Almost every chemical reaction in a cell is catalyzed by a class of proteins called enzymes.  Catalysts increase the rates of reactions that are already energetically favorable by lowering the activation energy (see Figure 2-27). In the test tube, catalysts such as charcoal and platinum facilitate reactions but often at high temperatures, at extremes of high or low pH, or in organic solvents. In contrast to these harsh conditions, enzymes must catalyze chemical reactions in the mild conditions of a cell: 37 °C, pH 6.5–7.5, and aqueous solvents. As we just discussed, all antibodies belong to the immunoglobulin family of proteins and have a similar structure. Enzymes, however, are a structurally diverse group of proteins that have evolved through unrelated and highly divergent mechanisms.

The ability of enzymes to function as catalysts under conditions where nonbiological catalysts would be ineffectual is exemplified by two striking properties: their enormous reaction rates and their specificity. Quite often, the rate of an enzymatically catalyzed reaction is 10⁶–10¹² times that of an uncatalyzed reaction under otherwise similar conditions. The specificity of an enzyme denotes its ability to act selectively on one substance or a small number of chemically similar substances, the enzyme’s substrates. Enzyme specificity depends on a close fit between substrate molecules and their binding sites on an enzyme. 

Enzymatic specificity is usually quantified in relative terms; that is, the reaction with a good substrate may occur, for example, 10,000 times faster than it does with a poor substrate. The catalytic action of an enzyme on a given substrate can be described by two parameters: K_m (the Michaelis constant), which measures the affinity of an enzyme for its substrate, and V_max, which measures the maximal velocity of the reaction at saturating substrate concentrations. Equations for K_m and V_max are most easily derived by considering the simple reaction

For an enzyme with a single catalytic site, Figure 3-26a shows how the rate of product formation depends on [S] when [E] is kept constant. At low concentrations of S, the reaction rate is proportional to [S]. As [S] is increased, the rate does not increase indefinitely in proportion to [S]; rather, it eventually reaches a maximum velocity V_max. The value of V_max is independent of [S], but is proportional to [E] and to the catalytic constant k_cat, which is an intrinsic property of the individual enzyme. Halving [E] reduces the reaction rate at all values of [S] by half. Both V_max and K_m for a particular enzyme and substrate can be determined from experimental curves of reaction velocity versus substrate concentration, as illustrated in Figure 3-26.

Most reactions in cells do not occur independently of one another or at a constant rate. Instead, the catalytic activity of enzymes is so regulated that the amount of reaction product is just sufficient to meet the needs of the cell. As a result, the steady-state concentrations of substrates and products will vary depending on cellular conditions. The flow of material in an enzymatic pathway is controlled by several mechanisms, some of which also regulate the functions of nonenzymatic proteins.

One of the most important mechanisms for regulating protein function entails allosteric transitions changes in the tertiary and/or quaternary structure of a protein induced by binding of a small molecule, which may be an activator, inhibitor, or substrate. Allosteric regulation is particularly prevalent in multimeric (multisubunit) enzymes. Some multimeric enzymes are composed of identical subunits, each containing an active site and, often, a distinct regulatory site. Other enzymes comprise structurally different subunits; in these, active sites and regulatory sites may be located on different subunits.

Many multimeric enzymes undergo allosteric transitions that alter the relationship of the subunits to one another. A wellunderstood enzyme illustrating this mechanism is aspartate transcarbamoylase (ATCase). This bacterial enzyme catalyzes the first step in the pyrimidine biosynthetic pathway:

ATCase, which is composed of six catalytic subunits and six regulatory subunits, exists in an active R state and inactive T state (Figure 3-28). The equilibrium between these states is shifted toward the inactive T state by binding of cytidine triphosphate (CTP), an end product of the pyrimidine pathway, to the regulatory subunits. Thus CTP is an allosteric inhibitor of ATCase. The CTP-induced allosteric transition in ATCase is an example of feedback inhibition, whereby an enzyme that catalyzes an early reaction in a multistep pathway is inhibited by an ultimate product of the pathway. Clearly, this type of regulation prevents accumulation of pyrimidines in excess of what the cell needs for DNA synthesis.

The mechanism of feedback inhibition helps regulate most biosynthetic pathways; that is, the final product of the pathway inhibits the enzyme that catalyzes the first step, thus preventing both production of the intermediate products and unnecessary metabolic activity. Feedback inhibition of enzyme function is reversible. If the concentration of free feedback inhibitor (e.g., CTP) falls, the bound inhibitor dissociates from the regulated enzyme, which then reverts to its active conformation. The binding of a feedback inhibitor to an enzyme and its subsequent release can be described by the equilibrium binding constant K_i, which is similar to the Michaelis constant K_m used to describe substrate binding.

In many cases, especially when a protein binds several molecules of one ligand, the binding is graded; that is, binding of one ligand molecule affects the binding of subsequent ligand molecules. Such cooperative allostery, or cooperative binding, permits many multisubunit proteins to respond more efficiently to small changes in ligand concentration than would otherwise be possible. In positive cooperativity, sequential binding is enhanced; in negative cooperativity, sequential binding is inhibited.