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CBG PANT Replication, transcription and translation > CBG Lecture 6: RNA Processing > Flashcards

CBG Lecture 6: RNA Processing Flashcards

1
Q

what is RNA processing

A

any posttranscriptional modifications to RNA

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2
Q

which type RNA is only modified in eukaryotes

A

mRNA

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3
Q

how is tRNA processed

A

methylation

pseudouridylation

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4
Q

how is rRNA processed

A

cleavage
methylation
multiple copies of rRNA to mRNA because no translational amplification

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5
Q

where are eukaryotic ribosomes made

A

in the nucleolus

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6
Q

what can you see in a microscope when looking at ribosomes being made

A

5S rRNA ‘christmas trees’

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7
Q

outline the anatomy of prokaryotic mRNA

A

5’ UTR, SDS (Shine Delgarno Sequence) ———STOP-3’ UTR

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8
Q

what is a shine delgarno sequence

A

ribosomal binding site in prokaryote

helps recruit the ribosome to mRNA to initiate protein synthesis by aligning ribosome with start codon

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9
Q

where abouts is an SDS

A

-8 of AUG start codon in mRNA

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10
Q

is mRNA monocistronic in prokaryotes or eukaryotes

A

mRNA is monocistronic in eukaryotes

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11
Q

define monocistronic

A

only one coding region

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12
Q

define polycistronic

A

often several coding regions

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13
Q

which mRNA is polycistronic

A

prokaryotes

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14
Q

name some start codons

A

AUG

GUG

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15
Q

name some stop codons

A

UAA
UGA
UAG

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16
Q

outline anatomy of eukaryotic mRNA

A 
heavily modified and monocistronic 
m7G 5'  7methylguanosine cap as part of 5' UTR
start
normally 1 code
stop 
3' UTR with polyadenosine 3' tail
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17
Q

which eukaryotic mRNAs dont contain a polyadenosine tail
what do they have instead
what is the result of this

A

histone associated mRNA
have a stem loop structure at 3’ end
less stable and shorter half life c. few mins-half hour

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18
Q

when is the polyA tail added

A

post transcriptionally - not directly encoded in the gene

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19
Q

what is the eukaryotic polyA tail analogous to in prokaryotes?

A

SDS - shine delgarno sequence

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20
Q

on what circumstances can mRNA leave nuclear pore

A

if it has a 5’ cap
polyA tail
been properly spliced

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21
Q

what is the purpose of the 5’ 7methylguanosine cap

A

provides protection in the nucleus, ribosome binding site
confers stability-stops degrading
viruses lack 5’ cap therefore humans cant differentiate between viral and human mRNA

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22
Q

what is the purpose of the A200 polyA tail

A

slows degradation of mRNA in
cytoplasm
export through nuclear pores
tells the time mRNA should survive and whereabouts mRNA should be
increase length of tail = increase survival time

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23
Q

what is the typical half life of a polyA tail in mRNA

A

t1/2 = 10hours

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24
Q

when does polyA tail formation occur (temporally)

A

immediately during/after transcription

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25
Q

outline steps of polyA tail formation

A
  1. cleavage CPSF (Cleavage and polAdenylation specificity factor) and CStF (Cleavage stimulation factor) terminates transcription
  2. Polyadenylation by PAP (polyadenosine polymerase) in nucleus
  3. Ribonucleoprotein formation by PABP (polyadenosine binding protein) which binds to cytoskeletal motors
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26
Q

outline steps of polyA tail destruction

A

1,Deadenylation in cytoplasm by DAN (deadenylating nuclease)

2. destruction by exosome

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27
Q

outline order of all the specificity factors/proteins/enzymes involved in polyA tail formation and destruction

A
  1. CPSF and CStF
  2. PAP
  3. PABP
  4. DAN
  5. exosome
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28
Q

what do sequences in the 3’UTR do

A

target mRNA to specific places in the cytoplasm

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29
Q

what does 3’UTR of vasopressin mRNA do

A

directs vasopressin mRNA to dendrites in hypothalamus and PABP binds to cytoskeletal motors

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30
Q

how does premRNA become mature

A

its spliced to remove introns and ligate exons

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31
Q

which are expressed; introns or exons

A

exons

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32
Q

how are introns removed from premRNA

A

spliced out and discarded

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33
Q

what are premRNA coding regions composed of

A

introns and exons

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34
Q

what catalyses splicing

A

the spliceosome

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35
Q

what is splicing

A

removing of introns from premRNA by spliceosomes the ligating exons

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36
Q

what is a spliceosome

A

a complex of small nuclear ribonucleoproteins snRNP

it is a ribozyme

37
Q

when does splicing occur

A

although post transcriptional, it is concurrent

38
Q

what could introns be

A

remains of parasitic sequences in the form of mitochondria

39
Q

what bases does an intron commonly have at 5’ and 3’ end

A

GU @ 5’
AG @ 3’
branch point always contains adenine

40
Q

what is the branch point

A

adenosine critical part of removal process

41
Q

how are introns released from premRNA

A

in the form of an intron lariat which is immediately degraded

42
Q

what is snRNA

A

small nuclear RNA associated with proteins, called U particles

43
Q

what are U particles

A

snRNPs -> small nuclear ribonucleoproteins (snRNA + protein)

