Secondary metabolite

Secondary metabolites are organic compounds produced by bacteria, fungi, or plants which are not directly involved in the normal growth, development, or reproduction of the organism. Unlike primary metabolites, absence of secondary metabolites does not result in immediate death, but rather in long-term impairment of the organism's survivability, fecundity, or aesthetics, or perhaps in no significant change at all. Specific secondary metabolites are often restricted to a narrow set of species within a phylogenetic group. Secondary metabolites often play an important role in plant defense against herbivory and other interspecies defenses. Humans use secondary metabolites as medicines, flavorings, pigments, and recreational drugs.[1]

Secondary metabolites aid a host in important functions such as protection, competition, and species interactions, but are not necessary for survival. One important defining quality of secondary metabolites is their specificity. Usually, secondary metabolites are specific to an individual species,[2] though there is considerable evidence that horizontal transfer across species or genera of entire pathways plays an important role in bacterial (and, likely, fungal) evolution.[3] Research also shows that secondary metabolic can affect different species in varying ways. In the same forest, four separate species of arboreal marsupial folivores reacted differently to a secondary metabolite in eucalypts.[4] This shows that differing types of secondary metabolites can be the split between two herbivore ecological niches.[4] Additionally, certain species evolve to resist secondary metabolites and even use them for their own benefit. For example, monarch butterflies have evolved to be able to eat milkweed (Asclepias) despite the toxic secondary metabolite it contains.[5] This ability additionally allows the butterfly and caterpillar to be toxic to other predators due to the high concentration of secondary metabolites consumed.[5]

Human health implications

Most polyphenol nutraceuticals from plant origin must undergo intestinal transformations, by microbiota and enterocyte enzymes, in order to be absorbed at enterocyte and colonocyte levels. This gives rise to diverse beneficial effects in the consumer, including a vast array of protective effects against viruses, bacteria, and protozoan parasites.[6]

Secondary metabolites also have a strong impact on the food humans eat. Some researchers believe that certain secondary metabolite volatiles are responsible for human food preferences that may be evolutionarily based in nutritional food.[7] This area of interest has not been thoroughly researched, but has interesting implications for human preference. Many secondary metabolites aid the plant in gaining essential nutrients, such as nitrogen. For example, legumes use flavonoids to signal a symbiotic relationship with nitrogen fixing bacteria (rhizobium) to increase their nitrogen uptake.[5] Therefore, many plants that utilize secondary metabolites are high in nutrients and advantageous for human consumption.


Most of the secondary metabolites of interest to humankind fit into categories which classify secondary metabolites based on their biosynthetic origin. Since secondary metabolites are often created by modified primary metabolite synthases, or "borrow" substrates of primary metabolite origin, these categories should not be interpreted as saying that all molecules in the category are secondary metabolites (for example the steroid category), but rather that there are secondary metabolites in these categories.

Plant secondary metabolites

Plants are capable of producing and synthesizing diverse groups of organic compounds and are divided into two major groups: primary and secondary metabolites. Secondary metabolites are metabolic intermediates or products which are not essential to growth and life of the producing plants but rather required for interaction of plants with their environment and produced in response to stress. Plant secondary metabolites can be divided into four major classes: terpenes, phenolics, glycosides and alkaloids.[8]

