Secondary metabolites


Contributing author

Andras Keszei


Secondary metabolism is generally defined as everything that’s not primary metabolism, but that’s not a specific enough definition to be useful. An alternative definition might be: everything that’s not absolutely necessary for survival and reproduction in an optimal (glasshouse) environment. And yet, that’s not really specific enough either. The definition of secondary metabolites is therefore open to interpretation. Some secondary metabolites are critical to plant survival, some less so.

Traditionally the classical groups of secondary metabolites are the Terpenes, Phenolics, and Alkaloids.

Terpene secondary metabolites include:

  • Monoterpenes such as pinene, cineole, menthol, linalool, limonene
  • Sesquiterpenes such as valencene, santalol, polygodial, zingiberene,
  • Diterpenes including steviol, taxol, jathophane, croton aldehyde
  • Triterpenes, such as cardiac glycosides, saponins
  • Apocarotenoids such as -ionone, strigolactones

Phenolic secondary metabolites include:

  • Flavonoids such as anthocyanins, flavanols, flavones, flavanones and condensed tannins
  • Phenylpropanoids including cinnamic acid, caffeic acid, ferulic acid
  • Hydolysable tannins such as salicin, gallates, lignin, etc
  • Coumarins

Alkaloid secondary metabolites are nitrogen base containing organic compounds, becoming biologically active in alkaline conditions. These include:

  • Caffeine, theine, and theobromine which are all CNS stimulants.
  • Nicotine, morphine, cocaine, and mescalin, CNS depressants,
  • Finally, capsaicine, piperine, and sanshool, “Heat” flavour compounds which containt unmyelinated C-type neuron stimulants are also alkaloid secondary metabolites.

Other (alkaloid secondary metabolites) include:

  • Glucosinolates which produce thiocyanates and are found in mustard, (e.g. wasabi, from the Brassicaceae)
  • Cyanogenic glycosides which produce hydrogen cyanide and are found in the rosacae, cassava, sorghum, eucalypts.
  • Anthraquinones which are found as glycosides in cassia – laxative

Roles of secondary metabolites in plant function

Secondary Metabolites despite their name play important roles in ecological interactions, in response to environmental effects and as structural elements.

Ecological roles of secondary metabolites

Ecological roles of secondary metabolites include interactions with other plants of the same species, with plants from different species, with herbivores, with pollen and seed dispersal vectors and with symbionts. In interactions secoanry compounds are generally classified as Kairomones if the are detrimental to producing organism, as allomones if they are detrimental to receiving organismor as synomones if they are beneficial to both producing and receiving organism

Kairomones include strigolactones which are produced by the roots of many types of plants and actually induce the germination of the seeds of root parasitic Striga spp. Phellandrene produced by some eucalypts attracts Christmas beetles which are high impact herbivores.

Allomones include FPCs in the leaves of eucalypts cause nausea in possums.

-triketones in manuka leaf litter prevent the germination of seeds (allelopathy).

And, cyclic diketones found in Australian terrestrial orchids trick wasps into pollen dispersal with no reward.

Synomones include flavonoids exuded by the roots of Fabaceae which attract they symbiotic bacteria necessary for the formation of root nodules. Likewise, anthocyanins and chalcones in flowers attract pollinators and maize sesquiterpenes released on herbivory attract parasites of the herbivore to the benefit of both plant and parasite.

Environmental roles of secondary metabolites

Secondary metabolites also may have environmental roles. For example, isoprene and mono-terpene hydrocarbons protect the thylakoid membranes to maintain photosynthesis in high temperatures. These compounds are responsible for the “blue haze” over the Blue Mountains in Southeast Australia. Antioxidants such as flavonoids and carotenoids protect against free radicals generated by UV radiation.

And quercitol (a carbohydrate) helps maintain osmotic balance in drought affected eucalypts.

Structural roles of secondary metabolites

Lastly, secondary metabolites can play important structural roles. Lignin, in wood is technically a secondary compound. Lignin contributes to structural rigidity and height in woody species. Other structural secondary metabolites include calcium oxalate and silicate, which are important in defensive structures in some species.


Thus, while secondary metabolites are classically defined as not being essential for the survival of the individual, they can be central to survival and performance of many many species. By quantifying secondary metabolites in plant tissues researchers gain insight into environmental effects and the evolution of plant interactions, to name just a couple important processes.


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