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

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Flashcards in Exam 3: Ch 8 Pre-mRNA Processing & Transport Across Nuclear Envelope Deck (77):
1

functional RNAs are exported to the cytoplasm as components of _____________

ribonucleoproteins

2

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

stability of the mRNAs in the cytoplasm

rate of their translation

3

are cytokine mRNAs unstable?

yes

4

why are mRNAs encoding proteins required in large amounts extremely stable

so multiple proteins can be transcribed from each mRNA

5

miRNA

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

regulate stability and inhibit translation of target mRNAs

6

RNAi

RNA interference

leads to degradation of RNA using siRNA

viral RNA in infected cells

degradation of transposon-encoded RNA

7

siRNA

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

8

RNA knockdown

using siRNA to inhibit translation of a specific mRNA by degradation

9

post-transcriptional gene control

all the mechanisms that regulate gene expression after transcription

includes stability and translation rate

10

hnRNA

heterogeneous nuclear RNA

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

11

snRNA

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

12

pre-tRNA

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

may have an intron in the anti-codon loop

13

pre-rRNA

long rRNA precursor that is processed into mature rRNA

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

14

snoRNA

small nucleolar RNA

base pair with complementary regions of pre RNA

directs cleavage of RNA chain and base modification

15

order of RNA processing

capping

polyadenylation

splicing

16

why is RNA processing important

protect pre-mRNA from enzymes that digest uncapped RNAs

17

co-transcriptional

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

18

ribonucleoprotein (RNP) complexes

proteins that are always associated with mRNAs

19

order of RNP complexes

pre-mRNP

nuclear mRNP

cytoplasmic mRNP

20

when is the 5' cap added to nascent RNAs

after transcription initiation

21

purpose of 5' cap

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

22

hnRNP

heterogeneous ribonucleoprotein particles

nuclear proteins + hnRNA

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

23

how were hnRNP proteins discovered?

UV radiation causes cross-links btw RNA bases and proteins

chromatography recovered proteins

monoclonal Ab specific for major proteins

24

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

yes

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