How ribosomes decode mRNA Flashcards

1
Q

Mutation in Arg-minus mutant strains affect enzymes in what pathway?

A

Arginine biosynthetic pathway

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2
Q

When streptomycin is present, do Arg-minus mutants grow in the absence of arginine or not?

A

They grow in the absence of arginine

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3
Q

How does the ‘leaky’ mutant affect the growth of Arg-minus mutants in the absence of arginine?

A

Growth is slow

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4
Q

Does low streptomycin enhance or prevent growth of the Arg-minus mutants?

A

It enhances it

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5
Q

Does low streptomycin enhance or prevent growth of the Arg-minus mutants?

A

It enhances it

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6
Q

Give examples of other strains of mutant that are derived from the ‘leaky’ mutant and which the additional mutations involve altered ribosomes

A
  • SM-resistant (SM-R) strains = non-leaky

- Other mutations (ram) increased leakiness

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7
Q

Who discovered that SM caused ‘misreading’ of mRNA in vitro?

A

Julian Davies, Walter Gilbert and Luigi Gorini

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8
Q

What can be deduced from the work of Julian Davies, Walter Gilbert and Luigi Gorini?

A
  • mRNA can be misread by ribosomes
  • Misreading is enhanced by a drug (streptomycin) that binds to ribosomes
  • Mutations resulting in altered ribosomes can either reduce or enhance misreading
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9
Q

What can be deduced from the work of Julian Davies, Walter Gilbert and Luigi Gorini?

A
  • mRNA can be misread by ribosomes
  • Misreading is enhanced by a drug (streptomycin) that binds to ribosomes
  • Mutations resulting in altered ribosomes can either reduce or enhance misreading
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10
Q

Ribosomes don’t just catalyse protein synthesis, they monitor and control what?

A

Fidelity of mRNA decoding

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11
Q

Ribosomes don’t just catalyse protein synthesis, they monitor and control what?

A

Fidelity of mRNA decoding

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12
Q

What happens to the aa-tRNA if they are cognate?

A

Retained in A site

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13
Q

What happens to the aa-tRNA if they are non-cognate?

A

Ejected from ribosome

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14
Q

GTP hydrolysis in either case (when aa-tRNA is retained or ejected) is proofreading at what?

A

At a cost

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15
Q

The ribosome has evolved to deliver what?

A

Optimal growth rate

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16
Q

The ribosome has a need versus what accuracy?

A

Need versus cost accuracy

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17
Q

Ribosomes must generate what to enable codon-anticodon pairing?

A

A water-free zone

18
Q

Ribosomes do not distinguish cognate versus non-cognate pairs merely by counting what?

A

H-bonds

19
Q

Do ribosomes know what they are looking for or not?

A

Yes

20
Q

In order for ribosomes to monitor codon-anticodon pairs, they require a what?

A

‘Decoding site’

21
Q

In order for ribosomes to monitor codon-anticodon pairs, they require a what?

A

‘Decoding site’

22
Q

Where is the decoding site?

A

On the 30S/40S ribosomal subunit where codon-anticodon recognition occurs

23
Q

What is ‘accommodation’?

A

When the aa-tRNA enters the A site properly

24
Q

What happens to the tRNA component as the ternary complex binds to the ribosome?

A

It gets distorted

25
Q

What happens to the tRNA component as the ternary complex binds to the ribosome?

A

It gets distorted

26
Q

In the decoding site of the ribosome, incoming tRNA within ternary complex can be:

A
  • Cognate: a perfect match to the mRNA codon
  • Near-cognate: a near-perfect match to the mRNA codon
  • Non-cognate: a mismatch to the mRNA codon
27
Q

What did Venki Ramakrishnan research?

A

The selection of aa-tRNA in ribosomal decoding site

28
Q

What did Venki Ramakrishnan research?

A

The selection of aa-tRNA in ribosomal decoding site

29
Q

What does the ribosome monitor during aa-tRNA selection?

A

Base pair geometry

30
Q

What does the ribosome measure base-pair geometry on?

A

The minor groove side of prospective codon-anticodon pairs and in this way determines whether such base-pairs are complementary

31
Q

Inspection of the major groove of the DNA helix reveals what?

A

The sequence of dsDNA or dsRNA

32
Q

Inspection of the minor groove of the DNA helix reveals what?

A

Whether a base-pair obeys Watson-Crick complementary pairing

33
Q

Inspection of the minor groove of the DNA helix reveals what?

A

Whether a base-pair obeys Watson-Crick complementary pairing

34
Q

The ribosomal proofreading of aa-tRNA selection in decoding site involves what?

A

2 independent selection steps separated by an irreversible event (GTP hydrolysis_Tu-GDP departure)

35
Q

What can happen to the ternary complex [aa-tRNA-EFTu-GTP] during the first selection step?

A

Can be lost/ejected

36
Q

What can happen to the aminoacyl-tRNA during the second step?

A

Can be lost

37
Q

What is the overall error frequency in aa-tRNA selection and is this an acceptable error frequency?

A

~1 in 10^4

This is an acceptable error frequency

38
Q

What is another name for the ‘pre-A site’?

A

The ‘A/T site’

39
Q

What is the ‘pre-A site’?

A

The preliminary site into which the ternary complex binds

40
Q

What happens in selection 1?

A

Ternary complex containing non-cognate tRNA is rejected

41
Q

What happens between selection 1 and selection 2?

A

GTP hydrolysis and then accommodation of aa-tRNA

42
Q

What happens in selection 2?

A

aa-tRNA containing near-cognate tRNA is rejected