All there is needed to know about RNA Flashcards
mRNA
carries genetic information
tRNA and rRNA
translate mRNA into protein
snRNA
mRNA processing
snoRNA
modification of rRNA and tRNA, mRNA editing,
genomic imprinting
microRNA
gene regulation
are eukaryotic mRNAs mono or polycistronic?
eukaryotes have molycistronic mRNA
Prokarytoes have ___ mRNA
ponocystronic
can both Prokaryotes and Eukaryotes get multiple protein products from one mRNA?
Yes
how many RNA polymerases do Prokaryotes have?
one
name the eukaryotic RNA Polymerases and their respective functions
RNA Pol 1: rRNA (not 5sRNA)
RNA Pol2: mRNA, most snRNA, some snoRNA, and miRNA
RNA Pol3: tRNA, 5sRNA, snRNA, some snoRNA
5s RNA
part of large subunit of ribosome
what does alpha-amanitin from mushrooms do?
binds to RNA Polymerase II inhibiting gene expression
what are three important places for Prokaryotic transcription?
- TCTTGACA site where the initial RNA holoenzyme can bind
- TATAAT (Pribnow box): where transcription bubble forms
- +1 site downstream of TATAAT site where transcription officially starts
describe the complicated eukaryotic promoter region
-CAAT: where RNA Pol II and transcription factors associate
-TATA (Hogness box): like 25 bp upstream from +1 site
enhancers/silencers: can be close or even very far away from promoter region it acts on
RNA has the same directionality and sequence (except U for T) as the ___ strand
coding strand
what protein do some Prokaryotes depend on for termination of transcription
Rho
Rifamycin
- treats bacterial infections by inhibiting their RNA Polymerase
- *not super effective against fungi infections since they are eukayotic and their RNA Poly is different and is protected in nucleus but may still have some effects
Dactinomycin
- binds DNA to block movement of RNA Pol
- effects BOTH Pro and Euk
does Prokaryotic mRNA undergo processing?
NOPE
describe the types of activities that are classified as RNA processing
- Capping
- hnRNP association
- Splicing
- 4 3.’ end processing end processing
- Transport
state the 4 consensus sequences of an intron
Donor: 5’ GU
Branching site: A
Poly pyrimidine stretch
Acceptor: 3’ AG site
what are the four functions provided to the mRNA molecule by the RNA cap?
- stabilize RNA/ protection from 5’ - 3’ degradation
- enhance translation
- nuclear transport
- splicing of first intron
what is the spliceosome?
- where pre-mRNA splicing takes place
- composed of snRNPs and pre-mRNA
- –> snRNPs are snRNAs and associated proteins
describe 3’ end processing
-cleavage and poly adenylation of Euk pre-mRNAs
what is the AAUAAA region involved in 3’ end processing?
-hexonucleotide sequence where PAP and CPSF can bind
10-30 NTs down from the AAUAAA region is the ________ which is most often CA
-cleavage site
further yet downstream from CA cleavage site is ___
GU rich region
what happens if distance between AAUAAA and the GU rich region exceeds 40 NT??
-3’ end processing is nill
what two ridiculously crazy phenomena occur in RNA editing?
a C can be converted to U
an A can be converted to Inosine
how is it ensured that mRNA nucleocytotransport is unidirectional?
-some hnRNP proteins bind to mRNA molecule in the nucleus and unbind as mRNA reaches cytoplasm
what do introns do to genetic diversity?
-increase genetic diversity by potentially offering different splice sites which can result in different proteins being formed
Since introns get spliced out anyway, can mRNAs that normally have introns do just as well if introns are taken out altogether??
NO. introns have usefull functions
state the function of introns
- stimulate 3’ end processing
- keep nuclear mRNA stable
- help with transport
- help with capping
Beta-globin genes are intron dependent genes. mRNA of Beta-globin will not accumulate if introns are taken out, what can help??
-insertion of TK sequence into 5’ UTR region
RNA decay:
deadenylation-dependent
remove poly A tail and degrades from 3’ end
RNA decay:
deadenylation independent
- remove cap
- degrades from 5’ end
DICER
cuts up dangerous double stranded RNA which is a huge red flag!!
RISC
picks up si RNA and can then find the chump responsible for it and destroy it
describe 5 possible combinations of RNA splicing
- exon skipping
- alternate 5’ donor site (3’ end stays consistent)
- alternative 3’ acceptor site (5’ end stays same)
- intron retention
- mutually exclusive exons
describe the players and processes involved in splicing repression!
hnRNPs can bind to splicing suppressor sequences (ISS or ESS) and prevent snRNPs from doing their splicing thing
describe the players and processes involved in splicing activation!
SRs can bind to splicing enhancer sites (both ISE and ESE) and facilitate splicing
does alternative splicing in UTR regions affects the structure of a protein??
absolutely not.
However, regulatory regions in UTR can alter mRNA levels and alter protein levels.
COX-2 RNA has ___ poly A sites
2
proximal and distal poly A sites
why is the COX-2 RNA distal poly A site more unstable?
-the distal poly A site includes in the final transcript sequences that bind destabilizing factors like tristetraprolin
which poly A site might a cancerous tissue use for COX-2?
- proximal poly A site
- would make a more stable mRNA product leading to more inflammatory effects
what relation does calcitonin and CGRP have?
- same pre-mRNA transcript
- alternative 3’ end processing in different tissues leads to different functional proteins
RNA and Disease:
Systemic lupus erythematosus
Autoimmune reaction to snRNPs (small nuclear ribonuclear proteins – snRNAs and associated proteins)
what is the role of snRNPs
small nuclear ribonuclear proteins catalyze splicing
Frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) results from an altered ratio of tau protein… explain how this happens and why that might lead to disease
- Mutations in exon 10 of tau gene increase exon inclusion through altered alternative splicing
- Alters ratio of tau isoforms in the brain, believed linked to disease
- Therefore, disease is most likely due to altered ratio of normal tau protein isoforms
Myotonic Dystrophy is caused by
•Caused by expanded CTG repeat in the 3’ UTR of DMPK, a protein kinase gene (CUG repeat in the mRNA)
-this leads to less DMPK which is needed for appropriate muscle-specific RNA splicing
Spinal Muscular Atrophy
•1 in 10,000 births, second most common fatal autosomal recessive disorder after cystic
fibrosis, most common genetic cause of childhood mortality, progressive degeneration of spinal
cord neurons.
On each chromosome 5q13, how many SMN genes are there?
2 (SMN1 and SMN2) so for normal 2n person, 4 SMN genes total
Spinal Muscular Atrophy
•1 in 10,000 births, second most common fatal autosomal recessive disorder after cystic
fibrosis, most common genetic cause of childhood mortality, progressive degeneration of spinal
cord neurons.
Describe the normal relationship between SMN 1 and SMN 2
normally SMN1 is active and SMN2 is inactive due to splicing
what usual mutation causes Hutchinson-Gilford Progeria Disease
codon 608 of lamin A/C gene where GGC gets mutated to GGU…. remember 5’GU Acceptor???? Yeah.. this leads to cryptic 5’ splice site in exon 11 causing a GAIN of FUNCTION mutation of progerin
