eukaryotic genes and gene expression

Question 1

how can nucleosomes be separating?

Answer 1

incubating them with DNAse enzyme

Question 2

nucleosome core is an octomer what are the subunits

Answer 2

2X H2A
2X H2B
2X H3
2X H4

Question 3

which histone proteins are slightly lysine - rich

Answer 3

H2A

H2B

Question 4

which histone proteins are arginine rich

Answer 4

H3

H4

Question 5

which histone proteins are LYSINE rich

Answer 5

H1

Question 6

what is linker DNA bound to

Answer 6

histone H1

Question 7

what is protruding from the nucleosome

Answer 7

4 core histone with N-termini tails

Question 8

what does H1 do

Answer 8

helps pack the chromatin into further fibres

Question 9

histone N-termini tails can be modified by

Answer 9

phosphorylation,
acetylation,
methylation

Question 10

these modifications regluate gene expression because

Answer 10

if the histones are packed to tightly, no other factors can interrogate the chromosome and transcription is silenced

Question 11

acetylation what happens

Answer 11

the K/R are aceytlated on histone tail neutralises positive charge

Question 12

what does modification via phosphorylation do

Answer 12

introduces a negative charge

Question 13

Non coding RNA (ncRNA)

Answer 13

rRNA

tRNA

Question 14

prokaryotes what happens

Answer 14

RNA pol 2 explores until sigma sub-unit recognizes a promoter sequence upstream

Question 15

what happens after initiation of trancription

Answer 15

sigma subunit falls off

Question 16

AA interaction with base pairs in the major groove

Answer 16

asp- Hbond acceptor with N-H on A base (very stable thats why it is key in TF
arg- Hbond donor with 2 N-H to O and N of G base

Question 17

pol 1
pol 2
pol 3

Answer 17

rRNA nucleolus
mRNA, snRNA nucleoplasm
5S rRNA, tRNA nucloplasm

Question 18

eukaryotic transcription initiation

Answer 18

TAF (TF2D) transcription activation protein binds to TATA + accessory factors, TF, and then recruitment of RNA polymerase 2

Question 19

what do enhancers do

Answer 19

stimulate promoter activity

Question 20

what do both promoters and enhancers contain

Answer 20

sequcence mofits to which TF can bind

Question 21

how does activation of transcription work

Answer 21

activator recruits HAT

and HAT acetylates histone tails

Question 22

2 effects of HAT

Answer 22

looser chromatin structure make promotor region more accessible
TF2D binds more strongly to acetylated nucleosomes

Question 23

activation also causes

Hat do they recruit

Answer 23

the activator to recruit chromatin remodeling complex

increasing mobility of neucleosome and makes promoter accessible

Question 24

what are the 4 TFs dna binding domains

Answer 24

Homeodomain
leucine zipper
zinc finger
helix-loop-helix

Question 25

homeodomain what is it

Answer 25

helix 2 and 3 form a helix turn helix

helix 3 makes sequence specific interactions with major groove of DNA

Question 26

zinc finger what is it

Answer 26

formed by beta sheets and alpha helix
2 cysteines and 2 histidines complex a zinc atom
alpha helix contacts DNA in major groove

Question 27

helix loop helix what is it

Answer 27

N terminal long alpha helix contacting major groove of dna

dimerisation: short and long alpha helix combined

Question 28

leucine zipper protein what is it

Answer 28

N terminal part of Long alpha helix contacting major groove of dna
dimerisation: C terminal leucine zipper domain (a helix where every 7th AA is leucine)

Question 29

C-jun protein, what happens when 2 leucine zippers interact

Answer 29

leucines are on one side of the helix so when there are 2 helices hydrophobic interactions cause the zipper fomation

Question 30

activation of tancription

Answer 30

clustered control region
cooperative binding
combinatorial control
signalling pathway

Question 31

repression of transcription

Answer 31

insulators
competition
inhibition
direct repression
indirect mechanisms

Question 32

clustered control region what is it

Answer 32

each gene has its own local regulatory element

also has a local locus control region required for orderly expression

Question 33

modes of cooperative activator binding

Answer 33

interaction of A and B facilitates cooperative binding to DNA
interaction via mediator facilitates cooperative binding to DNA

Question 34

transcription during hypoxia eg of modes of cooperative activator binding

Answer 34

at normal O2 levels HIF1 alpha is destroyed

at low levels the heterodimer can form and activate transcription at genes with hypoxia response element in promoters

Question 35

modes of cooperative activator binding 2

Answer 35

factor A binds and recruits chromatin remodeler

A binding causes slight unwinding and B can now bind

Question 36

combinatorial control principle

Answer 36

each gene receives several signals
each gene represented by a TF
the same TF may control a number of genes

Question 37

JAK (kinase)/Stat pathway what happens

Answer 37

cytosine binds to a receptor
receptor gets phosphorylated by JAK
STAT now binds to receptor and gets phosophrylated
phosphorylated STAT dimer translocates into the nucleus, activates target genes

Question 38

RAS pathway what happens

Answer 38

ligand binds to tyrosine kinase which then autophosphorylates
Grb and SOS actvate the small GTPase RAS
RAS triggers the MAP kinase cascade
MAP kinase can phosphorylate transcriptional factors

Question 39

gene silencing

Answer 39

turned off by lack of activators and transcription machinery
off state is reinforced by DNA methylation
methyl C binding proteins are bound
methyl C binding proteins recruit HDACs and chromatin remodeling complex