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Fundamentals Of Life Science > Histones and Packaging > Flashcards

Histones and Packaging Flashcards

1
Q

Why does DNA need to be packaged?

A

So biological processes can be carried out

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2
Q

How many bases does one complete double turn of double-helical DNA contain?

A

10

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3
Q

Why does DNA need to be unwound?

A

To allow access to machinery for replication and transcription

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4
Q

How many bases does the human haploid genome contain?

A

3 x 10^9 bases

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5
Q

Approximately how much DNA sin each diploid cell?

A

2m

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6
Q

What is the role of chromatin?

A

To package DNA

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7
Q

What is chromatin made up of?

A

Nucleosomes (which are made up of histones)

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8
Q

What factors do histones affect?

A

Isolation
Characterisation
Biochemical properties

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9
Q

What is the composition of chromatin?

A

DNA
Proteins (mainly histones)
RNA (not coding for proteins)

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10
Q

What is the most common nuclear protein?

A

Histones (very abundant)

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11
Q

What is the role of histones?

A

Packaging

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12
Q

What is the ratio between histones and DNA

A

1:1

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13
Q

What is the non-histone chromatin protein used for?

A

Scaffolding

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14
Q

What is the role of RNA in the nucleosome?

A

Used when the nucleosome is acting as a signalling molecule to either allow or prevent transcription

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15
Q

What are the four core histones?

A

H4 H3 H2A H2B

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16
Q

What is the linker histone?

A

H1

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17
Q

Which is the least conserved histone?

A

H1

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18
Q

Which are the most highly conserved histones?

A

H4 and H3

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19
Q

What are the properties of histones and how do they help carry out their role in packaging?

A

-Very small
-V highly positively charged
-highly conserved
Ideal for packaging as DNA is v negatively charged

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20
Q

How many amino acids difference is there in H2A and H2B

A

2

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21
Q

What is the first level of packaging?

A

Nucleosome

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22
Q

What is the second level of packaging?

A

10nm fibre

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23
Q

What does the nucleosome consist of?

A 
2 x H2A 
2 x H2B 
2 X H3 
2 X H4
1 H1 
200bp DNA
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24
Q

What determines the packaging of DNA?

A

How the histones interact

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25
Q

What is the cononical nucleosome?

A

The normal contribution of histones

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26
Q

How many base pairs of DNA fit in the nucleosome?

A

146 base pairs of DNA left handed super helix

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27
Q

How many base pairs of DNA wraps around the nucleosome?

A

146

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28
Q

What happens to the other base pairs that are not wrapped around the nucleosome?

A

The extra DNA either side of the nucleosome is used to link one nucleosome to another nucleosome (only time DNA is in a naked state)

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29
Q

What is the total protein content of the nucleosome?

A

108kDa

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30
Q

What is the DNA path around the nucleosome?

A

1.8 superhelical turns to the left

31
Q

How does the heterodimerisation of histones H3 and H4 occur?

A

Histone handshake motif
2 molecules of each histone bind as a tetramer
Forms a horseshoe shape

32
Q

How do H2A and H2B associate with the complex?

A

They form dimers above and below the tetramer

33
Q

What could a change any of the four histones cause?

A

It would change the interaction of dimers which could change the core octameric structure which could make it less stable

34
Q

How does DNA wrap about the octameric core?

A

It wraps around in a left handed super coil (even though DNA is a right handed helix)

35
Q

What does the fact that DNA does not run smoothly around the nucleosome mean?

A

Means that pockets form which allow for the increased accessability of transcription factors binding.

36
Q

What happens if the canonical nucleosome is altered?

A

The path taken by the DNA will change which is vital during transcription and transcription because DNA needs to be used as a template so must be able to unravel from the nucleosome

37
Q

How many variants does H2 have (and name them)?

A 
At least four 
H2AZ 
macroH2A 
H2AX 
H2A.Bbd
38
Q

When would histone variants be used?

A

if you want to activate or suppress gene transcription by changing the canonical nucleosome

39
Q

What is the role of H2AZ?

A

Used to increase gene activity by making the association between H2B:H2A and H3:H4 less stable and so the DNA is more losely packed and hence able to be accessed by more transcription factors.

40
Q

What is the role of macroH2A?

