Eukaryotic transcription 3-3/5/7/10

what is attenuation regulation

gene regulation mechanism ex. TRP operon

what does element refer to

DNA sequence

why is attenuation regulation only found in prokaryotes

because transcription and translation are coupled

what are transcription factors

DNA binding proteins in eukaryotes

what are transcription factors analogous to in prokaryotes (bacteria)

sigma factors

what does eukaryotic RNA polymerase I do

makes rRNA

what does eukaryotic RNA polymerase II do

makes mRNA

what does eukaryotic RNA polymerase III do

makes tRNA and rRNA

what are promoter elements

sequence of DNA that regulates gene expression by direction RNA pol. to correct transcription start site, binding sites for TF’s

what are control elements

non-coding DNA sequence that regulates gene expression, enhances or repress transcription by influencing the activity of RNA polymerase

how do binding factor (BF) proteins interact with control/usptream elements

bind to specific DNA sequences to regulate transcription efficiency and recruit the machinery

what does UBF stand for

upstream binding factor (binds to control element and core element)

What does UCE stand for

upstream control element

whats the naming process for transcription factors

roman numeral = polymerase, letter = exactlybun which TF for Pol x

what is a poly A tail

a bunch of adenine (A) nucleotide added to the 3’ end of eukaryotic mRNA after transcription

what is the purpose of a Poly A tail

to help make a loop withe 5’ cap in cytoplasm so protect against degradation

what is an intron

part of mRNA that’s not translated

what is an exon

coding region of the mRNA

what is RNA splicing

cutting out the introns so it can move outside of the nucleus

what does TBP stand for?

transcription binding protein

what binds to the prometer

TF before the gene

what does BRE and DPE stand for?

BRE = B response element, DPE = downstream protein binding element (DNA)

what does CTD mean

C terminal domain

how does Ctd aid in transcription

puts 5‘ cap on, splices to remove introns, adds the poly A tail, has to be phosphorylated for transcription to happen

what are enhancer sequences

sequnces of DNA that TBP bind to

what are transcritpion activators

TBP - transcription binding proteins

what are mediatiors

20 proteins combined to hold everything together

what are the differences in abortive initiation in eukaryotes vs. prokaryotes

Eukaryotes: RNA made and released when not phosphorylated. prokaryotes: blocked mRNA exit with sigma factor

what are the steps to 5’ capping

1. 1. CBP (cap binding protein) attaches to CTD, and CBP grabs 5’ end of mRNA as it comes out 2. 5’ guanylyl transferase grabs guanlyl group and puts cap on 5’ end 3. CBC (cap binding complex) holds on to the cap of the 5’ end unitl RNA is finished 4. CBP and 5’ G-transferase leaves

what is the purpose of gyanlyltransferae

grabs the guanlyl group and puts the cap on 5’ end

what does the Poly A signal sequnce do

elements that signal to put on the A’s

where is the poly A signal sequence

3’ untranslated region of mRNA, upstream (before) cleavage site

what are the 4 proteins needed for Poly A syntheses and what are their functions

Poly A factors (PAF) - recognize signal sequence and attached to CTD, Endonuclease - RNA specific, only cuts when attached to poly A factor Poly A polymerase (PAP)- only makes A’s, Poly A binding Protein (PABP)- bind to RNA, protect poly A tail

what are the two ways that eukaryotes terminate transcription

Hairpin termination, Torpedo termination

what is hairpin termination

hairpin downstream push against pol. and causes strand to be pulled so RNA pol. doesn’t have anything to hold onto, most common, sequence will indicate

what is torpedo termination

after RNA is cut after poly A tail there is still some RNA coming out so Xra2 grabs RNA from backside, chops everything up and catches up to pol. and shoves pol. so the rest of the RNA comes out

what is Xra2 and how is it involved in termination

exonuclease that chops up excess RNA to be recycled and ends transcription when no hairpin is present

what will happen to the RNA polymerase CTD after either termination method

it dephosphorylates, drops of DNA, and drops off 5’ cap, CBC, and RNA

what is alternative splicing and what does it allow eukarytoic cells to do

splicing out the middle exon - changes gene expression

in terms of RNA splicing, what is the Branch point and where is it found

a hairpin that bends for ligation

describe the 3 steps of intron removal

1. 1. fold at branch point 2. cut 3. ligate exons to each other (covalent bonds) and ligate introns to each other to make lariot (can be degraded)

what do snRNA have to do with splicing

folds into shapes to hold onto the sequences, reads sequnces and determines where to cut, keeps it all together, attached with snRNP’s

what are snRNA

small nuclear RNA

what are snRNP’s

Small Nuclear RNA protein

what is the function of karytopherins,

protien used to move snRNA in and out of nucleus

within the category of karyopherin’s what do importins and exportins do

importins - bring snRNA into nucleus, Exportins - bring snRNA’s out of nucleus

does splicing occur before or after transcription

either but can’t leave nucleus until finished