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BIMM 112 > Midterm Review > Flashcards

Midterm Review Flashcards

1
Q

core particle

A

146bp

nucleosome with directly interacting DNA

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2
Q

chromatosome

A

166

nucleosome with H1

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3
Q

nucleosome

A

180-200, repeating unit of chromatin; histone and dna

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4
Q

translational position

A

positioning of histone relative to DNA; check with MNase, which breaks down linker DNa

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5
Q

rotational positioning

A

position of DNA relative to histone– flexibility, AT

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6
Q

core histones

A

lack poly A tails

made in s phase

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7
Q

variant histones

A

synthesized throughout cell cycle
have poly a tails
more evolutionarily conserved
affect transcription, regulation, DNA repair, chromatin organization/compation

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8
Q

HMGB

A

HMB1box

affinity to 4 way junction structures, stim. binding of other DNA binding protiens

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9
Q

HMGN

A

nucleosome binding domain

specifically binds to nucleosomes, gene activation

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10
Q

HMGA

A

AT hook

binds minor groove of DNA using AT hook, bends DNA

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11
Q

H5

A

variant of H1

chromatin compaction and repression; avians and amphibians

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12
Q

H2Az

A

H2A

transcriptional regulation, chromatin segregation

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13
Q

H2Ax

A

H2a

DNA repair, phosphorylated– gamma form, marker for DNA damage

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14
Q

H3.3

A

H3

transcription, active genes

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15
Q

CENP-A

A

h3 variant

centromere function

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16
Q

H4

A

no sequence variant, S phase independent version

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17
Q

H3K4me3

A

observed at active promoters

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18
Q

H3K36me3

A

seen in downstream transcribed region of active genes

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19
Q

H3K4me1 and H3K27ac–

A

seen at active transcriptional enhancers

20
Q

H3K9me3

A

heterochromatin

21
Q

H3K27me3

A

associated with polycomb-mediated repression

22
Q

histone acetylases

A

use AcCoa

23
Q

rpd/HDAC

A

use nothing

24
Q

Sir2/SirT/HST deacetylase

A

NAD+

25
Q

methylases

A

s-adenosyl methionine

26
Q

LSD-1/JHDM demethylase

A

FAD/Fe(II)

27
Q

heterochromatin

A

doesnt condense in interphase, repetitive DNA, condensed throughout cell cycle, replicates late s-phase

28
Q

euchromatin

A

most single copy of DNA, decondenses interphase, replicates throughout S

29
Q

HP1

A

heterochromatin protein, binds H3K9met

30
Q

HMGA with heterochromatin

A

localized predominantly to heterochromatin

31
Q

PEV- position effect variegation

A

-euchromatic genes repressed by spreading heterochromatin

32
Q

Su(var)

A

suppressor of PEV; promotes heterochromatin

33
Q

E(var)

A

enhancer of PEV; enhances when mutated. decreases heterochromatin, activates euchromatic genes

34
Q

Su(var)2-5

A

encodes HP1

35
Q

Su)var)3-9

A

H3K9 methylase, HP1 binds to chrome with methylated H3K9

36
Q

RNA-seq

A

genome-wide sequence of steady state RNA

  1. poly_A selection, fragmentation
  2. cDNA strand synth
  3. end-repair, phosphorylate, A-tailing
  4. adapter ligation
37
Q

RPKM

A

reads per kb exon per million reads, normalizes number of reads

38
Q

GRO-seq

A

global run on sequencing, total level of nascent RNA, ongoing transcription

39
Q

ChIP-seq

A

antibodies; fixation, fornication, immunoprecipation, hydrolysis, analysis

40
Q

ICE chip

A

chip followed by illumina sequencing

41
Q

MNase-seq

A

reveals canonical nucleosomes, primarily cleaves AT

42
Q

MPE-seq

A

little sequence specificity, but locates non-canonical chromatin particles
reveals pre-nucleosome like particles

43
Q

DNase-seq

A

genome-wide DNase 1; recognizes 1 sequence, cleaves 20bp away

44
Q

ATAC-seq

A

genome-wide chromatin accessibility analysis; nextera

  • tagmentation, DNA fragmentation and ligation
  • alternative to MNase/DNase
  • less cells
45
Q

3C

A

Chromosome-conformation capture

-crosslink–> digest–> ligate–> PCR

46
Q

HI-C

A

crosslink, cut, fill ends with biotin, ligate, purify and shear, pull down biotin, sequence by pair ending

47
Q

chloroquinine

A
  • induces positive supercoiling
  • nicked dna will still be relaxed
  • malaria treatment
  • to see assembled chromatin

BIMM 112 (5 decks)

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