hey there!:
A) Knowing theatre the protease is showing the highest activity at pH 4-6, implies that the amino acid that amino acid that it is acting in is an amino acid with a basic side chain. Therefore, the residues can be any one of the three basic amino acids being histidine, arginine or lysine , having basic side chains at neutral pH.
b) The mechanism of reaction of cysteine proteases is as follows:
First step in the reaction is the deprotonation of a thiol in the cysteine proteases's active site by an adjacent amino acid with a basic side chain, which might be a histidine residue. This is followed by a nucleophilic attack by the anionic sulfur of the deprotonated cysteine on the substrate carbonyl carbon.
Here, a part of the substrate is released with an amine terminus, restoring the His into a deprotonated form, thus forming a thioester intermediate, forming a link between the carboxy-terminal of the substrate and cysteine, resulting in thiol formation. Thus the name thiol proteases. The thioester bond is then hydrolyzed into a carboxylic acid moiety while again forming the free enzyme.
C) cysteine proteases have a pka of 8-9 but when they are deprotonated by a His residue, their pka would come down to 6-8, which would be their optimal pH for functioning. This is because there is a deprotonation of the thiol group , later restoring the HIS deprotonated form and then formation of a thioester bond. This thioester bond when hydrolysed will a carboxylate moeity , which is responsible for bringing the pH down towards a more acidic side.
d) at the optimal pH , the fraction of deprotonated cysteine and protonated B will be equal which will change with the change in pH.
Hope this helps!
