eukaryotic genes and gene expression Flashcards
how can nucleosomes be separating?
incubating them with DNAse enzyme
nucleosome core is an octomer what are the subunits
2X H2A
2X H2B
2X H3
2X H4
which histone proteins are slightly lysine - rich
H2A
H2B
which histone proteins are arginine rich
H3
H4
which histone proteins are LYSINE rich
H1
what is linker DNA bound to
histone H1
what is protruding from the nucleosome
4 core histone with N-termini tails
what does H1 do
helps pack the chromatin into further fibres
histone N-termini tails can be modified by
phosphorylation,
acetylation,
methylation
these modifications regluate gene expression because
if the histones are packed to tightly, no other factors can interrogate the chromosome and transcription is silenced
acetylation what happens
the K/R are aceytlated on histone tail neutralises positive charge
what does modification via phosphorylation do
introduces a negative charge
Non coding RNA (ncRNA)
rRNA
tRNA
prokaryotes what happens
RNA pol 2 explores until sigma sub-unit recognizes a promoter sequence upstream
what happens after initiation of trancription
sigma subunit falls off
AA interaction with base pairs in the major groove
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
pol 1
pol 2
pol 3
rRNA nucleolus
mRNA, snRNA nucleoplasm
5S rRNA, tRNA nucloplasm
eukaryotic transcription initiation
TAF (TF2D) transcription activation protein binds to TATA + accessory factors, TF, and then recruitment of RNA polymerase 2
what do enhancers do
stimulate promoter activity
what do both promoters and enhancers contain
sequcence mofits to which TF can bind
how does activation of transcription work
activator recruits HAT
and HAT acetylates histone tails
2 effects of HAT
looser chromatin structure make promotor region more accessible
TF2D binds more strongly to acetylated nucleosomes
activation also causes
Hat do they recruit
the activator to recruit chromatin remodeling complex
increasing mobility of neucleosome and makes promoter accessible
what are the 4 TFs dna binding domains
Homeodomain
leucine zipper
zinc finger
helix-loop-helix
homeodomain what is it
helix 2 and 3 form a helix turn helix
helix 3 makes sequence specific interactions with major groove of DNA
zinc finger what is it
formed by beta sheets and alpha helix
2 cysteines and 2 histidines complex a zinc atom
alpha helix contacts DNA in major groove
helix loop helix what is it
N terminal long alpha helix contacting major groove of dna
dimerisation: short and long alpha helix combined
leucine zipper protein what is it
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)
C-jun protein, what happens when 2 leucine zippers interact
leucines are on one side of the helix so when there are 2 helices hydrophobic interactions cause the zipper fomation
activation of tancription
clustered control region
cooperative binding
combinatorial control
signalling pathway
repression of transcription
insulators competition inhibition direct repression indirect mechanisms
clustered control region what is it
each gene has its own local regulatory element
also has a local locus control region required for orderly expression
modes of cooperative activator binding
interaction of A and B facilitates cooperative binding to DNA
interaction via mediator facilitates cooperative binding to DNA
transcription during hypoxia eg of modes of cooperative activator binding
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
modes of cooperative activator binding 2
factor A binds and recruits chromatin remodeler
A binding causes slight unwinding and B can now bind
combinatorial control principle
each gene receives several signals
each gene represented by a TF
the same TF may control a number of genes
JAK (kinase)/Stat pathway what happens
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
RAS pathway what happens
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
gene silencing
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
