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LS3 final > lec 12 > Flashcards

lec 12 Flashcards

1
Q

how genomes exist during interphase

A

chromatins

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2
Q

how do genomes exist during cell division

A

chromosomes

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3
Q

what are chromosomes

A

condensed chromatins which get duplicated before cell division

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4
Q

what are chromatids

A

sister duplicate chromosomes

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5
Q

euchromatin

A

lighter in color because it’s less condensed

Contains actvely transcribed genomic regions

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6
Q

Heterochromatin

A

darker because it’s more condensed

Includes centromeres and telomeres which are not actively transcribed

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7
Q

how does chromatin structure affect the transcription activity of genes?

A

Less condensed chromatin (euchromatin) is more active and transcribed more readily than the more condensed heterochromatin

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8
Q

what is the chromatin structural unit

A

nucleosomes

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9
Q

what does Metaphase chromosome look like

A

like X (the way you picture a chromosome) on the scale of 1400 nm

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10
Q

chromosome at 700 nm

A

condensed scaffold-associated chromatin which is all loopy with a scaffold backbone (see at 300 nm)

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11
Q

interphase chromosome

A

extended scaffold associated chromatin

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12
Q

what does a zoomed in chromatin fiber look like

A

packed nucleosomes (little balls packed together)

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13
Q

what do zoomed in packed nucleosomes look like

A

“beads on a string” basically beads with string looped around each

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14
Q

what is the string portion of ‘beads on a string’ nucleosomes

A

double helix DNA

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15
Q

what are nucleosomes

A

DNA histone particles

147 bp DNA wrapped around 8 core histones

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16
Q

what are histones

A

basic proteins rich is arg and lys (basic binds tightly to (-) charged DNA)

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17
Q

what are the core histones

A

H2A, H2B, H3, H4 (11-15 kD) each is a protein chunk which is a part of the ‘bead’

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18
Q

What connects nucleosomes?

A

50 bp linker DNA and linker histones H1 (~21 kD)

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19
Q

what does chromatin structure explain

A

where DNA hangs out inside the nucleus

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20
Q

what does the dsDNA in chromosomes consist of

A

gene families, simple seq DNA, spacer DNA, and introns

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21
Q

What affects the position of nucleosomes?

A

The number of linker histone H1, histone modification, and chromosome remodeling proteins

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22
Q

What allows binding of TBP and RNAP?

A

The fact that DNA of an active promoter is usually free of nucleosomes

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23
Q

Is nucleosome localization stagnant or dynamic?

A

Dynamic - the nucleosome ‘moves’

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24
Q

What can change the location and density of nucleosomes?

A

The chromatin remodeling process

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25
Q

What accomplishes the chromatin remodeling?

A

The function of histone modifying enzymes and chromatin remodeling proteins

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26
Q

What does linker histone (H1) do?

A

Inhibits transcription

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27
Q

How does H1 (linker histone) repress transcription?

A

By occupying the position of DNA to prevent binding of transcription activators and RNAP

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28
Q

How did we find out an active promoter is free of nucleosomes?

A

Use restriction enzymes to cut a circular viral minichromosome within the promoter and enhancer region and have another enzyme cut a site opposite in another minichromosome. Look under microscope and see the cut within P/E has nuclesome free DNA at the ends, but the cut opposite P/E has has nucleosome free DNA in the center. Therefore, P/E is free of nucleosomes

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29
Q

What does chromatin remodeling (chromosome remodeling) do and what is it dependent on?

A

Changes the chromatin architecture and it dependent on ATP

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30
Q

What does it mean to remodel chromatin?

A

Change the position, density, or architecture of core nucleosomes

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31
Q

What causes the chromatin remodeling?

A

Histone replacement, histone protein modifications, nucleosome unwrapping and migration

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32
Q

What are some chromatin remodeling proteins which consume ATP?

A

SWI/SNF, SWR, ISWI, INO80, NuRD

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33
Q

What effect can chromatin remodeling have on transcription?

A

It can activate or repress it.

