Control of Gene Express I

Question 1

housekeeping proteins, glucose metabolism

Answer 1

common proteins

Question 2

RNA seq results

Answer 2

specifically limited proteins,..; hemoglobin

Question 3

What are thing assoicated with post transcription ?

Answer 3

alternative splicing dystrophin gene, post translational modification

Question 4

transcription factors

Answer 4

gene regulatory proteins

Question 5

Recognition sequence for regualtory proteins

Answer 5

TGATAG

Question 6

Recognition sequences can be?

Answer 6

proximal or distal to first exon

Question 7

Regulatory protiens associate with?

Answer 7

major grooves

Question 8

What recognizes a specific DNA sequence?

Answer 8

a gene regulatory proteins

Question 9

Possible binds to major groove

Answer 9

H bond donors
H bond acceptors
methyl groups
H atoms

Question 10

What do gene regulatory proteijns read?

Answer 10

the outside of the DNA helix…10-20 interactions

Question 11

Neccessary modules for transcrtiption factors

Answer 11

activation module and a DNA biding module

Question 12

What modules might a trasnctiption factor have?

Answer 12

dimerization module or regulatory module

Question 13

simplest most common DNA binding motif

Answer 13

helix turn helix

Question 14

helix turn helix

Answer 14

two alpha helices connected by short chain of aa that make the turn at fixed angles

Question 15

What is the longer helix?

Answer 15

recognition module-DNA binding module… fits into major groove

Question 16

What dose side chains of aa recognize in helix turn helix?

Answer 16

DNA motif

Question 17

How does H t H bind Dna?

Answer 17

symmetric dimers

Question 18

found in tandem clusters?

Answer 18

Zn finger domains

Question 19

stabalizes interaction w DNA

Answer 19

zn finger domain… has multiple contact points

Question 20

dimerization domain
activation domain
DNA binding domain

Answer 20

Leucine zipper motif

• two alpha helical binding domains
• dimerizes through leuicine zipper region homo or hetero

Question 21

what does Leu zipper interact with?

Answer 21

hydrophobic aa side chains

Question 22

what forms zipper strucutre?

Answer 22

aa leu every 7 aa

• grabs dna like clothes pin
• activation domain overlaps dimer domain

Question 23

consists of a short alpha chain connected by a loop to a second longer alpha chain

Answer 23

helix loop helix domain

Question 24

what there domains does HLH have?

Answer 24

dna bidning, dimerization, activation

Question 25

gene control region consists of?

Answer 25

DNA region involved in regulating and intitating transcription of a gene
-includes promoter
and regulatory seq

Question 26

promoter

Answer 26

trancription factors and RNA poly II assembly

Question 27

Activation

Answer 27

DNA looping and a mediator complex allot the gene regulatory proteins to interacti w the proteins that assemble at the promoter

Question 28

what do gene activator protieins modify?

Answer 28

local chromatin structure

Question 29

easier to remove histones

Answer 29

histone acetylation

Question 30

What do nucleosomes remodeling and histone removal favor?

Answer 30

transctitoin initiation by increasing accessibility of DNA to other prtoins

Question 31

KNow

Answer 31

actiavtion of a gene

Question 32

Gene repressors inhibit in two ways

Answer 32

1. competitive DNA binding
   2masking the activation surface- binds to actiavtion domain of the activator protein
   3direct interaction w tracrtipion factors-binds to DNA and blocks assembly of general trasncrition factors

Question 33

way 4 repressors work

Answer 33

recruitment of chromatin remodeling complex

-returns promotrer to the pretranscritional nucleosome state

Question 34

5 repressor works

Answer 34

recruitment of histone deacetylases

-hard to remove deacetlyated histone from promoter

Question 35

repressor way 6

Answer 35

recruitment of histone methyl transferase

-methylates histones- bond to proteins which act to maitina chromatin in a transcritionally silent form