This chapter provides the chemical basis for understanding how enzymes function and how this understanding can be used to control the action of enzymes for the purposes of transforming foods, producing food ingredients, and maintaining, enhancing, and monitoring food quality. Lipoxygenase action is generally considered to have detrimental effects on food and lipid quality. The chapter deals with the characterization and manipulation of enzyme activity endogenous to foods, a continuing challenge to food scientists. It describes some of the important commercial applications of proteolytic enzymes. The chapter focuses on the multiplicity of reaction and ancillary pathways of fatty acid transformation and associated roles of lipoxygenase-mediated processes in food quality. It also focuses on controlling endogenous enzymes that can have desirable or undesirable impact on food quality. Temperature, pH, and water activity are the most important environmental factors that influence enzyme activity, and changes in these parameters comprise the principal physical means to control enzyme action in food matrices.