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CMB2001 > lecture 3 > Flashcards

lecture 3 Flashcards

1
Q

what are the 3 ways activators promote transcription

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

what makes transcription more difficult in eukaryotes

A

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

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3
Q

whats the basic function of chromatin

A

to compact DNA

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4
Q

what small basic protein composes chromatin

A

histones

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5
Q

what are the two types of histones

A

core histones and linker histones

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6
Q

what are the 4 types of core histones

A

H2A, H2B, H3, H4

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7
Q

they have a globular domain made up of

A

alpha helices and loops

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8
Q

the also have an N terminal tail rich in

A

lys + arg

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9
Q

the globular domain folds into a

A

histone fold

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10
Q

the histone folds from different core histones interacts to form a

A

handshake interaction

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11
Q

what is an octamer

A

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

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12
Q

the core histones form repeating units called

A

nucleosomes

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13
Q

whats a nucleosome

A

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

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14
Q

does DNA passes directly from one nucleosome to the next

A

yes (10nm fibre)

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15
Q

what binds to the DNA between nucleosomes

A

linker histones such as histone H1

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16
Q

how thick is chromatin

A

30nm fibre

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17
Q

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

A

transcription in the naked DNA not in the chromatin template

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18
Q

chromatin structure is dynamic meaning

A

it can be remodeled and re organised for transcription to occur

19
Q

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

A

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

20
Q

histone variants are

A

alternative histones to the core histones

21
Q

they are expressed at

A

low levels

22
Q

all conventional histones have variants except ?

A

H4

23
Q

histone variants change

A

structural and functional properties of the nucleosome

24
Q

post-translational modification of histones is

A

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

25
Q

the modification state of the histone dictates the

A

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

26
Q

what are the major possibilities explaining how this works

A
  1. could alter chromatin folding/structure
  2. could control the recruitment of non histone proteins to chromatin (affects the transcription machinery)
27
Q

what is histone acetylation mediated by

A

HATS (histone acetyl transferases)

28
Q

histone acetylation occurs on?

A

lysine residues in the N terminal tail

29
Q

what is histone acetylation reversed by

A

HDACs (histone deacetylases), through hydrolysis

30
Q

high levels of acetylation correlates with

A

high levels of transcription

31
Q

2 major types of HATs

A

GNAT family and MYST family

32
Q

how are HATs recruited to chromatin

A

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

33
Q

some HATs are part of the general transcription machinery

A
34
Q

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

A

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

35
Q

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

A

bromodomains are usually found in proteins that promotes transcription

36
Q

bromodomain Bdf1 binds acetylated H4

A

and recruits TFIID

37
Q

histone methylation can occur on

A

lysine and arginine residues

38
Q

what proteins methylates lysine

A

histone lysine methyl transferases (HKMTs)

39
Q

HKMTs add up to how many methyl groups

A

3

40
Q

what do lysine demethylases do

A

reverse the methylation of lysine

41
Q

does methylation affect the charge of the lysine

A

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

42
Q

methylated lysines act as binding sites for binding modules eg

A

chromo domains

43
Q

methylation on H3 Lys9 and H3 Lys27 causes

A

repression of transcription

44
Q

methylation of H3 Lys4 and H3Lys36 causes

A

activation of transcription

CMB2001 (21 decks)

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