Part II

Metabolism refers to all the biochemical reactions that occur in a cell or organism. The study of bacterial metabolism focuses on the chemical diversity of substrate oxidations and dissimilation reactions (reactions by which substrate molecules are broken down), which normally function in bacteria to generate energy. Also within the scope of bacterial metabolism is the study of the uptake and utilization of the inorganic or organic compounds required for growth and maintenance of a cellular steady state (assimilation reactions). These respective exergonic (energy-yielding) and endergonic (energy-requiring) reactions are catalyzed within the living bacterial cell by integrated enzyme systems, the end result being self-replication of the cell. The capability of microbial cells to live, function, and replicate in an appropriate chemical milieu (such as a bacterial culture medium) and the chemical changes that result during this transformation constitute the scope of bacterial metabolism.
The bacterial cell is a highly specialized energy transformer. Chemical energy generated by substrate oxidations is conserved by formation of high-energy compounds such as adenosine diphosphate (ADP) and adenosine triphosphate (ATP) or compounds containing the thioester bond

(acetyl ~ SCoA) or succinyl ~ SCoA. ADP and ATP represent adenosine monophosphate (AMP) plus one and two high-energy phosphates (AMP ~ P and AMP ~ P~ P, respectively); the energy is stored in these compounds as high-energy phosphate bonds. In the presence of proper enzyme systems, these compounds can be used as energy sources to synthesize the new complex organic compounds needed by the cell. All living cells must maintain steady-state biochemical reactions for the formation and use of such high-energy compounds.
Kluyver and Donker (1924 to 1926) recognized that bacterial cells, regardless of species, were in many respects similar chemically to all other living cells. For example, these investigators recognized that hydrogen transfer is a common and fundamental feature of all metabolic processes. Bacteria, like mammalian and plant cells, use ATP or the high-energy phosphate bond (~ P) as the primary chemical energy source. Bacteria also require the B-complex vitamins as functional coenzymes for many oxidation-reduction reactions needed for growth and energy transformation. An organism such as Thiobacillus thiooxidans, grown in a medium containing only sulfur and inorganic salts, synthesizes large amounts of thiamine, riboflavine, nicotinic acid, pantothenic acid, pyridoxine, and biotin. Therefore, Kluyver proposed the unity theory of biochemistry (Die Einheit in der Biochemie), which states that all basic enzymatic reactions which support and maintain life processes within cells of organisms, had more similarities than differences. This concept of biochemical unity stimulated many investigators to use bacteria as model systems for studying related eukaryotic, plant and animal biochemical reactions that are essentially "identical" at the molecular level.
From a nutritional, or metabolic, viewpoint, three major physiologic types of bacteria exist: the heterotrophs (or chemoorganotrophs), the autotrophs (or chemolithotrophs), and the photosynthetic bacteria (or phototrophs) (Table 4-1). These are discussed below.
Heterotrophic Metabolism
Heterotrophic bacteria, which include all pathogens, obtain energy from oxidation of organic compounds. Carbohydrates (particularly glucose), lipids, and protein are the most commonly oxidized compounds. Biologic oxidation of these organic compounds by bacteria results in synthesis of ATP as the chemical energy source. This process also permits generation of simpler organic compounds (precursor molecules) needed by the bacteria cell for biosynthetic or assimilatory reactions.

The Krebs cycle intermediate compounds serve as precursor molecules (building blocks) for the energy-requiring biosynthesis of complex organic compounds in bacteria. Degradation reactions that simultaneously produce energy and generate precursor molecules for the biosynthesis of new cellular constituents are called amphibolic.
All heterotrophic bacteria require preformed organic compounds. These carbon- and nitrogen-containing compounds are growth substrates, which are used aerobically or anaerobically to generate reducing equivalents (e.g., reduced nicotinamide adenine dinucleotide; NADH + H+); these reducing equivalents in turn are chemical energy sources for all biologic oxidative and fermentative systems. Heterotrophs are the most commonly studied bacteria; they grow readily in media containing carbohydrates, proteins, or other complex nutrients such as blood. Also, growth media may be enriched by the addition of other naturally occurring compounds such as milk (to study lactic acid bacteria) or hydrocarbons (to study hydrocarbon-oxidizing organisms).