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BIMM 112 > Final Study guide > Flashcards

Final Study guide Flashcards

1
Q

nucleosome

A

repeating units of chromatin, with histone and DNA

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2
Q

core particle

A

147bp

histone octamer with directly interacting DNA

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3
Q

chromatosome

A

166bp

histone octamer with H1 and interacting DNA

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4
Q

nucleosome repeat length

A

average amount of DNA per nucleosome

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5
Q

nucleosome dyad

A

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

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6
Q

heterochromatin

A

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

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7
Q

euchromatin

A

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

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8
Q

nucleosome tetramer

A

-2 H3’s and 2 H4’s (more conserved)

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9
Q

nucleosome dimer

A

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

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10
Q

core histones

A

have globular domain with N-terminal tails

H2A and H2B have C-terminal tails

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11
Q

Active Histones/DNA

A

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

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12
Q

Repressed Histones/DNA

A

H3K: 27/9me3

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13
Q

Acetylation enzyme and cofactor

A 
Histone acetyl-transferases (HATS), 
acetyl coenzyme  (AcCoA)
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14
Q

deactylases

A

Rpd3/HDAC (no cofactor)

-Sir2/SirT/HST–> cofactor–> NAD+

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15
Q

methylation enzyme and cofactor

A 
histone methyltransferases (HMT's)
S-adenosyl-methionine
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16
Q

demethylases

A

LSD-1–> cofactor–> FAD

JHDM–> cofactor–> Fe(II)

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17
Q

ChIP absence/loss of signal

A

entire histone lost, methylation lost, something blocks antibody

18
Q

bivalent chromatin domains

A

genes transcriptionally poised (cancer/stem cells)

19
Q

weird ChIP antibody problem

A

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

20
Q

translational positioning

A

position of nucleosome relative to DNA

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

21
Q

rotational positioning

A

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
22
Q

Histone 1

A
  • 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
23
Q

S-phase regulated histones

A

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

24
Q

S-phase independent histones

A

synthesized throughout cell cycle, mRNA has poly-A tails

25
Q

oldest histones

A

histone variants, other histones evolved from those

26
Q

S-phase

A

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

27
Q

Histone Variant: H1’

A

chromatin compation and repression

28
Q

Histone Variant: H5

A

“super H1” in avian and amphibian erythrocytes; chromatin compaction and repression

29
Q

Histone Variant: H2Az

A

transcriptional regulation, chromosome segregation

30
Q

Histone Variant: H2Ax

A

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

31
Q

H3.3

A

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

32
Q

CenP-A

A

H3 variant, involved in centromere function

33
Q

H4

A

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

34
Q

High Mobility Group Proteins

A
  • 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
35
Q

HMGB: 25-30kDa

A
  • 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
36
Q

HMGN: 10kDa

A
  • 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
37
Q

HMGA

A
  • bind to DNA minor groove via AT hook motif
  • bend DNA
  • associated with formation of heterochromatin
38
Q

MeCP2

A

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

39
Q

epigenetics

A

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

40
Q

DNMT1

A

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

BIMM 112 (5 decks)

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