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Secondary metabolites are organic compounds that are not directly involved in the normal growth, development, or reproduction of an 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. 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, and recreational drugs.
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. 
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.
Small "small molecules"
- Alkaloids (usually a small, heavily derivatized amino acid):
- Hyoscyamine, present in Datura stramonium
- Atropine, present in Atropa belladonna, Deadly nightshade
- Cocaine, present in Erythroxylon coca the Coca plant
- Scopolamine, present in the Solanaceae (nightshade) plant family
- Codeine and Morphine, present in Papaver somniferum, the opium poppy
- Tetrodotoxin, a microbial product in Fugu and some salamanders
- Vincristine & Vinblastine, mitotic inhibitors found in the Rosy Periwinkle
- Terpenoids (come from semiterpene oligomerization):
- Glycosides (heavily modified sugar molecules):
- Natural phenols:
- Phenazine-1-carboxylic acid (and derivatives)
- Biphenyls and dibenzofurans are phytoalexins of the Pyrinae
- Penicillin, present in Penicillium fungi
Big "small molecules", produced by large, modular, "molecular factories"
- Fatty acid synthase products :
- Nonribosomal peptides:
- Hybrids of the above three:
Non-"small molecules" - DNA, RNA, ribosome, or polysaccharide "classical" biopolymers
- Ribosomal peptides:
- Secondary metabolism
- Hairy root culture, a strategy used in plant tissue culture to produce good quantities of valuable secondary metabolites
- Primary metabolite
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