Bioorganic Reactions

It is not essential to have a background in enzymology or biochemistry to gain at least an introductory-level understanding of many biosynthetic processes, so this book does not deal with enzymology or enzyme structure or function in any significant way, even though much of the chemistry we will be examining depends almost entirely on enzyme catalysis. Nevertheless, we will refer to enzyme catalysis and the names of specific enzymes throughout the text as we examine biosynthetic processes and reactions in significant detail. So what exactly are enzymes? Simply put, enzymes are naturally occurring proteins that catalyze various biochemical reactions in living systems. As we will see, many of the reactions they catalyze are familiar organic reactions, but have specific purposes and target structures. Generally speaking, enzymes catalyze organic reactions by lowering transition state energies or raising ground state energies of reactants in much the same way as nonenzymatic catalysts in laboratory chemical reactions, though in the case of enzyme catalysis, rate enhancements of as much as 1023 have been reported, far exceeding rate enhancements currently achievable by conventional chemical means. Understanding the interaction of enzymes and substrates (reactants) to form an enzyme–substrate complex (E–S complex) is fundamental to having some appreciation for how enzymes carry out their work. While overly simplistic, the “lock-and-key” model of enzyme–substrate interaction provides an intuitive context for understanding the remarkable substrate specificity of enzyme-mediated reactions. Thus, so-called enzyme active sites or binding sites (the “lock”) will only accept certain specific substrate structures (the “key”), with shape, conformation, intermolecular forces, and other factors determining the lock-and-key fit. Enzymes not only catalyze specific kinds of reactions, they can act specifically on certain compounds or classes of compounds or functional groups, often showing remarkable selectivity and stereospecificity, especially in the recognition and/or introduction of chirality centers in organic molecules. In terms of nomenclature, enzyme names always end with an ase suffix and are typically named in accordance with the substrate they act upon and/or the kind of reaction process they catalyze.