The cry1Ab gene produces the insect control protein Cry1Ab, a delta-endotoxin. The Cry1Ab protein produced by the Bt maize is identical to that found in nature and in commercial Bt spray formulations. Cry proteins, of which Cry1Ab is only one, act by selectively binding to specific sites localized on the lining of the midgut of susceptible insect species. Following binding, pores are formed that disrupt midgut ion flow, causing gut paralysis and eventual death due to bacterial sepsis. Cry1Ab is lethal only when eaten by the larvae of lepidopteran insects (moths and butterflies), and its specificity of action is directly attributable to the presence of specific binding sites in the target insects. There are no binding sites for the delta-endotoxins of B. thuringiensis on the surface of mammalian intestinal cells, therefore, livestock animals and humans are not susceptible to these proteins.

In plants, the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (abbreviated EPSPS) plays a key role in the biochemical pathway that results in the synthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. This enzyme is only present in plants and microorganisms, such as bacteria and fungi, and is not present in animals and humans. The simple amino acid analogue glyphosate selectively inhibits the activity of the EPSPS enzyme, thus shutting off aromatic amino acid synthesis. Because these amino acids are needed for protein synthesis, which is required for plant growth and maintenance, the application of glyphosate quickly results in plant death. EPSPS is not present in mammals, birds or aquatic life forms, which do not synthesize their own aromatic amino acids. For this reason, glyphosate has little toxicity to these organisms.

A gene encoding a glyphosate-tolerant form of the EPSPS enzyme was isolated from the CP4 strain of Agrobacterium tumefaciens, a common soil bacterium, and introduced into the maize genome using micro-particle bombardment. MON802 contains a third gene that codes for a modified version of the enzyme glyphosate oxidase (GOX), which accelerates the normal breakdown of glyphosate into two non-toxic products, aminomethylphosphonic acid (AMPA) and glyoxylate. AMPA is the principal breakdown product of glyphosate and is degraded by several microorganisms, while glyoxylate is commonly found in plant cells and is broken down by the glyoxylic pathway for lipid metabolism. The GOX encoding gene (goxv247) was isolated from the bacterium Ochrobactrum anthropi strain LBAA.