Enzymes are specialized proteins, which accelerate or catalyze a biochemical reaction. Each enzyme catalyzes a specific reaction and is regulated by competitive and noncompetitive inhibitors and/or by allosteric molecules. Multiple enzymes can catalyze a series of consecutive reactions, known as pathways, to produce and/or break down complex biological molecules. Examples include amino acid synthesis and degradation, the coordinated reactions involved in protein synthesis, and the urea cycle. Problems with enzyme pathways can not only lead to disease but also offer the opportunity for disease treatment via medications, which target specific points in these pathways.

Enzyme Reactions

Enzymes bring together one or more molecules, called substrates, to form a resulting molecule called a product (Figure 5-1). Most enzymes catalyze one specific reaction. However, some multipart enzyme complexes catalyze a series of step-by-step reactions—the first enzyme passes its product, now a new substrate, to a second enzyme that is part of the complex, the second passes its product to a third and so on. Enzymes are responsible for many essential reactions in the human body; in fact, there are from 20,000 to 25,000 total human genes, with about 25% of them producing enzymes. It is not surprising that problems with enzymes are caused by or result in diseases.

The concept of enzyme kinetics allows an exact description of the enzymatic reaction, including the influence of substrate and product molecules and how fast the enzyme catalyzes the reaction and the impact. More advanced enzyme kinetics allows the mathematical expression of how other molecules such as cofactors, inhibitors, and activators (see below) affect the enzyme reaction.

For example, as discussed in Chapter 1, specific amino acids form an enzyme’s primary structure and, therefore, secondary to quaternary structure. These structures, in turn, form substrate-binding sites (also known as the “active site”) to accommodate the substrates, their chemical reaction, and the departure of the product. Substrates and products can both be a hydrophobic, hydrophilic, charged, uncharged, or neutral molecule, or a combination of the above. Mutations that result in the change of an amino acid or amino acids that make the substrate pocket can drastically change the enzyme’s activity. For example, a hydrophobic substrate will easily enter an enzyme pocket that is lined with hydrophobic amino acids. However, if one of these hydrophobic amino acids is changed to a highly charged amino acid, the substrate may not be able to enter the pocket and the enzyme may no longer function. How well the substrate interacts with the substrate-binding site represents the “affinity” of the enzyme for the substrate. The stronger the affinity, the less substrate is needed to achieve a certain rate of reaction. This concept is important if a mutation changes the substrate-binding site and lowers the affinity. This concept is illustrated in Figure 5-1.

The number of molecules of substrate increases or decreases the likelihood of the substrate interacting with the enzyme and, therefore, the rate of the reaction. When all of the enzyme molecules have substrate occupying the binding sites, the enzyme is said to be saturated by substrate and the rate of the reaction is maximized. If lower amounts of substrate are present, the reaction would also be slower than normal, potentially leading to clinical manifestations. If a disease state causes a molecule to abnormally increase in concentration, it may become a substrate for an enzyme with which it would normally not react.

The final factor that decides maximum rate of the reaction is the efficiency at which an enzyme can catalyze a single reaction. Enzyme mutations can diminish this efficiency, although, in rare instances, a mutation can increase activity. Likewise, the cell has regulatory molecules that can change the rate of the reaction by decreasing or increasing the efficiency of the enzyme.

Cofactors

Enzyme reactions often require additional molecules called cofactors (Figure 5-2). Examples of these cofactors include vitamins, nicotinamide adenine dinucleotide (NADH), nicotinamide adenine dinucleotide phosphate (NADPH), flavin adenine dinucleotide (FADH2), and coenzyme A (CoA). For example, during an enzyme reaction, NADH or NADPH donates a hydrogen atom as well as electrons to the product and becomes NAD+ or NADP+, respectively, and are then released. FADH2 also donates electrons and two hydrogen atoms to produce FAD. Conversely, NAD+, NADP+, and FAD accept electrons to become the respective reduced forms. Some inorganic metal ions such as iron (Fe), copper (Cu), calcium (Ca), manganese (Mn), magnesium (Mg), or zinc (Zn) also serve as cofactors for reactions. Metal ions may contribute or accept an electron (e.g., Fe2+ → Fe3+) or their associated charge may simply provide essential stabilization for the chemical reaction without changing the metal.