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Building a phenotype - lectures > L4 RNA Makes Protein > Flashcards

L4 RNA Makes Protein Flashcards

1
Q

What is a 5’ UTR and a 3’ UTR?

A

Refers to either of the two sections either side of the coding sequence (the open reading frame) in an mRNA

5’ UTR is the leader sequence
3’ URT is the trailer sequence

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2
Q

What is an open reading frame?

A

The coding sequence of mRNA (a reading frame that contains no stop codons)

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3
Q

Wobble base

A

When the third amino acid is irrelevant

Eg. Alanine can be 
GCA
GCC
GCG
GCU
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4
Q

How is the ORF translated? And why is it like this?

A

I’m sets of three bases (codons)

Because it gives 64 possibilities of codes which is more than enough for 20 different amino acids to be coded for

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5
Q

What is the start codon

A

AUG
Methionine

Found as the first codon of the ORF

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6
Q

What are the stop codons ?

A

UAA
UAG
UGA

Don’t encode for any amino acids

Found as the last codon of the ORF

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7
Q

Give an example of something that uses a slightly different codon table

A

Mitochondria (use a slightly different codon table than in the cytoplasm)

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8
Q

How many Reading frames does each RNA have?

A

Three

However the start codon only occurs in one of the frames and so it determines the start of the correct ORF

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9
Q

Where is the start codon found in prokaryotes?

A

After the Shine-Dalgarno sequence

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10
Q

Which start codon determines the start of the frame in eukaryotes?

A

The first start codon found from the 5’ end of the mRNA

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11
Q

What is the sequence of the Shine-Dalgarno box?

A

5’ -AGGAGG- 3’

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12
Q

How does polycistronic mRNA work?

A

The shine dalgarno box sequence can occur multiple times in an mRNA sequence in prokaryotes.

This means in a single mRNA sequence there can be multiple proteins encoded (because multiple shine dalgarno sequences mean multiple sections of start codons)

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13
Q

What type of mRNA do prokaryotes have?

A

Polycistronic mRNA

Where multiple proteins are encoded for by a single mRNA

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14
Q

What type of mRNA do eukaryotes have?

+ what 2 otehr things does it have

A

Monocistronic RNA
(A single protein is encoded by the mRNA sequence)

5’ cap
Poly A tail

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15
Q

How can we locate the right Reading frame (cos there are 3 potential ones)

A

3/64 are stop codons
On average there are 16/1000 stop codons
ORF shouldn’t contain any stop codons
So we can estimate the correct frame that’s being translated because it’s the one where there are no stop codons in a section of about 1000 nucleotides

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16
Q

4 types of mutation

A

Silent
Missense
Nonsense
Frameshift

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17
Q

Silent mutation

A

Usually occurs in the last AA

UAU —> UAC (still encodes for tyrosine)

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18
Q

Missense mutation

A

UAU —> UCU (serine I stead of tyrosine) changed AA

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19
Q

Nonsense mutation

A

Introduces a stop codon
Eg. Tyrosine AUU can easily become AUG
Results in premature translation

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20
Q

Frameshift mutations

A

Caused by insertion or deletion of nucleotides (but if three nucleotides added/deleted frame stays the same)

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21
Q

Role of tRNA

A

Decodes the mRNA sequence into a protein sequence

Pairs anticodons and codons

Brings in charged AA

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22
Q

tRNA structure

A 
At 3’ end there is a CCA where the amino acid becomes linked to this last A base 
Anticodon loop (middle loop) binds to the codon
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23
Q

What’s special about tRNAs recognising codons ?

A

In a cell there are about 30-40 tRNAs but as we know there are 64 codons

So one tRNA can recognise multiple different codons

24
Q

What can uracil be chemically modified to?

A

Pseudouracil
Thymidine
Dihhdroudine

25
Q

What can adenine be chemically modified to?

A

Inosine

Can bond uracil and cytosine both still pyramidine bases

26
Q

What can guanine be chemically modified to?

A

Methylguanine

27
Q

Explain how one tRNA can recognise several different codons ?

A

tRNA has a wobble base which is chemically modified after the tRNA is made

This changes the base into another base (other than the 4 main ones) which has the ability to bind to multiple bases, for example, uracil AND cytosine. (This is the case with inosine)

28
Q

What shape does tRNA fold into?

A

L shape
Activated AA at 3’ end of L shape
Anticodon at other end

29
Q

Explains tRNA biogenesis (three things)

A

tRNAs are spliced our form the precursor tRNA using ribozymes:

  • RNAse P (splices at the 5’ end)
  • RNAse D (splices at the 3’ end)

CCA is added to 3’ end by nucleotidyl transferase

Base modifications are guided by small nucleolar RNAs (snoRNAs) - RNA modifying RNA example of RNA word relic

Only after all of these does the tRNA have a charged amino acid added to it

30
Q

How is tRNA charged?

