Question

1. What is the turnover number? How would you calculate it?

2. Which amino acids are small and hydrophobic? Large and hydrophobic? What type of binding site (meaning what amino acids would it contain) would bin a negatively charged amino acid? A positively charged one? A small hydrophobic one? A large hydrophobic one?

Answer 1

Ans. #1. Turnover number is the rate of product formation per unit time per unit enzyme concentration.

Turnover number (Kcat) = Vmax / [E]_t

where, [E]_t = concentration of enzyme in reaction mixture

            Vmax = Maximum velocity attained in reaction mixture.

#2. A. Amino acids with small, hydrophobic side chains – Glycine, Alanine, Valine, Isoleucine, cysteine.

Amino acids with large, hydrophobic side chain = Tryptophan, Phenylalanine,

#2. B. Oppositely charged particles attract each other whereas the particles with same charge repel each other.

So, amino acids with positively charged side chain (Lys, His, Arg) at the binding site would bind to a negatively charged amino acid.

#2. C. Amino acids with negatively charged side chain (Glutamic acid, aspartic acid) at the binding site would bind to a positively charged amino acid.

#2. D. Unlike charged residues where binding if facilitated by opposite charge on the participating residues, the hydrophobic molecules interact through van del Waals interactions.

A hydrophobic side chain interacts with another hydrophobic residue irrespective of the size. That is, a residue with small hydrophobic side chain bind to another residue with small hydrophobic side chain as well as large hydrophobic side chain; and vice-versa.

So, hydrophobic residues like Gly, Ala, Val, Ile, etc. can bind to the incoming hydrophobic residues irrespective of the size of side chain, only if the incoming substrate can make its path into the binding pocket.