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34
Q

Summary of chromatin remodeling process

A

chromatin remodeling complexes hydrolyze ATP to change the nucleosome position or density

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35
Q

Mechanisms which facilitate chromatin remodeling (4)

A
  1. Mobilize nucleosome position (sliding)
    1. Dissociation of DNA-histone contact (unwrapping)
    2. Remove core histones (histone eviction)
      Replace common core histones; e.g. H2A –> H2AZ isoform (histone variant exchange)
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36
Q

How does chromatin remodeling by core histone exchange work?

A

A remodeler protein repositions nucleosome to allow for a nucleosome free region and another remodeler protein faciliates replacement of core histone in the flanking nucleosomes of the nucleosome free region

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37
Q

Why would you want to remodel chromatin?

A

Nucleosomes tightly packed by common core histones have low transcription acitivity, but with a stable, nucleosome-free region, active transcription can occur

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38
Q

How do histone modifications facilitate chromatin remodeling?

A

They can loosen histone attachment to DNA, making it easier for the remodeling proteins

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39
Q

What’s an example of a histone modification and what facilitates it?

A

Histone tail acetylation by histone acetyltransferase

40
Q

What is a histone tail and where is it located?

A

N-terminal 11-36 amino acids of core histones; not buried inside the nucleosome

41
Q

How can the same residue of a histone be multiply modified?

A

By different chemical reactions under different conditions

42
Q

What will the same chemical modification on different residues of a histone do?

A

Possibly have different effects on transcription

43
Q

What are histone codes?

A

The combined pattern of histone modifications

44
Q

What does the histone code H3R2mK4mK9acK14ac mean?

A

Histone H3 with Arg2 methylated, Lys4 methylated, Lys 9 acetylated, and Lys 14 acetylated

45
Q

When is histone code important to transcription?

A

In vivo

46
Q

What are the four major histone modifications?

A

Acetylation, methylation, phosphorylation, and ubiquination

47
Q

What’s an acetyl group?

A

-C=OCH3

48
Q

What’s a methyl group?

A

CH3

49
Q

Whats a phosphoryl group?

A

-OPO3 2-

50
Q

Whats a ubiquitin group?

A

A squiggly clump

51
Q

What is acetylation?

A

Addition of an acetyl group to LYSINE residues

52
Q

How does acetylation affect histones?

A

Have fewer positive charges so interact less strongly with DNA

53
Q

How does acetylation differ in euchromatin and heterochromatin?

A

In euchromatin it’s hyperacetylated (common) while in heterochromatin it’s hypoacetylated (rare)

54
Q

Where does methylation occur?

A

Often the same Lys residue as acetylation and in Arg

55
Q

How do methylation and acetylation interact?

A

Often compete in Lys residues

56
Q

What does phosphorylation do?

A

Introduces negative charges

57
Q

What does poly-ubiquitination do?

A

Leads to degradation of ubiquintinated proteins

58
Q

What is mono-ubiquitination?

A

Adding 1 Ubq; is not a degradation signal and is part of histone code

59
Q

What acetylates histones

A

Histone acetylatransferase (HAT)

60
Q

How does histone acetyltransferase (HAT) work?

A

Transfers acetyl groups from donor acetyl-CoA to lysine (not arginine) residues

61
Q

What deacetylates histones?

A

Histone deacetylase (HDAC)

62
Q

What effect does lysine acetylation have on histone?

A

Neutralzies positive charges of histone which tends to reduce interactions between neighboring nucleosomes, which decreases overall chromatin condensation so it usually activates transcription

63
Q

How is HAT related to transcription?

A

Transcription co-activators often recruit HAT to activate transcription

64
Q

How is HDAC related to transcription?

A

Transcription co-repressors often recruit HDAC to repress transcription

65
Q

What proteins assist HAT recruiting?

A

When Max binds Myc, the dimer recruits HAT to acetylate histones and activate transcription

66
Q

What proteins assist HDAC recruiting?

A

When Max binds to Mad, the dimer recruits HDAC to deacetylate histones which suppresses transcription

67
Q

What does Mad1 dow hen it interacts with the Sin3-HDAC2 compelex?

