ENZYMES

Enzymes are biological catalysts, and although they are subject to the same laws of chemistry and physics that govern the behavior of other substances, they differ from ordinary chemical catalysts in several important respects:

1. Higher rates of reaction. Enzymes typically speed up rates of reaction by factors of 106 to 1012 over uncatalyzed reactions, and are several orders of magnitude greater than chemically catalyzed reactions.
2. Conditions of reactions. Enzymatically catalyzed reactions occur at relatively low temperatures (rarely above 45 degrees C) and at neutral pHs. Efficient chemical catalysis often requires very high temperatures and pressures and extremes of pHs.
3. Greater reaction specificity. Enzymes have a vastly greater degree of specificity with respect to their substrates than do chemical catalysts. Enzymes are highly specific in both binding their substrates and in catalyzing their reactions.
4. Capacity for regulation. The catalytic activities of many enzymes vary in response to the concentration of substances other than their substrates. The mechanisms of these regulatory processes include allosteric control and variation of the amounts of enzymes synthesized.

THE FORMATION OF THE ENZYME-SUBSTRATE COMPLEX

The forces through which substrates and other molecules bind to enzymes are the same as those forces that determine the conformation of proteins: hydrogen and ionic bonding, and hydrophobic interactions. In general, an active site consists of an indentation or cleft on the surface of an enzyme molecule that is complementary in shape to the substrate (spatial complementarity). Moreover, the amino acid R-groups that form the active site are arranged to interact specifically with the substrate in an attractive manner (chemical complementarity). Molecules that differ in shape and chemistry from the substrate cannot form enzyme substrate complexes that lead to the formation of products. X-ray studies indicate that the active site of most enzymes are largely preformed but that most of them exhibit at least some degree of induced fit upon binding the substrate.

An enzyme-substrate complex illlustrating both the spatial and chemical complementarity between enzymes and their substrates. Hydrophobic groups are represented by an H in a black circle; lines represent hydrogen bonds.

ENZYMES CAN BE INHIBITED BY SPECIFIC MOLECULES

The inhibition of enzymatic activity by specific small molecules and ions is important because it serves as a major control mechanism in biological system. Also, many drugs and toxic agents act by inhibiting enzymes.

Inhibitors are substances that bind to an enzyme in a way that alters its activity or efficiency. Enzyme inhibition can be either reversible or irreversible. As the names suggest, an irreversible inhibitor binds tightly to the enzyme and dissociates from the enzyme very slowly. A reversible inhibitor dissociates rapidly from the enzyme inhibitor complex.

Two classes of reversible inhibitors can be distinguished: competitive and noncompetitive inhibitors. A competitive inhibitor is a substance that competes directly with the normal substrate for the active site of an enzyme. Once bound, the inhibitor masks the active site and prevents the normal substrate molecules from binding. Often competitive inhibitors structurally resemble the normal substrate and specifically bind to the active site, but fail to react. Because the presence of the inhibitor reduces the concentration of free enzyme available for substrate binding, the overall reaction rate will slow. Noncompetitive inhibitors, by contrast, bind to a site other than the active site and prevent the enzyme from catalyzing reactions. The binding of the inhibitor does not block substrate binding, but it does inactivate the enzyme. Because the inhibitor effectively decreases the concentration of active enzyme available for catalysis, the reaction rate will slow.

How can you determine whether or not an inhibitor is a competitive or noncompetitive inhibitor? Competitive inhibition can be overcome if the concentration of substrate is sufficiently high so that most of the active sites of the enzyme are filled by substrate rather than by inhibitor. But because the noncompetitive inhibitor binds at a site other than the active site, noncompetitive inhibition cannot be overcome by increasing the substrate concentration.

Some Features of Active Sites

The active site of an enzyme is the region that binds the substrates (and the prosthetic group, if any) and contributes the residues that directly participate in the making and breaking of bonds. These residues are called the catalytic groups. Although enzymes differ widely in structure, specificity, and mode of catalysis, a number of generalizations concerning their active sites can be stated:

1. The active site takes up a relatively small portion of the total volume of an enzyme. Most of the amino acid residues in an enzyme are not in contact with the substrate. This raises the intriguing question of why enzymes are so big. Nearly all enzymes are made up of more than 100 amino acid residues, giving them a molecular weight greater than 10,000 and a diameter of more than 25Å.
2. The active site is a three-dimensional entity. The active site of an enzyme is not a point, a line, or even a plane. It is an intricate three-dimensional form made up of groups that come from different parts of the linear amino acid sequence--indeed, residues far apart in the linear sequence may interact more strongly than adjacent residues in the amino acid sequence. In lysozyme, the important groups in the active site are contributed by residues numbered 35, 52, 62, 63, and 101 in their linear sequence of 129 amino acids.
3. The specificity of binding depends on the precisely defined arrangement of atoms in an active site. A substrate must have a matching shape to fit into the site. Emil Fischer's metaphor of the lock and key, stated in 1890, has proven to be an essentially correct and highly fruitful way of looking at the stereospecificity of catalysis. However, recent work suggests that the active sites of some enzymes are not rigid. In these enzymes, the shape of the active site is modified by the binding of substrate. The active site has a shape complementary to that of the substrate only after the substrate is bound. This process of dynamic recognition is called induced fit.
4. Substrates are bound to enzymes by relatively weak forces.
5. Active sites are clefts or crevices. In all enzymes of known structure, substrate molecules are bound to a cleft or crevice from which water is largely excluded. The cleft also contains several polar residues that are essential for binding and catalysis. The nonpolar character of the cleft enhances the binding of substrate. In addition, the cleft creates a microenvironment in which certain polar residues acquire special properties essential for their catalytic role.

Download Printable (PDF) Version

Back to Main Menu / Previous Objective / Next Objective /