Chromatin Structure

Question 1

How is DNA organized?

Answer 1

into hierarchies of chromatin structures to form chromosomes

Question 2

What is chromatin?

Answer 2

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

Question 3

What are histones?

Answer 3

DNA binding proteins that compact the chromosomal DNA

Question 4

What a histones rich in?

Answer 4

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

Question 5

How many times does DNA wrap around histone?

Answer 5

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

Question 6

What are the four core histones?

Answer 6

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

Question 7

What is the function of the H3-H4 tetramer?

Answer 7

associates with DNA

Question 8

What is the function of the H2A-H2B dimers?

Answer 8

associate to form the octamer

Question 9

What is the core nucleosome?

Answer 9

about 146 bp of DNA wrapped around the octamer

Question 10

What happens after the octamer is removed?

Answer 10

leaves the DNA negatively supercoiled (left handed)

Question 11

What is the function of negative supercoiling?

Answer 11

facilitates strand separation

Question 12

What is the function of histone tails?

Answer 12

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

Question 13

What does each histone have?

Answer 13

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

Question 14

How long are histone tails?

Answer 14

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

Question 15

What is the function of H2A.X?

Answer 15

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

Question 16

What is the function of CENP-A?

Answer 16

replaces histone H3 in nucleosomes at the centromere

Question 17

What is the first level of chromatin compaction?

Answer 17

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

Question 18

What is H1?

Answer 18

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

Question 19

What happens to the compaction in interphase?

Answer 19

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

Question 20

What are euchromatins?

Answer 20

relatively decondensed regions stains lightly

Question 21

What are heterochromatins?

Answer 21

more compacted regions stain more darkly

Question 22

What are examples of heterochromatin?

Answer 22

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

Question 23

How does chromatin structure affect cellular processes?

Answer 23

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

Question 24

What are histone side chains subject to?

Answer 24

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

Question 25

What are the affects of modification?

Answer 25

1. recruit specific proteins 2. unstructured histone tails

Question 26

What is the function of histone acetyltransferases (HATs)?

Answer 26

add acetyl groups to lysine side chains

Question 27

What is the function of histone deacetylases (HDACs)

Answer 27

remove the acetyl groups

Question 28

What is the function of methytransferases (HMTs)?

Answer 28

add methyl groups to lysine and arginine side chains

Question 29

What is the function of histone demethylases?

Answer 29

remove the methyl groups

Question 30

What is the function of acetylation?

Answer 30

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

Question 31

What is the function of bromodomains?

Answer 31

recruit other proteins like nucleosome remodeling complexes

Question 32

Euchromatin has _ acetylation than heterochromatin?

Answer 32

more

Question 33

How many methyl groups can be added to a lysine?

Answer 33

three methyl groups

Question 34

How many methyl groups can be added to an arginine?

Answer 34

two methyl groups

Question 35

What is associated with silent chromatin?

Answer 35

methylation of lysine 9 in the H3 tail

Question 36

What is associated with active chromatin?

Answer 36

methylation of H3 lysine 4

Question 37

What is the function of chromodomains?

Answer 37

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

Question 38

What allows cell growth?

Answer 38

phosphorylation of H3 serine 10

Question 39

What allows for chromosome condensation?

Answer 39

phosphorylation of H3 serine 10 and serine 28

Question 40

What is histone code?

Answer 40

unique combinations of modification that define certain chromatin states

Question 41

What does chromatin packing present?

Answer 41

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

Question 42

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

Answer 42

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

Question 43

What are the functions of boundary elements?

Answer 43

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

Question 44

When do heterochromatin stop spreading?

Answer 44

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

Question 45

What are chromatin loops?

Answer 45

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