lecture 3

Question 1

what are the 3 ways activators promote transcription

Answer 1

1. promote binding of an additional activator.
2. stimulate complex assembly (pol II to bind to TATA)
3. release stalled RNA pol II

Question 2

what makes transcription more difficult in eukaryotes

Answer 2

the DNA is not naked it is packaged in a protein complex called chromatin

Question 3

whats the basic function of chromatin

Answer 3

to compact DNA

Question 4

what small basic protein composes chromatin

Answer 4

histones

Question 5

what are the two types of histones

Answer 5

core histones and linker histones

Question 6

what are the 4 types of core histones

Answer 6

H2A, H2B, H3, H4

Question 7

they have a globular domain made up of

Answer 7

alpha helices and loops

Question 8

the also have an N terminal tail rich in

Answer 8

lys + arg

Question 9

the globular domain folds into a

Answer 9

histone fold

Question 10

the histone folds from different core histones interacts to form a

Answer 10

handshake interaction

Question 11

what is an octamer

Answer 11

central H3-H4 tetramer and 2 flanking H2A-H2B dimers

Question 12

the core histones form repeating units called

Answer 12

nucleosomes

Question 13

whats a nucleosome

Answer 13

around 147 bp of DNA wrapped twice around an octamer of histone proteins

Question 14

does DNA passes directly from one nucleosome to the next

Answer 14

yes (10nm fibre)

Question 15

what binds to the DNA between nucleosomes

Answer 15

linker histones such as histone H1

Question 16

how thick is chromatin

Answer 16

30nm fibre

Question 17

to show that chromatin inhibits transcription they added Pol II and TFs to naked DNA and to chromatin

Answer 17

transcription in the naked DNA not in the chromatin template

Question 18

chromatin structure is dynamic meaning

Answer 18

it can be remodeled and re organised for transcription to occur

Question 19

what are the 3 main mechanisms for modulating th structure of chromatin

Answer 19

histone variants, post-translational modification of histones, ATP dependent chromatin remodeling

Question 20

histone variants are

Answer 20

alternative histones to the core histones

Question 21

they are expressed at

Answer 21

low levels

Question 22

all conventional histones have variants except ?

Answer 22

H4

Question 23

histone variants change

Answer 23

structural and functional properties of the nucleosome

Question 24

post-translational modification of histones is

Answer 24

modification of the N terminal tails (eg acetylation, methylation, ubiquitination, phosphorylation)

Question 25

the modification state of the histone dictates the

Answer 25

transcriptional state of the DNA. referred to as the histone code

Question 26

what are the major possibilities explaining how this works

Answer 26

1. could alter chromatin folding/structure 2. could control the recruitment of non histone proteins to chromatin (affects the transcription machinery)

Question 27

what is histone acetylation mediated by

Answer 27

HATS (histone acetyl transferases)

Question 28

histone acetylation occurs on?

Answer 28

lysine residues in the N terminal tail

Question 29

what is histone acetylation reversed by

Answer 29

HDACs (histone deacetylases), through hydrolysis

Question 30

high levels of acetylation correlates with

Answer 30

high levels of transcription

Question 31

2 major types of HATs

Answer 31

GNAT family and MYST family

Question 32

how are HATs recruited to chromatin

Answer 32

many HATs contain a specific subunit that interacts with activators and therefore the activator brings the HATs the promoters

Question 33

some HATs are part of the general transcription machinery

Question 34

positive charge gets reduced on lysine changes a result of acetylation meaning

Answer 34

the positively charge lysine cant interact with the negatively charged DNA so the chromatin is less compacted therefore easier for transcription

Question 35

acetylation of lysine also allows bromodomain proteins to recognise the DNA and for them to be recruited

Answer 35

bromodomains are usually found in proteins that promotes transcription

Question 36

bromodomain Bdf1 binds acetylated H4

Answer 36

and recruits TFIID

Question 37

histone methylation can occur on

Answer 37

lysine and arginine residues

Question 38

what proteins methylates lysine

Answer 38

histone lysine methyl transferases (HKMTs)

Question 39

HKMTs add up to how many methyl groups

Answer 39

3

Question 40

what do lysine demethylases do

Answer 40

reverse the methylation of lysine

Question 41

does methylation affect the charge of the lysine

Answer 41

no, meaning it has only a small effect on chromatin structure

Question 42

methylated lysines act as binding sites for binding modules eg

Answer 42

chromo domains

Question 43

methylation on H3 Lys9 and H3 Lys27 causes

Answer 43

repression of transcription

Question 44

methylation of H3 Lys4 and H3Lys36 causes

Answer 44

activation of transcription