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

on DNA, desigate which RNA pol. can bind

what are control elements

non-coding sequence that regulates gene expression, influences the activity of RNA polymerase

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

bind to the element and to the core sequence, (one of the UCE, the other on the core sequence) will bind to each other, bending DNA. Then TF factors bind to the bent section and recruit RNA pol to start transcription

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 with 5’ cap in cytoplasm to protect against degradation

what is an intron

part of mRNA that’s not translated

what is an exon

coding region of the mRNA, exit nucleus

what is RNA splicing

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

what does CTD mean

c terminus domain

how does CTD aid in tranlsation

part of RNA pol. coordinates putting the 5’ cap, splicing, and adding poly A tail

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

DNA sequences that TFs bind to - regulate promoter sequence from long distance

what are transcritpion activators

Upstream od the promoter and bind to enhancer sequences, bind to mediator proteins, pull mediator protein so that the transcription factors can pull the DNA strands apart more easily

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. CBP attaches to CTD 2. CBP grabs 5’ end of mRNA as it comes out 3. 5’ guanylyl transferase grabs guanylyl group and puts cap on 5’ end 4. CBC holds on to the cap of the 5’ end until RNA is finished 5. 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

downstream of stop codon, on 3’ end

what are the 4 proteins needed for Poly A syntheses

PAF, Endonuclease, PAP, PABP

what is PAF and what does it do

Poly A factor - Recognize signal sequence and attached to CTD

what does an endonuclease do specifically for Poly A tail

RNA specific, only cuts when attached to poly A factor

what is PAP and what does it do

Poly A polymerase - only makes A’s on 3’ end of mRNA after it has been cut from pol.

what is PABP and what does it do

Poly A binding Protein - 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 and 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 off DNA, 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, in intron region

describe the 3 steps of intron removal

1. fold at branch point 2. cut 3. ligate exons to each other (covalent bonds) and ligate introns to each other to make lariat (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 - in nucleas and amke strucrues to fold introns so they can be cut in right spot

what are snRNP’s

Small Nuclear RNA protein - made in cytoplams and are attached to snRNA

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