Final Study guide

Question 1

nucleosome

Answer 1

repeating units of chromatin, with histone and DNA

Question 2

core particle

Answer 2

147bp

histone octamer with directly interacting DNA

Question 3

chromatosome

Answer 3

166bp

histone octamer with H1 and interacting DNA

Question 4

nucleosome repeat length

Answer 4

average amount of DNA per nucleosome

Question 5

nucleosome dyad

Answer 5

halfway point of core particle DNA around histone pt. with a 2-fold rotational symmetry

Question 6

heterochromatin

Answer 6

dense material lining nuclear envelope; in mitosis, chromatin highly condensed–> mitotic chromosomes
-rich in repetitive DNA, replicates late S-phase, more evenly spaced nucleosomes

Question 7

euchromatin

Answer 7

thread-like material found throughout nucleoplasm, remains decondensed during interphase
-more single-copy DNA, replicates throughout S, less evenly spaced nucleosomes, contains majority of genes

Question 8

nucleosome tetramer

Answer 8

-2 H3’s and 2 H4’s (more conserved)

Question 9

nucleosome dimer

Answer 9

1 H2A and 1H2B make dimer (2x), more varied

Question 10

core histones

Answer 10

have globular domain with N-terminal tails

H2A and H2B have C-terminal tails

Question 11

Active Histones/DNA

Answer 11

H2K: 4/36/79me3, 4me1; H3K27ac

Question 12

Repressed Histones/DNA

Answer 12

H3K: 27/9me3

Question 13

Acetylation enzyme and cofactor

Answer 13

Histone acetyl-transferases (HATS), 
acetyl coenzyme  (AcCoA)

Question 14

deactylases

Answer 14

Rpd3/HDAC (no cofactor)

-Sir2/SirT/HST–> cofactor–> NAD+

Question 15

methylation enzyme and cofactor

Answer 15

histone methyltransferases (HMT's)
S-adenosyl-methionine

Question 16

demethylases

Answer 16

LSD-1–> cofactor–> FAD

JHDM–> cofactor–> Fe(II)

Question 17

ChIP absence/loss of signal

Answer 17

entire histone lost, methylation lost, something blocks antibody

Question 18

bivalent chromatin domains

Answer 18

genes transcriptionally poised (cancer/stem cells)

Question 19

weird ChIP antibody problem

Answer 19

H2K56ac found at DNA exit/entry point, but rare so antibody instead detects H3K9ac and H3K27ac

Question 20

translational positioning

Answer 20

position of nucleosome relative to DNA

-determine by: indirect end-labeling, genome-wide MNAse-seq–> nonspecific digestion of naked DNA w/ MNase

Question 21

rotational positioning

Answer 21

position of DNA relative to core histone/orientation of DNA helix to surface of histone

• detemine by: DNase1: cuts at minor groove (every 10bp or every turn of DNA), cuts only if minor groove facing away from histone, when run through gel–> 10bp ladder
• TA pairs–> better DNA bending

Question 22

Histone 1

Answer 22

• promotes compaction of chromatin into 30nm fibers
• present in metazoans (amphibian/avian: H5)
• globular region binds at nucleosome dyad interacting with nucleosome core and linker DNA

Question 23

S-phase regulated histones

Answer 23

synthesized S-phase, mRNA lacks poly-A tail, normal histone

Question 24

S-phase independent histones

Answer 24

synthesized throughout cell cycle, mRNA has poly-A tails

Question 25

oldest histones

Answer 25

histone variants, other histones evolved from those

Question 26

S-phase

Answer 26

histone proteins packing DNA pulled apart to make DNA accessible for replication after, DNA needs histones to replace

Question 27

Histone Variant: H1'

Answer 27

chromatin compation and repression

Question 28

Histone Variant: H5

Answer 28

"super H1" in avian and amphibian erythrocytes; chromatin compaction and repression

Question 29

Histone Variant: H2Az

Answer 29

transcriptional regulation, chromosome segregation

Question 30

Histone Variant: H2Ax

Answer 30

DNA repair--> DNA ds breaks--> phosphorylation of H2Ax @ conserved C-terminal Ser by ATM and ATR kinase *phosphorylated form H2Ax: gamma H2Ax, marker for DNA damage

Question 31

H3.3

Answer 31

transcription, differs by 4 AA residues from S-phase H3, but 100% conserved from drosphilia-->humans

Question 32

CenP-A

Answer 32

H3 variant, involved in centromere function

Question 33

H4

Answer 33

no sequence variant, but theres an S-phase independent H4

Question 34

High Mobility Group Proteins

Answer 34

- nuclear non-histone chromosomal proteins - involved in DNA related activities like transcription, replication, repair - can be extracted from nuclei at 0.35M salt, soluble in 2% trichloroacetic acid

Question 35

HMGB: 25-30kDa

Answer 35

- 3 domains: 2 N-terminal globular domains--> HMG-1 boxes, and 1 acidic C-terminal - one molecule per 2 nucleosomes - binds with high affinity to 4-way junction DNA - stim. binding of seq-specific DNA binding proteins

Question 36

HMGN: 10kDa

Answer 36

- present in vertebrates - highly charged proteins - N-terminus high in basic AA, C terminus high in acidic AA - 2 high affinity binding sites on each nucleosome, specific nucleosome binding proteins

Question 37

HMGA

Answer 37

- bind to DNA minor groove via AT hook motif - bend DNA - associated with formation of heterochromatin

Question 38

MeCP2

Answer 38

methyl-CpG binding protein -will form complex with HDAC, or directly block TF binding, may recruit CREB-1 for activation

Question 39

epigenetics

Answer 39

gene expression state maintained throughout cell division, modification of DNA are passed on after DNA replication, no change in DNA sequence ex) inactive X chromosome

Question 40

DNMT1

Answer 40

DNA methyl transferase 1, re-establish CpG methylation of hemi-methylated DNA right after DNA replication