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Cellular and Molecular Biology > Exam 3: Ch 8 Pre-mRNA Processing & Transport Across Nuclear Envelope > Flashcards

Exam 3: Ch 8 Pre-mRNA Processing & Transport Across Nuclear Envelope Flashcards

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1
Q

functional RNAs are exported to the cytoplasm as components of _____________

A

ribonucleoproteins

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2
Q

for protein coding genes, the amount of protein produced depends on 2 things

A

stability of the mRNAs in the cytoplasm

rate of their translation

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3
Q

are cytokine mRNAs unstable?

A

yes

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4
Q

why are mRNAs encoding proteins required in large amounts extremely stable

A

so multiple proteins can be transcribed from each mRNA

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5
Q

miRNA

A

micro RNA: ~22 bp long that base pair extensively, but not completely with mRNA

regulate stability and inhibit translation of target mRNAs

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6
Q

RNAi

A

RNA interference

leads to degradation of RNA using siRNA

viral RNA in infected cells

degradation of transposon-encoded RNA

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7
Q

siRNA

A

short interfering RNA: ~22 bp long that are perfectly complementary to an mRNA sequence

inhibit translation of specific mRNA through RNA knockdown

cleave target RNA, leading to rapid degradation

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8
Q

RNA knockdown

A

using siRNA to inhibit translation of a specific mRNA by degradation

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9
Q

post-transcriptional gene control

A

all the mechanisms that regulate gene expression after transcription

includes stability and translation rate

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10
Q

hnRNA

A

heterogeneous nuclear RNA

include pre-mRNA and RNA processing intermediates with 1+ introns

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11
Q

snRNA

A

5 small nuclear RNAs that function in removing introns from pre-mRNA by RNA splicing

2 small nuclear RNAs that substitute for the 1st two at rare introns

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12
Q

pre-tRNA

A

tRNA precursor has more transcribed bases at the ends than mature tRNA

may have an intron in the anti-codon loop

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13
Q

pre-rRNA

A

long rRNA precursor that is processed into mature rRNA

cleavage, removing bases from ends of cleaved product, modification of bases

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14
Q

snoRNA

A

small nucleolar RNA

base pair with complementary regions of pre RNA

directs cleavage of RNA chain and base modification

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15
Q

order of RNA processing

A

capping

polyadenylation

splicing

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16
Q

why is RNA processing important

A

protect pre-mRNA from enzymes that digest uncapped RNAs

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17
Q

co-transcriptional

A

pre-mRNA processing occurs in nucleus while nascent mRNA is being transcribed

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18
Q

ribonucleoprotein (RNP) complexes

A

proteins that are always associated with mRNAs

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19
Q

order of RNP complexes

A

pre-mRNP

nuclear mRNP

cytoplasmic mRNP

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20
Q

when is the 5’ cap added to nascent RNAs

A

after transcription initiation

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21
Q

purpose of 5’ cap

A

mark RNA as pre-mRNA to protect from digestion by enzymes

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22
Q

hnRNP

A

heterogeneous ribonucleoprotein particles

nuclear proteins + hnRNA

help with RNA processing: splicing, polyadenylation, export through nuclear pores to cytoplasm

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23
Q

how were hnRNP proteins discovered?

A

UV radiation causes cross-links btw RNA bases and proteins

chromatography recovered proteins

monoclonal Ab specific for major proteins

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24
Q

can hnRNP binding to pre-mRNA make it more accessible?

