When cyanogenic plants are injured, hydrogen cyanide (HCN) is liberated. This cyanogenesis is initiated by any decompartmentation, resulting in the contact of cyanogenic glycosides and the corresponding β-glucosidases. The related hydrolysis produces unstable hydroxynitriles which decay to HCN and a carbonyl. This treatise reviews the various plant biological, biochemical and molecular facets of cyanogenic glucosides; special emphasis is put on the new and actual aspects of their biosynthesis. In the past, this complex conversion of amino acids via aldoximes to cyanogenic glucosides was described as so-called channelled biosynthesis. Yet, later on, it was shown that this multi-step biosynthesis is performed by only two multi-functional cytochrome P450 enzymes, which are located in the ER. Subsequently, the resulting unstable hydroxynitriles are glucosylated by soluble cytosolic glucosyltransferase. Just recently, the ‘missing link’ between the cytochrome-dependent synthesis and the final glucosylation step could be elucidated in Birger Møller's lab by the discovery of a metabolon that comprises all biosynthetic steps. Thus, the old concept of ‘channelled biosynthesis’ does apply again.

Glucosinolates, which resemble cyanogenic compounds in many aspects, are characterized by the liberation of mustard oils, a complex mixture of isothiocyanates, thiocyanates and related nitriles. Degradation takes place when tissues of glucosinolate-containing plants are damaged and cells are destroyed. Glucosinolates and their degradation products are important factors in plant defence against herbivores, as well as against pathogens. The biosynthesis of glucosinolates includes three independent phases: first, the chain elongation of amino acids; second, conversion of the precursor amino acid via aldoximes into glucosinolates; and, finally, further modifications of the resulting glucosinolates. In the past, for a long time the formation of aldoximes from amino acids was discussed controversially and three different pathways had been proposed, one involving flavin-containing mono-oxygenases, another one membrane-bound peroxidases and a third one in which – similar to the biosynthesis of cyanogenic glucosides – the aldoximes are produced by cytochrome P450s. Meanwhile, due to the tremendous progress by molecular biology and molecular genetics, it was shown that only the P450-related synthesis is relevant. This review emphasizes on the biochemical and molecular aspects of glucosinolate biosynthesis, but does also outline the mustard oil formation, its ecological relevance and important nutritional aspects.

Apart from the amino acids present in proteins, numerous other amino acids occur in plants. Whereas some of them are known to be intermediates in various pathways of primary metabolism, others are regarded as typical secondary metabolites with the corresponding ecological functions. In contrast to the comprehensive knowledge of cyanogenic glucosides and glucosinolates, far less is known about the biology and biochemistry of non-protein amino acids (NPAAs). The corresponding part of this chapter reviews the recent knowledge on the various aspects of NPAAs, including their biosynthesis and metabolism and their putative ecological significance.