Exam 3: Ch 8 Cytoplasmic Post-Transcriptional Control & rRNA/tRNA Processing Flashcards
miRNA
short single stranded RNA that hybridize to 3’ UTR of target mRNA
imperfect binding
inhibits translation of the target mRNA
siRNA
short interfering RNA (single stranded) aids RNAi
causes degradation of target mRNA
pri-miRNA
very long transcript for one or more miRNAs
Exportin5
nuclear transporter that moves pre-miRNAs out of the nucleus through FG-domain of nucleoporin
Dicer
cytoplasmic RNA-specific RNase
acts with TRBP (Tar binding protein) for RNA to process pre-miRNA into double-stranded miRNA
RNA-induced silencing complex (RISC)
complex of 1 strand of double-stranded miRNA and a protein called Argonaute
binding of multiple RISCs to an mRNA
inhibits translation initiation through P bodies
P body
sites of translational repression of mRNA bound by miRNA-RISC complexes
mRNA degradation in cytoplasm
contain decapping enzyme, exonucleases, and activators of decapping enzyme
do RNAi bind perfectly to complementary mRNA to induce degradation?
yes
RNAi
double stranded RNA induces degradation of all cellular RNAs that have a sequence matching one of the double stranded RNAs
difference between RISC associated siRNA and miRNA
siRNA: base pairs perfectly with target RNA and induces cleavage
miRNA: recognizes target with imperfect base pairing and results in inhibition of translation
the ________ protein is responsible for cleavage of target RNA
Argonaute
1 domain is homologous to RNase H enzymes that degrade RNA of an RNA-DNA hybrid
does RNAi protect against viruses and transposons?
yes
plasmodesmata
cytoplasmic connections between plant cells that traverse the cell walls between them
transfer of siRNA
siRNA knockdown
one strand of ds siRNA with single stranded regions generates mature siRNA RISC complexes without inhibition of protein synthesis
researches use synthetic ds siRNA to knockdown expression of specific genes in human cells
cytoplasmic polyadenylation
oocytes have mRNAs with short polyA tails that cant be translated
upon fertilization of the egg, the mRNAs are stabilized and a long polyA tail is added
cytoplasmic polyadenylation element (CPE)
U rich area where CPE-binding protein (CPEB) binds to signal polyadenylation
CPEB in neurons
postsyn neuron remembers which axon was stimulated, and leads to local synthesis of new proteins help the synapse
due to CPEB being present in dendrites…stimulates polyadenylation –> translation of mRNA in dendrites
what does the concentration of an mRNA depend on
rate of synthesis
rate of degradation
how can cytokine synthesis occur in bursts?
transcription of their genes is rapidly turned on or off
mRNAs have short half-lives
3 pathways of cytoplasmic degradation
deadenylation-dependent pathway
deadenylation-independent decapping pathway
endonucleolytic pathway
deadenylation-dependent pathway (most mRNA)
length of poly A tail slowly decreases with time from deadenylating nuclease
when short enough, tail can’t be stabilized by PABPI
decapping enzyme removes cap and exonuclease degrades
deadenylation-independent decapping pathway
special 5’ sequences make the cap sensitive to decapping enzyme
short bursts like cytokines
endonucleolytic pathway
RNAi pathway
doesn’t involve decapping or deadenylation
rapamycin
antibiotic that suppresses immune response in organ transplant patients
TOR pathway (target of rapamycin)
active mTOR stimulates overall protein synthesis by phosphorylating 2 critcal proteins that regulate translation
aids in synthesis of translation factors and tRNAs
eases assembly of ribosomes
Rheb
a small monomeric G protein that regulates mTOR
active when bound to GTP (activates mTOR)
autophage/macrophagy
degradation of cytoplasmic components in starved cells
this process is inhibited by mTOR in growing cells when there are enough nutrients
eIF2 kinase
regulates global rate of cellular protein synthesis
trimeric G protein (GTP/GDP)
translation initiation factor brings charged tRNA to P site
how to inhibit eIF2 kinase
phosphorylation at a serine
some mRNAs can still be transcribed even though eIF2 has been phosphorylated
ex. chaperone proteins that refold proteins after cellular stress
adenovirus and PKR (protein kinase RNA)
normally inhibition of protein synthesis helps stop producing progeny virions
adenovirus virus-associated RNA binds to PKR with high affinity and stop protein kinase acitibty to prevent inhibition
ferritin
intracellular iron-binding protein that binds and stores excess cellular iron
iron response element-binding protein (IRE-BP)
controls iron concentration by regulating translation of one mRNA and degradation of another
regulates ferritin and transferrin receptor
mRNA surveilance
mechanisms that help cells avoid translation of improperly processed mRNA
nonsense mediated decay (NMD)
causes degradation of mRNAs where 1 or more exons have been incorrectly spliced
rapid degradation of mRNAs with stop codons before the last splice junction
protein localization
mRNAs being translated in regions where the protein is actually needed
sequences in 3’ UTR direct this
__% of total RNA in rapidly growing cells is rRNA
80%
__% of total RNA in rapidly growing cells is tRNA
15%
where does ribosome formation take place
nucleolus, some nucleoplasm, final steps in cytoplasm
quality control step in ribosome formation
before nuclear export
ensures only functional ribosomal subunits are exported to the cytoplasm
pre-rRNA transcription unit
encodes the subunits of the large and small ribosome
synthesis and processing occurs in nucleolus
how can so many pairs of ribosomal subunits (40/sec in yeast) be synthesized, processed, and transported
pre-rRNA genes are packed with RNA pol I transcribing the gene simultaneously
snoRNAs
small nucleolar RNAs
hybridize to pre-rRNA and form snoRNPs to aid processing
AAA ATPase family
class of proteins involved in large molecular movements
ex. folding of large rRNA into proper conformation
what organisms have self-splicing group I introns
mitochondrial and chloroplast pre-rRNA
mRNA from E. coli bacteriophages
bacterial tRNA primary transcrips
group I self-splicing sequences use ______ as a cofactor
guanosine
ribozyme
RNA with catalytic ability
pre-tRNAs undergo extensive modification in the _____
nucleus
mature cytosolic tRNAs are produced from larger precursors (pre-tRNAs) synthesized by RNA pol _ in the ______
RNA pol III, nucleoplasm
what is present in all pre-tRNAs that isnt in mature tRNAs
a 5’ sequence of variable length
5’ end of mature tRNA is generated from endonucleolytic cleavage specified by the tRNA 3D structure by RNase P
3 modifications that happen to pre-tRNAs
base modification
cleavage
splicing
mechanism of pre-tRNA splicing is different than self-splicing introns and spliceosomes
splicing is catalyzed by protein, not RNA
intron is excised in 1 step of simultaneous cleavage at both ends of the intron
hydrolysis of GTP and ATP is required to join the two tRNA halves back together
which exportin moves mature tRNAs through NPCs
exportin-t
nuclear body
specialized nuclear domains that aren’t surrounded by membrane
regions of high concentrations of specific proteins and RNAs
ex. nucleoli: sites of ribosomal subunit synthesis
Cajal nuclear body
site of RNP-complex assembly for spliceosomal snRNPs and other RNPs
nuclear speckle nuclear body
discovered using Ab immunofluorescence to snRNPs
storage of snRNPs
promyelocytic leukemia (PML) nuclear body
discovered using Ab immunoflurorescence
sites of assembly and modification of protein complexes for DNA repair and apoptosis
ex. p53 tumor suppressor protein
defense vs. DNA viruses and post-translational modification
other nucleoli functions
assembly of immature SRP RNP complexes involved in protein secretion and ER membrane insertion
also export of these to the cytoplasm