A

It represses transcription

68
Q

What happens when Mac binds to Mad1

A

the Max-Mad1 dimer recruits HDAC2 via the Sin3 bridge and HDAC2 deacetylates histones around the promoter region, resulting in transcription inhibition

69
Q

Examples of transcriptional co-repressors

A

histone deacetylases

70
Q

Examples of transcriptional co-activators:

A

histone acetyltransferases

71
Q

What happens with hypoacetylated chromosomes?

A

Repressed chromatin and no transcription

72
Q

What happens with abundant histone acetylation?

A

Active chromatin and transcription occurs

73
Q

What happens to the thryoid receptor without thyroid hormone?

A

The thyroid receptor bind co-repressor NcoR to recruit Sin3, which binds HDAC to deacetylate histone and repress transcription

74
Q

What happens to the thyroid receptor in the presence of thyroid hormone?

A

The thyroid receptor binds to a co-activator which is a HAT complex what acetylates histone to activate transcription

75
Q

What’s an example of a repressor converted to an activator?

A

Thyroid receptor is a repressor without thyroid hormone, but with thyroid hormone, the histones are acetylated and transcription is activates

76
Q

How can you use ChIP to identify chromatin DNA bound by a protein in vivo?

A

Fix chromatins, cut with ultrasonication or nuclease, immunoprecipitate with antibodies to transcription factor or modified histones; PCR the DNA from the promoter – the DNA of chromatin fragments bound by the protein will produce the PCR product

77
Q

How did we find out histone acetylation occurs before transcription?

A

Infected cells with a virus and isolated chromatin at different stages of infection then ChIP against TBP or acetylated histone and PCR – see the acetylation occurred after viral infection but before TBP binding and mRNA expression

78
Q

How does histone acetylation affect DNA-TBP interaction?

A

Shows that the transcription repressor Mad/Max co-repressor recruits HDAC to deactylate histone and suppress transcription but TBP recruits HAT to acetylate the histones at the promoter – ultimate level of transcription is dependent of balance between HDAC and HAT

79
Q

Where can a histone be methylated?

A

At lysine and arginine residues

80
Q

What do methyltransferases (HMT) do?

A

Transfer 1-3 methyl groups from donor SAM to lys or arg residues of histone tails

81
Q

What effect does methylation have on charges of lysine and arginine and whats the resulting effect?

A

Doesn’t reduce the positive charges so does not reduce nuclesome condensation

82
Q

What effect does hsistone methylation often have in general?

A

Chromatin condensation and transcription inactivation (but not always!)

83
Q

Example of histone methylation repressing transcription:

A

H3K9 is methylated and binds to a chromosome remodeling protein which recruits HMT which methylates the next nucleosome at the same spot which eventually results in chromatin condensation (heterochromatin) which can cause gene silencing unless gene is insulated

84
Q

What is the prokaryotic holoenzyme of RNAP

A

alpha, beta, beta’, w, sigma factor

85
Q

What is the closed complex in prokaryotic transcription?

A

Holoenzyme + promoter DNA

86
Q

What is the recognition seq and location for promoters in prokaryotic transcription?

A

TATA box at -10 position

87
Q

Where are DNA regulatory elements located for prokaryotic transcription?

A

Usually close to or within the promoter and transcribed region

88
Q

What regulates prokaryotic transcription?

A

A few transcription factors, changing of sigma factors, or RNAP for phages

89
Q

What don’t prokaryotes have that eukaroyotes do in regards to transcription?

A

Histones, nucleosomes, complex chromatin structures

90
Q

Components of eukaryotic transcription?

A

Three RNAP

91
Q

Which RNAP transcribes mRNAs in eukaroyotes?

A

RNAPII

92
Q

What is the holoenzyme of RNAPII in prokaryotes compared to eukaroyotes?

A

More subunits and requires TFIIs

93
Q

What is the preinitiation complex in eukaryotic transcription?

A

Holoenzyme + TFIID + promoter DNA

94
Q

Where are DNA regulatory elements located for eukaryotic transcription?

A

May be close to, within, or far away from promoter or transcribed region?

95
Q

What regulates eukaryotic transcription?

A

Many transcription factors, co-activators, co-repressors, nucleosome position/density, histone codes, and aspects of chromatin structure

LS3 final (1 decks)

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