A

Aminoacyl-tRNA-synthetase

Links the amino acid to the adenine base in CCA of the tRNA

One synthetase for each AA (20). This means that a synthetase must be able to recognise different codons which code for the same amino acid.

Nowadays: tRNA is charged with an AA and this is done by a protein

Before: good evidence it could have been down by RNA before. Flexizyme ribozyme discovered which could charge tRNA with AA

31
Q

?

A

tRNA bound to glutamyl-tRNA-synthetase

One end of the synthetase enzyme recognises the anticodon on the tRNA (this synthetase is specific to the anticodon so it can bring the correct AA)

At 3’ end of tRNA is where the amino acid is linked to the 3’ OH of the tRNA

32
Q

What’s the first step of the two step coupling of an amino acid to a tRNA?

A

Adenylation (activation) of the amino acid
- carboxyl group of AA reacts with phosphate in ATP so that pyrophosphate (two phosphates) is released and an ATP molecule with only one phosphate is now attached to the AA (see diagram in slide)

*example of an RNA based molecule (ATP) activating a small molecule (AA) - example of RNA work relic

33
Q

What’s the second step of the two step coupling of an amino acid to a tRNA?

A

Transfer of the activated amino acid to the 3’ OH of the tRNA

(Same enzyme catalyses this)

34
Q

What happens is incorrect AA is bound to tRNA?

A

If error found, enzymes can hydrolyse bond between AA and tRNA so no tRNA with the wrong AA is produced

35
Q

Structure of ribosome

A 
Made of RNA and protein
Small and large subunit 
80% of RNA in a cell is rRNA
Prokaryotes 20AA/sec
Eukaryotes 8AA/sec
36
Q

Where does peptide synthesis occur

A

Large subunit of ribosome

37
Q

Large ribosomal subunit

A

Oldest part of ribosome (from time when RNA was making peptides but not proteins)

Need evolution of small subunit to guide process and provide template for protein synthesis

38
Q

Ribosome facts

A

30 nanometers

39
Q

Polyribosome

A

Multiple ribosomes present on a single mRNA

40
Q

S unit

A

Svedburg unit

41
Q

Prokaryote ribosome

A

Large subunit - 50S

Small - 30S

42
Q

Eukaryotic ribosome

A

Large subunit - 60S

Small - 40S

43
Q

A site

A

Amino acyl site

Brings in tRNA with charged AA

44
Q

P site

A

Peptidyl site

Contains tRNA that carries the peptide

45
Q

E site

A

Exit site

tRNA that is in the exits site, it’s uncharged because the amino acid has been removed (added to the peptide) and this tRNA is about to leave

46
Q

Where does anticodon-codon pairing occur?

A

Small sub unit near mRNA

47
Q

Where does protein synthesis occur?

A

In the large sub unit at the peptidyl transfer centre

48
Q

What are the three steps of translation

A

Initiation
Elongation
Termination

49
Q

Initiation

A

1) small ribosomal subunit recognises and binds to the shine dalgarno sequence in the mRNA of prokaryotes (mRNA - rRNA interaction)
2) tRNA molecule charged with AA methionine binds with the start codon AUG that come after the SD sequence

Note: in prokaryotes the first methionine coded for because of the start codon has a blocked N terminus

3) large subunit binds to the complex of the tRNA with the charge amino acid (binds with the charge tRNA in the P site)

50
Q

Elongation

A

1) tRNA bringing in a new AA binds to A site which puts it in close provoking to the already present peptide
2) peptide bond formed
3) translocation: ribosome shifts one codon in 3’ direction so the empty uncharged tRNA is now in the E site and ready to exit
4) empty tRNA exits E site

51
Q

Peptide bond formation

A

tRNA carrying amino acid, amino group of this AA reacts with the carboxyl group of the already present peptide in the P site.

52
Q

How does RNA catalyse peptide bond formation?

See slides

A

Base in ribosomal RNA that removes a proton from a nitrogen on the activated amino acid and creates a hydroxyl group !???????????

53
Q

X

A

X

54
Q

Termination

A

Occurs at stop codon

1) Release factor binds to stop codon
2) peptidyl-tRNA bond is hydrolyse so the final peptide product is released
3) both subunits, the tRNA and the RF dissociate from mRNA

55
Q

What RNA world relics does translation involve?

A 
mRNAs 
tRNAs and snoRNAs
rRNAs
RNAse P
Adenylate-aa (activation of an AA through an adenylate)
56
Q

Proteins involved

A 
tRNA synthétases
RNAse D
Initiation factors 
Elongation factors 
Release factors
57
Q

Why did proteins not takeover translation completely?

A

RNA is a relic from the past, probably irreplaceable part of current machinery, example of a living fossil that life has been built on

Building a phenotype - lectures (36 decks)

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