As we explained in Chapter 1, organic chemistry is the study of compounds that contain car bon. Nearly all organic compounds also contain hydrogen; most also contain oxygen, nitro gen, or other elements. Organic chemistry concerns itself with the way in which these atoms are bonded together into stable molecular structures, and the way in which these structures change in the course of chemical reactions. Some molecular structures are shown below. These molecules are all amino acids, the con stituents of proteins. Look at the number of carbon atoms in each molecule and the way they are bonded together. Even within this small class of molecules there’s great variety—glycine and alanine have only two or three carbon atoms; phenylalanine has nine.

Lysine has a chain of atoms; tryptophan has rings.

In methionine the atoms are arranged in a single chain; in leucine the chain is branched. In proline, the chain bends back on itself to form a ring.

Yet all of these molecules have similar properties—they are all soluble in water, they are all both acidic and basic (amphoteric), they can all be joined with other amino acids to form proteins. This is because the chemistry of organic molecules depends much less on the num beror the arrangement of carbon or hydrogen atoms than on the other types of atoms (O, N, S, P, Si...) in the molecule. We call parts of molecules containing small collections of these other atoms functional groups, simply because they are groups of atoms that determine the way the molecule works. All amino acids contain two functional groups: an amino (NH2 or NH) group and a carboxylic acid (CO2H) group (some contain other functional groups as well).

That isn’t to say the carbon atoms aren’t important; they just play quite a different role from those of the oxygen, nitrogen, and other atoms they are attached to. We can consider the chains and rings of carbon atoms we find in molecules as their skeletons, which support the functional groups and allow them to take part in chemical interactions, much as your skeleton supports your internal organs so they can interact with one another and work properly.

We will see later how the interpretation of organic structures as hydrocarbon frameworks supporting functional groups helps us to understand and rationalize the reactions of organic molecules. It also helps us to devise simple, clear ways of representing molecules on paper. You saw these structural diagrams in Chapter 1, and in the next section we shall teach you ways to draw (and ways not to draw) molecules—the handwriting of chemistry. This section is extremely important because it will teach you how to communicate chemistry, clearly and sim ply, throughout your life as a chemist.