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Bio 200 > RNA processing > Flashcards

RNA processing Flashcards

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1
Q

4 steps

A

5’cap
cleavage
polyadenylation
splicing

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1
Q

5’cap

A

during pausing of transcription

  • A 7’ methylguanylate cap is added to the 5’ terminal nucleotide through an unusual 5’- 5’ triphosphate linkage (on first ribonucleotide with GTP)
  • In animal cells and in higher plants the 2’hydroxyl of the ribose group of the first base is methylated.
  • In vertebrates the second nucleotide is also methylated.

CTD Ser 5 phosphorylation bind with capping enzyme

CTD ser2 phosphorylation

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2
Q

cap function

A

Addition of the cap:
-protects the pre-mRNA from degradation
-facilitates nuclear export
-assists recognition by translation factors

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3
Q

Ser-5 phosphorylation ensures

A

only RNAs transcribed by Pol II
(mostly mRNAs) are capped

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4
Q

Serine 2 phosphorylation recruits additional proteins

A

Splicing factors
Polyadenylation factors
Export factors

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5
Q

poly(A) signal

A

3‘ AAUAAA xxxxx G/U sequence
recognition and binding site

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6
Q

cleavage and polyadenylation factors

A

CPSF, CStF, CFI, CFII

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7
Q

formation of poly (A) tail

A

poly(A) polymerase (PAP) add~12 A residues
nuclear poly (A) binding protein
(PABPN1) which catalyzes the rapid addition of ~200 A residues.

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8
Q

Are all mRNA transcripts polyadenylated?

A

All mRNAs are polyadenylated except histone mRNAs…
they have unique secondary structure in their 3’ UTRs

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9
Q

hnRNPs

A

heterogeneous nuclear ribonucleoprotein particles)

contribute to polyadenylation, export to cytoplasm, splicing

containing one or more RNA binding domains and often also one or more intrinsically disordered protein domains.

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10
Q

Three functions of hnRNPs

A
  • Association with hnRNPs prevent the formation of sequence-specific secondary structures through
    base pairing. The hnRNPs impose a uniform structure that processing enzymes can recognize.
  • hnRNPs can regulate pre-mRNA splicing. Many premRNAs can be spliced in more than one way, and
    hnRNPs bound in or near splice sites can promote or repress their use.
  • hnRNPs function in RNA transport as some can cycle in and out of the nucleus.
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11
Q

Splicing

A

The GU AG rule…
The A of the Branch point is also highly conserved…

lariat structure
two transesterification reactions

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12
Q

small nuclear RNAs (snRNAs)

A

U1 snRNA: bind with 5’splicing site (GU)
U2 snRNA: bind with branch point

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13
Q

Spliceosome

A

U1U2
U4/5/6
U1/4 leave
U2/5/6: 2 transesterification

no ATP input

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14
Q

exception for splicing

A

self-splicing: most plant
Au….AC introns (not GU…. AG)
trans-splicing

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15
Q

rRNA process

A

snoRNAs

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16
Q

tRNA process

A

remove 5’end
short segment at loop removed
CCA add to 3’end
extensive modification

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17
Q

exon definition

A

SR proteins: bind with ESE
interact with U2AF65 AF35 U1
U2AF65 AF35 interacts with U2
AF35 bind the splice site

18
Q

sxl-lethal

A

female sxl protein bind to pre-mRNA before exon3, female exclude exon3
exon 3 have inframe stop codon: not functional

19
Q

sxl-lethal with Tra

A

female sxl protein bind to Tra pre-mRNA before exon 2, female exclude exon2
exon 2 have inframe stop codon: not functional
only female produce Tra protein, activate the splicing site at the end of exon 4 of dsx
female: dsx 3/4 with poly A
male: dsx 3/5

20
Q

affext exon definition

A

affect splicing site
produce new site
interfere with SR protein, cause exon skipping

21
Q

RNA editing

A

A to I
C to U

22
Q

protein inport

A

cargo protein has NLS
bind with importin in cytoplasm
go into nucleus
active RAN-GTP replace importin
back to cytoplasm
RNA-GDP

23
Q

protein export with exportin 1

A

cargo protein has NES
exportin bind with RAN-GTP go into nucleus
bind cargo
go out to cytoplasm
RNA-GDP

24
Q

RNAs require RAN

A

tRNA
ribosomal subunit
specific mRNA with hnRNP

25
Q

RAN-independent

A

NXF1/NXT1 bind with SR protein
go out nucleus

26
Q

RNA remodel

A

in nucleus:
CBC PABPN1

in cytoplasm
eIF4E PABPC1

27
Q

SR protein mediate RNA export

A

Npl3 (SR protein)
Glc7 (phosphorase, facilitate binding of the transporter)
NXF1/NXT1
Sky 1 Kinase: phosphorylates Npl3

28
Q

RNA survellience

A

Non-sense mediated decay (NMD)
stop codon before last exon

Non-stop decay
lack of stop codon

No-go decy
stalled because damage or secondary structure

29
Q

Non-sense mediated decay (NMD)

A

UPF3: part of exon-juction complex
go to cytoplasm with mRNA
ribosome displace UPF3

but if stop codon downstream UPF3, ribosome fall off

mRNA with UPF3 trigger RNA degradation

30
Q

wooble base

A

G: C U
U: A G
I: C A U

31
Q

translation iniation

A

tRNAi Met + eIF2-GTP

tRNAi Met + eIF2-GTP +40S+eIF1/3/5/1A (43S)

eIF4E: cap-binding protein
eIF4G: bind to eIF3, poly A binding protein
eIF4A: remove secondary structure
eIF4B: enhance A activity
mRNA

scanning
find and bind with AUG:form 48S

eIF complex leave (only 1A and 5B-GTP stay)
large subunit bind
5B-GDP
form 80S

32
Q

translation elongation

A

EF1alpha -GTP
GTP hydrolysis
amino acid chain remove to A site
EF2-GTP：move to E site

33
Q

translation termination

A

eRF1 with eRF3-GTP
cleavage and release

34
Q

RNA degradation

A

deadenylation- dependent
deadenylation- independent
endonuclease- mediate

35
Q

deadenylation- dependent

A

deadenylase complex
DCP1/2 XPN1： 5-3
exosome: 3-5

36
Q

deadenylation- independent

A

AU rich 3‘UTR
Rsp28B and Edc 3
DCP 1/2
XRN 1

37
Q

endonuclease- mediate

A

endonuclease cut
DCP1/2 XRN1
exosome

38
Q

TfR regulation

A

high iron：degradation
low iron：IRE-BP bind with 3‘ UTR IRE
block degradation

39
Q

miRNA

A

Pol II synthesize pri-miRNA
dsRNA hairpin
Drosha：pre-miRNA
exportin 5 take to cytoplasm
Dicer cleave
one strand bind Argonacute protein in RISC

40
Q

early embryo regulation

A

CPE cytoplasmic polyadenylation element
CPEB bind CPE
recruit Maskin
Maskin bind with eIF4E
prevent eIF4E bind eIF4G
prevent recruit ribosome

41
Q

later embryo

A

CPEB phosphorated
release Maskin
recruit eIF4
CPSF and PAP lengthen poly A
bind with eIF4E
eIF4E bind eIF4G
recruit ribosome

42
Q

Ferritin

A

aconitase： activate at low iron
bind 5‘UTR IRE
block eIF4A and scanning

43
Q
A

Bio 200 (5 decks)

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