This initial chapter describes the differences between bacterial and archaeal cells and the rational for establishing the three-domain system to classify life forms. The phenotypic changes in microorganisms due to horizontal gene transfer are discussed. Physiological unity in prokaryotes with variations in cell morphology and growth characteristics is reviewed. The periplasm in bacteria is characterized and cell structures isolated from disrupted bacterial cells are outlined. Characterization of enzymes includes graphic expression to determine enzyme rate and substrate affinity.