A

Placed in nucleosome on inactive X chromosome (one X chromosome is turned off so will be enriched in macroH2A to keep it turned off)

41
Q

What is the role of H2ABbd?

A

Placed on active X chromosome so keep it active

42
Q

What is the role of H2AX?

A

Signals to repair broken DNA so it’s not transferred into the next generation

43
Q

What percentage identity does H2A have with H2AZ?

A

60% (low)

44
Q

How does the use of H2AZ instead of H@A increase gene transcription?

A
  1. Amino acids are different so the interaction stability is lowered between H2AZ and H2B
  2. Alters the interaction of the H2A/H2B dimer with the H3/H4 tetramer
  3. DNA wrapped around nucleosome not as strongly so transcription can easily occur
  4. H2AZ tail is also longer which affects interactions in central core
45
Q

How many variants are there of H3?

A

5 (but very little difference between them)

46
Q

What are the variants of H3?

A 
H3.3
H3A 
H3.2 
CenpA 
H3.lt
47
Q

What is the role of CenpA?

A

It is enriched at the centromeres and telomeres where there are no genes so you can attach the chromosome or at the telomers to protect the genome

48
Q

What are histone variants used for?

A

To alter the packaging of DNA

49
Q

What does replacement of H3 with H3.3 cause?

A

marks actively transcribed loci by replication independent nucleosome assembly

50
Q

What do variants of H3 and H2A differentiate between?

A

chromatin at centromeres, active genes and heterochromatin

51
Q

When is there no gene expression?

A

Metaphase (most highly condensed state

52
Q

Describe the 10nm fibre

A

A series of nucleosomes linked by linker DNA

53
Q

What is the packing ratio in the 10nm fibre?

A

6-7

54
Q

What does the length of the linker DNA depend on?

A

cell type and species

55
Q

Describe the structure of the 30nm solenoid?

A
  • 10nm coiled
  • histone H1 binds and stops the DNA from slipping
  • 6 nucleosomes per turn
  • packing ratio of 40
56
Q

Describe the structure of the 300nm solenoid?

A
  • Each loop contains between 60-100 kb of DNA tethered by non-histone scaffolding proteins
  • protein scaffolding allows the DNA to condense further
  • non-histone proteins keep space between loops and prevent crossing
  • packing ratio of 680
57
Q

Describe the structure of the 700nm fibre

A
  • loops of chromatin coil again to form a coiled coil
  • scaffold has loops of 30nm loops
  • packing ratio of 10^4
58
Q

What is the final level of packaging?

A
  • metaphase chromsome

- whole of DNA completely inaccessible to transcription or replication machinery

59
Q

What levels of packaging can transcription occur at?

A

Up to 30nm as long as transcription factors can associate

60
Q

What are the two types of chromatin?

A

Heterochromatin and euchromatin

61
Q

Where is heterochromatin present?

A

Telomers and centromeres

62
Q

what is heterochromatin?

A

Very highly compacted chromatin, very rarely contains genes within in it (usually a gene poor region)

63
Q

In a interphase cell how would you distinguish between heterochromatin and euchromatin?

A

Heterochromatin- dense staining regions (highly compacted)

Euchromatin-light staining regions

64
Q

What are the two types of heterochromatin?

A

Constitutive and facultative

65
Q

What types of genes are contained within constitutive heterochromatin?

A

Poorly expressed genes

66
Q

What is facultative heterochromatin often associated with?

A

Morphogenesis or differentiation

67
Q

Why don’t you want to put a gene into heterochromatin?

A

Because once its there you can’t transcribe it

68
Q

Is constitutive heterochromatin the same or different in every cell?

A

same

69
Q

Does facultative stay the same or change?

A

Change

70
Q

When is heterochromatin replicated?

A

Later in S phase of the cell cycle

71
Q

What type of chromatin configuration does euchromatin have?

A

open configuration

72
Q

When is euchromatin replicated?

A

Early in S phase (more accessible to replication machinery)

73
Q

What types of gene does euchromatin contain?

A

Transcriptionally active and inactive genes

74
Q

What are each of the levels of DNA packaging?

A 
Level 1 - Nucleosome
Level 2 - 10nm Fibre (beads on a string)
Level 3 - 30nm Solenoid
Level 4 - 300nm Solenoid
Level 5 - 700nm Fibre
Level 6 - Metaphase chromosome

Fundamentals Of Life Science (26 decks)

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