The parent Bt11 line of maize was developed to resist European Corn Borer (Ostrinia nubilalis) by producing its own insecticide. This event was genetically engineered through introduction of the cry1Ab gene, isolated from the common soil bacterium Bacillus thuringiensis (Bt). The cry1Ab gene produces the insect control protein Cry1Ab, a delta-endotoxin. The Cry1Ab protein expressed in Bt11 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 from 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 delta-endotoxins of B. thuringiensis on the surface of mammalian intestinal cells, therefore, livestock animals and humans are not susceptible to these proteins.

In addition to insect resistance, Bt11 was developed to allow for the use of glufosinate ammonium, the active ingredient in phosphinothricin herbicides (Basta®, Rely®, Liberty®, and Finale®) as a weed control option, and as a breeding tool for selecting plants containing the cry1Ab gene. Bt11 contains the pat gene, isolated from a common soil actinomycete Streptomyces viridochromogenes. This gene allows for the production of the enzyme phosphinothricin N-acetyltransferase (PAT) which confers tolerance to glufosinate. The PAT enzyme in maize line Bt11 converts L-phosphinothricin (PPT), the active ingredient in glufosinate ammonium, to an inactive form. In the absence of PAT, application of glufosinate leads to reduced production of the amino acid glutamine and increased ammonia levels in the plant tissues, resulting in the death of the plant. The PAT enzyme is not known to have any toxic properties.

The parent GA21 line of maize was genetically engineered, by particle acceleration (biolistic) transformation, to be tolerant of glyphosate-containing herbicides. The isolated endogenous maize epsps gene was modified through site-directed mutagenesis, such that its encoded enzyme was insensitive to inactivation by glyphosate, and inserted into the inbred AT maize variety. The modified maize line permits farmers to use glyphosate-containing herbicides for weed control in the cultivation of maize.

Glyphosate specifically binds to and inactivates the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which is part of an important plant biochemical pathway called the shikimate pathway. The shikimate pathway is involved in the biosynthesis of the aromatic amino acids tyrosine, phenylalanine and tryptophan, as well as other aromatic compounds. When conventional plants are treated with glyphosate they cannot produce the aromatic amino acids essential to their survival. The EPSPS enzyme is present in all plants, bacteria and fungi, but not in animals, which do not synthesize their own aromatic amino acids. Thus, EPSPS is normally present in foods derived from plant and microbial sources.