequence
5. surface of the protein is extensively complementary to the surface of the DNA region to which it binds
6. series of contacts is made with the DNA involving 4 possible configurations

Question 3

Typical gene regulatory protein-DNA interaction involves _____ interactions

Answer 3

10-20

Question 4

Describe the helix turn helix DNA binding motif

Answer 4

simplest, most common
two alpha helices connected by short chain of amino acids that make long turn at fixed angle
longer helix= recognition module- DNA binding module - fits into major groove

Question 5

Explain the zinc finger domain

Answer 5

DNA binding motif includes Zn atom
binds to major groove of DNA
found in tandem clusters 
stabilizes interaction with DNA
multiple contact points

Question 6

Explain the leucine zipper motif

Answer 6

-two alpha helical DNA binding domain
-grabs DNA like clothespin
-activation domain overlaps dimer domain
-interactions between hydrophobic amino acid side chain
-

Question 7

Explain the helix loop helix domain

Answer 7

consists of short alpha chain connected by a loop to a second longer alpha chain
can occur as homo or heterodimers
three domains or modules of protein: DNA binding domain, dimerization domain, activation domain

Question 8

What is hereditary spherocytosis?

Answer 8

hemolytic anemia characterized by spherical and fragile red blood cells that lyse and release hemoglobin

Question 9

HS is ____ inherited

Answer 9

dominantly

Question 10

What does the erythrocyte membrane Skelton (EMS) do?

Answer 10

confers property of durability and stability to RBCs

Question 11

HS can be mutation in zinc finger protein gene _____

Answer 11

Klf1

Question 12

KLF1 zinc finger protein binds to ______ of all genes in EMS, which _____

Answer 12

promoters; turns them on

Question 13

What is the mutation in KLF1 that leads to HS?

Answer 13

mutation of non functioning KLF1 Zn finger protein which leads to no EMS made, leading to HS

Question 14

What is the HS mutation sequence?

Answer 14

RER to RDR

which is GAA to GAT or Glu to Asp

Question 15

HS KLF1 finger domain 2 binds to the ______ strand and leads to no ______

Answer 15

opposite; transcription

Question 16

What is EMSA?

Answer 16

electrophoretic mobility shift assay

Question 17

Describe EMSA

Answer 17

mix radioactive DNA fragment with protein extract from cell
run electrophoretic gel
proteins with DNA attached migrate according to size
shift of radioactive band when protein is bound to DNA
isolate protein to identify

Question 18

What does affinity chromatography do?

Answer 18

isolate DNA binding protein

purification of sequence specific binding proteins

Question 19

What is CHIP?

Answer 19

chromatin immuno- precipitation

Question 20

What does CHIP do?

Answer 20

allows identification of the sites in the genome that a known regulatory protein binds to

Question 21

What is the gene control region?

Answer 21

DNA region involved in regulating and initiating transcription of a gene, includes the promoter

Question 22

_____ and _____ assemble at the promoter

Answer 22

RNA polymerases and general transcription factors

Question 23

What is a mediator?

Answer 23

serves as an intermediary between gene regulatory proteins and RNA polymerase II

Question 24

DNA _____ and a _____ complex allow the gene regulatory proteins to interact with the proteins that assemble at the promoter

Answer 24

looping; mediator

Question 25

How does nucleosome remodeling and histone removal favor transcription?

Answer 25

increasing accessibility of DNA to proteins