Nucleotides are used by cells to build genes. Genes are DNA and RNA molecules that function as templates for ribosome enzymes assembling proteins out of amino acids. DNA and RNA are each built from a set of four nucleotides: adenine, guanine, cytosine, and thymine for DNA; and adenine, guanine, cytosine, and uracil for RNA. A sequence of three nucleotides, known as a codon, encodes for one amino acid by selectively binding with it. For example, the nucleotide sequence GAA will selectively bind with the amino acid molecule glutamate.

All nucleotides in DNA and RNA share a common “connector”, making it possible for a single enzyme to assemble thousands of nucleotides together into a long strand. This connector consists of a pentose sugar with one or more phosphate groups. Here, the standard connector is shown in green as a cytosine nucleotide chemically bonds with a thymine nucleotide, releasing a water molecule in the process. A different enzyme can be used to take a strand of nucleotides apart.

Because we are building one generic nucleotide, orotidine 5'-monophosphate (OMP), to represent all nucleotides, codon encoding is not included in Petri Dish’s cell model.