Alkaloids are a large group of nitrogen-containing compounds, examples of which are known to occur in approximately 20 percent of all flowering plants. Closely related plant species often contain alkaloids of related chemical structure. The primary metabolites from which they are derived include amino acids such as tryptophan, tyrosine, and lysine. Alkaloid biosynthetic pathways can be long, and many alkaloids have correspondingly complex chemical structures. Alkaloids accumulate in plant organs such as leaves or fruits and are ingested by animals that consume those plant parts. Many alkaloids are extremely toxic, especially to mammals, and act as potent nerve poisons, enzyme inhibitors, or membrane transport inhibitors. In addition to being toxic, many alkaloids are also bitter or otherwise bad-tasting. Therefore, the presence of alkaloids and other toxic secondary metabolites can serve as a deterrent to animals, which learn to avoid eating such plants.

Sometimes domesticated animals that have not previously been exposed to alkaloid-containing plants do not have acquired avoidance mechanisms, and they become poisoned. For example, groundsel contains the alkaloid senecionine, which has resulted in many recorded cases of livestock fatalities due to liver failure. More frequently, over time, natural selection has resulted in animals developing biochemical mechanisms or behavioral traits that lead to avoidance of alkaloid-containing plants.

In other, more unusual cases, animals may evolve a mechanism for sequestering (storing) or breaking down a potentially toxic compound, thus

"disarming" the plant. For instance, caterpillars of the cinnabar moth can devour groundsel plants and sequester senecionine without suffering any ill effects. Moreover, the caterpillars thereby acquire their own weapon against predators: the plant-derived alkaloid stored within their bodies. Over time, plants acquire new capabilities to synthesize additional defense compounds to combat animals that have developed "resistance" to the original chemicals. This type of an "arms race" is a form of coevolution and may help to account for the incredible abundance of secondary metabolites in flowering plants.

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