Question

Essay Question: Discuss the moleculear interactions in the active site that allow the substrate to bind to the enzyme. Please be descriptive.

Answer 1

The active site of an enzyme corresponds to the region where a substrate bind to the enzyme during enzymatic reaction. Even though the active sites resembles 10-20 % of the protein (enzyme), only 3-4 amino acids actively participates in the catalytic reaction and form catalytic sites, rest of the amino acids contributes to the three-dimensional structure. Enzymes are specifically designed to respond particular substrate, as the catalytic active sites are very specific to substrate. Usually, the active site found into the grooves or tunnel of the enzyme. Interestingly, the nature of the active sites or amino acids does not change after reactions and they reduced the activation energy of the reaction which results faster and efficient reaction or higher turnover due to more number of substrate with enough energy to participate in reaction.

There are two theory proposed for the enzyme substrate binding: lock and key hypothesis & induced fit hypothesis. According to the lock and key hypothesis, proposed by Emil Fischer, enzyme active site and substrate have stable complementary structure due to which the exactly fit to each other, with strong affinity and highest catalytic efficiency. On the other hand, induced fit hypothesis, proposed by Daniel Koshland's, suggest both active site and substrate structure are not complementary, in fact active site undergoes into a transformational change to significantly bind with substrate. This theory suggest active site surface is flexible and it under went to conformation changes upon binding to the substrate.

Typically, most of the enzyme has two binding sites where specific substrate binds and re-oriented for catalysis. The initial binding of the substrate involves temporal non-covalent interaction as both should not repel during initial binding. Due to this reason binding sites mostly contain non-polar amino acids. The binding/interaction between substrate and active site involves four forces/non-covalent interactions which hold the substrate and keep it in proper orientation. a) Van der Waals force: this is a week force formed between opposite charged substrate and amino acids within catalytic sites.

b) Hydrogen bond: involves dipole-dipole interaction between substrate and amino acids of catalytic sites, where positively charged hydrogen form bond with negatively charged oxygen or sulphur.

c) Electrostatic interaction: in aqueous medium, when both opposite charged substrate and amino acids within catalytic sites.

d) Hydrophobic interaction: It happens when hydrophobic groups which are water repelling groups curl inside into a aqueous medium leaving hydrophilic group outside exposed to the aqueous medium.