eQuilibrator Classic Reactions

This is an introduction to the most central reactions and pathways of metabolism through the lens of biochemical thermodynamics. For the sake of simplicity, we focus on the thermodynamic principles of heterotrophic metabolism - the metabolism of organisms like E. coli, yeast, humans and octopi that consume organic carbon compounds to provide both energy and carbon for their continued growth, homeostasis and reproduction. Phototrophic and chemotrophic metabolisms are equally interesting and important (perhaps more so from an evolutionary and environmental perspective) but we will not cover them in detail here. At least in this version.

While there are many links between the sections of “eQuilibrator Classic Reactions,” this document is intended to be read in order, starting with simple concepts like ATP hydrolysis and building up to more complex pathways like respiration, glycolysis and the TCA cycle. You can refer to the FAQ document for a glossary of common terms used on eQuilibrator.

Contents:

• Energy Currency and ATP Hydrolysis
• Thioester Bonds are Energetic Too
• The Oxidation of Glucose
• Plants Make Glucose from CO₂
• Glycolysis and Fermentation
  • NADH as an Electron Carrier
  • Ethanol Fermentation
  • Mixtures of Fermentation Products
  • Glycolysis in Gory Detail
• Respiration
  • Alternative Respiratory Pathways
• Transamination for Making Amino Acids
• Metabolism of Alkanes and Fatty Acids
  • Example of Octane Breakdown
  • Energy Balance in Octane Breakdown
  • Fatty Acid Metabolism
• The TCA Cycle
  • Metabolism of Acetyl-CoA
  • Constructing the TCA Cycle
    • α-Ketoglutarate to Oxaloacetate
  • Oxaloacetate back to α-Ketoglutarate
  • Anaplerotic Reactions
  • pH Dependence
• References