All posts by Chris Wolverton

Secondary Compounds

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 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.


How do leaves transduce light into chemical energy?

Responses to Stimuli

How do plants respond to environmental cues?

  • Gravity sensing: How does a plant convert an acceleration force into cellular information?
  • Auxin Transport: How is the distribution of this hormone targeted to individual cells?
  • Gravity signaling: What is the chain of events that leads to gravitropic curvature?
  • Phototropism: How does a light gradient cause differential growth?
  • Photomorphogenesis: What is light-induced development, and how is it regulated?
  • Touch Sensing: How does a plant detect an object and grow around it?

Cell Walls

One of the most prominent features of plant cells is their cell wall. While many organisms produce some kind of extracellular matrix that is important in cell function, almost every cell made by a plant is surrounded by a rigid mixture of cellulose and other polysaccharides and proteins. The cell wall allows the formation of high hydrostatic pressure known as turgor pressure.


Cellulose is the major load-bearing structural component of the cell wall. In chemical terms, cellulose is β1→4-linked glucose dimers called cellobiose. These dimers repeat in long chains, which are crystallized with other such chains during synthesis to form microfibrils. Think of a microfibril as yarn, and individual chains as the threads that are spun into a yarn.

chemical structure of cellobiose

One of the peculiarities of cellulose in the cell wall is that it is not synthesized inside the cell and deposited in the apoplast by vesicles. Rather, cellulose is synthesized by a complex spanning the plasma membrane and extruded into the apoplast. These rosette-shaped structures, called terminal complexes, are made up of many individual cellulose synthase enzymes working in concert to produce a microfibril. Terminal complexes travel along a network of cortical microtubules that determine the pattern of deposition of cellulose microfibrils. Direct evidence for this hypothesis came from visualizing the interaction between microtubules and a part of the cellulose synthase enzyme complex.


Other Wall Components

In addition to cellulose, plant cell walls include a wide variety of polysaccharides and structural proteins. The polysaccharides include hemicelluloses and pectins, both of which are diverse groups of complex, branched carbohydrates. Unlike cellulose, neither of these constituents is manufactured directly in the cell wall, but both follow the more traditional intracellular synthesis followed by secretion. These polysaccharides function to stabilize the interaction between cellulose microfibrils through H-bonding.

cartoon diagram of cell wall components

Pardez AR, Somerville CR, Ehrhardt DW (2006) Visualization of Cellulose Synthase Demonstrates Functional Association with Microtubules. Science 312:1491-1495 See a collection of time-lapse movies.


How do plants grow?

  • Principles of Growth: How do plants create a complex body plan?
  • Meristems: How do these specialized regions of cell division make a plant?
  • Cell fate determination: Do cells inherit their identity, or is it the product of position?
  • Cell walls: What role do cell walls play in growth and development?
  • Cell expansion: What controls the timing and direction of cell expansion?
  • Water potential: How does water provide the driving force for cell growth?
  • Organ formation: How does a jumble of cells become organized for a specific function?