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Biochem - Year 1 Biomed > Translation Gene Expression (ecoli) > Flashcards

Translation Gene Expression (ecoli) Flashcards

1
Q

What does degenerate code mean

A

64 codons code for 20 amino acids so more corona for 1 amino acid

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2
Q

What are the 3 stop codons which don’t code for a amino acid

A

UAA UAG UGA

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3
Q

Which 2 things can AUG code for

A

Formyl methionine (initiator trna)

Methionine

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4
Q

Is the code always universal?

A

No some exceptions eg mitochondria have different codons

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5
Q

Explain the structure of trna

A

5’ monophosphate molecule
Clover shape

D loop 
T loop 
Anticodon site 
Variable arm 
AA acceptor site
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6
Q

What codon is on the amino acid acceptor site usually and is it 5’ or 3’ end

A

CCA

It’s 3’ end meaning an OH is present

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7
Q

What are the 4 modified bases on the trna and name the most useful one

A

Ribo thymidine

Pseudo uridine

Dihydro uridine

INOSINE (most useful)

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8
Q

What is the process called of amino acids joining trnas

A

Aminoacylation of trna

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9
Q

Which enzyme catalyses aminoacylation

A

Trna synthetase

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10
Q

Explain the process of aminoacylation of a trna

A

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

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11
Q

Why is the ester bond formed by the amino acid and the amino acid acceptor site important

A

The energy of the ester bond is used to form a peptide bond

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12
Q

What is an amp molecule attached to the carboxyl of amino acid called

A

Aminoacyl adenylate

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13
Q

Why is there 2 classes of trna synthetases (class I and class II)

A

Both specific for 10 AA each
Interact with trna differently
Eg threonyl trna synthetase = for threonine

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14
Q

What are identity elements on trna?

A

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

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15
Q

How many different trnas for amino acids are there

A

40

Eg leucyl trna(leu)

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16
Q

Why do trna synthetases need to distinguish between amino acids aswell?

A

Because they can be similar eg threonine and serine

Threonyl synthetase needs to distinguish

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17
Q

How is proof reading done to allow the right amino acids to attach to trna

A

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

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18
Q

What does the editing and acylation site do on trna synthetases

A

Editing - cleaves small AA

Acylation - cleaved too large AA

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19
Q

What is the serine trna called before and after acylation

A

Trna ser before

Seryl trna ser (aminoacyl trna)

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20
Q

How are trnas specific to 1 amino acid on the mrna codon sequence

A

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

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21
Q

What is the wobble hypothesis

A

Because only 40 trnas but 64 codons for 20 amino acids, the trna anticodons need to change/pair with more than 1 codon

22
Q

Which base changes on the anticodon in the wobble hypothesis

A

The 3rd base on anticodon (at 5’)

23
Q

What are the H bonds called in wobble hypothesis

A

Non standard H bonds (between the 5’ base on trna and 3’ on mrna)

24
Q

Why is inosine important in the wobble hypothesis

A

It binds to either A,C or U on the codon

25
Q

What happens if the wobble base is A?

A

Converted to inosine by anticodon deaminase enzyme

26
Q

What 2 bases arent found at the wobble base site (3’)

A

A and U

Deaminase converts A to inosine

27
Q

Which codon bases does G bind to

A

C or U

28
Q

Explain the structure of inosine and how it helps to bind to A,C and U

A

It’s a purine

Has 1 double bond oxygen allowing it to bind to C,U and A with 2 bonds

29
Q

What are ribosomes made of

A

Ribonucleotide proteins

Rrna and proteins

30
Q

What is the large subunit made up of

A

50S

23s rrna + 5srrna

31 proteins

31
Q

What is the small subunit made up of

A

30s

21 proteins

16s rrna

32
Q

What does S mean

A

Svedberg unit

33
Q

Which 2 rrna are important in translation

A

23s in the large 50s subunit

16s in the small 30 s subunit

34
Q

Which initiator trna starts translation

A

Formyl-methionyl trnaF

F met trna

35
Q

What occurs first in initiation of translation

A

Methionine and trna f are joined by trna synthetases to form amino acyl trna (normal acylation steps)

(Methionyl trna met)

36
Q

How is met trna f turned into formyl methionine trna f met

A

Methionine is formylated by formyl transformase enzyme

Formyl tetrahydrofolate is turned into tetrahydrofolate

= formyl methionine trna f

37
Q

What happens once the 30s ribosome binds to the shine dalgarno sequence (ending AUG)

A

Allows attachment of Fmet trna f

Fmet trna binds to the AUG by the anticodon h bonding

38
Q

What happens in initiation once f met trna binds to AUG

A

The 50s ribosome binds forming the 70s initiation complex

39
Q

How is the 16s rrna on the 30s ribosome (small subunit) important in initiation

A

Forms comp base pairs with the shine dalgarno sequence so the 30s subunit can bind and bring Fmet trna

40
Q

Name the 3 initiation factors and which one is bound to GTP

A

IF1, IF2, IF3

IF2 is bound to a GTP

41
Q

What happens to initiation factors in initiation

A

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

42
Q

What is needed to produce the 70s initiation complex

A

GTP hydrolysis (the GTP on the IF2 factor)

43
Q

What are the 3 subunits of the 50s ribosome called

A

E - exit site
P- peptidyl site
A- aminoacyl site

44
Q

What happens in elongation

A

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

45
Q

Which 2 elongation factors are needed for a new aminoacyl trna to be transferred to A site

A

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

46
Q

How is EF - G elongation factor needed to translocate the ribosome

A

EF -G needed

GTP is hydrolysed and then this allows for the EF G to be free and allow further translocation

47
Q

How is a peptide bond formed

A

The amine NH2 group of a new amino acid attacks the carbonyl ester O bond on the previous aminoacyl trna

48
Q

What catalyses formation of peptide bond

A

The 23s rrna on the 50s ribosome

49
Q

Which 3 release factors attach to termination codons (UAA, UGA, UAG) allowing cleavage of polypeptide

A

RF1, RF2, RF3.GTP

50
Q

Explain steps of termination using Release factor 1 and 3.GTP

A

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

51
Q

What allows ribosome dissociation at terminator sequence

A

RRF ribosome release factor

And EF-G and GTP hydrolysis

Biochem - Year 1 Biomed (21 decks)

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