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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
Q

are there specific hnRNPs in the nucleus and in the cytoplasm?

A

yes

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26
Q

RNA recognition motif (RRM), RNP motif, RNA-binding domain (RBD)

A

found in hnRNPs and other RNA-binding proteins

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27
Q

KH motif

A

found in hnRNP K proteins and other RNA-binding proteins

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28
Q

splicing in short vs. long transcription units

A

short: follows cleavage and polyadenylation of pre-mRNA
long: starts before transcription of gene is done

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29
Q

which RNA sequences are retained in mature mRNA

A

near 5’ cap and near poly A tail

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30
Q

how were introns discovered

A

electron microscopy of RNA-DNA hybrids of adenovirus DNA and the mRNA encoding hexon

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31
Q

splice-site

A

exon-intron junctions

32
Q

during splicing _____ base pair with pre-mRNA

A

snRNA U1, 2, 4, 5, 6 and ~6 proteins each

~170 proteins

33
Q

U1 binds to which part of pre-mRNA for splicing

A

5’ end

34
Q

spliceosome

A

a large RNP complex made of the 5 splicing snRNPs and other proteins on a pre-mRNA

~170 proteins and ~100 splicing factors

35
Q

consensus sequence

A

a moderately conserved short sequence at splice sites flanking introns in pre-mRNA

36
Q

splicing occurs at short, conserved sequences in pre-mRNA via 2 _____________ rxns

A

transesterification

37
Q

in transesterification splicing, introns are removed as ______ structures

A

lariat (lasso) intermediate

5’ G of intron joined to adenosine (A residue) near 3’ end

38
Q

branch point

A

the adenosine residue in the lariat structure that forms an RNA branch

39
Q

exon-junction complex

A

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
Q

REF

A

RNA export factor

an hnRNP that helps export processed mRNP from uclus to cytoplasm

41
Q

nonsense-mediated decay

A

hnRNPS that help degrade wrongly spliced mRNAs

42
Q

trans-splicing

A

construction on mRNA by splicing together separate RNA molecules

occurs in 2 types of protozoans

uses snRNPs

43
Q

CTD

A

carboxyl termianl domain

found in RNA pol II

very long

44
Q

exonic splicing enhancers (ESE)

A

sequences within exons that show where the splice sites are

SR proteins interact

45
Q

SR protein

A

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
Q

cross-exon recognition complex

A

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
Q

self-splicing

A

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
Q

which domains in group II introns can be trans-acting and like snRNAs and why is this important

A

domain I and V

shows that group II introns may have evolved into trans-acting snRNAs that perform the same function (splicing)

49
Q

do snRNPs stabilize the geometry of snRNAs and intron nucleotides required to catalyze pre-mRNA splicing?

A

yes, in theory

50
Q

which mRNAs dont have a poly A tail

A

histone mRNAs

51
Q

early studies of pulse-labeled adenovirus and SV40 RNA demonstrated…

A

that A residues are added to a 3’ OH produced from cleavage of a longer transcript

52
Q

3’ cleavage and polyadenylation uses…

A

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
Q

what degrades RNA introns that are processed out of pre-mRNAs and improperly spliced/polyadenylated pre-mRNAs?

A

nuclear exoucleases through hydrolysis

11 of these exonucleases form an exosome (helicases too)

54
Q

nuclear cap binding complex

A

protects 5’ cap from exosome degradation

55
Q

alternative splicing generates…

A

transcripts with different combinations of exons

make isoform proteins (ex. fibronectin)

56
Q

a cascade of regulated RNA splicing controls fruit fly ____________ __________

A

sexual differentiation

57
Q

what is Sx1 protein encoded by sex-lethal gene

A

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
Q

transformer (Tra) protein

A

encoded by transformer gene in female drosophilia

allows processing of pre-mRNA from double-sex gene –> Dsx protein

59
Q

male vs. female Dsx protein

A

longer than female

transcriptional repressor that inhibits expression of genes for female development

female represses genes for male development

60
Q

splicing _______ and _________ control splicing at alternative sites

A

repressors, enhancers

ex. fruit flies Dsx protein / fibronectin by hepatocytes vs. fibroblasts

61
Q

RNA binding sites for splicing repressors are usually

A

hnRNPs

can also occur in exons: exonic splicing silencers

62
Q

RNA binding sites for splicing enhancers are usually

A

SR proteins

can also occur in introns: intronic splicing enhancers

63
Q

complex regulation of alternative RNA splicing through ____-_______ modifications of ______ factors play a significant role in modulating _____ ______

A

post-translational, splicing factors

neuron function

ex. Ca activated K channel in hair cells

64
Q

RNA editing

A

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
Q

apoB gene

A

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
Q

LDL has apoB___ on its surface

A

apoB-100

deliver cholesterol to tissues by binding LDLr

67
Q

RNA editing in mammals

A

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
Q

fully processed mRNAs in nucleus are bound to hnRNPs in complexes called…

A

nuclear mRNPs

69
Q

before an mRNA can be translated, it must be exported out of the _____ to the _____

A

nucleus, cytoplasm

70
Q

nuclear pore complex (NPC)

A

large, symmetrical structures made of 30 different proteins called nucleoporins

71
Q

FG-nucleoporin

A

line the central channel through the NPC

semi-permeable barrier lets small molecules only diffuse

72
Q

mRNPs are transported through the NPC by…

A

mRNP exporter

uses REF (RNA export factor), a component of the exon-junction complex

also uses SR proteins

73
Q

direction of mRNP export from the nucleus is controlled by…

A

phosphorylation and dephosphorylation of mRNP adapter proteins like REF

74
Q

pre-mRNAs in _____ are not exported from the nucleus

A

spliceosomes

incompletely spliced mRNAs associate with hnRNPs in the spliceosomes

75
Q

HIV ___ protein regulates the transport of unspliced viral mRNAs

A

REV protein

76
Q

constitutive transport element (CTE) in retroviruses other than HIV

A

binds to mRNP exporter to allow transport of unspliced retroviral RNA

77
Q

Rev protein

A

binds to Rev-response element (RRE) and allows unspliced and singly spliced HIV mRNAs through the NPC

Cellular and Molecular Biology (34 decks)

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