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RNA Processing - Coggle Diagram
RNA Processing
Bacterial RNA Processing
Transcription and Translation are simultaneous and occur in the cytoplasm bc no nucleus.
No capping
No splicing
Splicing = removal of introns
No PolyA Tails
ORF1 + ORF2 + ... = an operon if they are all on the same mRNA
Why is it good to have multiple products on one mRNA?
Keep shit together that works together
turn on/off expression only once per unit of working parts
increased efficiency
helpful bc mRNA has a very short half life (minutes)
Parts of mRNA
Open reading frame (ORF)
start codon is at beginning of first ORF
5' untranslated region (UTR)
contains information on protein folding and ribosome loading
UTR's do not get translated into amino acids
there's a triphosphate here
3' UTR
determines speed of degradation
No introns
Eukaryotic RNA Processing
mRNA has to exported out of the nucleus before translation.
ribosomes are in the cytoplasm outside of the nucleus
exportation allows more regulation
Parts of mRNA
25.9% introns
1.5% protein coding
Processing takes place in the CTD tail of RNAP (aka still in the nucleus) via the following modifiers (in order). Processing is co-transcriptional.
promoter escape
DNA repair
capping
the 5' cap is called 7-methyl-G
functions of 7-methyl-G
signal for nucleus export
assists in ribosome loading
promotes mRNA circularization
the cap sticks to the polyA tail
protection from RNAase because mRNA is now unrecognizable to the enzyme
increases mRNA half-life
3 enzymatic steps all occur at C-terminus
RNA triphosphate removes gamma phosphate from the 5' end
guanylyltransferase adds GMP Moiety to the beta phosphate on the 5' end of another mRNA
leads to condensation reaction called 5' to 5' joining
methyltransferase adds the 7-methyl-G cap to mRNA
occurs during transcription
splicing = removal of introns from pre-mRNA
Quick Facts
average human gene has 8 introns
average exon length = 150bp
average intron length = 3000bp
muscles have the most introns
Largest pre-mRNA is 2,400,000 nt long
pre-mRNA = mRNA before splicing
pre-mRNA binds to DNA's non-introns and the introns stick out in loops to be cleaved later
transcription rate = 50 nt/sec
bigger mRNA's tend to have a longer half-life and lower abundance
Splicing factors are on the CTD tail and this process is co-transcriptional
Splicing vs Alternative Splicing
Splicing includes all of the exons
Alternative Splicing excludes one or more exons to make a totally different gene products
same gene can code for different products based on splicing behavior
variance in splicing pattern leads to different products (called isoforms)
Variation is based on which poly A site is acknowledged
Order of exons is NEVER scrambled
Functions of Introns
coding and can sometimes become exons
code for functional RNA
allows alternative splicing
Types of splicing
Group 1 Introns (NOT Covered)
Group 2 Introns (NOT Covered)
Nuclear pre-mRNA Splicing
Most common
Mechanism
1) Branch point A at 2' OH attacks phosphate at 5' splice site
this makes a covalent bond
forms lariat structure
transesterification reaction 1 catalyzed by U2, U5, and U6
Activates 5' splice site
2) Activated 5' splice site attacked 3' splice site
transesterification rxn 2 catalyzed by U2, U5, and U6
free 3'OH at 5' splice site attacks phosphate of next exon at 3' splice site
3) Intron lariat is released and degraded
4) exons are spliced together
Recognition sites for nuclear pre-mRNA splicing
5' splice site with a GU
3' splice site with an AG
Branch point A with a 2' OH
Enzymes = snRNP's
enzymes = nonspontaneous rxn
100-300 nt RNA + proteins = snRNP
Roles of snRNP's
recognition of 5' splice site and branchpoint A
bring 5' splice site and 2'OH of branchpoint A together
bring 3'OH upstream of the exon's 5' splice site so it's close to the phosphate of the 3' splice site
Catalyzes transesterification reactions
Order of rxns carried out by snRNP's
1) U1 binds at 5' splice site of GU of intron
2) U2 binds to branchpoint causing A to bulge out
3) U1 + U2 complex brings 2'OH to the 5' spice site
4) U4 + U5 + U6 complex joins the U1 + U2 complex
U1 and U4 are displaced
U2 is at branchpoint A
5) proximity of the 2' OH and 5' splice site leads to transesterification rxn 1 catalyzed by U2, U5, and U6
6) transesterification rxn 2 is catalyzed by U2, U5, and U6
exons spliced togetehr
intron lariat is released
Very energy intensive
interactions can be any combination of RNA and protein interactions (protein::protein, RNA::RNA, or RNA::protein)
polyA tail addition (polyadenylating)
DNA codes for polyA sequence and transcribes it onto RNA
sequence = 50-250 A's all in a row
steps of polyA tail addition
Pol II transcribes the polyA tail
CTD associated endonuclease binds to mRNA
cuts 20-40 nucleotides downstream
3' OH is freed
3' OH is bound by polyA polymerase (PAP)
PAP adds the polyA tail
PolyA binding protein (PABP) coats the polyA tail and protects the mRNA
increases mRNA half-life
promotes circularization
sticking to the cap
Cistronic-ness
Polycistronic = when one mRNA makes multiple gene products
only polycistronic if multiple gene products are made
Makes operons
Monocistronic = when one mRNA makes one product
Remember there can be multiple open reading frames/exons but if they only make one product, they are still monocistronic
Typically, eukaryotic mRNA is monocistronic
Most regulation occurs during transcription
