Chromatin And Gene Expression

Question 1

How do we have so many types of cells with the each having the same genetic material?

Answer 1

• via turning gene on and off
• having unique gene pattern
• same info can be used in different ways
• epigenetic modification (in response to environmental stress)

Question 2

Ways of Silencing a gene

Answer 2

Temporary - Histone methylation* - depends, can also activate gene (normally H3K9/27)
Permanently - DNA methylation

Question 3

Levels of gene expression control

Answer 3

1. Transcriptional level (rate limiting and most important)
2. RNA processing control (splicing, adding caps/tails)
3. Export/ localisation control
4. Translational control - ribosomal
5. PTM - e.g. MicroRNA

Question 4

Define genes

Answer 4

Genes are transcriptional units that are composed of structural and functional info coding for a protein and regulatory element, respectively

Question 5

Promoter

Answer 5

Essential in initiating transcription at LOW level

Positioned just upstream of target gene and is where RNA pol II binds

Question 6

Enhancers

Answer 6

Enhancers are regulatory DNA sequences that can be found upstream, downstream or even within the gene and allows FINE TUNING of gene expression. They often respond to external signals

Question 7

Types of PTM and what they do on histone tail and DNA

Answer 7

1. Acetylation - loosen chromatin (activate gene transcription)
2. Methylation - if histone then can activate or silence gene. If on DNA - permanently silent gene (no known DMT in specialised cell)
3. Phosphorylation
4. ADP-ribosylation - cross talk between PTM and core histone
5. Ubiquitination - allow crosstalk with another histone modification

Question 8

Regulatory elements often LACK nucleosomes - why?

Answer 8

More accessible for TF to bind

Question 9

Nucleosome composition

Answer 9

H1 linker + 2(H2A+H2B +H3+H4)

Question 10

Function and characteristics of histone N’ tail

Answer 10

Highly flexible and one of the most modified structure
Unstructured - no fixed structure within cell
Interact with DNA and can alter DNA path around the nucleosome
Great PTM site to fine tune gene expression

Question 11

Acetylation of histone occurs on what type of residue?

Answer 11

e- amino acids (e.g. Lysine, arginine) at the N term of ALL4 core histones

Question 12

Order of histone acetylation in lysine

Answer 12

H4 - K16 / K12 or K8 / K5 (‘K16-4-4(-4+1)’)

H3 - K18 / k23/ k14 / k9 / k27 (‘1823-149-27’)

Question 13

Histone methylation sites

Answer 13

H3 K4/9/27 - K4 (Active)
H4 K20
H1 K26

Normally tri.me.

Question 14

Permanently silencing a gene requires

Answer 14

Tri me. H3 K9/27
DNA methylation
H3K27 binds to PRC2 (PcG) which contains EZH2, EZH2 binds to H3K27 and permanently silence gene. PRC1 then ubiquitinate H2A to mark cell as permanently off

Question 15

What is ontology

Answer 15

Ontology defines the function of a gene and it’s functional relationship as well as interaction with other genes. (Which can be mapped out in a list

Question 16

Acetylation occurs on all 4 core histones

Answer 16

Yes

Question 17

What are the amino acids class that is often preferred to be acetylated amen methylated

Answer 17

e-amino acids

Lysine arginine

Question 18

Methylation on arginine is

Answer 18

Symmetrical

Question 19

Level of acetylation controls

Answer 19

The level of gene expression

Question 20

N’ phospholinkage

Answer 20

Histidine arginine and lysine

Question 21

O phospholinkage

Answer 21

Threonine tyrosine serine

Question 22

EZH2 has what ability

Answer 22

Deacetylation and methylation activity

Binds to H3k27

Question 23

Transcription initiation at low level is controlled by

Answer 23

Basal and core promotor upstream of the gene

Question 24

The promotor serve as a site of what

Answer 24

Site for RNA polymerase recognition.

Question 25

Higher level control of transcription initiation is by what

Answer 25

Enhancers which can fine tune gene expression and respond to the external environment

Question 26

TF contains wiggle room which is the combination of motifs that determines the type of TF that binds to it

Answer 26

T

Question 27

Transcription level is available till what level of e DNA

Answer 27

3rd level - 30nm

Question 28

If TF can bind to motifs it can recruit what to unwind DNA

Answer 28

Chromatin remodellers which requires energy

Question 29

Major and Minor groove serve as what fit TF

Answer 29

Binding site

Question 30

Define epigenetics

Answer 30

The study of inheritable changed in the gene expression of cellular phenotypes which is caused by mechanisms other than DNA changes

Question 31

After development how many percentage of gene is active

Answer 31

10-20%

Question 32

Arg acetylation often are

Answer 32

Symmetrical

Question 33

Asymmetrical acetylation occurs on where

Answer 33

Lysine residues

Question 34

Define gene expression

Answer 34

Gene expression is the process by which information of a gene is used in the synthesis of a functional gene product. The product is often a protein from coding regions and a functional regulatory unit if from a non coding region

Question 35

Define genes

Answer 35

Genes are transcriptional unit which is composed of structurwl and functional information crowing for protein and regulatory elements repectively

Question 36

TATABOX Features

Answer 36

A promotor
About 50% of genes use it
8 bp long
-35–10 upstream of gene

Question 37

Histone tail is one of the most modified and flexible structure

Answer 37

t