Secondary metabolite

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 metabolities 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.

Categories
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):
 * Azadirachtin, (Neem tree)
 * Artemisinin, present in Artemisia annua Chinese wormwood
 * tetrahydrocannabinol, present in Cannabis
 * Steroids (Terpenes with a particular ring structure)
 * Saponins (plant steroids, often glycosylated)
 * Glycosides (heavily modified sugar molecules):
 * Nojirimycin
 * Glucosinolates
 * Natural phenols:
 * Resveratrol
 * Phenazines:
 * Pyocyanin
 * Phenazine-1-carboxylic acid (and derivatives)

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

 * Polyketides:
 * Erythromycin
 * Discodermolide
 * Fatty acid synthase products :
 * FR-900848
 * U-106305
 * phloroglucinols
 * Nonribosomal peptides:
 * Vancomycin
 * Thiostrepton
 * Ramoplanin
 * Teicoplanin
 * Gramicidin
 * Bacitracin
 * Hybrids of the above three:
 * Epothilone
 * Polyphenols

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

 * Ribosomal peptides:
 * Microcin-J25