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FLC > Chromatin & Histone Structure > Flashcards

Chromatin & Histone Structure Flashcards

1
Q

Define what chromatin is

A

The chromosomes and the associated proteins

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2
Q

What are histones?

A

The proteins the DNA winds around

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3
Q

What do the 4 levels of DNA packaging consist of?

A

1 - Nucleosomes = DNA + Histones
2 - 30nm fibres
3 - 80 - 100nm fibres
4 - mitotic chromosomes

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4
Q

What do chromosomes consist of?

A

DNA
Histone proteins
Non histone proteins
Non coding RNA

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5
Q

How is DNA packaged in interphase?

A

As nucleosomes

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6
Q

Why is DNA so compact?

A

Lots of DNA is tightly packed in higher order structures around the histone core

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7
Q

What is meant by higher order DNA structure?

A

The 4 levels of DNA packaging

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8
Q

When extracted at physiological salt concentration, how is the chromatin arranged?

A

As 30nm thick fibre

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9
Q

What is needed for higher order structures to form?

A
  • Linker histones
  • Histone tail interaction with adjacent nucleosomes
  • Binding of packaging proteins to histone tails
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10
Q

Why is the chromatin structure not static?

A

Nucleosomes have to be removed from DNA in front of the polymerase and replaced behind the polymerase, during Replication / Transcription

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11
Q

What are histone remodelling factors?

A

Enzymes that remove and replace nucleosomes

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12
Q

List the features of facultative heterochromatin

A
  • contains non expressive genes of that cell type
  • DNA tightly packaged as heterochromatin
  • Can be packaged as euchromatin in other cell types
    (expressed)
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13
Q

How is facultative heterochromatin regulated?

A

By chemical modifications of lysine residues in histone tails

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14
Q

Give examples of lysine modifications that can occur

A
  • methylation

- acetylation

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15
Q

What ensures the DNA histone complex doesn’t fall

apart?

A

Chromosomes are treated to extract histones and most non histone proteins. They appear as DNA loops attached to scaffold (tightly bound proteins)

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16
Q

Which method can be used to investigate chromatin structure?

A

DNase digestion

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17
Q

How does DNAse digestion work?

A

DNAse I cuts double stranded DNA

Histone binding protects DNA from digestion

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18
Q

Where on the DNA does the DNAse work?

A

On DNAse I sensitive sites (HSS)

19
Q

What DNAse I sensitive sites (HSS) are there on DNA?

A
  • Histone free DNA sequence
  • Naked DNA/ binding transcription factors
  • Promoters/ enhancers
20
Q

How do transcription proteins still access the DNA strand

despite its highly packaged structure?

A

TFs open up the chromatin structures, recruit basal TFs to enable transcription to occur

21
Q

How do Transcription factors regulate transcription?

A
  1. TFs bind to promoter (and enhancer)
  2. Recruit general basal transcription factors
  3. Assemble initiation complexes
  4. Recruits RNA polymerase
22
Q

How do TFs recruit chromatin modifying enzymes?

A

Via nulceur co - activator (NCoA)

or nucleur co - repressor (NCoR)

23
Q

What modifications do chromatin modifying enzymes carry out?

A

Acetylation

24
Q

Is acetylation of chromatin more prevalent in euchromatin

or heterochromatin?

A

Many Lysine residues in Euchromatin histones are acetylated

Heterochromatin histones are largely unacetylated

25
Q

What is the role of Histone Acetyl Transeferases (HAT)?

A
  • acetylate lysine residues on histones

- lead to unpacking of chromatin

26
Q

What is the job of (HDACs) Histone deacetylases?

A

Deacetylate histones leading to compaction of chromatin

27
Q

Where are thyroid hormones produced in the body?

A

Thyroid glands

28
Q

What allows the hormones to bind to Thyroid hormone receptors (THRs)?

A

Hormones are very hydrophilic so pass through membrane and bind to their receptors

29
Q

What is the role of the DNA Binding Domain on the THR (Thyroid Hormone Receptor)?

A

Binds specific Thyroid response element (TRE)

- acts as a regulatory TF

30
Q

What happens in the absence of the thyroid hormone?

A

NCoR binds to HDAC and DNA methylated
causes repression of genes
chromatin packed tightly

31
Q

What are the 3 domains on a Thyroid Hormone Receptor?

A
  • Activation Domain
  • DNA binding Domain
  • Ligand Binding Dimerisation Domain
32
Q

What is the significance of thyroid hormones?

A

Have major effects on metabolism

33
Q

What is the significance of the TRE (thyroid response element)?

A

TRE binds a thyroid receptor protein dependent on the presence of the hormone

34
Q

What occurs when thyroid hormone is available?

A

Hormone binds to thyroid receptor
Undergoes conformational change
Allowing NCoA to bind and recruit HAT and HMT
Chromatin opens up to be transcribed

35
Q

What does the Ligand Binding Dimerisation Domain do?

A

Binds the thyroid hormone

36
Q

What are HMTs and what is their role?

A

Histone Methyl Transferases

- methylate histone tails

37
Q

Describe and explain what HDMs are and their role

A

Histone Demethylases

- demethylate histones

38
Q

How many times can a lysine residue be methylated?

A

Lysine residue can be mono, di, or tri- methylated

39
Q

What effect does methylating lysine residues have?

A

Dependent on the residue it can either cause

  • chromatin condensation (H3K9me3)
  • chromatin decondensation (H3k9me1)
40
Q

What is the histone code?

A

The hypothesis that the transcription DNA is partly regulated by the modifications to histone proteins, especially on their unstructured ends.

41
Q

Which code reading proteins are domains found by?

A

Related domains are found in multiple code reading proteins

e. g.
- bromodomain bind to acetylated lysines
- chromo/ tudordomain bind to methylated lysines

42
Q

How is the histone code read?

A

By binding proteins

43
Q

Are histone marks read singularly?

A

They’re not read in isolation

there are multiple lysine residues on each histone with multiple histone modifications

FLC (34 decks)

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