Topic 2, Lecture 2 Flashcards
Nucleosome are static or dynamic?
dynamic
why are they stated to be dynamic
bc they are (breathing) not tightly wrapped
how long in milliseconds do nucleosomes exist wrapped and unwrapped?
250 milliseconds wrapped
10-50 milliseconds unwrapped
at what rate are nucleosomes unwrapped?
from each end at a rate of about 4 times per second
If the protein has high affinity for sequence, the sequence specific DNA binding protein bind to the nucleosome when DNA is
unwrapped
cis vs trans
cis- before promoter region
trans- binds to neighbor to control different genes
promoter
site of general transcription factor and RNA polymerase assembly
aka pre initiation complex
cis-regulatory sequence- (enhancer) and how far?
regulatory sequence located up to 50,000 bp away from start site- controls the rate of pre-initiation assembly at the start site.
section of random exposure
binding site for sequence specific DNA binding protein
what is the purpose of spacer DNA
to provide flexibility
all of the other proteins located on the drawing are known at the
general transcription proteins and they are all non-specific
tata box
immediately upsteam from +1 site -30bp away from +1 site
what is responsible for decondensation?
transcription regulators which are
histone modifying enzymes and chromatin remodeling complexes
the transcription regulators are just binding sites for
the histone and chromatin-remodeling complex
what are the ways that affect chromatin structure?
sliding
histone- removal
histone variants
Chromatin remodeling enzyme
binds to DNA
induces association of DNA from nucleosomes
causes the nucleosome to slide , exposing specific DNA sequences
this sliding needs energy, and can be cis-regions
END GAME:
can completely disassemble
or replace via variant histones
How do Histone variants work
work histone chaperones
composed of aspartate and glutamate
not a function of protein folding but just keep things apart
Histone chaperones can do what?
replace histones with weaker histones for looser packing
remove whole histones or switch out bc purpose is to expose and decompose
T/F: chromosome remodeling complexes play a critical role in the initiation of a gene transcription.
FALSE
what are transcription activators?
Proteins that promote the binding of additional regulators
what do they do?
recruit RNA polymerase to promote
release RNA polymerase from pause
what kind of modifications can we do to the histone tails?
Methylation
only lysine; leads to condensation, creates heterochromatin, addition methyl to lysine
(preserves the + charge)
acetylation
only lysine; leads to decondensation; creates euchromatin, additon of acetyl removes + charge from lysine
phosphorylation
only serine and threonine; leads to decondensation, creates euchromatin (additon of phosphate)
what is the histone code
sum total of all modifications together
depends on the histone modifying enzyme that binds to the transcription factor
dimmer that controls condensations
Histone deacetylase
removal of acetyl (recondense)
histone methyltransferase
transfer methyl to histone (lock that baby with positive charge)
what are the two domains of the transcription factors?
activation/ repressor domain:
not-specific (no actual activation)
DNA binding domain
determines where binding occurs, gets activation domain to correct spot
what is a cofactor?
things that bind to the activation or repression domain, the activation is not specific at all, it activates wherever it is put.
DNA BINDING DOMAIN is very SPECIFIC.
what groove does the transcription factor bind to?
major groove
because there is more information present/ more potential
more specificity/ tighter binding
