Translation Gene Expression (ecoli) Flashcards
What does degenerate code mean
64 codons code for 20 amino acids so more corona for 1 amino acid
What are the 3 stop codons which don’t code for a amino acid
UAA UAG UGA
Which 2 things can AUG code for
Formyl methionine (initiator trna)
Methionine
Is the code always universal?
No some exceptions eg mitochondria have different codons
Explain the structure of trna
5’ monophosphate molecule
Clover shape
D loop T loop Anticodon site Variable arm AA acceptor site
What codon is on the amino acid acceptor site usually and is it 5’ or 3’ end
CCA
It’s 3’ end meaning an OH is present
What are the 4 modified bases on the trna and name the most useful one
Ribo thymidine
Pseudo uridine
Dihydro uridine
INOSINE (most useful)
What is the process called of amino acids joining trnas
Aminoacylation of trna
Which enzyme catalyses aminoacylation
Trna synthetase
Explain the process of aminoacylation of a trna
ATP is hydrolysed into AMP + PPi
An amino acid is joined by an AMP molecule by the carboxyl group of the amino acid (COOH-P)
Forms an AMINOACYL ADENYLATE
The aminoacyl adenylate (amino acid and an AMP molecule) then reacts with the trna 3’ OH
Forms an ester bond and AMP is released
The trna now is an aminoacyl trna
Why is the ester bond formed by the amino acid and the amino acid acceptor site important
The energy of the ester bond is used to form a peptide bond
What is an amp molecule attached to the carboxyl of amino acid called
Aminoacyl adenylate
Why is there 2 classes of trna synthetases (class I and class II)
Both specific for 10 AA each
Interact with trna differently
Eg threonyl trna synthetase = for threonine
What are identity elements on trna?
Elements of the trna clover shape which is used by synthetases to identify what trna it is eg trna Alanine has a GU bp at the top
How many different trnas for amino acids are there
40
Eg leucyl trna(leu)
Why do trna synthetases need to distinguish between amino acids aswell?
Because they can be similar eg threonine and serine
Threonyl synthetase needs to distinguish
How is proof reading done to allow the right amino acids to attach to trna
There is an editing site which cleaves too small amino acids
An acylation site cleaved too large amino acids
The amino acid acceptor site will move amongst these 2 sites to stop the wrong amino acid binding
What does the editing and acylation site do on trna synthetases
Editing - cleaves small AA
Acylation - cleaved too large AA
What is the serine trna called before and after acylation
Trna ser before
Seryl trna ser (aminoacyl trna)
How are trnas specific to 1 amino acid on the mrna codon sequence
Their anticodon forms H bonds with the mrna codon eg AUG on mrna is UAC on the anticodon
This is then met trna which adds methionine
What is the wobble hypothesis
Because only 40 trnas but 64 codons for 20 amino acids, the trna anticodons need to change/pair with more than 1 codon
Which base changes on the anticodon in the wobble hypothesis
The 3rd base on anticodon (at 5’)
What are the H bonds called in wobble hypothesis
Non standard H bonds (between the 5’ base on trna and 3’ on mrna)
Why is inosine important in the wobble hypothesis
It binds to either A,C or U on the codon
What happens if the wobble base is A?
Converted to inosine by anticodon deaminase enzyme
What 2 bases arent found at the wobble base site (3’)
A and U
Deaminase converts A to inosine
Which codon bases does G bind to
C or U
Explain the structure of inosine and how it helps to bind to A,C and U
It’s a purine
Has 1 double bond oxygen allowing it to bind to C,U and A with 2 bonds
What are ribosomes made of
Ribonucleotide proteins
Rrna and proteins
What is the large subunit made up of
50S
23s rrna + 5srrna
31 proteins
What is the small subunit made up of
30s
21 proteins
16s rrna
What does S mean
Svedberg unit
Which 2 rrna are important in translation
23s in the large 50s subunit
16s in the small 30 s subunit
Which initiator trna starts translation
Formyl-methionyl trnaF
F met trna
What occurs first in initiation of translation
Methionine and trna f are joined by trna synthetases to form amino acyl trna (normal acylation steps)
(Methionyl trna met)
How is met trna f turned into formyl methionine trna f met
Methionine is formylated by formyl transformase enzyme
Formyl tetrahydrofolate is turned into tetrahydrofolate
= formyl methionine trna f
What happens once the 30s ribosome binds to the shine dalgarno sequence (ending AUG)
Allows attachment of Fmet trna f
Fmet trna binds to the AUG by the anticodon h bonding
What happens in initiation once f met trna binds to AUG
The 50s ribosome binds forming the 70s initiation complex
How is the 16s rrna on the 30s ribosome (small subunit) important in initiation
Forms comp base pairs with the shine dalgarno sequence so the 30s subunit can bind and bring Fmet trna
Name the 3 initiation factors and which one is bound to GTP
IF1, IF2, IF3
IF2 is bound to a GTP
What happens to initiation factors in initiation
IF3 and IF1 and IF2 (with GTP) bind to the 30s when it recognises the shine dalgarno
When the Fmet trna is bound to AUG, the IF 3 dissociates
The IF2 and IF1 are displaced when the 50s subunit binds to form a 70s complex
What is needed to produce the 70s initiation complex
GTP hydrolysis (the GTP on the IF2 factor)
What are the 3 subunits of the 50s ribosome called
E - exit site
P- peptidyl site
A- aminoacyl site
What happens in elongation
A new aminoacyl trna is added to the A site on the 70s initiation complex
A peptide bond forms between the only aminoacyl trna AA and the new at the A site (using the ester bond energy)
The ribosome then translocates and deacylated trna will exit via the exit site
Which 2 elongation factors are needed for a new aminoacyl trna to be transferred to A site
Ef- Tu bound to GTP allows a new aminoacyl trna to be transferred to A site
When GTP is hydrolysed, EF-Ts is needed to remove gdp to stop EF Tu sticking
How is EF - G elongation factor needed to translocate the ribosome
EF -G needed
GTP is hydrolysed and then this allows for the EF G to be free and allow further translocation
How is a peptide bond formed
The amine NH2 group of a new amino acid attacks the carbonyl ester O bond on the previous aminoacyl trna
What catalyses formation of peptide bond
The 23s rrna on the 50s ribosome
Which 3 release factors attach to termination codons (UAA, UGA, UAG) allowing cleavage of polypeptide
RF1, RF2, RF3.GTP
Explain steps of termination using Release factor 1 and 3.GTP
RF1 will bind to the termination codon on mrna
This stops further movement of the 70s initiation complex
GTP from the RF3 is then hydrolysed to cleave the polypeptide from the trna
The deacylated trna is then also removed
Ribosome dissociates
What allows ribosome dissociation at terminator sequence
RRF ribosome release factor
And EF-G and GTP hydrolysis
