All plants produce chemical compounds as part of their normal metabolic activities. These include primary metabolites, such as sugars and fats, found in all plants, and secondary metabolites found in a smaller range of plants, some useful ones found only in a particular genus or species. Pigments harvest light, protect the organism from radiation and display colors to attract pollinators.

The functions of secondary metabolites are varied. For example, some secondary metabolites are toxins used to deter predation, and others are pheremones used to attract insects for pollination. Phytoalexins protect against bacterial and fungal attacks. Allelochemicals inhibit rival plants that are competing for soil and light.

Plants synthesize a bewildering variety of phytochemicals but most are derivatives of a few biochemical motifs.

Alkaloids contain a ring with nitrogen. Many alkaloids have dramatic effects on the central nervous system. Caffeine is an alkaloid that provides a mild lift but the alkaloids in datura cause severe intoxication and even death.

Phenolics contain phenol rings. The anthocyanins that give grapes their purple color, the isoflavones, the phytoestrogens from soy and the tannins that give tea its astringency are phenolics.

Turpenoids are built up from terpene building blocks. Each terpene consists of two paired isoprenes. The names monoterpenes, sesquiterpenes, diterpenes and triterpenes are based on the number of isoprene units. The fragrance of rose and lavender is due to monoterpenes. The carotenoids produce the reds, yellows and oranges of pumpkin tomatoes

Glycosides consist of a glucose moiety attached to an aglycone. The aglycone is a molecule that is bioactive in its free form but inert until the glycoside bond is broken by water or enzymes. This mechanism allows the plant to defer the availability of the molecule to an appropriate time, similar to a safety lock on a gun. An example is the cyanoglycosides in cherry pits that release toxins only when bitten by a herbivore.