19: Flashcards
Transcription units
-entirety of dna that is being transcribed
-includes 5’ UTR and 3’ UTR
-all important for stabilizing rna
Where promoter intiates and where transcript ends is the whole unit
two types:
Simple transcription units:
Consitutive splicing- same product every time
-95%of genes: every transcript is spliced in order, splice sites occr and splicing happens in after
ex; B globulin
-splicing happens immediately
complex transcription units:
Alternative splicing
-lots of exons, exons can be spliced in different ways, u may not use all of them, may keep some introns, etc. Can make many varients then
-can happen after rna pol is finished making transcriot or as long as the rna pol is further down… NOT IMMEDIATELY
How do cells know which version of a protein to make (ie know which combo to use for altenrative splicing: which set of things they should keep in)
Every gene that has introns and exons have sequwnces that tell splicesomes where to splice and where not to but this is the same everywhere… ie all genes have the same splicing repressor sites and the spliciing sites so how do we control which is actually expressed so that differences in splicing can occur
-each junction requires a splicemsome to bind and mediate that slicing, way to bind tho is regulated by the use of activators and repressors (allows for different sewuxnes to be made)
-only way to differentiate these cells is the making of the activators and repressors that allow binding to these places (esssentially each cell will make different activators and different repressors which allow different sites to be spliced and not spliced leading to different genes
Splicing Activators: have rna binding motif rich in ARG/SER (SR PROTEINS), attract splicing machinery
Splicing repressors: dont have RS domain so they cannot recruit or attract splicing machiner
-block the use of splice specific sites
Binding sites called exonic(or intronic) ENHANCERS (sites that bind activaters). or SILENCERS (sites that bind repressors)
What are the regulating sequences on pre-mrna for alternative splicing
exonic (or intronic) splicing enhancers or silencers
-present on exons on introns to guid pos or neg regulators to bind splicesomes
-sites that bind activators or repressors
slide 6
RS motor
can bind to splicesome machinery if activator binds to sequence, if not it doesnt bind and stops
Fibronectin
can get various different types by using different activation and repressors
what is at the beginning and end of each splice
In constitutive:
GU at the beginning
AG at the end
In alternative:
AU
AC
why different?
splice junctions are different ebcause they iuse different sets of splicesomes
Calitonin and alternative spliciig
different c terminus in each
Two different types; one found in thyroid one found in neuronal cells
making a transcript smaller makes it more limited for alternative splicing patterns
What are other ways to process splicing
C terminus one from above
Alternative Polyadenylation : have many different sites of this , each cell will express different things that will go and splice at different points
-the tools that the cell has is what allows for different splicing (one cell may have protein A complex that allows for splicing at site B)
Inhibited Polyadenylation:
-ex U1 A
-esssentially what happens is that when there is alo t of the protein it goes and it binds to its own mrna , which causess a bunch of proteins to come and prevent polyadeylation (not cleavage) so the thing will still get spliced but when it does, there is no poly A tail added to the end of it so it will cause degredation
-these machinery cut it without adenylating it
-occurs when too much of the gene U1A is present
Trans splicing:
-essentially remember how usual spilcing without the complex, (second of the 3 ways from earlier ) work by an A (in middle going and attacked the G on one end and then that G goes and attacks the A on the other end, causing ti to be spliced. In trans, instead of the middle A attacking the G in that sequence, it goes to another strands G juncction and attacks that, so it takes the extron from another molecule and attached it to its own
-think a man isnt getting action form his wife, he goes to another women and gets her and adds it to him
TRANSPORT THROUGH NUCLEAR PORE
Nucleus: double membrane
-there are proteins that make up a NUCLEOPORE
What does a nucleopore do
allows transportation out/in of nucleus
-complex structure that is on the membrane that allows transport out and in
how does it regulate the mrna out:
remember: rna is cvered in nuclear proteins, the processing occurs, and there are proteins bound to it that it needs
When rna is ready to leave:
SHOULDNOT HAVE THINFS ON IT THAT IT DOESNT NEED ie splicesomes should not be on it if it is “ready”
ie if it doesnt have a cap or it has splicesomes on it
nucleopore detects these things and doesnt allow things to leave if it has things it should or isnt really readyyet
so what are the signals for not letting things out or for control ie
1)capping (make sure that it is)
2)lack of some protenis (make sure proteins like splicesomes are gone)
3) presence of some proteins
5’ cap is recognized by transport machinery , pore grabs on to it
as processed mrna transports through the nucleorpore, the nMRNPS are replaced by c mRNPS (cytoplasmic ribonucleoproteins), nuclear proteins shuttle back to nucleus
rna is never naked
What does pre mrna have on it recap review
snRNP (smallnucleo ribonucleoproteins
hnRNP (heterogen nucleo ribonucleoproteins) found around pre mrnsa
What is on processed mrna
Nuclear mRNPS (messenger rnps); ecpoerted along with the mrna, but as they pass thriugh nucleopore change into CYTOPLASMIC mRNPS
rna si never naked
is mrna sometimes transported to the different edges of a cell
yes think some neural cells, need the mrna to be on one end of it, we transport it to theend as mrnsa and then translate it there (not before so this prevents an overconcentrartion of proteins in one area)
Posttranscriptional / pretranslational control (events on/with mRNA before ribosomes)
1.Localization of mRNA (explained in card 16)
2.RNA editing
3.Post-transcriptional silencing by siRNA (shortinterfering) or miRNA
Translational control switch
-how efficently mrna is translated
RNA stability (degradation and stabilization)
-stabilizing it makes it have more protein expressio
-destablizing it allows for degredation
aWHy do we make proteins out of rna and not dna
Dna has all the genes sequences we need tomake proteins,
cant control protein levels by increasing or decfreaing dna
also, dna cannot be controlled in terms of how much proteins we make because we cannot increase or decrease the amount of dna, it is just like that
rna copies allow us to increase or decrease the amount of it allowing for varying concentrations of proteins to be made
