Topic 2, Lecture 2

Question 1

Nucleosome are static or dynamic?

Answer 1

dynamic

Question 2

why are they stated to be dynamic

Answer 2

bc they are (breathing) not tightly wrapped

Question 3

how long in milliseconds do nucleosomes exist wrapped and unwrapped?

Answer 3

250 milliseconds wrapped
10-50 milliseconds unwrapped

Question 4

at what rate are nucleosomes unwrapped?

Answer 4

from each end at a rate of about 4 times per second

Question 5

If the protein has high affinity for sequence, the sequence specific DNA binding protein bind to the nucleosome when DNA is

Answer 5

unwrapped

Question 6

cis vs trans

Answer 6

cis- before promoter region
trans- binds to neighbor to control different genes

Question 7

promoter

Answer 7

site of general transcription factor and RNA polymerase assembly
aka pre initiation complex

Question 8

cis-regulatory sequence- (enhancer) and how far?

Answer 8

regulatory sequence located up to 50,000 bp away from start site- controls the rate of pre-initiation assembly at the start site.

Question 9

section of random exposure

Answer 9

binding site for sequence specific DNA binding protein

Question 10

what is the purpose of spacer DNA

Answer 10

to provide flexibility

Question 11

all of the other proteins located on the drawing are known at the

Answer 11

general transcription proteins and they are all non-specific

Question 12

tata box

Answer 12

immediately upsteam from +1 site -30bp away from +1 site

Question 13

what is responsible for decondensation?

Answer 13

transcription regulators which are
histone modifying enzymes and chromatin remodeling complexes

Question 14

the transcription regulators are just binding sites for

Answer 14

the histone and chromatin-remodeling complex

Question 15

what are the ways that affect chromatin structure?

Answer 15

sliding
histone- removal
histone variants

Question 16

Chromatin remodeling enzyme

Answer 16

binds to DNA
induces association of DNA from nucleosomes
causes the nucleosome to slide , exposing specific DNA sequences
this sliding needs energy, and can be cis-regions

END GAME:

can completely disassemble
or replace via variant histones

Question 17

How do Histone variants work

Answer 17

work histone chaperones
composed of aspartate and glutamate
not a function of protein folding but just keep things apart

Question 18

Histone chaperones can do what?

Answer 18

replace histones with weaker histones for looser packing
remove whole histones or switch out bc purpose is to expose and decompose

Question 19

T/F: chromosome remodeling complexes play a critical role in the initiation of a gene transcription.

Answer 19

FALSE

Question 20

what are transcription activators?

Answer 20

Proteins that promote the binding of additional regulators

Question 21

what do they do?

Answer 21

recruit RNA polymerase to promote
release RNA polymerase from pause

Question 22

what kind of modifications can we do to the histone tails?

Answer 22

Methylation
only lysine; leads to condensation, creates heterochromatin, addition methyl to lysine
(preserves the + charge)
acetylation
only lysine; leads to decondensation; creates euchromatin, additon of acetyl removes + charge from lysine
phosphorylation
only serine and threonine; leads to decondensation, creates euchromatin (additon of phosphate)

Question 23

what is the histone code

Answer 23

sum total of all modifications together
depends on the histone modifying enzyme that binds to the transcription factor
dimmer that controls condensations

Question 24

Histone deacetylase

Answer 24

removal of acetyl (recondense)

Question 25

histone methyltransferase

Answer 25

transfer methyl to histone (lock that baby with positive charge)

Question 26

what are the two domains of the transcription factors?

Answer 26

activation/ repressor domain:
not-specific (no actual activation)

DNA binding domain
determines where binding occurs, gets activation domain to correct spot

Question 27

what is a cofactor?

Answer 27

things that bind to the activation or repression domain, the activation is not specific at all, it activates wherever it is put.

DNA BINDING DOMAIN is very SPECIFIC.

Question 28

what groove does the transcription factor bind to?

Answer 28

major groove

because there is more information present/ more potential
more specificity/ tighter binding