Chromatin Flashcards
what binds to the receptor to activate the signaling pathway to promote PKA
ligand
what one type of cell can give rise to at least 220 different cell types
stem cells
stem cells can give rise to how many different types of cells
220
what are the two different structures of DNA
euchromatin and heterochromatin
what is the point of epigenetic regulation
to read genetic information in different manors enabling to generate the different cells of our body
embryonic stem cells can form how many different layers
3
what are the three layers embryonic stem cells can form
mesoderm
endoderm
ectoderm
what are the 4 different cell types
multipotent
primitive progenitor
lineage committed
specialised blood
what do cells require before becoming specialised blood cells
further differentiation
injuries, tissue damage, tissue regeneration, sun exposure, ischemia, require what in order to regenerate
the cellular processes have to occur simultaneously and therefore require coordination
what enables stem cells and progenitor cells to re enter into proliferation and then differentiate
epigenetic regulations
what to epigenetic regulations enable stem and progenitor cells to do
to re enter into proliferation and then differentiate
what does epigenetic regulations enable stem cells and progenitor cells to differentiate into
regenerate tissue
epigenetic enables to read the genetic information in different manners, what is this called
cell plasticity or genome reprogramming
what is the human genome made out of
DNA
where is DNA stored
the nucleus of eukaryotic cells
how does a heterochromatin appear on a histogram compared to euchromatin
darker
heterochromatin contains what kind of DNA
compacted (inactive)
euchromatin contains what kind of DNA
opened (active)
why is euchromatin open?
so it can be read
what structure do the euchromatin have
double stranded helical
DNA is complexed with histones to form what
nucleosomes
each nucleosome consists of how many histones
8
how many times does the DNA wrap around the 8 histones
1.65 times
a chromatosome consists of what
a nucleosome plus the H1 histone
the nucleosome folds up to produce what
a 30 nm fiber
the 30 nm fiber forms loops averaging what length
300nm
the 300nm fibers are compressed and folded to produce a fiber at what width
250 nm wide fiber
tight coiling of the 250 nm fiber produces the chromatid of what
a chromosome
why can’t heterochromatin genes be read
they are closed
what 8 histones form a nucleosome
2 H3
2 H4
2 H2A
2 H2B
nucleosomes are what level of DNA packing
1st level
what charge of amino acids are in a nucleosome
positive
where do the nucleosomes bind tightly to and what charge
negatively charged DNA
what is an example of 2nd level packing
solenoids/chromatin
in a solenoid, H1 histones aggregate causing what
6 nucleosomes to coil together
solenoids stack on top of each other forming what
a chromatin fiber
where do chromatin fibers attach themselves to
wall of the nuclear membrane
when chromatin fibers are attached to the wall of the nuclear membrane what do they form
loops by binding to nuclear membrane proteins
in the nucleus of a non dividing cell chromatin fibers form what
discrete chromosone territories
chromosome territories are correlated with what
gene densities
territories of chromosome domains that are relatively gene rich tend to be located towards what
towards the interior of the nucleus
the interaction of DNA/nucleosomes is regulated by what
histone modifying enzymes that induce post translational modifications
name examples of histone modifying enzymes
histone acetyl transferase (HAT)
Acetyl co A
HOW are the histone modifying enzymes produced (HAT and Acetyl coA)
glycolysis on lysine
what does lysine do in order to regulate the strength of the binding of histone to DNA and opens genes to be expressed
its a positive amino acids which binds strongly to negatively charged DNA
what does lysine do once it has bound to the negatively charged DNA
regulates the bindings of histones to the DNA and opens chromatins/genes to be expressed
how are the expression of histone modifying genes and the activity of the histone modifying enzymes regulated
by cellular receptors and by energy metabolism
acetylation/deacetylation of the positively charged amino acid lysine regulates what
interaction of negatively charged phosphate on DNA
what processes regulate the interaction with negatively charged phosphate on DNA
acetylation/deacetylation
HAT enzymes catalyse the transfer of what to what
acetyl group from acetyl co A
how is acetyl co a produced
in the TCA cycle
where are the epsilon amino groups of lysines located
in the N terminus of histones
what does acetylation involve
abolishes the positive charge on lysine interacting with the negatively charged phosphate on the DNA backbone
acetylation reduces what
the strength of the interaction histone/DNA
interactions of DNA/nucleosome is regulated by PTM but what is this induced by
cell sigaling receptors and energy metabolism
acetylation is an example of what process
PTM
arginine and lysine can exist as what structures
mono, di, or tri-methylated
what is methylation an example of
PTM
what happens when a lysine is ubiquitinated
increases the size of lysine
what is phosphorylation an example of
PTM
phosphorylation can do what and why
repulses histone and DNA due due to the the several negative charges
histones are modified where
on the N terminus and C terminal domains
what is the process that neutralises the positive charge of arginine
deimination or citrunillation
what does demination (citrunillation) do to arginine
neutralises the positive charge, weakening the interaction with the negatively changed DNA, resulting in the opening of the chromatin
methylation of lysine and arginine do what
regulates the hydrophobic interactions with histones
weakens the interactions between histones and DNA
histone modifying enzymes are expressed in what manner
tissue-dependant manner
what do histone modifying enzymes do
open or close access to a gene
regulating gene expression
for gene expression to occur (transcription) the enzymes that synthesise RNA (RNA polymerase) must attach to what
a promotor region
what enzymes synthesises RNA
RNA polymerase
promotors contain specific DNA sequences called what
response elements
how many different types of RNA polymerase are there
3
the RNA polymerase auto assemble together to form what
RNA transcription machinery that binds and opens the double stranded DNA helix and then slide along the helix
this opens and closes the DNA while synthesising the RNA molecule
what are transcription factors
proteins that bind to specific DNA on a specific sequence to recruit the RNA polymerase to this specific location of the genome and initiate the transcription
transcription factors can bind to what 3 things
promotos, enhancers, or silencers
what are enhancers
DNA sequences localalised in non coding regions (everything that is not an exon) to increase the chance that transcription of a particular gene will occur
what are silencers
opposite of enhancers
made of DNA and bind to transcription factors like enhancers but they inhibit or abolish the gene transcription
