These also known as secondary products or natural products, these are organic compounds that are not directly involved in the normal growth, development or reproduction of organisms and are not directly involved with photosynthesis, respiration, solute transport, translocation, protein synthesis, nutrient assimilation, or differentiation, or the formation of carbohydrates, proteins and lipids. Unlike primary metabolites, absence of secondary metabolites results not in immediate death, but in long-term impairment of the organism’s survivability/fecundity or aesthetics, or perhaps in no significant change at all. Secondary metabolites are often restricted to a single species or a narrow set of species within a group, whereas primary metabolites are typically found throughout the plant kingdom. In most cases, secondary metabolites have been found not to be simply metabolic waste products, but instead to play important roles in plant defences against pathogens or herbivores and in other aspects of plants ecology.

These ecological roles include:

  1. Protecting against animal herbivory (being eaten by herbivores including insects) and infection (by microbes).
  2. Aiding pollinators and seed-dispersing animals by serving as attractants in smell, color or taste.
  3. Aiding in plant-plant competition (including allelopathy) and in plant microbe symbiosis.

These compounds can have a deleterious or beneficial effects in plants intended for human consumption. The main groups are:

  1. Terpenes
  2. Phenolics
  3. Nitrogen compounds

Allelopathy Plants synthesizing phenolics (including caffeic acid and ferulic acid) and other secondary metabolites may impart these to the soil in the form of fallen leaves, decaying litter and root secretions. The inhibiting effects of these substances on germination or growth of neighboring plants is termed allelopathy and can lead to better fitness through increased access to light, water and nutrients. The study of allelopathy in agriculture is important with respect to maximizing crop yields. However, it is difficult to unravel the precise ecological function of most “secondary” metabolites, though this designation often implies an ecological role. In the introduced invasive weed Spotted knapweed (Centaurea maculosa), it is a polyphenolic tannin, catechin, that serves as its primary allelopathic root exudate.

Secondary metabolism

This part deals with hydrophobic compounds such as waxes, cutins and suberin. These contribute to the formation of the casparian strip, cuticle and other water structures. In addition, it deals with compounds termed as secondary metabolites that have no direct function in growth, development and reproduction of plants. Some of their uses are:

  • Defenses against pathogens (including bacteria, fungi, viruses and nematodes) and herbivorous predators (such as arthropods and other animals). Which is done by means of barrier substances, toxins and other means of defenses.
  • Pigments (such as anthocyanins)
  • Structural supports (such as lignin)

Many of the secondary metabolites have real or purported commercial or other uses as insecticides, fungicides, pharmaceuticals, herbs, medicinal, dietary supplements and “nutraceuticals”, flavoring and scents and industrial materials. Some are used as extracted products, while some are useful when genetically increased, decreased, or redistributed in crop plants, in order to enhance yields, diminish applied insecticides, improve edibility, etc.

Waxes, Cutins and Suberin Plants use these substances to create hydrophobic barriers, to limit water loss from transpiration, to divert water absorbed by roots into the symplast and (at least to a modest degree) to help deter invaders. Plants native to arid habitats have thicker cuticles, but other plants subjected to dry conditions also increase their cuticle thickness. Some pathogenic fungi penetrate the cuticle mechanically, or secrete cutinase that hydrolyze cutin and assist them in penetrating the cuticle.

All plant parts exposed to the atmosphere are coated with the layers of lipid material that reduce water loss and help block the entry of pathogenic fungi and bacteria. The principal types of coatings are cutin, suberin and waxes. Cutin is found on most above ground parts; suberin is present on underground parts, woody stems and healed wounds. Waxes are associated with both cutin and suberin. The outermost layer of a leaf include (from inside out)

  • The cell wall and middle lamella of the epidermis.
  • The cuticular layer (cutin, wax and CHO polymers such as pectin, cellulose, etc.).
  • The cuticle proper (cutin and wax).
  • The outermost layer of surface wax.

Waxes are complex mixtures of (mostly) non-polymeric long-chain (25-35 carbon) hydrophobic lipids, usually consisting of straight aliphatic alkanes and alcohols (primary and secondary) but also aldehydes, ketones, esters and free fatty acids. They are found on the outer surface of leaves, in the cuticle mixed with cutin and in the cuticular layer and are also found with suberin.

Waxes in the cuticle are secreted as droplets from the epithermal cells. The surface layer is often crystallized in the form of small rods, tubes or plates of wax, which enhance the repellency of water and the self-cleansing properties of the surface (the so-called Lotus effect or super hydrophobicity, in which the contact angles formed with water on leaves of Lotus japonicus or taro measure up to 170°C).

Cutin consists of polymeric macromolecules- many waxy long-chain fatty acid polyester polymers. Cutin covers the aerial surfaces of most plants in the cuticular and cuticle layers. Cutin joins the barrier role and consists of non-saponifiable polymers of long-chain hydrocarbons. Suberin is found in roots and other underground parts, as well as woody stems, sites of leaf abscission and healed wounds. In roots, it forms the Casparian strip (Casparian band) of the endodermis, which forces water entering the stele of root into the symplast. Suberin is a polymer of uncertain structure, formed from long chain components including dicarboxylic acids and phenolic compounds, using ester linkages and is often mixed with waxes. It is a main constituent of the cork (phellem, the outermost layer of the bark or periderm). It is named after the Cork Oak, Quercus suber.