Chapter Summary


  • The Calvin cycle fixes CO2 by reductive condensation with ribulose 1,5-bisphosphate. The Calvin cycle is used by cyanobacteria and chloroplasts and by some lithotrophs and photoheterotrophs.
  • 14C radiolabel and paper chromatography were first used to identify intermediates of the Calvin cycle.
  • Rubisco catalyzes the condensation of CO2 with ribulose 1,5-bisphosphate. The six-carbon intermediate immediately splits into two molecules of 3-phosphoglycerate (PGA), which are activated by ATP and reduced by NADPH to glyceraldehyde 3-phosphate (G3P).
  • One of every six G3P is converted to glucose or amino acids. The other five molecules of G3P undergo reactions to regenerate ribulose 1,5-bisphosphate.
  • Carboxysomes sequester and concentrate CO2 for fixation by the Calvin cycle. CO2 levels regulate gene expression for carboxysome transporters and the Calvin cycle.


  • The reductive, or reverse, TCA cycle fixes CO2 in some anaerobes and archaea.
  • Anaplerotic reactions in all organisms regenerate TCA cycle intermediates by fixing CO2.
  • The acetyl-CoA pathway in anaerobic bacteria and methanogens fixes CO2 by condensation to form acetyl-CoA.
  • The 3-hydroxypropionate cycle in chloroflexus and in some hyperthermophilic archaea fixes CO2 in a cycle generating the intermediate 3-hydroxypropionate.


  • Fatty acid biosynthesis involves successive condensation of malonyl-ACP groups formed from acetyl groups tagged with acyl carrier protein (ACP) and a carboxylate. Each successive malonyl group is transferred onto the growing acyl chain, with release of CO2. The condensation reaction is catalyzed by acetyl-CoA carboxylase.
  • The growing acyl chain is dehydrogenated. Each added unit is hydrogenated by two molecules of NADPH unless an unsaturated kink is required.
  • Some fatty acids are partly unsaturated. An unsaturated kink may be generated by a special dehydratase, which forms the alkene double bond between the third and fourth carbons.
  • Fatty acid biosynthesis is regulated by the levels of acetyl-CoA carboxylase and by the stringent response to carbon starvation. Bond saturation is regulated by temperature and other environmental factors.
  • Polyesters for energy storage are synthesized by cyclic elongation of polyalkanoates.
  • Polyketide antibiotics are synthesized by modular enzymes.


  • Oxidized or reduced forms of nitrogen, such as nitrate, nitrite, and ammonium ions, can be assimilated by bacteria and plants. Assimilation competes with dissimilatory reactions that obtain energy.
  • Nitrogen gas (N2) is fixed into ammonium ion (NH4+) only by some species of bacteria and archaea, never by eukaryotes.
  • Nitrogenase enzyme includes a protein containing an iron-sulfur core (Fe protein) and a protein containing a complex of molybdenum, iron, and sulfur (FeMo protein). Electrons acquired by Fe protein (with energy from ATP) are transferred to FeMo protein to reduce nitrogen.
  • Four cycles of reduction by NADPH or an equivalent reductant are required to reduce one molecule of N2 to two molecules of NH3. At neutral pH, NH3 is protonated to NH4+.
  • Oxygen inhibits nitrogen fixation. Bacteria and plants have various means of separating nitrogen fixation from aerobic respiration, such as heterocyst development or temporal separation.
  • Regulation of nitrogen fixation by nitrogen and oxygen levels occurs via NtrC and sigma-54 regulation of transcription.


  • Amino acid biosynthesis requires numerous different enzymes to catalyze many unique conversions. Structurally related amino acids branch from a common early pathway.
  • Metabolic intermediates from glycolysis and the TCA cycle initiate amino acid biosynthetic pathways.
  • Ammonium ion is assimilated by TCA intermediates, such as oxaloacetate into glutamate. Glutamate assimilates ammonium ion to form glutamine. Transamination is the donation of NH4+ from one amino acid to another, such as glutamine transferring ammonia to oxaloacetate to make aspartate.
  • Arginine biosynthesis requires multiple steps of NH3 transfer and carbon skeleton condensation.
  • Aromatic amino acids are built from a common pathway that branches out. Their biosynthesis is regulated tightly at both transcriptional and translational levels.
  • Purines are built as nucleotides attached to a ribose phosphate. Several single-carbon groups are assimilated, including CO2—a phenomenon suggesting an ancient pathway. Pyrimidines are made from aspartate, and then added onto PRPP.
  • Nonribosomal peptide antibiotics are built by modular enzymes analogous to those that build polyketides.


  • Tetrapyrroles are conjugated ring systems made up of pyrroles, each five-membered ring including one nitrogen positioned to coordinate a central metal ion. Tetrapyrrole derivatives include chlorophylls, hemes, hemoglobin, and cyanocobalamin.
  • The glutamate pathway or the glycine-succinate pathway condenses eight molecules of 5-aminolevulinic acid into four linked pyrroles. The linked pyrroles are cyclized to uroporphyrinogen III, the foundation of most biologically active tetrapyrrole derivatives.
  • Biosynthesis is regulated by nutritional and environmental needs. Tetrapyrrole biosynthesis takes lots of energy, so these products are synthesized only when necessary.