sonia RNA biology - processing, translation

Question 1

Comparing mRNA molecules from human and Escherichia coli cells, which of the following is typically NOT true?
A human mRNA has a special 5’ cap, while a bacterial mRNA does not.
B human mRNA has a poly-A tail, while a bacterial mRNA does not.
C human mRNA may undergo alternative splicing, while a bacterial mRNA cannot.
D human mRNA contains noncoding sequences, while a bacterial mRNA does not.
E typical human mRNA encodes one protein, while some bacterial mRNAs encode several different proteins.

Answer 1

option D - bacteria mRNA also has noncoding sequences

Noncoding, untranslated regions (UTRs), upstream of the initiation codon and downstream of the termination codon, are found in mRNAs from bacteria and humans, although bacterial UTRs are typically short compared to human mRNAs

Question 2

why is regulating gene expression important in organisms?

Answer 2

particularly in complex organisms like eukaryotes, they can regulate when where and the amount of protein produced
TIME, SPACE AMOUNT

Question 3

describe ways in which you can post transcriptionally regulate gene expression?

Answer 3

only EUKARYOTES undergo RNA processing/post transcriptional modifications

1. splicing of introns- dependent or independent
2. 5’ capping, 3’ polyadenlyation
3. RNA editing - apop48/100, amylotrophic lateral schlerosis

Question 4

what does rna processing mean?

Answer 4

any modification to the mRNA molecule following transcription (only happens in eukaryotes
> generally refers to 5’capping, 3’polyAdenylation, splicing, rna editing

Question 5

how does RNA processing happen cotranscriptionally. What signals the machinery to begin?

Answer 5

carboxy terminal domain phosphorylation promotes promoter clearance/transcription terminatIon of RNA pol2
also signals to the 5’ capping enzyme complex and polyA cleavage factors to the nascent mRNA

as the premRNA transcript elongates, splicing occurs immediate too

THIS IS UNIQUE TO RNA POL 2

Question 6

describe the 5’ end cap

Answer 6

it is a 7-methylguanosine (m7GnnP)
capping begins when the emerging mRNA is 22-40 bp long and mediated by CEC
the methylguanosine joined to the rest of the mRNA molecule by a 5 to 5 linkage (with all 3 phosphates) instead of a 5-3 linkage

Question 7

how does the cap get added to the mRNA

Answer 7

• capping enzyme complex* made up of 3 enzymes
  1. rna triphosphatase cleaves the gamma phosphaste from the mRNA at 5’ end
  2. rna guanyltransferase adds a GMP to the resulting diphophate
  3. methyltransferase methylates guanosine

CEC interacts with the RNA pol||

Question 8

amongst protecting mRNA from exonuclease degradation, aiding translation initiation and splicing and polyadenlyation,why else is the 5’ cap important?

Answer 8

it can facilitate NUCLEAR EXPORT of mRNA
> the CBC bound to the 5’ cap is recognised by the nuclear pore complex
== allows mRNA to leave nucleus/export and be translated by ribosome

Question 9

what is cis acting and transacting sequences?

can you give an example of them with relation to polyadenlyation>

Answer 9

cis acting - dna sequences: AAUAAA and G/U rich region
> the cleavage site is found between these sequences

transacting - proteins/ multi-subunit protein complexes that bind to cis acting signals
cleavage+polyadenylation factor (CPSF) cleavage and stimulation factor (CstF)

Question 10

describe process of polyadenlylation

Answer 10

1. pre- mRNA is cleaved by CPSF which recognised the AAUAAA consesus sequcence
2. CstF helps to stimulte this cleavage as it regonsied the GU rich sequcne
3. polyadenylate polymerase catalyses the addition of 100-250 adenosines to this 3’ free end. nteracts with CPSF

Question 11

what is the importance of alternative polyadenlyation

Answer 11

APA describes mechanism of gene regulation that generates distinct 3′ ends in transcripts made by RNA polymerase II.
> most APA sites found in the 3’ UTR so mRNA is same length but the stability or translation efficieny can be regulated this way
> contribute to genetic diversity by increasing size of the proteome/creating different mRNA transcripts if APA signals are found throughout the mRNA

Question 12

what is the biological importance of polyadenlyation

Answer 12

> protects pre-mRNA from being degraded by exonuclease activity
can help efficiency of translation by using the PABP which creates a closed loop mRNA and tethers eIF4F to the start of mRNA

Question 13

distinguish between mutations and RNA editing

Answer 13

mutation - change in the DNA base sequence
RNA editing- change to the open reading frame of the mRNA molecule
so RNA editing is a form of epigentic modification

Question 14

describe mechanisms in which RNA editing can occur

Answer 14

via base deamination where the amino group is replaced by an oxygen
> uses specific deaminases A-i C-U

or INDELS which then create a new open reading frame for that RNA transcript

Question 15

why is 5’ capping important in premRNA

Answer 15

can help to stabilise mRNA and protect it from exonucelase degradation
aids with splicing and polyadenylation – how??

also crucial for translation initiation as it acts as a docking station for ribosome. enables the eIF4E to bind to the 5’ end of pre mRNA transcript

Question 16

before forming the 43 pre-initiation complex (40S+ternary complex), the 40S ribosome binds to other eIF. What are they and why?

Answer 16

binds to eIF1, 1A and 3
> this helps to seperate the 60S and 40S subunits and prevents reassociation of them until after the initiation codon has been found (scanning)

Question 17

what is the ternary complex made of? Why

Answer 17

~ translation intiation~
eIF2
GTP - when hydrolysed by eiF5 generates energy to release the initiation factors allowing 60S subunit to bind = 80S complex! == allow elongation phase of translation to occur
tRNA18 - encoded Methioninie

Question 18

what is eIF4F and what is function?

Answer 18

if it has number 4 in it its part of the cap binding complex
> eIF4E which binds to the 5’ cap and binds to
> eIF4G which can bind to eIF3 allowing recruitment of pre-initiation 43S complex to the mRNA
> eIF4A/B helicase and cofactor which help with scanning to find the initiation codon

Question 19

how do miRNA regulate gene expression?

Answer 19

by entering the RISC complex, they can target specific mRNA
> cleave mRNA
> destabilize mRNA by removing the polyAAA and if there is incomplete complimentary then inhibits translation
> maybe inhibit transcription

Question 20

how does complimentary base pairing affect prokaryotic translation?

Answer 20

so if there is strong ribosomal binding i.e there is complete complementarity between the SDalgarnoS and the antiSDS on the rRNA the more efficient the translation

as the high affinity pairing will enbale the mRNA to recruit the 16S ribosome more quicker

Question 21

which of the following uses a spliceosome
A alternative polyadenylation
B spliceosome dependent splicing
C rna editing
D spliceosome independent splicing

Answer 21

OPTION B

spliceosome is a protein:rna complex
> made up of 5 rna which then combine with proteins to create 5 different snRNPs

Question 22

what does snRNA

and snRNP

Answer 22

small nuclear RNAS - u1,2,4,5,6

small nuclear ribonucleoproteins = spliceosome components for spliceosome dependent splicing