Chapter Summary


  • Energy enables cells to build ordered structures out of simple molecules from their environment.
  • The free energy change (ΔG) includes enthalpy (ΔH), the heat energy absorbed or released; and –TΔS, the product of temperature and entropy change (ΔS).
  • Negative values of ΔG show that a reaction may drive the cell’s metabolism. The sign of ΔG depends on the relative magnitude of ΔH and –TΔS.


  • The direction of reaction is determined by the molecular stability of reactants and products and by entropy change associated with number of products, gaseous products, or products with multiple forms.
  • Concentrations of reactants and products affect ΔG. The lower the concentration ratio of products to reactants, the more negative the value of ΔG.
  • A concentration gradient stores energy. Solutes run down their concentration gradient unless energy is applied to reverse the flow.
  • Cellular thermodynamics involves changing reactant and product concentrations and coupling energyyielding reactions with energy-spending reactions.
  • Reaction pathways with ΔG near zero can drive microbial growth.


  • Catabolic pathways organize the breakdown of large molecules in a series of sequential steps coupled to reactions that store energy in small carriers such as ATP and NADH.
  • ATP and other nucleotide triphosphates store energy in the form of phosphodiester bonds.
  • NADH, NADPH, and FADH2 each store energy associated with an electron pair that carries reducing power.
  • Enzymes catalyze reactions by lowering the ΔG required to reach the transition state. They couple energy transfer reactions to specific reactions of biosynthesis and cell function.


  • Fermentation, respiration, and photoheterotrophy are forms of catabolism. In fermentation, the catabolite is broken down to smaller molecules without an inorganic electron acceptor. Respiration requires an inorganic terminal electron acceptor such as O2 or nitrate. In photoheterotrophy, catabolism is supplemented by light absorption.
  • Carbohydrates or polysaccharides are broken down to disaccharides, and then to monosaccharides. Sugars and sugar derivatives, such as amines and acids, are catabolized to pyruvate.
  • Pyruvate and other intermediary products of sugar catabolism are fermented, or they are further catabolized to CO2 and H2O through the TCA cycle (in the presence of a terminal electron acceptor).
  • Lipids and amino acids are catabolized to glycerol and acetate, as well as other metabolic intermediates.
  • Aromatic compounds such as lignin and benzoate derivatives are catabolized to acetate through different pathways, such as the catechol pathway.


  • Glucose is catabolized by three related pathways of stepwise degradation of glucose to pyruvate. In the absence of oxygen, completion of catabolism requires generation of fermentation products.
  • In the Embden-Meyerhof-Parnas (EMP) pathway, glucose is activated by two substrate phosphorylations, and then cleaved to two three-carbon sugars. Both sugars eventually are converted to pyruvate. The pathway produces 2 ATP and 2 NADH.
  • In the Entner-Doudoroff (ED) pathway, glucose is activated by one phosphorylation, and then dehydrogenated to 6-phosphogluconate. 6-Phosphogluconate is cleaved to pyruvate and a three-carbon sugar, which enters the EMP pathway to form pyruvate. The ED pathway produces 1 ATP, 1 NADH, and 1 NADPH.
  • In the pentose phosphate shunt, 6-phosphogluconate is converted to a series of sugars, each containing three to seven carbons—including fructose 6-phosphate, which reenters the EMP pathway.
  • Intermediates of sugar catabolism may serve as substrates for biosynthesis of amino acids and other cell components.
  • Glucose catabolism is reversible, enabling cells to build glucose from small molecules. Glucose biosynthesis uses some enzymes of glycolysis in reverse, but also requires enzymes that bypass irreversible steps in the catabolic pathway.
  • Fermentation is the completion of catabolism without the electron transport system and a terminal electron acceptor. The electrons from NADH are restored to pyruvate or its products in reactions that generate fermentation products, including alcohols and carboxylates, as well as H2 and CO2. Fermentation has applications in food, industrial, and diagnostic microbiology.
  • Acetyl-CoA is a key intermediate in several fermentation pathways.


  • The pyruvate dehydrogenase complex (PDC) removes CO2 from pyruvate, generating acetyl-CoA. Two electrons are transferred to NAD+, forming NADH + H+. PDC activity is a key control point of metabolism, induced when carbon sources are plentiful and repressed under carbon starvation and low oxygen.
  • The tricarboxylic acid cycle (TCA cycle) converts the acetyl group to 2 CO2 and 2 H2O in the presence of a terminal electron acceptor such as O2 to receive the electrons associated with the hydrogen atoms.
  • Acetyl-CoA enters the TCA cycle by condensing with oxaloacetate to form citrate. A series of enzymes sequentially removes carbon dioxide and water molecules and generates 2 NADH, FADH2, and ATP. Each reaction step couples energy-yielding to energy-storing events.
  • NADH and FADH2 transfer electrons to the electron transport system and ultimately the terminal electron acceptor, such as O2. Electron transport generates a transmembrane proton potential that powers the membrane-embedded ATP synthase to make ATP.
  • Respiration consists of substrate catabolism plus oxidative phosphorylation, the process of electron transport and ATP generation.


  • Catabolism of aromatic molecules by bacteria and fungi recycles lignin and other important substances within ecosystems. Toxic pollutants are also degraded.
  • Benzoate undergoes aerobic catabolism to catechol. The catechol ring is cleaved, generating acetyl-CoA, which enters the TCA cycle.
  • Anaerobic catabolism of benzoate involves activation by HS-CoA and reduction of NADP+ to NADPH.
  • Polycyclic aromatic hydrocarbons (PAHs) are degraded slowly by microbes. PAH catabolism has exciting potential applications for bioremediation of toxic pollutants.
  • Aromatic catabolism by environmental microbes is an important field of research. Research techniques include genetic and genomic analysis, chromatography of radiolabeled substrates, and NMR spectroscopy.