Quinones and amino acids are usually compartmentally separated in living systems, however there are several junctions in which they meet, react and influence. It occurs mainly in wounded, cut or crushed plant material during harvest, ensiling or disintegrating cells. Diffusing polyphenols are oxidized by polyphenol oxidases (PPOs) to quinonic compounds, which associate reversibly or irreversibly with amino acids and proteins. The reaction takes place with the free nucleophilic functional groups such as sulfhydryl, amine, amide, indole and imidazole substituents. It results in imine formation, in 1,4-Michael addition via nitrogen or sulphur and in Strecker degradation forming aldehydes. The formation and activity of quinone-amino acids conjugates influences the colour, taste, and aroma of foods. Physical and physiological phenomena such as browning of foods, discoloration of plants during processing, alteration of solubility and digestibility, formation of humic substances, germicidal activity, cytotoxicity and more occur when quinones from disintegrating cells meet amino acids. The mechanisms of toxicity and the pathways by which PCBs may be activated and act as a cancer initiator include oxidation to the corresponding quinones and reaction with amino acids or peptides. Sclerotization of insect cuticle is a biochemical process involving also the reaction between quinones and amino acid derivatives.