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BISC 320 > Chromatin Structure > Flashcards

Chromatin Structure Flashcards

1
Q

How is DNA organized?

A

into hierarchies of chromatin structures to form chromosomes

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2
Q

What is chromatin?

A

refers to the combination of proteins (histones) and DNA to comprise chromosomes; also RNA or other proteins

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3
Q

What are histones?

A

DNA binding proteins that compact the chromosomal DNA

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4
Q

What a histones rich in?

A

lysine and arginine that are positively charged to stabilize the DNA-histone interaction

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5
Q

How many times does DNA wrap around histone?

A

wraps 1.8 turns around the octamer in a left handed manner to form a nucleosome

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6
Q

What are the four core histones?

A

H2A, H2B, H3, and H4 (2 of each)

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7
Q

What is the function of the H3-H4 tetramer?

A

associates with DNA

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8
Q

What is the function of the H2A-H2B dimers?

A

associate to form the octamer

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9
Q

What is the core nucleosome?

A

about 146 bp of DNA wrapped around the octamer

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10
Q

What happens after the octamer is removed?

A

leaves the DNA negatively supercoiled (left handed)

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11
Q

What is the function of negative supercoiling?

A

facilitates strand separation

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12
Q

What is the function of histone tails?

A
  1. regulate nucleosome packing and interactions and chromatin structure and function
  2. interact with other nucleosomes to compact DNA further
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13
Q

What does each histone have?

A

an N-terminal “tail” that extends outwards between the DNA coils

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14
Q

How long are histone tails?

A

up to 25 amino acids in length and have an undefined structure

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15
Q

What is the function of H2A.X?

A

phosphorylated at sites of DNA double-strand breaks and is thought to recruit repair machinery

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16
Q

What is the function of CENP-A?

A

replaces histone H3 in nucleosomes at the centromere

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17
Q

What is the first level of chromatin compaction?

A

the 10nm fiber, which arises from nucleosome association with DNA, and has a “beads on a string” appearance; nucleosomes are separated by “liner region” of 20-60 bases; 10nm is folded further into 30 nm fiber

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18
Q

What is H1?

A

a linker histone that binds to the linker DNA in between successive nucleosomes, helping compaction of the 30 nm fiber; then compacted further into compact chromosomes in which large looks of chromatin are anchored to a central scaffold

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19
Q

What happens to the compaction in interphase?

A

when chromosomes are relatively uncondensed and genes are being transcribed, there is a range of compaction along the chromsome

20
Q

What are euchromatins?

A

relatively decondensed regions stains lightly

21
Q

What are heterochromatins?

A

more compacted regions stain more darkly

22
Q

What are examples of heterochromatin?

A
  1. telomeres (special DNA at the ends of chromosomes) and centromeres
  2. regions with highly repetitive DNA sequences
23
Q

How does chromatin structure affect cellular processes?

A
  1. rearrangements that place an origin of replication into heterochromatin result in late replication
  2. recombination involves breaking DNA and joining it to a different molecule. Heterochromatic regions experience less recombination, which can protect the genome
  3. CENP-A is needed to form a functional centromere, which is needed for proper chromosome separation
24
Q

What are histone side chains subject to?

A

modification that act as signals during regulation: acetylation, methylation, phosphorylation, and ubiquitylation

25
Q

What are the affects of modification?

A
  1. recruit specific proteins
  2. unstructured histone tails
26
Q

What is the function of histone acetyltransferases (HATs)?

A

add acetyl groups to lysine side chains

27
Q

What is the function of histone deacetylases (HDACs)

A

remove the acetyl groups

28
Q

What is the function of methytransferases (HMTs)?

A

add methyl groups to lysine and arginine side chains

29
Q

What is the function of histone demethylases?

A

remove the methyl groups

30
Q

What is the function of acetylation?

A
  1. removes the positive charge from lysine side chains, affects interactions with negative DNA
  2. generates binding sites for bromodomain proteins, bind specifically to acetyl-lysines
31
Q

What is the function of bromodomains?

A

recruit other proteins like nucleosome remodeling complexes

32
Q

Euchromatin has _ acetylation than heterochromatin?

A

more

33
Q

How many methyl groups can be added to a lysine?

A

three methyl groups

34
Q

How many methyl groups can be added to an arginine?

A

two methyl groups

35
Q

What is associated with silent chromatin?

A

methylation of lysine 9 in the H3 tail

36
Q

What is associated with active chromatin?

A

methylation of H3 lysine 4

37
Q

What is the function of chromodomains?

A

bind to specific methylated lysines, and are often associated with transcriptional silencing

38
Q

What allows cell growth?

A

phosphorylation of H3 serine 10

39
Q

What allows for chromosome condensation?

A

phosphorylation of H3 serine 10 and serine 28

40
Q

What is histone code?

A

unique combinations of modification that define certain chromatin states

41
Q

What does chromatin packing present?

A

a barrier to proteins that need to access DNA, and hence inhibits processes like transcription

42
Q

ATP-dependent nucleosome remodeling complexes increase the accessibility of DNA by:

A
  1. sliding the histone octamer along the DNA
  2. removing the histone octamer and transferring it elsewhere
  3. introducing loops into the DNA
43
Q

What are the functions of boundary elements?

A
  1. act as physical barriers to heterochromatin
  2. can be specific sequences to which proteins bind that are regulators of histone modifications
44
Q

When do heterochromatin stop spreading?

A

until a boundary element is reached (H3 is deacetylated, lysine 9 is methylated, and a chromatin silencing protein binds)

45
Q

What are chromatin loops?

A

each loop contains one type of chromatin, and the loop is anchored in the nuclear periphery which is another boundary element

BISC 320 (20 decks)

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