In Petri Dish, cells take in glucose, O2, PO32-, NH4+, and CO2 from the environment, and then use those basic molecules to build phospholipids for plasma membranes, amino acids for proteins, and nucleotides for genes. Glucose is also broken down for energy. Every molecule that a cell needs must either be taken in from the environment or built from molecules taken in from the environment.

Cells build molecules using series of chemical reactions known as metabolic pathways. All of the metabolic pathways in a cell form a metabolic network. The diagram below represents the core metabolic network of a cell in Petri Dish. If any of these chemical reactions were missing, then the cell would be unable to grow or reproduce. However, players can extend this core metabolic network to give their cells more capabilities.

The red arrows in the diagram represent the pathway for cellular respiration, the green arrows for amino acid synthesis, the blue arrows for nucleotide synthesis, and the purple arrows for phospholipid synthesis.

The metabolic pathways in Petri Dish have been simplified. Steps have been combined and most cofactors have been eliminated. Because of this, some chemical reactions do not balance, especially in terms of hydrogen atoms. Including cofactors, such as NAD+ (C21H27N7O14P2) or Coenzyme A (C21H36N7O16P3S), would drastically increase the size and complexity of the core metabolic network because cells would have to be able to build those molecules. And in the case of Coenzyme A, we would also need a source for sulfur. Where possible, we have made sure that our chemical reactions do balance for carbon, nitrogen, oxygen, and phosphorous atoms.