Chapter 4

Question 1

Organization level 1A = nucleosome (11nm)

Answer 1

Octamer- a core of 8 positively charged histones
DNA ( -) coils around this octamer 1.8 times or 147 nucleotides
This makes the DNA fold 7 times then the original one and 11nm thick ( 2nm thick originally)

Question 2

Organization level 1B = beads on a string

Answer 2

The octamer has 4 tyoes of histone
-Histone 2A
- histone 2B
- histone 3
- histone 4
2 of each 
There is a fifth type - histone 1 - linker histone, links adjacent nucleosomes on a string
The histones are highly conserved
There is only 2 aa difference out of 102 btw pea and cow H4

Question 3

Organization level 2 - solenoid structure (30nm)

Answer 3

Assembly of nucleosome into a compact chromatin fibre of packed nucleosome
This makes this the dna 30nm more thicker
It compacts by 40 folds

Question 4

Organization level 3 - radial chromatin loops(300nm)

Answer 4

When the solenoid structure further copacts to supercoil loops and held by non histone proteins.
The loops are stabilized and maintained by cohesin non histone proteins acting as a clamp
TheDNA stand associate to nucleur matrix which is a protein fibre framework . This is many fibrous proteins lining the inside of nuclear membrane
Loops are of 20000 to100000 bases

Question 5

How can a nuclear scaffold observed

Answer 5

By removing all the DNA and all the histones

Question 6

Organizational level 3B - rosettes 300nm

Answer 6

The spacial arrangement of loops is maintained by the attachment of DNA to an insoluble network of scaffold proteins
Forming chromosomal scaffold
These loops gather together to form rosettes

Question 7

Organization level 4- mitotic chromosome - chromatids - 700nm

Answer 7

Occurs in mitotic phase - also have looped domain structure
10000 folds
Condensin protein
More condense then interphase
Nucleus not present
Also occurs at centromere - alpha satellite

Question 8

Types of chromatin

Answer 8

Euchromatin- inner in the nucleus
Constitutive chromatin outer , repetetive sequence
Facultative chromatin outer

Question 9

Chromatin structure of euchromatin and constitutive chromatin study the paper

Answer 9

DNase sensitive
Irregular nucleosome
Accessible to nucleosome

DNase insensitive
Regular nucleosome array less
Accessible to nucleosome

Question 10

Presence of genes
Meiotic combinations
Study the paper

Answer 10

Eu
High variable
Normal
Cons
Low
Low

Question 11

What are the mechanisms by which chromosome looses

Answer 11

Chromatin remodelling - reposition of DNA to expose / hide DNA
Chemical modification to chromatin- remodel chromatin from closed to open structures

These are epigenetic meaning outside of DNA, envr or outside factors causing on/off of genes

Question 12

Open chromatin and closed chromatin

Answer 12

Open chromatin 
-relaxes association between DNA and nucleosome
- regulatory protein have access to DNA sequence 
- transcriptionally active
Closed chromatin 
- DNA sequence covered by nucleosomes
- regulatory proteins don’t have access
-transcriptionally inactive

Question 13

Remodelling of the chromatin

Answer 13

An ATP dependent chromatin remodelling complex uses ATP to loosen DNA around nucleosome and move it along the histone, exposing / hiding genes

Question 14

Chemical modification of histones - reversible

Answer 14

Addition of a chemical group, at the N terminus tail by covalent bonds
Acetylation
Methylation
Phosphorylation

Function
Interaction of histones
Compactness of dna
Recruit other proteins , and inactive transcription

Question 15

Acylated histones

Answer 15

Looser dna , transcriptionally active

Question 16

PhosphoryLated histones

Answer 16

Inc or dec winding of dna on histone

Question 17

Methylated

Answer 17

Affects the accessibility of DNA to processing enzymes by binding organizational structures eg nuclear matrix
Eg methylation of histone H3 helps form heterochromatin