An enzyme attracts substrates to its active site, catalyzes the chemical reaction by which products are formed, and then allows the products to dissociate (separate from the enzyme surface). The combination formed by an enzyme and its substrates is called the enzyme–substrate complex. When two substrates and one enzyme are involved, the complex is called a ternary complex; one substrate and one enzyme are called a binary complex. The substrates are attracted to the active site by electrostatic and hydrophobic forces, which are called noncovalent bonds because they are physical attractions and not chemical bonds.

As an example, assume two substrates (S₁ and S₂) bind to the active site of the enzyme during step 1 and react to form products (P₁ and P₂) during step 2. The products dissociate from the enzyme surface in step 3, releasing the enzyme. The enzyme, unchanged by the reaction, is able to react with additional substrate molecules in this manner many times per second to form products. The step in which the actual chemical transformation occurs is of great interest, and, although much is known about it, it is not yet fully understood. In general there are two types of enzymatic mechanisms, one in which a so-called covalent intermediate forms and one in which none forms.

In the mechanism by which a covalent intermediate—i.e., an intermediate with a chemical bond between substrate and enzyme—forms, one substrate, B―X, for example, reacts with the group N on the enzyme surface to form an enzyme-B intermediate compound. The intermediate compound then reacts with the second substrate, Y, to form the products B―Y and X.

Many enzymes catalyze reactions by this type of mechanism. Acetylcholinesterase is used as a specific example in the sequence described below. The two substrates (S₁ and S₂) for acetylcholinesterase are acetylcholine (i.e., B―X) and water (Y). After acetylcholine (B―X) binds to the enzyme surface, a chemical bond forms between the acetyl moiety (B) of acetylcholine and the group N (part of the amino acid serine) on the enzyme surface. The result of the formation of this bond, called an acyl–serine bond, is one product, choline (X), and the enzyme-B intermediate compound (an acetyl–enzyme complex). The water molecule (Y) then reacts with the acyl–serine bond to form the second product, acetic acid (B―Y), which dissociates from the enzyme. Acetylcholinesterase is regenerated and is again able to react with another molecule of acetylcholine. This kind of reaction, involving the formation of an intermediate compound on the enzyme surface, is generally called a double displacement reaction.

Sucrose phosphorylase acts in a similar way. The substrate for sucrose phosphorylase is sucrose, or glucosyl-fructose (B―X), and the group N on the enzyme surface is a chemical group called a carboxyl group (COOH). The enzyme-B intermediate, a glucosyl–carboxyl compound, reacts with phosphate (Y) to form glucosyl-phosphate (B―Y). The other product (X) is fructose.

In double displacement reactions, the covalent intermediate between enzyme and substrate apparently influences the reaction to proceed more rapidly. Because the enzyme is unaltered at the end of the reaction, it functions as a true catalyst, even though it is temporarily altered during the enzymatic process.

Although many enzymes form a covalent intermediate, the mechanism is not essential for catalysis. One substrate (Y) reacts directly with the second substrate (X―B), in a so-called single displacement reaction. The B moiety, which is transformed in the chemical reaction, is involved in only one reaction and does not form a bond with a group on the enzyme surface. The enzyme maltose phosphorylase, for example, directly affects the bonds of the substrates (B―X and X), which, in this case, are maltose (glucosylglucose) and phosphate, to form the products, glucose (X) and glucosylphosphate (B―Y).

Covalent intermediates between part of a substrate and an enzyme occur in many enzymatic reactions, and various amino acids—serine, cysteine, lysine, and glutamic acid—are involved.

The Michaelis-Menten hypothesis

If the velocity of an enzymatic reaction is represented graphically as a function of the substrate concentration (S), the curve obtained in most cases is a hyperbola. The mathematical expression of this curve, shown in the equation below, was developed in 1912–13 by German biochemists Leonor Michaelis and Maud Leonora Menten. In the equation, V_M is the maximal velocity of the reaction, and K_M is called the Michaelis constant,

The shape of the curve is a logical consequence of the active-site concept; i.e., the curve flattens at the maximum velocity (V_M), which occurs when all the active sites of the enzyme are filled with substrate. The fact that the velocity approaches a maximum at high substrate concentrations provides support for the assumption that an intermediate enzyme–substrate complex forms. At the point of half the maximum velocity, the substrate concentration in moles per litre (M) is equal to the Michaelis constant, which is a rough measure of the affinity of the substrate molecule for the surface of the enzyme. K_M values usually vary from about 10⁻⁸ to 10⁻² M, and V_M from 10⁵ to 10⁹ molecules of product formed per molecule of enzyme per second. The value for V_M is referred to as the turnover number when expressed as moles of product formed per mole of enzyme per minute. The binding of molecules that inhibit or activate the protein surface usually results in similar types.

Enzymes are more efficient than human-made catalysts operating under the same conditions. Because many enzymes with different specificities occur in a cell, adequate space exists only for a few enzyme molecules catalyzing one specific reaction. Each enzyme, therefore, must be very efficient. One molecule of the enzyme catalase, for example, can produce 10¹² molecules of oxygen per second. The catalytic groups at the active site of an enzyme act 10⁶ to 10⁹ times more effectively than do analogous groups in a nonenzymatic reaction.

The reason for the great efficiency of enzymes is not completely understood. It results in part from the precise positioning of the substrates and the catalytic groups at the active site, which serves to increase the probability of collision between the reacting atoms. In addition, the environment at the active site may be favorable for reaction—that is, acidic and basic groups may act together more effectively there, or some strain may be induced in the substrate molecules so that their bonds are broken more easily, or the orientation of the reacting substrates may be optimal at the enzyme surface. The theories that have been formulated to account for the high catalytic efficiency of enzymes, although reasonable, still remain to be proved.