Question

1. Explain how covalent catalysis contributes to the function of the serine protease.
2. Examine each of the different major classes of proteases. In what way is the mechanism of each class similar, and different, to the serine protease mechanism?

Answer 1

Ans.1:  Serine proteases are involved in an enormous number of biological processes.These are Proteolytic enzyme with a serine residue (Ser) in its active site.Serine is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines.Serine proteases cleave peptide bonds in proteins, in which serine serves as the nucleophilic amino acid at the enzyme's active site.

Covalent Catalysis is one of the four strategies that an enzyme will use to catalyze a specific reaction, which involves the formation of a transient covalent bond between a substrate and a residues in the enzyme active site or with a cofactor.Covalent catalysis occurs when the substrates in an enzymatic reaction become temporarily covalently attached to the enzyme during the catalytic reaction. In this reaction the enzyme contains a reactive group, usually a nucleophilic residue which reacts with the substrate through a nucleophilic attack.In covalent catalysis, an additional covalent intermediate is added to the reaction, and helps to reduce the energy of transition states in the later stages of the reaction. The productive arrangement of catalytic residues in the serine protease active site is optimized not only to position ser residue but also to subtly shift the position of His residue as the cycle progresses, to favor catalysis.

Example: Chymotrypsin is an example of the use of covalent catalysis in serine protease function.

Ans.2: Proteases are a protein-digestive enzyme that cleaves protein through hydrolysis, the addition of water to the peptide bond. Although hydrolysis of the peptide bond is thermodynamically favored, it is still a slow reaction without the enzyme.

There are Four major class of Proteses, they are:

(i) Serine Proteases- Serine Proteases use serine residue to create a nucleophilic amino acid that cleaves the peptide bond. They are responsible for various functions such as blood clotting, and digestion.

(ii)Cysteine Protease-  Cysteine Proteases is one of proteases enzyme that cleave protein by cleave the peptide bond.It polarizes the peptide carbonyl group to get it activated for attack, and upon attack by the nucleophile, a stabilizing tetrahedral intermediate is generated. But different from chymotrypsin enzyme, in this enzyme, a cysteine residue, activated by histidine residue play a nucleophilic attack the peptide bond.

Eg: Papain is a protein-cleaving enzyme derived from papaya fruit

(iii)Aspartyl protease- Aspartyl proteases are one of the eukaryotic protease enzymes that catalyze peptide substrates using aspartate residue. It is usually in an acidic pH range which is inhibited by pepstatin.On the active sites of aspartyl proteases, there are aspartic acid residues that work together to promote a water molecule to attack the peptide bond. One of the aspartic acid residues will activate the water molecule by attracting the hydrogen atom of water. The other aspartic acid residue will polarize the carbonyl group on the peptide making it easier to attack.

Eg: Renin, an enzyme that supports the regulation of blood pressure.

(iv)Metalloproteases- Metalloproteases contain an active site that has a bound metal ion.The metal ion activates a water molecule to carry out a nucleophilic attack on a carbonyl peptide bond. A base is present to help deprotonate the metal-bound water.Bound to the active site is a base that pulls a proton from the water molecule bound to the metal in order to turn the water molecule into a nucleophile to attack the peptide bond.

Eg: Carboxypeptidase A and B, as well as thermolysin, which are digestive enzymes.