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Mol Bio - Exam 1 > Molecular Structure of Genes and Chromosomes 2 (L9) > Flashcards

Molecular Structure of Genes and Chromosomes 2 (L9) Flashcards

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1
Q

chromatin

A

complex of DNA and protein that makes up the chromosome

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2
Q

nucleosome

A

147 bp of DNA wrapped 1 2/3 times around histones (2 each of H2A, H2B, H3, H4) - building block of chromatin

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3
Q

why do DNA and histones associate with each other?

A

histones have many basic aa’s (+) and DNA is (-)

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4
Q

linker DNA

A

b/w beaded nucleosome - 10 to 90 bps

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5
Q

how are nucleosomes stacked?

A

30 nm diameter double helix of nucleosomes stacked with H1 histone

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6
Q

what do all histones have?

A

flexible N-terminal tails (19-39 residues) on H3, H4

N and C-terminal tails on H2A, H2B

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7
Q

post-translational modifications of nucleosomes

A

phosphorylation, methylation, acetylation, ubiquitination

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8
Q

significance of acetylation

A

charge is neutralized -> DNA destabilized -> transcription activated

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9
Q

significance of methylation

A

charge is not changed -> DNA stabilized -> transcription inactivated

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10
Q

decondensed vs. condensed chromatin

A

decondensed: gene expression
condensed: no gene expression

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11
Q

regulation of acetylation

A

HATS (histone acetyltransferases) - add Ac onto Lys

HDACS (histone deacetylases) - remove Ac

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12
Q

where do acetylation and methylation occur?

A

on Lys side chain - epsilon amino group

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13
Q

what test can be used to determine the status of chromatin?

A

DNase 1 sensitivity assay of the nuclei DNA

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14
Q

number of times methylation can occur

A

three times on one amino group

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15
Q

regulation of methylation

A

HMTs (histone methyltransferases)

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16
Q

two types of chromatin in nucleus

A

euchromatin: active/open
heterochromatin: inactive/condensed

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17
Q

euchromatin

A

active/open - related to histone acetylation on H3 tails

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18
Q

what is the exception in euchromatin?

A

tri-methylation of Lys4 on H3 related to activation

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19
Q

heterochromatin

A

inactive/condensed - related to histone methylation - 2 H3 tails are tri-methylated

20
Q

what is HP1

A

heterochromatin protein 1 - chromodomain and chromoshadow domain

21
Q

what does HP1 recognize w/ chromodomain?

A

H3K9Me3 (trimethylated Lys 9 on H3)

22
Q

what does HP1 recognize w/ chromoshadow domain?

A

allows for oligomerization of HP1 proteins -> aggregation -> forms heterochromatin

23
Q

what else can HP1 also recruit?

A

HMTs -> spread area of methylation

24
Q

function of boundary elements

A

isolate action of HP1 so there are regions of condensed and noncondensed DNA

25
Q

TFIID

A

one of the first proteins bound to the promoter to promote transcription - recognizes acetylated Lys’s w/ bromodomain

26
Q

how is animal cloning accomplished?

A

SCNT - somatic cell nuclear transfer

27
Q

what is the epigenetic process that gives rise to variations in outcome of cloning?

A

random X chromosome inactivation (Barr body)

28
Q

MeCP2

A

methyl CpG binding protein 2 - recognizes methylated C, recruits HDAC and HMT, changes post-translational modification to inactivated state of gene transcription

29
Q

euchromatin vs. heterochromatin: what cell types have each?

A

stem cells: more euchromatin

differentiated cells: more heterochromatin

30
Q

iPS cells (induced pluripotent stem cells)

A

pluripotency induced in already differentiated cells - done by transcription factors

31
Q

what are iPS cells used for?

A

cloning; studying disease mechanisms in dish and also by correcting defect - create many fixed cells and put them back into patient (cell therapy)

32
Q

ChIP - chromatin immunoprecipitation

A

only region that was originally decondensed will be bound to antibody - then secondary antibody for primary antibody -> use to get sequence info

33
Q

what does the ChIP sequence tell?

A

get sequence info from pieces - see what sequences are associated w/ heavily Ac-proteins -> genes here in decondensed state -> most likely are expressed

34
Q

what happens to chromatin during metaphase of mitosis?

A

condensation into chromosomes

35
Q

cytogenetics

A

study of the structure and function of cell, especially the chromosomes

36
Q

karyotyping

A

study of the number and appearance of chromosomes - each chromosome has unique banding pattern

37
Q

what stain is used for karyotyping?

A

Giesma stain - shows G bands and R bands: G bands have more stain

38
Q

what is one clinical application of karyotyping?

A

to detect chromosomal aberration

39
Q

what causes CML?

A

transloation b/w chromosomes 9 and 22: Philadelphia chromosome - makes a new gene (oncogenic BCR-ABL tyrosine kinase) that is always on -> cancer

40
Q

FISH - fluorescent in situ hybridization

A

like southern blot

41
Q

SKY - special karyotyping

A

probes recognize a particular chromosome - use a different colored dye on each chromosome and see where translocations occur

42
Q

ChIP steps

A
  1. isolate and shear chromatin mechanically
  2. add antibody-specific for acetylated N-terminal histone tail
  3. immunoprecipitate
  4. release immunoprecipitated DNA and assay by PCR
43
Q

three elements for inheritance and replication of chromosomes

A
  1. autonomously replicating sequences (ARS) - “origin of rep”
  2. centromere - helps replicated plasmid to split into daughter cells
  3. telomere - allows linear plasmid to replicate
44
Q

telomeres and DNA replication problem

A

lagging strand requires RNA primer to bind fragments -> so every time you replicate, the strand should get shorter… so you have telomeres

45
Q

telomerase action

A

add TEL sequence to ends of chromosome by reverse transcription followed by translocation-hybridization

46
Q

parts of telomerase-RNA complex

A
  • ssDNA at terminus of telomere
  • catalytic site for dNTP addition
  • telomerase protein
  • telomerase-associated RNA template

Mol Bio - Exam 1 (10 decks)

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