Transcription 3 Flashcards

1
Q

How is the barrel shaped core histone octamer made?

A
  1. Two H3/H4 dimers form.2. These form a tetramer. 3. Two H2A/H2B dimers form and bind to the tetramer.
    This is a predefined order of assembly.
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2
Q

What is the Nucleosome Core Particle (NCP)?

A

A histone octamer with DNA wrapped around it.

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3
Q

How many base pairs of DNA interact with a histone octamer?

A

146bp

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4
Q

How do histones interact with DNA?

A

Histones are cationic (lots of Lys/Arg) so bind to the negatively charged DNA backbone. Histones select the regions of DNA that are easiest to bend. Histones bind to the minor groove of DNA.

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5
Q

What is the chromatosome?

A

A nucleosome with the H1 linker histone bound, fixing the octamer to the DNA.

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6
Q

Why does nucleosome distribution vary between chromosomal loci?

A

Nucleosome binding is sequence dependent. Histone octamers can migrate to allow transcription.

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7
Q

What is a DNA solenoid?

A

Chromatin that has been condensed by zig-zag folding into a 30nm fibre. Helix consisting of 11nm nucleosome beads. Positively charged histone N termini extend from the nucleosome centre and bind to DNA on neighbouring nucleosomes.

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8
Q

How is the solenoid stabilised?

A

By H1 binding.

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9
Q

How much are sequential NCPs rotated in a solenoid?

A

By 71°.

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10
Q

What does the extent of solenoid compaction depend on?

A

Depends on the cellular environment. If transcription is needed the solenoid opens up.

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11
Q

How many nucleosomes are there per helical turn in a solenoid?

A

6

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12
Q

What regions of DNA do scaffold proteins bind to?

A

AT-rich regions.

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13
Q

How is the DNA scaffold further condensed?

A

By generating supercoils.

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14
Q

What does a chromosome consist of?

A

Helically packed loops of 30nm fibres

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15
Q

What is euchromatin?

A

Condensed chromatin that is transcriptionally active. Contains the largest proportion of genes in a chromosome. Not all transcribed at the same time, untranscribed regions may exist in the solenoid structure.

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16
Q

What is heterochromatin?

A

Condensed chromatin that is less transcriptionally active than euchromatin.

17
Q

What is faculative chromatin?

A

Chromatin that can be changed from heterochromatin to euchromatin.

18
Q

What is constitutive chromatin?

A

Chromatin that is condensed as heterochromatin throughout the cell cycle.

19
Q

Describe the histone fold.

A

Long central alpha helix connected to 2 shorter terminal helices. Forms a stable X shaped structure when dimerised.

20
Q

Approximately how many turns of DNA are there around each nucleosome?

A

1.7 turns

21
Q

How is DNA wrapped around a nucleosome?

A

Tightly wrapped. DNA remains on the outside of the nucleosome disc like structure. DNA strands lie in parallel.

22
Q

Why can’t transcription factors bind when DNA is wrapped tightly around nucleosomes?

A

Tight wrapping causes distortion of grooves and loss of shape complementarity.

23
Q

What is the role of the linker histones?

A

Stabilise interactions between nucleosomes in compacted chromatin.

24
Q

What does the H1 linker histone do?

A

Connects the entry and exit points of DNA on each nucleosome. Optimises the angle of each histone so that they naturally line up to form a helix.

25
Q

Where can histones be acetylated?

A

On conserved lysines in the N termini of H3 and H4.

26
Q

How does histone acetylation regulate transcription?

A

When acetylated histones become neutral and chromatin opens, allowing transcription factor binding.

27
Q

What are the enzymes that control acetylation of histones?

A

Histone acetyltransferase and Histone deacetylase.

28
Q

How can some gene specific transcription factors to bind in compact chromatin?

A

Can recognise the target sequence in compact chromatin, recruit HATs to open chromatin and activate transcription.

29
Q

How can methylation of CpG islands prevent transcription?

A

Methyl-CpG binding protein binds and recruits HDAC to condense the chromatin.