A

yes

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25
are there specific hnRNPs in the nucleus and in the cytoplasm?
yes
26
RNA recognition motif (RRM), RNP motif, RNA-binding domain (RBD)
found in hnRNPs and other RNA-binding proteins
27
KH motif
found in hnRNP K proteins and other RNA-binding proteins
28
splicing in short vs. long transcription units
short: follows cleavage and polyadenylation of pre-mRNA long: starts before transcription of gene is done
29
which RNA sequences are retained in mature mRNA
near 5' cap and near poly A tail
30
how were introns discovered
electron microscopy of RNA-DNA hybrids of adenovirus DNA and the mRNA encoding hexon
31
splice-site
exon-intron junctions
32
during splicing _____ base pair with pre-mRNA
snRNA U1, 2, 4, 5, 6 and ~6 proteins each ~170 proteins
33
U1 binds to which part of pre-mRNA for splicing
5' end
34
spliceosome
a large RNP complex made of the 5 splicing snRNPs and other proteins on a pre-mRNA ~170 proteins and ~100 splicing factors
35
consensus sequence
a moderately conserved short sequence at splice sites flanking introns in pre-mRNA
36
splicing occurs at short, conserved sequences in pre-mRNA via 2 _____________ rxns
transesterification
37
in transesterification splicing, introns are removed as ______ structures
lariat (lasso) intermediate 5' G of intron joined to adenosine (A residue) near 3' end
38
branch point
the adenosine residue in the lariat structure that forms an RNA branch
39
exon-junction complex
after RNA splicing a group of hnRNP proteins stays bound to spliced RNA 20 nt away from each exon-exon junction one of the hnRNPs is REF
40
REF
RNA export factor an hnRNP that helps export processed mRNP from uclus to cytoplasm
41
nonsense-mediated decay
hnRNPS that help degrade wrongly spliced mRNAs
42
trans-splicing
construction on mRNA by splicing together separate RNA molecules occurs in 2 types of protozoans uses snRNPs
43
CTD
carboxyl termianl domain found in RNA pol II very long
44
exonic splicing enhancers (ESE)
sequences within exons that show where the splice sites are SR proteins interact
45
SR protein
family of RNA-binding hnRNPs that interact with (ESEs) with an RRM RNA-binding domain long stretches of protein-protein interaction domains of serine and arginine (RS) domains
46
cross-exon recognition complex
complex of SR proteins, snRNPs and other splicing factors that assemble on an exon allows for precise specification of exons in long pre-mRNAs
47
self-splicing
some introns are removed on their own in nonphysiologcal test tube conditions group I introns in rRNA genes of protozoans group II introns in mitochondria/chloroplasts
48
which domains in group II introns can be trans-acting and like snRNAs and why is this important
domain I and V shows that group II introns may have evolved into trans-acting snRNAs that perform the same function (splicing)
49
do snRNPs stabilize the geometry of snRNAs and intron nucleotides required to catalyze pre-mRNA splicing?
yes, in theory
50
which mRNAs dont have a poly A tail
histone mRNAs
51
early studies of pulse-labeled adenovirus and SV40 RNA demonstrated...
that A residues are added to a 3' OH produced from cleavage of a longer transcript
52
3' cleavage and polyadenylation uses...
poly(A) polymerase (PAP) binds to complex before cleavage can occur multiple poly(A) binding protein copies (PABPII) adds to short poly A tail added by PAP
53
what degrades RNA introns that are processed out of pre-mRNAs and improperly spliced/polyadenylated pre-mRNAs?
nuclear exoucleases through hydrolysis 11 of these exonucleases form an exosome (helicases too)
54
nuclear cap binding complex
protects 5' cap from exosome degradation
55
alternative splicing generates...
transcripts with different combinations of exons make isoform proteins (ex. fibronectin)
56
a cascade of regulated RNA splicing controls fruit fly ____________ __________
sexual differentiation
57
what is Sx1 protein encoded by sex-lethal gene
Sx1 found only in females binds to a pre-mRNA and allows splicing of exon 3 (males keep exon 3 which codes stop) Sx1 proteins allows splicing of transformer gene pre-mRNA
58
transformer (Tra) protein
encoded by transformer gene in female drosophilia allows processing of pre-mRNA from double-sex gene --> Dsx protein
59
male vs. female Dsx protein
longer than female transcriptional repressor that inhibits expression of genes for female development female represses genes for male development
60
splicing _______ and _________ control splicing at alternative sites
repressors, enhancers ex. fruit flies Dsx protein / fibronectin by hepatocytes vs. fibroblasts
61
RNA binding sites for splicing repressors are usually
hnRNPs can also occur in exons: exonic splicing silencers
62
RNA binding sites for splicing enhancers are usually
SR proteins can also occur in introns: intronic splicing enhancers
63
complex regulation of alternative RNA splicing through ____-_______ modifications of ______ factors play a significant role in modulating _____ ______
post-translational, splicing factors neuron function ex. Ca activated K channel in hair cells
64
RNA editing
a type of pre-mRNA processing where the sequence of a pre-mRNA is altered, changing the mature mRNA mitochondria of protozoans/plants and chloroplasts
65
apoB gene
encodes two alternative forms of a serum protein for uptaking and transporting cholesterol apoB-100 (liver) and apoB-48 (intestine) defect can lead to atherosclerosis
66
LDL has apoB___ on its surface
apoB-100 deliver cholesterol to tissues by binding LDLr
67
RNA editing in mammals
changes apoB pre-mRNA to synthesize a shorter apoB-48 the cell-type specific expression of the 2 types of apoB result from editing of apoB pre-mRNA (intestinal only)
68
fully processed mRNAs in nucleus are bound to hnRNPs in complexes called...
nuclear mRNPs
69
before an mRNA can be translated, it must be exported out of the _____ to the _____
nucleus, cytoplasm
70
nuclear pore complex (NPC)
large, symmetrical structures made of 30 different proteins called nucleoporins
71
FG-nucleoporin
line the central channel through the NPC semi-permeable barrier lets small molecules only diffuse
72
mRNPs are transported through the NPC by...
mRNP exporter uses REF (RNA export factor), a component of the exon-junction complex also uses SR proteins
73
direction of mRNP export from the nucleus is controlled by...
phosphorylation and dephosphorylation of mRNP adapter proteins like REF
74
pre-mRNAs in _____ are not exported from the nucleus
spliceosomes incompletely spliced mRNAs associate with hnRNPs in the spliceosomes
75
HIV ___ protein regulates the transport of unspliced viral mRNAs
REV protein
76
constitutive transport element (CTE) in retroviruses other than HIV
binds to mRNP exporter to allow transport of unspliced retroviral RNA
77
Rev protein
binds to Rev-response element (RRE) and allows unspliced and singly spliced HIV mRNAs through the NPC

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