44
Q

what are the steps of splicing

A
  1. premRNA cleaved @ 5’ end (AG) of intron. U1 attaches to complementary sequence
  2. Cut end attaches to the conserved branch point by pairing G and A nucleotieds from 5’ end and branch point respectively to form a lariat
  3. G and A bases bond via transesterificatoin
  4. U2 and U4/U6 position the 5’ end and the branch point close together
  5. U5 brings 3’ end closer, cut and join 5’ end by transesterification
  6. adjoining exons covalently bind and lariat is released with U2, U5 and U6
45
Q

what is a lariat

A

a looped strucure of the conserved branch region and intron

46
Q

name main U particles involved in splicing

A

U1 bind 5’ donor
U2 binds bridge
U4/U6 rechecks donor
U5 binds 3’ acceptor

47
Q

where could spliceosome have evolved from

A

self splicing bacterial introns, which could have arrived in eukaryotes as parasites brought in by the protomitochondrion

48
Q

what are capping splicing and tailing factors associated with

A

the CTD of RNAP2 in eukaryotes

49
Q

what processing does RNAP2 do

A

capping, splicing and tailing factors

50
Q

what does CTD do

A

acts as a staging post for more splicosomes

51
Q

what is the CTD

A

the carboxy terminal domain and its the largest subunit of RNAP2

52
Q

what does RNAP require to make mRNA

A

ATP generally

53
Q

what is alternative splicing useful for

A

to produce more than one protein from a single gene

54
Q

how does alternative splicing produce more than one protein from a single gene

A

can have a standard splice - remove all intron
or skip an exon, remove all introns
or leave intron in and translate

55
Q

why do humans have 25k genes but 90k polypeptides

A

due to alternative splicing

56
Q

which undergoes more splicing, E.coli or Homo sapiens

A

Humans

57
Q

what generates antibodies and BCRs from the same immunoglobin gene

A

interplay of tailing and splicing from the same immunoglobin gene

58
Q

how many types of rRNA do eukaryotes have

A

4 types: 28s, 18s, 5.8s and 5s

59
Q

how many types of rRNA do bacteria have

A

3 types: 23s, 16s,5s

60
Q

how are bacterial rRNAs made

A

formed by the process of a single prerRNA transcript

61
Q

how is eukaryotic mature rRNA made

A

by cleaving of pre-rRNA and for 5s type, its formed by the process of a single pre rRNA transcript

62
Q

what does ribosomal RNA
processing involve

what do they do

A

the use of small nucleolar ribonucleoproteins snRNPs which catalyse pseudouridinylation and methylation of rRNAs

63
Q

what sequence do all tRNAs have at their 3’ end

why

A

CCA sequence which is the site for amino acid attachments

64
Q

what are ribozymes

A

catalytic RNA

65
Q

what is wobble base pairing

A

tRNA base modification common in both euks and bac

66
Q

what modified tRNA nucleosides are there

A

dihydrouridine, pseudouridine, ribothymidine - formed by modificaiton of uridines
methylguanosine and inosine

67
Q

in bacteria, what can U wobble base pair with

A

A G I

68
Q

in eukaryotes, what can U wobble base pair with

A

I G

69
Q

what is the difference in wobble base pairing interaction between eukaryotes and bacteria due to

A

a result of small structural differences between prokaryotic and eukaryotic ribosomes

70
Q

how can RNA be regulated

A

by binding other RNAs - RNA interference

71
Q

what does RISC do

A

RNA induced silencing complex
cleaves mRNA complementary to miRNA or siRNA
also have an Argonaut portion which is an RNAse that can cleave any RNA that is complementary to its fragment

72
Q

why is the RNA specific response vital

A

vital in the response of cells to invading viruses: the mRNA of viruses can be specifically targeted by this method

73
Q

how is RNAi used in plants

A

used as a way of regulating their own genesL micro RNAs miRNA are transcribed from the plants’ own DNA

74
Q

what could RNAi help treat

A

human viral diseases and cancees

75
Q

what is the RNA specific response

A

dsRNA (eg. from viruses) is cleaved into fragments by and RNAse called Dicer and the small interfering RNA resulting from that (siRNA) fragments bind the RISC.
the argonaut portion of RISC is an RNAse that can cleave any RNA that is complementary to its fragments

76
Q

what is Dicer

A

an RNAse

77
Q

what does the the Argonaut portion of RISC do

A

RNAse that can cleave any RNA that is complementary to the fragment in its portion

78
Q

what does transferrin do

A

takes up iron from the blood

79
Q

what does ferritin do

A

sequesters excess iron

80
Q

what does cytosolic aconitase do? how is it double duty

A

binds ferritin mRNA at the RBS, which blocks ribosomes from binding

also it binds transferrin mRNAA which blocks an endonuclease site

81
Q

what happens when iron levels in the blood increase

A

the protein dissociates from both mRNAs leading to the degradation of the transferrin mRNA and expression of the ferritin mRNA

82
Q

what does an exonuclease do

A

nibbles at 3’ or 5’ ends of nucleic acid

83
Q

what does an endonuclease do

A

splits in the middle of a nucleic acid

84
Q

what is RNAP2 also known as

A

an mRNA factory

85
Q

what is the difference in production of BCR and antibodies due to

A

alternative splicing
T-cell stimulates the production of CStF.
truncated transcript cant splice out early stop codon: soluble antibody
full transcript splices out early stop codon and retains hydrophobic tail: membrane bound BCR

86
Q

what does T cell stimulate the production of

A

CStF

87
Q

what is the result of having a truncated transcript wrt. BCells/ABs

A

CStF cant splice out early stop codon therefore get a soluble antibody

88
Q

what is the result of having a full transcript (wrt. Bcells/ABs)

A

CStF splices out early stop codon and retains hydrophobic tail : BCR

CBG PANT Replication, transcription and translation (10 decks)

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