lecture 20--exam 5 Flashcards
(33 cards)
what are chromosomes made of? what is the complex called?
what is chromatin made of?
DNA, histones, non histone proteins
chromatin
8 histone proteins with DNA around it
what are the core histones? what is wrapped around them to form the ____ of DNA packing?
H2A H2B H3 H4
–DNA is wrapped around them to form octamer (2 of each) , which is the first level of DNA packing, called 10nm fiber OR nucleosome fiber
whaat the second level of DNA packing?
what are additional levels of packing referred to as?
nucleosome is coiled into thicker structures, referred to as 30nm fiber
higher order structures—> scaffolds where loops of 30nm fibers are anchored
how does chromatin restrict DNA?
contributes to keeping genes not being used silent + generates diverse arrays of expression patterns via use of combination of large number of transcription regulators
what are 6 levels of regulation in eukaryotic gene expression?
transcription inhibition
RNA processing—> alternative splicing because diff splice variants have diff functions
RNA transport–> from nucleus to cytoplasm
RNA stability–> half life of RNA varies + stability is based on sequences in the 5 + 3 UTR regions and length of poly A tail
translation efficiency–> various amounts of polypeptide based on RNA stability + efficiency
protein activation
what are the 3 cis-acting elements that work in eukaryotes and what are their functions?
promotor– TATA, which binds TBP, which is a part of basal transcription factor TF2D, after pol 2 recruitment, can start
promoter proximal elements: upstream of the TATA
enchancers: distant indépendant cis acting elements
- can be upstream or downstream or a gene, far or close OR in introns
-orientation independent, work in any orientation
-in yeast, calles upstream activation sequences UAS
what are the 3 trans acting factors (aka transcription factors) in DNA that BIND directly to DNA?
basal or general TF: part of RNA pol 2 that bind promoter
-regulate lots of genes and aren’t as specific
some can bind to proximal promoter elements
regulatory TF: bind enhancers away from the promoter region
+ are very specific and regulate far less genes
what are 3 trans acting factors than do NOT bind DNA directly, but bind proteins bound to DNA?
mediator—large protein that links TF’s bound to enhancers + basal transcription apparatus bound to promoter
coactivators– lack DNA binding domain
-bind TF bound to enchancers
corepreossors–lack DNA binding domain
bind + have negative affect on transcription
what are 2 basic mechanism that Tf’s use? ( can use one or both)
directly interact with basal transcription machinery ( RNA pol 2) OR mediator complex
open up chromatin to make it more accessible to RNA pol 2
what is euchromatin and heterochromatin, what are their activating + inactive mods?
what happens during cell cycle + during development ?
euchromatin: active + loose packed
accessible tot TF’s
less methylation in major groove
active: H3 lys4Me & H4 acetylation
hetero: tighlty packed, inactive
inaccessible to TF’s
more methylation in major groove
inactivating mods: H3lys9Methylation
cell cycle: interphase the chromatin is loose, but tight during mitosis
devlepement: can differ based on conditions
what is an enchancesome + what does it do?
aggregation of multiple proteins binding other proteins + binding enhancers
direct DNA bending into a loop that brings that enchancesome into contact with:
RNA pol +
tf bound at the core promoter
proximal promoter elements
what are pioneer factors?
first to bind reg modules + their binding facilitates the binding of additional transaction factors
what does the SHH gene direct + how does it generally work ?
production of fingers or toes + a role in brain organization
each is controlled by diff reg proteins + TF–> one combination binds enhancer in brain cells but a different combo can bind an alternative enchanter in limb cells
what is LCR? how does it work?
highly specialized enchancer elements that regulate transcription of multiple genes packaged into complexes of related genes –> ex is the reg region in B globin complex
–regulation of genes contain 4 cis acting reg sequences, HS1-Hs4 that bind proteins that direct formation of small DNA loops that bridge promoters of the B globin gene
how does GAL system work in yeast, how are they regulated?
what does Gal 4 bind to?
what does Gal4 interact with?
GAL1,7,10 have their own promoter, but genes are regulated by GAL4
GAL4 encodes Gal4 regulatory protein–> an activator
–UAS, which is upstream of the 4 GAL genes
-since Gal4 protein is continuously accessible, it interacts with Gal 80 (repressor), which binds it and inactives transcription
what are the two parts of the homodimeric Gal4?
how are Gal4 and Gal80 produced?
what causes Gal4 to be activated and get rid of Gal80?
1)DNA binding domain targets the UAS (similar in all)
2)activation domain is a target for Gal80
constitutively produced
–when galactose is present, Gal3 binds galactose and to Gal80, which alters Gal80 and makes it release Gal4, allowing for GAL gene transcription
what does GAL4 being activated lead to formation of?
what happens when glucose is present?
mediator, which is an enchansome that forms and makes a DNA loop which contact TF2D + RNA pol to allow transcription
-Mig1 is produced, which binds to a silencer by UAS, which represses UAS from directing initiation
what are insulator sequences?
how do they work?
possible mechanism?
cis acting sequences located to separate enchaners from promoters
protein binding sequences that direct enhancers to interact with the promoter and block them interacting with enhancers and other promoters
-can block enchancer action and turn off a gene
allowing formation of DNA loops with their intented target and enchancer and preventing loops between promoter + enchancer that is not its target
what are the regulated steps between CAP and GAL4?
CAP– DNA binding is regulated
GAL4– always bound to DNA, exposing of activation domain is regulated
what if regulatory sequences are not bound by histones?
-sequences will include linker sequences between nucleosomes + sequences with specific characteristic that prevent histones from binding
what do chromatin remodelers do?
what doe chomratin modifiers do?
change the distribution of the nuclesomes by being recruited to specific sites in the chromatin by trans acting factors that bind specific DNA
add or remove methyl or acetylene groups– commonly at lysines
what are open/ covered promoters?
open: constitute active genes like housekeeping genes & have a NDR (nucleosome depleted region), which does not have TAT box but an A/T tract that has ES (enhancer) that attracts transcription activators
Covered: regulated + have TATA in which nucleosomes + TAF fight for binding
what is open vs closed chromatin?
how can we tell the difference?
open: DNA with nucleusomes is relaxed, allowing access
closed: reg DNA is covered by nucleosomes, making it hard to get to
using DNAse1
–cuts DNA in open chromatin but is unable to do so in closed
what are chromatin remodelers? what 3 ways do they work?
protein complex that carry out chromatin remodeling by moving nucleosomes by:
sliding them along chromosome or removing them from DNA—– > uncover enhancers or promoters + associated with gene activation
-SWI/SNF complex
reorganizes nucleosomes by making the nucleosome reposition to a diff DNA sequence –> usually repress
-ISWI complex
change composition of histone Octomers–> replacing histone proteins with variant ones –> gene activation usually
-SWR1 complex
