Question

Under typical conditions, many essential biochemical reactions proceed so slowly that life could not exist without the presence of enzymes. Enzymes increase reaction rates through a wide variety of mechanisms. These mechanisms generally utilize the following strategies: improving the nucleophiles and electrophiles present in the catalytic R groups or substrates; stabilizing the extra electron density of the leaving group; and stabilizing transition states. Proteases are enzymes that break down proteins by hydrolyzing peptide bonds. Chymotrypsin is a protease found in the digestive tract that cleaves peptide bonds on the C-terminal side of large hydrophobic amino acids. Depicted below are a peptide substrate and the three catalytic residues within the chymotrypsin active site. Note that the 2-dimensional geometry is only roughly shown. R1 represents a large hydrophobic amino acid and R represents other amino acids. The R groups of the catalytic triad of aspartate (Asp102), serine (Ser195), and histidine (His57) are shown. Select the atoms that act as nucleophiles and electrophiles in the acylation phase of the reaction.

Select the 2 atoms that act as nucleophiles in the acylation phase. Note: As shown below, the nucleophilic atoms might be weak nucleophiles, but they become strong in the process of catalysis.

In the first step of the Chymotrypsin mechanism, an alkoxide ion on Ser195 attacks the carbonyl carbon of the peptide substrate. What aspects of the Chymotrypsin active site facilitate the formation of the alkoxide ion on Ser195?

I'm confused because I thought all the oxygens and nitrogens would be nucleophiles and the adjacent carbons would be electrophiles, I tried that but it didn't work

Answer 1

Concepts and reason

Enzymes are the biological catalysts that enhance the rate of biological reactions by lowering the activation energy required for the reaction to take place without being itself consumed in the reaction. A French chemist, Anselme Payen first discovered the enzyme, diastase in the year, 1833. The word enzyme was first used by Wilhelm Kuhne in the year, 1877.

Fundamentals

Enzymes are mostly proteins by nature and are known to catalyze more than 5,000 biochemical reactions. The enzymes act on the substrate and convert it into product. The active site of the enzyme interacts with the substrate to form an enzyme substrate complex.

This binding site of the enzyme consists of the amino acids, which give a three dimensional configuration to the active site that is unique for each substrate. The binding of the specific substrate only allows the reaction to proceed.

Serine proteases are the enzymes that act on the peptide bonds between the proteins. Some examples of serine proteases include Chymotrypsin, trypsin, elastase, etc. The enzyme chymotrypsin enhances the rate of hydrolysis and it does not catalyze the direct attack of water on peptide bond in a reaction. The reaction catalyzed by chymotrypsin occurs in two phases – acylation phase and deacylation phase.

The atoms that act as nucleophiles are nitrogen “N” of His57 and “O” of Ser195. The atoms that act as electrophiles are “H” on Ser195 and “C” on peptide substrate. The structure of active site of chymotrypsin is:

Aspartate (Asp 102), Serine (Ser 195), and Histidine (His 57) form the catalytic triad of the chymotrypsin. From the structure of active site of the chymotrypsin it can be seen that serine is bonded to histidine, which is further bonded to Aspartic acid. This bonding network favors the proton transfer between the His 57 and Ser 195. The formation of alkoxide ion on Ser 195 is favored by enhancing the basicity of His 57.

Ans: