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Michaelmas Term 1 > RNA Makes Protein > Flashcards

RNA Makes Protein Flashcards

1
Q

Why do we need proteins?

A

They are better catalysts

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2
Q

What two sections does mRNA contain?

A
  • ORFs (open reading frames)
  • UTRs (untranslated regions)
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3
Q

Describe ORFs

A

Contain 3 nucleotide codons, each for one aa

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4
Q

What is the wobble base?

A

The third base, that is often irrelevant for coding

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5
Q

Start codon

A

AUG

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6
Q

Stop codon

A
  • UAA
  • UAG
  • UGA
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7
Q

How is translation initiation achieved in prokaryotes?

A
  • polycistronic mRNA
  • ribosome binds to Shine-Dalgarno box
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8
Q

What is polycistronic mRNA?

A

Encodes multiple proteins

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9
Q

Shine-Dalgarno box

A

5’-AGGAGG-3’

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10
Q

How is translation initiation achieved in eukaryotes?

A
  • monocistronic mRNA with a 5’ cap and poly-A tail
  • ribosome binds to 5’ cap and scans for first AUG
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11
Q

What predicts which frame is translated in mRNA?

A
  • stop codon distribution
  • statistically, averages 3/64 codons, 3/192nts = 15.6 per 1000nt
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12
Q

Silent mutations

A
  • do not change aa sequence
  • ~1/3
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13
Q

Missense mutations

A
  • cause aa substitutions
  • ~2/3
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14
Q

Nonsense mutations

A
  • cause premature termination
  • <5%
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15
Q

Frameshifts mutations

A
  • Caused by indels
  • often truncate proteins
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16
Q

What is the function of tRNA?

A

To decode the mRNA sequence into protein sequence

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17
Q

What is the function of rRNA?

A

the main component of the ribosome - the translation machinery

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18
Q

tRNA facts

A
  • 15% of all cell RNA
  • 78-91nts
  • 31-41 per cell
  • 3’ end carries activated aa
  • clover shaped secondary structure
  • one tRNA can recognise several codon
  • ~20% is modified RNA bases
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19
Q

What is the 3’ end sequence of tRNA

A

CCA

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20
Q

What is the middle loop in tRNA?

A

The anticodon loop

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21
Q

List the modified RNA bases

A
  1. Dihydrouridine
  2. Inosine
  3. Ribothymidine
  4. Pseudouridine
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22
Q

Describe Pseudouracil

A

Has nitrogen replacing carbon 5

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23
Q

Describe inosine

A

O = relaxes NH2

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24
Q

Describe dihydrouridine

A

Loss of carbon chain

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25
Q

Describe methyl-guanine

A

Methylation of amine group

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26
Q

Structure of tRNA

A
  • folds in L shape
  • D- and TψCG-loops interact
  • anticodon on one end of L
  • activated aa on the other end of the L
  • flexibility (twisting) in variable loop
  • acceptor stem
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27
Q

tRNA biogenesis

A
  • tRNA precursors processed at 5’ end by ribozyme RNAse P
  • tRNA precursors processed at 3’ end by enzyme RNAse D
  • tRNA nucleotidyl transferase adds 3’ CCA
  • base modification of snoRNAs
  • splicing (for some)
28
Q

What are tRNA precursors?

A

Often tandem arrays with different tRNAs

29
Q

snoRNAs

A

small nucleolar RNAs

30
Q

Flexizyme

A

Artificial 42nt ribozyme that can charge tRNA with aa

31
Q

aminoacyl-tRNA synthetase

A

aaRS

32
Q

charging tRNA with activated aa is

A

a highly selective coupling reaction

33
Q

How is an amino acid activated

A
  • aminoacyl-tRNA synthetase catalyses ATP + amino acid -> AMP
34
Q

How many aaRS for each aa?

A

1

35
Q

How many aaRS are there?

