Amino acids are the building blocks of proteins. There are 22 standard amino acids used to build proteins, but we are going to represent all of them in Petri Dish with a single generic amino acid, glutamate. Glutamate can be used as a precursor to build other amino acids, such as alanine, aspartate, and glutamine, if necessary. In fact, we build aspartate from glutamate in our core metabolic network in order to build orotate for nucleotide synthesis.

Amino acid synthesis begins by diverting ketoglutarate from the cellular respiration pathway and combining it with NH4+ to build glutamate in step 1. Glutamate is then converted into our generic amino acid in step 2. We added this second step because glutamate is also an intermediate in the nucleotide synthesis pathway, so glutamate has to show up explicitly in the metabolic network.

The metabolic pathway for building glutamate in Petri Dish has been simplified. Here is a more detailed version of the actual pathway: