Cells Contain a Universal Set of Small Molecules

  Dissolved in the aqueous phase (cytosol) of all cells is a collection of 100 to 200 different small organic molecules (Mr ~100 to ~500), the central metabolites in the major pathways occurring in nearly every cell—the metabolites and pathways that have been conserved throughout the course of evolution. This collection of molecules includes the common amino acids, nucleotides, sugars and their phosphorylated derivatives, and a number of mono-, di-, and tricarboxylic acids. The molecules are polar or charged, water soluble, and present in micromolar to millimolar concentrations. They are trapped within the cell because the plasma membrane is impermeable to them—although specific membrane transporters can catalyze the movement of some molecules into and out of the cell or between compartments in eukaryotic cells. The universal occurrence of the same set of compounds in living cells is a manifestation of the universality of metabolic design, reflecting the evolutionary conservation of metabolic pathways that developed in the earliest cells.

There are other small biomolecules, specific to certain types of cells or organisms. For example, vascular plants contain, in addition to the universal set, small molecules called secondary metabolites, which play a role specific to plant life. These metabolites include compounds that give plants their characteristic scents, and compounds such as morphine, quinine, nicotine, and caffeine that are valued for their physiological effects on humans but used for other purposes by plants. The entire collection of small molecules in a given cell has been called that cell’s metabolome, in parallel with the term “genome”. If we knew the composition of a cell’s metabolome, we could predict which enzymes and metabolic pathways were active in that cell.