Plants synthesize a wide range of metabolites that are not known to be essential for their survival. Because they are not a part of primary metabolism, they are often lumped together in a category of metabolites called secondary compounds. This is an entirely artificial categorization given that there is no unifying characteristic of the entire group. Many of these compounds are involved in defense responses, but others produce pigments involved in pollinator attraction, and still others make up important photoprotective pigments in leaves that guard against damage due to high light conditions. Most of the secondary compounds are strongly oxidizing, and thus are sequestered in the vacuole after production to protect the proteins of the cytoplasm from damage.

While the structures and functions of these molecules are diverse, they can be grouped into 3 major classes based on common structure and biosynthetic pathways. The classes include the phenolic compounds, terpenes, and nitrogen-containing compounds. No single plant species makes a full complement of all secondary compounds, but each makes a select subset of them.

Phenolic compounds

Phenolic compounds are united by having a phenol group — a phenyl ring with a hydroxyl group. Such structures are assembled through the shikimic acid pathway, which branches off of primary metabolism through phosphoenolpyruvate in the respiration pathway and leads to the synthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Phenylalanine serves as the entry substrate to form the phenolic secondary compounds, with the first committed step being the deamination of phenylalanine by the enzyme phenylalanine ammonia lyase (PAL). The simplest resulting molecules are the simple phenolics, phenylpropanoids, and the precursors to lignin. When these simpler phenolics condense with a second phenyl ring, they form flavonoids, isoflavonoids, and flavonols.

One example of a common flavonoid is the family of pigment known as anthocyanins, which contribute the reds, purples, and blues to flower pigments. The different colors of anthocyanin pigments are the result of varying degrees of hydroxylation on one of the 2 rings of the flavonoid. Many other examples of flavonoids are encountered every day in the foods humans eat, specifically from the herbs and spices added to food for flavoring and spice. Flavonoids are the primary flavor constituents in such spices as cinnamon, ginger, cloves, nutmeg, coffee, and vanilla. These flavonoids probably serve as a deterrent to herbivorous insects and larger animals, and many also show antimicrobial properties.

Terpenes

Terpenes are long chain hydrocarbon molecules having 10-40 carbons. Most are toxic in some way to animals and so are deterrents to herbivory. In addition to these defense compounds, the plant hormones GA and ABA are examples of terpenes, as are the carotenoids, yellow-orange pigments involved in photosynthesis. Like the phenolic compounds, the terpenes are synthesized by a pathway that branches from respiration through either acetyl CoA or glyceraldehyde 3-phosphate and pyruvate. The results of either pathway are 5-carbon units that can be joined together in a variety of ways to produce the long chain structures associated with this class. As a consequence of this biosynthetic process, the terpenes always occur in multiples of 5 carbons (10, 15, 20, etc).

The monoterpenes are the smallest of the terpenes, composed of 10 carbons, and are often volatile essential oils found on the surface of leaves and stems. The familiar scent of pine, for example, is produced by α-pinene and β-pinene. Another familiar monoterpene is limonene, responsible for the lemon scent. In the case of both pine and citrus, these essential oils are found in a sub-epidermal duct or ‘oil gland’ where they are maintained until the tissue is disrupted. Most of the flavor compounds associated with the mint (Lamiaceae) family, including basil, oregano, mint, and thyme, are produced by monoterpene essential oils. In these examples, the oils are found in modified trichomes atop the surface of the leaf, where they are easily ruptured and released as a potential herbivore merely contacts the tissue.

Another class of terpene is the diterpenes (20 carbons) that are represented by pine resins, found in ducts throughout the stems of most pine species. Another important diterpene is the anti-cancer drug taxol, found in the bark of the Pacific Yew tree. This complex diterpene binds to microtubules and stabilizes them, resulting in an arrest of mitosis. The triterpenes (30 carbons) are large, complex structures that undergo ring condensation to form steroidal compounds and cardiac glycosides, so named because of their effects on vertebrate heart function. Several of these compounds are used to treat heart conditions, including digoxin, from the foxglove plant (Digitalis sp.) and oleandrin, from the oleander plant (Nerium oleander). Finally, the tetraterpenes (40 carbons) include latex and chicle.

N-containing compounds

Whereas representative molecules of both phenolics and terpenes are found in all plants, the nitrogenous compounds are only found in about 20% of plant species. Many nitrogenous compounds defend the plant through profound effects on the nervous system of animals, often interfering with nerve cell signaling in the central nervous system by binding to neurotransmitter receptors. Molecules such as nicotine, cocaine, heroin, and morphine are all alkaloids and act in this way. Other alkaloids such as those produced in the Nightshade family (Solanaceae) effect nerve cell signaling in the peripheral nervous system and can disrupt digestive processes of potential herbivores. In addition to the alkaloids, this class includes the cyanogenic glycosides. These potent deterrents release cyanide gas when the tissues containing the cyanogenic glycosides are ruptured.