Question

3a. The catalytic mechanism of an enzyme involves nucleophilic attack on the substrate by an active site cysteine. Normally, this cysteine has a pKa of 8.2. If the cytoplasm of the cell is pH 7.2 and the pH of the mitochondrial matrix is 8.2, predict whether this enzyme is a better catalyst in the cytoplasm or mitochondria. Explain

Answer 1

Answer -- catalytic mechanism of an enzyme envolves Nucliophilic attack on substrate by the amino acid of active side of enzyme. Those enzymes active side have cysteine ,best function equal or above PH compare to pk valu of side chain. Cysteine side chain pk value 8.2 so above or equal the PH it's side chain deprotonated ( donate H+ ) gives negative chage . These negatively charge side chain attack ( Nucliophilic) over the substrate and reaction continue. So cytoplasm PH 7.2 and mitochondrial matrix PH is 8.2 according to this PH enzyme perform best in mitochondrial matrix. But in an enzyme cysteine side chain pk value shift towards close to 7 due to microenvirment hece it perform reaction in cytoplasm.

For example_ Glyceraldehyde 3 phosphate dehydrogenase enzyme active site have cysteine amino acid and it catalize reaction Glyceraldehyde 3 phosphate to 1,3biphosphoglycerate.these reaction are glycolysis reaction and glycolysis occurs in cytoplasm.