Nucleosomes; chromatin and chromosome structure

Question 1

Length of DNA

Answer 1

3.4nm per turn
2 meters in each cell

Question 2

Why need structure for dna ?

Answer 2

to package DNA into a cell
to protect dna from breakage/chemical attack
to allow control access to only those parts that need to be active in cell

Question 3

Nucleosome structure

Answer 3

made of 4 diff histones
2 of each make octomer
dna wraps twice around octomer
h3 binds to h4
h2a binds h2b
h1 is lnker
tails extend out nucleosome

Question 4

structure after nucleosome h1

Answer 4

beads on a string
h1 binds to nucleosome core particle and linker dna and assists in packaging

Question 5

explain method to reveal nucleosome organisation

Answer 5

micrococcal nuclease digest
micrococcal nuclease cuts dna independently
dna is more accessible in linker regions
partial digest gives dna fragments with several nucleosomes
nucleosome spacing is regular but varies between species/cell type

Question 6

after beads on string

Answer 6

dna organised into 30nm fibre although this is contested

Question 7

after 30nm fiber

Answer 7

proteins forming chromosome scaffold caused looped domains to form in 30nm fibre

Question 8

overall level of organisaition of chromatin stages simplified

Answer 8

short region of DNA double helix
beads on a string form of chromatin
30nm chromatin fiber of packed nucleosome
section of chromosome in extended form - looped
condensed section of chromsome
entire mitotic chromosome

Question 9

what are the different regions of chromatin in cell

Answer 9

heterochromatin - inactive in gene expression
- constitutive(around centromere and telomere+satellite sequence, same in all cell types)
faculative(contains silent genes,regulated,differes between cell types

Euchromatin

Question 10

TADS

Answer 10

dna squence within a tad physically interact with each other more frequently than with sequences outside tad
probably involve interaction between ctcf protein and cohesin complex
keep different regions of chromatin functionall seperate

Question 11

Lads and NADS

Answer 11

Laminar associated domain (LADS) - associated with nuclear lamina
-gene poor and hetero chromatic
2 types of lads -constitutive and facultative

NADS - are regions of chromatin associated with the nucleolus

Question 12

How does chromatin open up ?

Answer 12

individual loops can decondense to allow easier access to regions of the DNA required for gene expression/replication/repair

Question 13

Chromatin asembly during transcription

Answer 13

Rna polymerase advances
DNA is displaced from octamer and forms closed loop
torsion ahead of RNA polymerase displaces octamer, which reinserts behind polymerase

displaced octamer never leaves DNA

Question 14

Chromatin assembly during DNA replication

Answer 14

Nucleosomes are removed ahead of replication fork
they are separated to the h3-h4 core tetramer and h2A, h2B
nucleosomes are replaced after the replication fork as a mixture of locally used old histones and new histones

Question 15

Histone remodeling in DNA repair

Answer 15

two main ones

eviction - nucleosome removed from dna near the break and then replaced after damage is repaired

sliding - the nucleosomes slide away from the area of dna damage and then slide back when repair is complete

Question 16

Histone remodelling

Answer 16

deposition composition - sliding

site exposure - repositioning
ejection and then unwrapping

altered- dimer exchange aka changing some parts of the octamer aka switching histones

Question 17

Four main familys involved in transcription

Answer 17

all have some domains in common such as DExx and HELK

Question 18

Replification specific modelers

Answer 18

Chromatin assembly factor
Anti silencing factor

Question 19

post translational modification of histones

Answer 19

Acetylation
methylation
phosphorylation
ubiquitination
sumoylation

most occur on lysine
some on argine
phos and ubiq only on serine /threonine

Question 20

histone modification

Answer 20

usually on tail
more on h3 and 4 vs h2a and b
can change histone property aka charge
can get different modification on same site
also several modification at same time

Question 21

Histone code hypothesis

Answer 21

speicifc patterns of modification on histone proteins can act as a code that regulated gene expression and other chromatin-dependent processes

Question 22

Histone modifying enzymes

Answer 22

Several enzymes that do the same thing
acetylations - acetylaresases and deacetylases

same thing for mtehylation

phosphorylation - kinases and phorylatsses

Question 23

Core histone variants

Answer 23

can have different size or domains or function
no variants of h4 and h2b

Question 24

h1 variants

Answer 24

occur in n and c tail domains of h1
variants have different in distribution and biophysical properties
but difference in function isnt well denied

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