Protein Biosynthesis + Carbohydrates

Question 1

Describe the structure of all RNA as well as the 4 nucleobases

Answer 1

Question 2

Describe the mechanism of amino acid addition to the 3’OH of tRNA for carrying

Answer 2

Requires ATP

Question 3

How do ribosomes make amide bonds?

Answer 3

Ribosomes catalyse the peptidyl transferase reaction

Next, the entire complex shifts to the left

1. The used tRNA at P moves to E and is ejected
2. The newly extended tRNA at A moves to P
3. A new tRNA attaches to the A site and is ready to be extended

Question 4

What was the proposed mechanism of peptidyl transferase?

Answer 4

It was originally thought that histidine in the active site of the ribosome functions as a base to deprotonate the amino group and initiate nucleophilic acyl substitution

Question 5

How was the structure of the ribosome determined and what was found out?

Answer 5

Using x-ray crystallography, the structure of the ribosome was derived

• Bragg’s law was used to derive the structure from various diffraction rays

It was found that the ribosome active site was made out of RNA and not amino acids/protein, so the histidine theory is disproved

Question 6

What is the mechanism of peptidyl transferase attributed to as of now?

Answer 6

• The catalytic activity is now attributed to an adenine residue/nucleobase
• This is why ribosomes are ribozymes (catalytic RNA) and not enzymes (catalytic proteins)

Question 7

What are glycoproteins?

Answer 7

Glycoproteins: proteins with short, branched carbohydrate chains bonded to the side chains of amino acids

Used for receptors, recognition, cell-cell interactions

Ex., blood group antigens A and B

Question 8

What are proteoglycans?

Answer 8

Proteoglycans (mucopolysaccharides): proteins with long, linear carbohydrate chains bonded to the side chains of amino acids

Typically found in connective tissue and cartilage

Question 9

What are peptidoglycans?

Answer 9

Peptidoglycans: long, linear carbohydrates crosslinked to short oligopeptides

Typically found in bacterial cell walls

Question 10

What are lipopolysaccharides?

Answer 10

Lipopolysaccharides: fatty acids linked to carbohydrates

Typically found in the outer envelope of Gram-negative bacteria

Question 11

What is a monosaccharide?

Answer 11

Monosaccharide (“one sugar”): a carbohydrate that cannot be hydrolysed in the lab to a simpler carbohydrate

Question 12

Describe the 2 main ways a monosaccharide is classified

Answer 12

1. According to their number of carbon atoms
   
   • A prefix indicating the number of carbons is followed by the suffix ose
     
     • Triose, tetrose, pentose, hexose
2. Based on the carbonyl group present
   
   • Aldoses have an aldehyde group (most common)
   • Ketoses have a ketone group (assumed to be on carbon 2 if not specified)
     
     1. Note that prefix keto = suffix ulose (ex., pentulose = ketopentose)