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
- Localization of mRNA to specific regions (pre-translational control)
All rna must be move from nucleus to cytoplasm
tRNA- nucleus to mitochondria
mRNA-nurse cell to oocyte (head and tail develop differently based on which genes are in different areas)
mRNA: cell to cell
Think drosophila:
nerve cells make proteins that is incolved in head development… so nerve cells makeit transport it to oocyteand in the ooycte it is transported to the anterior part of the egg in order to localize head development into the head region and not the body region (growth in the wrong place) (bicoid and oskar)
also: fibroblast, move like feet , need actin, if mrna for actin was made in nucleus and not transported it worul be a problem
ACTIN: made in nucleus, have a specific sequence called the ZIP code which tells proteins that have to be expressed at specific ends what they are (ie a protein for the posterior end will have a different ZIP code than proteins in the anterior end)
so rna is made, ZIP code binds to a paticular protein called ZBP whcih shuttles in and out of cell, acts as adapter and attaches it to cytoskeletonmotors (kinenens and dyneins)
what is ZIP code
encoded in 3] UTR and tells the mrna where it should belong to
- RNA editing (pretranslational)
-alteration in the sequence of the mrna
SOMETIMES rna in cytoplasm is different from rna in nucleus… WHY? it is modified and this ends up changing the sequence
Differenty ways:
a)U Deletion:
-all editing uses another rna
-mrna has string of U and an endonucleoside
-guide rna comes in and doesnt properly hybridize to the mrna and it loops out, and is single strnaded
-gets cut by endonuclease (the mrna) and then u get something that takes out the UUs and u have a ligase come in and glue the ends so now the U’s are gone and it is DELETED
b)U Insertion:
-original mrna has a guid rna with it, guide rna kicks out at a point (bc it only has partial complimentary so it is sticking out at this point)
-cugt it here, and Us are added and then it is ligased together
c) Deamination of A to I
exon and intron make a double stranded rna where u can get this weird protein that is edited as well
d) Deamination of C to U
-some cells have enzymes (or guide rna) to change it to U and this makes a stop codon instead, causing it to be shorter in other cells sonow has different function
- Post transcriptional gene silencing (PTGS) by small rna molecules
RNA INTERFERENCE: ability of small, double stranded or single stranded rna molecules to induce sequence specific gene silencing through binding
Once u have an mrna that has a 5’ cap (7MG) and 3’ tail, it is hard to control how much protein u make, only way to swithc it off is to degrade it… but what if we want it later on?
-can make a small part of it double stranded by synthesizing one part of it… this prevents ribosomes from translating it preventing degredation and preventing translation so it is just swithced off
SMall rna derived from genome: miRNA; usually involed in regulating gene expression of a cell
-made by making a hairpin structure of a oart if the gene we want to control and yeah
-cuts it and moved into cytoplasm
-processed into short double stranded rna
-one strand taken off and encorporated into RISC protein (rna in the protein hekps to guid it to a target side)
-will go to target gene and will prevent translation or cause cutting of it sometimes
Bacftiera and viruses
cuts a bit of virus dna
takes rna and puts it into RISC and now next time virus comes in it knows where to attack
short piece of rna is used as a guide to find the rna essentiatlly
miRNA: Natural antisnese RNA:
Sense rna: mrna
bottom strand: antisense rna, stops the mrna from being expressed
What are the roles of small rna
Regulatory factors
histone methylation
Suppression
Defense against viral infections (CRISPR)
How does bacteria protect itself from virus
cuts a bit of virus dna
takes rna and puts it into RISC and now next time virus comes in it knows where to attack
short piece of rna is used as a guide to find the rna essentiatlly
- Translationalcontrol switch
Ferritin : Ironstorage protein
-every single cell inbody needs iron,
we want to store iron or transport it… use ferriten
mrna of ferriten has sequence called Iron Responsive protein element, binds to protein that repsonds to iron… whe there is too much iron, it binds to IRE which binds to these areas and stop translation
Transferrin, when we dont have iron , these things bidn to it and u dont
- mRNA longetivity
3’ end is needed for bringing things exosomes, stabilize and in
needed like in cancer cells not there, soit stabilizes and inhi8bits differfent mrnas because oit doesnt have3] end.
