Protein Metabolism

Question 1

What makes up the majority of RNA?

Answer 1

rRNA is approximately 80% of RNA

Question 2

What do mRNA code for?

Answer 2

Proteins

Question 3

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

Answer 3

Protein synthesis

Question 4

What is the start codon?

Answer 4

AUG?

Question 5

What are the 3 stop codons?

Answer 5

UAA UAG UGA

Question 6

What does redundancy of the DNA mean?

Answer 6

There are as many as 6 codons for an amino acid

Question 7

What is a wobble position?

Answer 7

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

Question 8

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

Answer 8

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

Question 9

What causes changes in the reading frame?

Answer 9

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

Question 10

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

Answer 10

3 E.g. GCI CGA GCI CGU CGI CGC

Question 11

How do the codon and anticodon pair?

Answer 11

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

Question 12

What are the types of mutations that affect translation?

Answer 12

Missence mutation Nonsense mutations Insertion/deletions

Question 13

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

Answer 13

Frameshift mutations for non 3n changes

Question 14

What is a silent mutation?

Answer 14

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

Question 15

What is an aminoacyl-tRN synthetase?

Answer 15

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

Question 16

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

Answer 16

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)

Question 17

What is a charged tRNA?

Answer 17

tRNA is carrying an Amino acid

Question 18

What does tRNA specificity based on?

Answer 18

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

Question 19

How does aminoacyl-tRNA synthetase discriminate between different tRNA?

Answer 19

Through interactions with the acceptor stem and anticodon

Question 20

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

Answer 20

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

Question 21

How does the tRNA synthetase correct errors?

Answer 21

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

Question 22

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

Answer 22

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)

Question 23

What are ribosomes?

Answer 23

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

Question 24

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

Answer 24

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

Question 25

What are the initiation factors for prokaryotes?

Answer 25

IF1, IF2 and IF3

Question 26

What must happen before translation begins in prokaryotes?

Answer 26

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)

Question 27

What does IF3 do?

Answer 27

Prevents the 30S and 50S subunit from combining prematurely

Question 28

What does IF1 do?

Answer 28

Prevents the use of the A site in initiation

Question 29

What does IF2 do?

Answer 29

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

Question 30

What ribosome is for prokaryotes and which is for eukaryotes?

Answer 30

Pro: 70S Eu: 80S

Question 31

What is the nascent protein always attached to?

Answer 31

Always covalently bound to a tRNA during protein synthesis

Question 32

How does elongation occur in bacterial protein synthesis?

Answer 32

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

Question 33

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

Answer 33

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

Question 34

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

Answer 34

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

Question 35

What guides aminoacyl-tRNA to the A binding site?

Answer 35

EF-Tu (Elongation Factor - Thermally unstable)

Question 36

How is termination in translation done for prokaryotes?

Answer 36

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.

Question 37

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

Answer 37

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)

Question 38

What is the A site in a ribosome?

Answer 38

The Acceptor site, associated with mRNA codon

Question 39

What is the p site in ribosomes?

Answer 39

Peptide transferase site, associated with mRNA codon

Question 40

What is the E site in ribosomes?

Answer 40

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

Question 41

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

Answer 41

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

Question 42

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

Answer 42

16s rRNA