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

CBG Lecture 6: RNA Processing Flashcards

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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
outline steps of polyA tail formation
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
26
outline steps of polyA tail destruction
1,Deadenylation in cytoplasm by DAN (deadenylating nuclease) | 2. destruction by exosome
27
outline order of all the specificity factors/proteins/enzymes involved in polyA tail formation and destruction
1. CPSF and CStF 2. PAP 3. PABP 4. DAN 5. exosome
28
what do sequences in the 3'UTR do
target mRNA to specific places in the cytoplasm
29
what does 3'UTR of vasopressin mRNA do
directs vasopressin mRNA to dendrites in hypothalamus and PABP binds to cytoskeletal motors
30
how does premRNA become mature
its spliced to remove introns and ligate exons
31
which are expressed; introns or exons
exons
32
how are introns removed from premRNA
spliced out and discarded
33
what are premRNA coding regions composed of
introns and exons
34
what catalyses splicing
the spliceosome
35
what is splicing
removing of introns from premRNA by spliceosomes the ligating exons
36
what is a spliceosome
a complex of small nuclear ribonucleoproteins snRNP | it is a ribozyme
37
when does splicing occur
although post transcriptional, it is concurrent
38
what could introns be
remains of parasitic sequences in the form of mitochondria
39
what bases does an intron commonly have at 5' and 3' end
GU @ 5' AG @ 3' branch point always contains adenine
40
what is the branch point
adenosine critical part of removal process
41
how are introns released from premRNA
in the form of an intron lariat which is immediately degraded
42
what is snRNA
small nuclear RNA associated with proteins, called U particles
43
what are U particles
snRNPs -> small nuclear ribonucleoproteins (snRNA + protein)
44
what are the steps of splicing
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
what is a lariat
a looped strucure of the conserved branch region and intron
46
name main U particles involved in splicing
U1 bind 5' donor U2 binds bridge U4/U6 rechecks donor U5 binds 3' acceptor
47
where could spliceosome have evolved from
self splicing bacterial introns, which could have arrived in eukaryotes as parasites brought in by the protomitochondrion
48
what are capping splicing and tailing factors associated with
the CTD of RNAP2 in eukaryotes
49
what processing does RNAP2 do
capping, splicing and tailing factors
50
what does CTD do
acts as a staging post for more splicosomes
51
what is the CTD
the carboxy terminal domain and its the largest subunit of RNAP2
52
what does RNAP require to make mRNA
ATP generally
53
what is alternative splicing useful for
to produce more than one protein from a single gene
54
how does alternative splicing produce more than one protein from a single gene
can have a standard splice - remove all intron or skip an exon, remove all introns or leave intron in and translate
55
why do humans have 25k genes but 90k polypeptides
due to alternative splicing
56
which undergoes more splicing, E.coli or Homo sapiens
Humans
57
what generates antibodies and BCRs from the same immunoglobin gene
interplay of tailing and splicing from the same immunoglobin gene
58
how many types of rRNA do eukaryotes have
4 types: 28s, 18s, 5.8s and 5s
59
how many types of rRNA do bacteria have
3 types: 23s, 16s,5s
60
how are bacterial rRNAs made
formed by the process of a single prerRNA transcript
61
how is eukaryotic mature rRNA made
by cleaving of pre-rRNA and for 5s type, its formed by the process of a single pre rRNA transcript
62
what does ribosomal RNA processing involve what do they do
the use of small nucleolar ribonucleoproteins snRNPs which catalyse pseudouridinylation and methylation of rRNAs
63
what sequence do all tRNAs have at their 3' end | why
CCA sequence which is the site for amino acid attachments
64
what are ribozymes
catalytic RNA
65
what is wobble base pairing
tRNA base modification common in both euks and bac
66
what modified tRNA nucleosides are there
dihydrouridine, pseudouridine, ribothymidine - formed by modificaiton of uridines methylguanosine and inosine
67
in bacteria, what can U wobble base pair with
A G I
68
in eukaryotes, what can U wobble base pair with
I G
69
what is the difference in wobble base pairing interaction between eukaryotes and bacteria due to
a result of small structural differences between prokaryotic and eukaryotic ribosomes
70
how can RNA be regulated
by binding other RNAs - RNA interference
71
what does RISC do
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
why is the RNA specific response vital
vital in the response of cells to invading viruses: the mRNA of viruses can be specifically targeted by this method
73
how is RNAi used in plants
used as a way of regulating their own genesL micro RNAs miRNA are transcribed from the plants' own DNA
74
what could RNAi help treat
human viral diseases and cancees
75
what is the RNA specific response
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
what is Dicer
an RNAse
77
what does the the Argonaut portion of RISC do
RNAse that can cleave any RNA that is complementary to the fragment in its portion
78
what does transferrin do
takes up iron from the blood
79
what does ferritin do
sequesters excess iron
80
what does cytosolic aconitase do? how is it double duty
binds ferritin mRNA at the RBS, which blocks ribosomes from binding also it binds transferrin mRNAA which blocks an endonuclease site
81
what happens when iron levels in the blood increase
the protein dissociates from both mRNAs leading to the degradation of the transferrin mRNA and expression of the ferritin mRNA
82
what does an exonuclease do
nibbles at 3' or 5' ends of nucleic acid
83
what does an endonuclease do
splits in the middle of a nucleic acid
84
what is RNAP2 also known as
an mRNA factory
85
what is the difference in production of BCR and antibodies due to
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
what does T cell stimulate the production of
CStF
87
what is the result of having a truncated transcript wrt. BCells/ABs
CStF cant splice out early stop codon therefore get a soluble antibody
88
what is the result of having a full transcript (wrt. Bcells/ABs)
CStF splices out early stop codon and retains hydrophobic tail : BCR

CBG PANT Replication, transcription and translation (10 decks)

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