A
  • 20
  • some can recognise multiple tRNAs (because there are 31-41 tRNAs)
36
Q

Charging tRNA with activated aa mechanism

A
  • coupling of aa to 3’OH 
  • specific anticodon recognition creates an RNA-protein complex
37
Q

Describe the coupling of the aa to 3’OH of tRNA

A
  1. Adenylation of amino acid with ATP (pyrophosphate byproduct)
  2. Amino acid transfer to tRNA 3’OH, releasing AMP
  3. Hydrolytic editing to remove misincorporations
38
Q

Describe the error rate of hydrolytic editing

A

~10-6
- due to highly selective coupling

39
Q

Speed of translation in prokaryotes

A

17-21 aa/sec

40
Q

Speed of translation in eukaryotes

A
  • 6-9 aa / sec
  • 1-2 proteins per minute
41
Q

Describe the ribosomal large subunit

A
  • contains peptidyl transferase
  • possibly oldest part of ribosome
  • RNA -> peptides possible
42
Q

Describe the ribosomal small subunit

A
  • contains mRNA guide
  • probably evolved later
  • allows RNA -> proteins (true translation)
43
Q

How big are ribosomes?

A
  • big!
  • 30nm
  • can be seen under TEM
44
Q

Polyribosomes

A

Multiple ribosomes per mRNA (think beads on a string)

45
Q

What is the Svedberg unit?

A
  • S
  • non-metric unit for sedimentation coefficient
46
Q

What is Da?

A
  • Dalton
  • atomic mass
  • H = 1Da
47
Q

Where is tRNA in the ribosome?

A
  • A- site (amino acyl)
  • P- site (peptidyl)
  • E-site (Exit)
48
Q

What are the 3 steps of translation:

A

1) initiation at start codon
2) polypeptide elongation
3) termination at stop codon

49
Q

Describe translation initiation in bacteria

A
  • blocked N terminus
  • small subunit binds to Shine-Dalgarno
  • fMet-tRNA binds to AUG start codon
  • large subunit binds to fMet-tRNA in P-site
50
Q

What is a blocked N-terminus?

A

N-formyl methionine is used as the first amino acid

51
Q

What does translation initiation in bacteria involve at the small subunit?

A
  • mRNA-rRNA interactions
  • mRNA-tRNA interactions
52
Q

Describe elongation

A

1) acyl-tRNA loaded into A-site
2) peptidyl transfer
3) translocation, peptide-tRNA in P-site
4) empty tRNA exits E-site

53
Q

What happens during peptidyl transfer?

A

Peptide bond formation

54
Q

What is translocation during translation?

A

ribosome shifts one codon in 3’ direction

55
Q

Describe peptide bond formation

A
  • amino group of incoming amino acid attacks C-terminal carbonyl of peptidyl-tRNA
  • transfer of peptide into A-site
56
Q

How does RNA catalyse peptide bond formation?

A
  • rRNA adenine accepts proton from NH3+
  • donates proton to hydrolyse tRNA peptide in P-site
57
Q

The catalytic centre is

A

Adenosine

58
Q

Describe termination

A

1) RF binds to stop codon
2) peptidyl-tRNA bond hydrolysed; product release
3) subunits, tRNA and RF dissociate from mRNA

59
Q

RF

A
  • release factor
  • protein
60
Q

In what direction is RNA translated?

A

5’ -> 3’

61
Q

At what end is the untranslated leader?

A

5’

62
Q

At what end is the terminator?

A

3’

63
Q

Open reading frame is usually much longer than

A

1000 nucleotides

64
Q

Where does codon-anticodon coupling happen?

A

In the small subunit

65
Q

Where is the peptidyl transfer centre?

A

In the catalytic site, the large subunit

66
Q

Where is 16s rRNA

A

small subunit

67
Q

During termination, the bond between peptide and tRNA is

A

Hydrolysed

Michaelmas Term 1 (42 decks)

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