How ribosomes decode mRNA Flashcards
Mutation in Arg-minus mutant strains affect enzymes in what pathway?
Arginine biosynthetic pathway
When streptomycin is present, do Arg-minus mutants grow in the absence of arginine or not?
They grow in the absence of arginine
How does the ‘leaky’ mutant affect the growth of Arg-minus mutants in the absence of arginine?
Growth is slow
Does low streptomycin enhance or prevent growth of the Arg-minus mutants?
It enhances it
Does low streptomycin enhance or prevent growth of the Arg-minus mutants?
It enhances it
Give examples of other strains of mutant that are derived from the ‘leaky’ mutant and which the additional mutations involve altered ribosomes
- SM-resistant (SM-R) strains = non-leaky
- Other mutations (ram) increased leakiness
Who discovered that SM caused ‘misreading’ of mRNA in vitro?
Julian Davies, Walter Gilbert and Luigi Gorini
What can be deduced from the work of Julian Davies, Walter Gilbert and Luigi Gorini?
- 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
What can be deduced from the work of Julian Davies, Walter Gilbert and Luigi Gorini?
- 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
Ribosomes don’t just catalyse protein synthesis, they monitor and control what?
Fidelity of mRNA decoding
Ribosomes don’t just catalyse protein synthesis, they monitor and control what?
Fidelity of mRNA decoding
What happens to the aa-tRNA if they are cognate?
Retained in A site
What happens to the aa-tRNA if they are non-cognate?
Ejected from ribosome
GTP hydrolysis in either case (when aa-tRNA is retained or ejected) is proofreading at what?
At a cost
The ribosome has evolved to deliver what?
Optimal growth rate
The ribosome has a need versus what accuracy?
Need versus cost accuracy
Ribosomes must generate what to enable codon-anticodon pairing?
A water-free zone
Ribosomes do not distinguish cognate versus non-cognate pairs merely by counting what?
H-bonds
Do ribosomes know what they are looking for or not?
Yes
In order for ribosomes to monitor codon-anticodon pairs, they require a what?
‘Decoding site’
In order for ribosomes to monitor codon-anticodon pairs, they require a what?
‘Decoding site’
Where is the decoding site?
On the 30S/40S ribosomal subunit where codon-anticodon recognition occurs
What is ‘accommodation’?
When the aa-tRNA enters the A site properly
What happens to the tRNA component as the ternary complex binds to the ribosome?
It gets distorted
What happens to the tRNA component as the ternary complex binds to the ribosome?
It gets distorted
In the decoding site of the ribosome, incoming tRNA within ternary complex can be:
- 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
What did Venki Ramakrishnan research?
The selection of aa-tRNA in ribosomal decoding site
What did Venki Ramakrishnan research?
The selection of aa-tRNA in ribosomal decoding site
What does the ribosome monitor during aa-tRNA selection?
Base pair geometry
What does the ribosome measure base-pair geometry on?
The minor groove side of prospective codon-anticodon pairs and in this way determines whether such base-pairs are complementary
Inspection of the major groove of the DNA helix reveals what?
The sequence of dsDNA or dsRNA
Inspection of the minor groove of the DNA helix reveals what?
Whether a base-pair obeys Watson-Crick complementary pairing
Inspection of the minor groove of the DNA helix reveals what?
Whether a base-pair obeys Watson-Crick complementary pairing
The ribosomal proofreading of aa-tRNA selection in decoding site involves what?
2 independent selection steps separated by an irreversible event (GTP hydrolysis_Tu-GDP departure)
What can happen to the ternary complex [aa-tRNA-EFTu-GTP] during the first selection step?
Can be lost/ejected
What can happen to the aminoacyl-tRNA during the second step?
Can be lost
What is the overall error frequency in aa-tRNA selection and is this an acceptable error frequency?
~1 in 10^4
This is an acceptable error frequency
What is another name for the ‘pre-A site’?
The ‘A/T site’
What is the ‘pre-A site’?
The preliminary site into which the ternary complex binds
What happens in selection 1?
Ternary complex containing non-cognate tRNA is rejected
What happens between selection 1 and selection 2?
GTP hydrolysis and then accommodation of aa-tRNA
What happens in selection 2?
aa-tRNA containing near-cognate tRNA is rejected
