1.4 Eukaryotic Gene Regulation Flashcards
how many rnap do prokaryotes have
1
differentiate between the 3 rnap of eukaryotes, in regards to which genes they transcribe
rnapI: rRNA genes
rnapII: all protein coding genes
rnapIII: tRNA genes
transcription initiation in eukaryotes require many proteins named? and what do they do?
general transcription factors. they help position rnap at eukaryotic promoters
name is the general transcription factor of prokaryotes (that is apart of rnap)
sigma factor
eukaryotic genomes lack _______
operons
how many general tf (transcription factors) are involved in rnapII transcription
5: TFIID, TFIIB, TFIIF, TFIIE, TFIIH
eukaryotic dna is packaged into __________ which provides an additional mode of __________
chromatin, regulation
are gene regulatory proteins also a tf?
yes
the _______ acts as an intermediate between regulatory proteins and rnap
mediator
t/f can gene regulatory proteins act over very large distances
yes - through dna looping
coactivators and corepressors assemble on dna-bound gene regulatory proteins do not bind directly on dna, so where can they bind?
cis reg elements
describe the modular design of eukaryotic activator proteins
- dna binding domain (dbd) which recognizes specific DNA sequences
- activation domain (ad) which accelerates the freq/rate of transcription
you can mix and match dbds and ads, as long as the dbd can bind to the target which leads to activation of the tata box
how do activator proteins activate transcription
they attract position and modify gen tf, mediator, rnapII
they can do that by either directly acting on these components (attracts them to promoters like prokaryotic activators) or indirectly modifying chromatin structure
what is the basic structure of eukaryotic chromatin
nucleosomes
describe the structure of nucleosomes
dna wound around a histone octamer (h2a, h2b, h3, and h4)x2
the linker dna (10-80bp) is attached to h1 on one nucleosome, a nucleosome includes ~200 nucleotide pairs on dna and the dna that wraps around the core is approx 1217 bp long
how do nucleosomes pack
as compact chromatin fibers in a zigzag or solenoid model
when nucleosomes are packed, transcriptional machinery cannot assemble on promoters tightly packed in chromatin, how is this solved?
activator proteins can alter chromatin structure and increase promoter accessibility
how many ways can activator proteins alter chromatin
4
describe the purpose and process of nucleosome sliding
nucleosome structure can be altered by chromatin remodeling complexes in an atp dependent manner to increase promoter accessibility - it just moves the dna around to show the parts you wanna show
nucleosome removal and histone exchange requires cooperation with __________________
histone chaperones
describe the 2 methods of altering chromatin through histone chaperones
- remove histones which leads to more space. an optional step is to put an alternate protein using histone chaperone, which binds more loosely to help gen tfs get in there
- an atp dependent chromatin remodeling complex w a histone chaperon brings a histone and changes the prot for an exchange of h2a-h2b dimers which bind more loosely
what are the histone code
histone modifying enzymes produce specific patterns of histone modifications
what enzymes are involved in the addition of phosphate, acetyl, and methyl groups
phosphorylation: kinase
acetylation: acetyltransferase
methylation: methyltransferase
where do histone modifications occur
on specific aa of histone tails (usually on n terminus but c terminus is also possible)
which enzymes are nicknamed writers and why
histone modifying enzymes - they make specific modifications to histone tails
what can reader proteins do
can recognize specific modifications and provide meaning to the code
describe the steps of the human interferon gene regulation
- activator protein binds to chromatin DNA and attracts a histone acetyltransferase (HAT)
- HA acetylates lysine 9 of histone H3 and lysine 8 of histone h4 (h3k9 and h4k8)
- activator protein attracts a histone kinase (hk)
- hk phosphorylates serine 10 of histone h3 (h3s10). can only occur after acetylation of lysine 9.
- serine modification (phosphorylation) signals the acetyltransferase to acetylate lysine 14 of histone h3 - the histone code for transcription initiation is written
- tfIId and chromatin remodeling complex (reads the code) bind to modified histone tails and initiate transcription
can you skip steps in the human interferon gene regulation
no
unlike prokaryotes, eukaryotic repressor proteins rarely compete with _____ for access to dna
rnap
how can eukaryotic repressor proteins inhibit transcription (6)
- dna competitive binding: repressor with repression domain doesn’t allow the activator to bind to the active site bc it’s overlapped with where the repressor is
- masking the activation surface: the activator binds to the binding site but the head (activator surface) is blocked
- direct interaction with gen tf: repressor can inactivate the gen tf even if on the tata box
- recruitment of chromatin remodeling complexes: rolls the histone back up to prevent gene expression bc it cannot read it
- recruitment of histone deacetylases : modify the tails of histone
- recruitment of histone methyl transferase: modify tails of histone
when guided by gene regulatory proteins, histone reader and writer proteins can establish what
a repressive form of chromatin – the reader keep recruiting writers to write on the following histone tail = chromatin can be stabilized and histone code cna be spread
what spreads the histone code along chromatin
reader writer complexes
how do reader-writer complexes know to stop spreading the histone code
border sequences
what enzyme is attracted by readers to methylate nearby cytosines in dna
dna methylase
which nucleotide base is dna methylase doing to methylate
cytosines
describe epigenetic inheritance
methylation and further gene expression patterns can be inherited. the whole cell memory is semiconservative as if there are methylated cytosines on one strand then the other would be too
what do dna methyl binding proteins do
bind methyl groups and stabilize the structure
what does the methylation of cytosines do
blocks tf/rna poly from coming in = transcription repression
which of the following would you expect to see at the interferon gene promoter and accompanying histones if an activator protein was present, but histone kinase was inhibition
a. acetylated h3k9 and h4k8
b. acetylated h3k9 and h4k8; phosphorylated h3s10
c. a. acetylated h3k9 and h4k8; phosphorylated h3s10; tfiid and chromatin remodeling complex binding
d. no histone acetylation of phosphorylation
A. step 3 cannot happen and since you cannot skip steps you won’t see the following so it is only at a. there will be some histone acetylation or phosphorylation
