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Mcb1 > Protein Metabolism > Flashcards

Protein Metabolism Flashcards

1
Q

What makes up the majority of RNA?

A

rRNA is approximately 80% of RNA

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2
Q

What do mRNA code for?

A

Proteins

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3
Q

rRNAs form part of the structure of ribosomes and participate in what function?

A

Protein synthesis

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4
Q

What is the start codon?

A

AUG?

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5
Q

What are the 3 stop codons?

A

UAA UAG UGA

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6
Q

What does redundancy of the DNA mean?

A

There are as many as 6 codons for an amino acid

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7
Q

What is a wobble position?

A

Mean’s there is steric freedom at this site (typically an anticodon of an tRNA); other bases may pair This is position 1 of the anti codon but position 3 of the codon

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8
Q

Codons that differ in their first two bases have their own tRNA, why?

A

It may code for a different aa or due to steric hindrance Wobble position

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9
Q

What causes changes in the reading frame?

A

For a given mRNA any non-N3 insertions/deletions cause alteration of the reading frame

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10
Q

When the anticodon has an Inosine at position 1, how may different codons can it pair with?

A

3 E.g. GCI CGA GCI CGU CGI CGC

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11
Q

How do the codon and anticodon pair?

A

Anti parallel E.g Anticodon 3 2 1 U A G A U C 1 2 3 Codon Position 1 on the anticodon matches with position 3 of the codon

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12
Q

What are the types of mutations that affect translation?

A

Missence mutation Nonsense mutations Insertion/deletions

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13
Q

What happens in insertion and deletions in respect to the reading frame?

A

Frameshift mutations for non 3n changes

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14
Q

What is a silent mutation?

A

DNA base-pair substitutions which do not affect the amino acid coding

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15
Q

What is an aminoacyl-tRN synthetase?

A

An ezyme that carry out two couple reactions 1. Amino acid is activated by reaction with ATP to give an aminoacyl -AMP intermediate 2. Amino acids are coupled to tRNA’s by an ester linkage between the carboxyl group of the amino acid and the 2’ or 3’ OH of the 3’ A-residue of the tRNA

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16
Q

Why must enzymes be very precise? (Aminoacyl-tRNA synthetase)

A

They bridge between 3-letter codon code and specific amino acids Each enzyme is specific for one amino acid and one or more corresponding tRNAs (so ~20 enzymes)

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17
Q

What is a charged tRNA?

A

tRNA is carrying an Amino acid

18
Q

What does tRNA specificity based on?

A

On the specific bases in the anticodon and other bases elsewhere in the tRNA

19
Q

How does aminoacyl-tRNA synthetase discriminate between different tRNA?

A

Through interactions with the acceptor stem and anticodon

20
Q

What is the mechanism of aminacylation by aminocyl-tRNA synthetase?

A

Step 1. Amino acid activation by ATP with the release of phosphate Step 2. Binding the activated amino acid to terminal A residue of the tRNA

21
Q

How does the tRNA synthetase correct errors?

A

It moves the 3’ end of the amino acid from the synthesis site to the editing site and there the amino acid will be removed

22
Q

What is the mechanism for formylmethionyl-tRNA (fMet-tRNA(/f))?

A
  1. Initiator tRNA (tRNA (/f)) - first charged with methionine. 2. Formally group is transferred to the methionyl- tRNA (^fMet) from N10-formyltetrahydrofolate (Role of formulation of the amino group is that this Met can no longer inserted in the interior of the polypeptide chain)
23
Q

What are ribosomes?

A

Translation machines consisting of more than 20 different proteins no 3 or more different ribosomal RNA 70s = 50s + 30s 80s = 60s + 40s

24
Q

What are the components of 70s and 80s ribosomes?

A

70s: 50s(5s rRNA and 23S rRNA) and 30s ( 16S rRNA) 80s: 60s(5s, 28s, 5.8s rRNA) and 40s (18s rRNA)

25
Q

What are the initiation factors for prokaryotes?

A

IF1, IF2 and IF3

26
Q

What must happen before translation begins in prokaryotes?

A

Pairing of mRNA with the 3’ end of 16S rRNA, mediated by the Shine-Dalgarno sequence -6 bases upstream of he AUG Pairing of mRNA AUG with anticodon of the initiator mrthionyl-tRNA (^fMet)

27
Q

What does IF3 do?

A

Prevents the 30S and 50S subunit from combining prematurely

28
Q

What does IF1 do?

A

Prevents the use of the A site in initiation

29
Q

What does IF2 do?

A

Chaperones the anticodon onto the P site (where it’s suppose to go)

30
Q

What ribosome is for prokaryotes and which is for eukaryotes?

A

Pro: 70S Eu: 80S

31
Q

What is the nascent protein always attached to?

A

Always covalently bound to a tRNA during protein synthesis

32
Q

How does elongation occur in bacterial protein synthesis?

A

The cycle begins with peptidyl-tRNA in the P site. An aminoacyl-tRN guided by EF-Tu binds in the A site. When both sites re occupied a new peptide bond is formed by 23S rRNA The ribosomal subunits are translocated by elongation factor G, which moves the decay latex tRNA to the E site Deacylated tRNA is free to dissociate once in the E site

33
Q

What does 23S rRNA do during elongation of bacterial protein synthesis?

A

Forms a new peptide bond between an aminoacyl-tRNA and peptidyl-tRNA with peptidyl-transferase activate

34
Q

What does elongation factor g do in elongation of bacterial protein synthesis?

A

Moves the deacylated tRNA to the E site (from P)

35
Q

What guides aminoacyl-tRNA to the A binding site?

A

EF-Tu (Elongation Factor - Thermally unstable)

36
Q

How is termination in translation done for prokaryotes?

A

Termination of translation by release factors that are proteins with tRNA shapes. Binding of release factors force the peptide transferase to add water instead of an amino acid to the peptide tRNA.

37
Q

How many high energy phosphate bonds are consumed during translation of 1 amino acid?

A

Total of 4: 2 from ATP (when charging each tRNA with an amino acid) One GTP (for binding the charged tRNA to the ribosomal A-site) One GTP (for the translocation step) (Initiation and termination also require ATP/GTP)

38
Q

What is the A site in a ribosome?

A

The Acceptor site, associated with mRNA codon

39
Q

What is the p site in ribosomes?

A

Peptide transferase site, associated with mRNA codon

40
Q

What is the E site in ribosomes?

A

The exit site, not associated with mRNA codon, less well define in eukaryotic ribosomes

41
Q

What are the non-traditional base pairing seen in the wobble position? (This position is base 3 of codon and base 1 of anticodon)

A

On tRNA: on mRNA A: U G: C,U U: A,G C: G I: U,C,A

42
Q

What does the Shine-Dalgarno consensus sequence pair up with?

A

16s rRNA

Mcb1 (13 decks)

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