  • Terpenes constitute a large class of natural products which are composed from isoprene units. Terpenes are only hydrocarbons and terpenoids are oxygenated hydrocarbons. The general molecular formula of terpenes are multiple of (C5H8)n , where 'n' is number of linked isoprene units. Hence, terpenes are also termed as isoprenoid compounds. Classification is based on the number of isoprene units presentin their structure.
Number of isoprene units Name Carbon atoms
1 Hemiterpene C5
2 Monoterpene C10
3 Sesquiterpenes C15
4 Diterpene C20
5 Sesterterpene C25
6 Triterpene C30
7 Sesquarterterpene C35
8 Tetraterpene C40
More than 8 Polyterpene
  • A phenolic is a chemical compound characterized by the presence of aromatic ring structure bearing one or more hydroxyl groups. Phenolics are most abundant secondary metabolites of plants ranging from simple molecules such as phenolic acid to highly polymerized substances such as tannins. Classes of phenolics have been characterized on the basis of their basic skeleton.
No. of carbon atoms Basic skeleton Class
6 C6 Simple phenols
7 C6 - C1 Phenolic acids
8 C6 - C2 Acetophenone, Phenyle acetic acid
9 C6 - C3 Phenylepropanoids, hydroxycinnamic acid, coumarins
10 C6 - C4 Naphthoquinone
13 C6 - C1- C6 Xanthone
14 C6 - C2 - C6 Stilbene, anthraquinone
15 C6 - C3 - C6 Flavonoids, isoflavanoids
18 (C6 - C3 ) 2 lignans, neolignans
30 ( C6 - C3 - C6)2 Biflavonoids
  • A glycoside is a molecule in which carbohydrate is bound by a glycosidic bond to a non-carbohydrate moiety containing a hydroxyl group. The sugar most commonly found in glycosides is glucose. Among diverse group of glycosides three are most important. These are saponins, cardiac glycosides and cyanogenic glycosides.
  • Alkaloids: are a diverse group of nitrogen containing basic compounds. They are typically derived from plant sources and contain one or more nitrogen atoms. Chemically they are very heterogeneous. Based on chemical structures, they may be classified into two broad categories:

Small "small molecules"

Big "small molecules", produced by large, modular, "molecular factories"

Non-"small molecules": DNA, RNA, ribosome, or polysaccharide "classical" biopolymers

See also


  1. "Secondary metabolites - Knowledge Encyclopedia". Retrieved 2016-05-10.
  2. Pichersky E, Gang DR (October 2000). "Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective". Trends in Plant Science. 5 (10): 439–45. doi:10.1016/S1360-1385(00)01741-6. PMID 11044721.
  3. Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW (March 2009). "Genomic islands: tools of bacterial horizontal gene transfer and evolution". FEMS Microbiology Reviews. 33 (2): 376–93. doi:10.1111/j.1574-6976.2008.00136.x. PMC 2704930. PMID 19178566.
  4. Jensen LM, Wallis IR, Marsh KJ, Moore BD, Wiggins NL, Foley WJ (September 2014). "Four species of arboreal folivore show differential tolerance to a secondary metabolite". Oecologia. 176 (1): 251–8. doi:10.1007/s00442-014-2997-4. PMID 24974269.
  5. Croteau R, Kutchan TM, Lewis NG (2012-07-03). "Chapter 24: Natural products (secondary metabolites)". In Civjan N (ed.). Natural products in chemical biology. Hoboken, New Jersey: Wiley. pp. 1250–1319. ISBN 978-1-118-10117-9.
  6. Marín L, Miguélez EM, Villar CJ, Lombó F (6 April 2018). "Bioavailability of dietary polyphenols and gut microbiota metabolism: antimicrobial properties". BioMed Research International. 2015: 905215. doi:10.1155/2015/905215. PMC 4352739. PMID 25802870.
  7. Goff SA, Klee HJ (February 2006). "Plant volatile compounds: sensory cues for health and nutritional value?". Science. 311 (5762): 815–9. doi:10.1126/science.1112614. PMID 16469919.
  8. Pranav Kumar. (2013). Life Sciences : Fundamentals and practice. Mina, Usha. (3rd ed.). New Delhi: Pathfinder Academy. ISBN 9788190642774. OCLC 857764171.
  9. Chizzali C, Beerhues L (2012). "Phytoalexins of the Pyrinae: Biphenyls and dibenzofurans". Beilstein Journal of Organic Chemistry. 8: 613–20. doi:10.3762/bjoc.8.68. PMC 3343287. PMID 22563359.
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