The focus of this book is on organic chemistry in a biological context. At various points in our investigation of organic reactivity, however, we will also be considering some non-biological, laboratory counterparts of reactions that occur in living cells. The reason for this is two-fold: first of all, it is often instructive to compare and contrast similar reactions taking place in very different environments, and sometimes the similarities are quite striking. Secondly, even those who intend to pursue a career in the life or health sciences can benefit from some exposure to the kind of challenges that professional organic or medicinal chemists work on: if you are working as a biologist for a pharmaceutical company for example, you will be better able to appreciate the contributions of your chemist colleagues if you are able to make the intellectual connection between the reactions they are running in flasks and those that are taking place in the cells you are studying.
Below we briefly outline the differences between laboratory and biological reactions:
- Catalysts: The vast majority of biological organic reactions are catalyzed by enzymes. While chemists synthesizing molecules in the laboratory sometimes make use of enzyme-catalyzed reactions, it is much more common to use non-biological catalysts (often containing transition metals), acids or bases as catalysts, or no catalyst at all.
- Solvent: Biological organic reactions occur in the aqueous environment of the cell. In the laboratory, organic reactions can be run in a wide variety of solvents, ranging from the very nonpolar (such as hexane) to the very polar, such as methanol,water, or even ionic liquids. Most commonly, though, laboratory reactions are run in relatively non-polar solvents such as diethyl ether or dichloromethane.
- Reactant mixture: The aqueous environment of a cell is an extremely complex mixture of thousands of different biomolecules in solution at low concentrations (usually nanomolar to millimolar), whereas the components of a laboratory reaction have usually been purified, and are present in much higher concentrations.
- Temperature: Biological reactions take place within a narrow temperature range specific to the organism: a little too cold and the enzymes catalyzing the reactions are 'frozen', a little too hot and the enzymes will come unfolded, or 'denature'. Laboratory reactions can be run at a variety of temperatures, sometimes at room temperature, sometimes at the boiling point of the solvent, and sometimes at very low temperatures (such as when a reaction flask is immersed in a dry ice-acetone bath).
- pH: Biological reactions take place in aqueous solution buffered to a specific pH: about pH 7 for most living things. Accordingly, highly acidic or basic species are unlikely to be reactants or intermediates in a biological reaction mechanism. Laboratory reactions are often carried out in the presence of strong acids or bases.