Bio-inspired, hybrid architectures employing quantum dots (QDs) appended with functionally active biomolecules such as enzymes have the potential to be utilized in numerous applications. Some examples include nanosensors for medical diagnostics, chemical/biological threat detection, as well as “bio-factories” in complex industrial synthetic processes. The main advantage in creating these nanofactories is increased rates in catalysis and efficiency when enzymes are associated with nanoscaffolds, as shown in numerous studies. However, the mechanism for this enhancement remains elusive. Gaining a fundamental, mechanistic understanding of enzyme-QD nanostructures is important in the development of numerous device applications. In this work, we review an array of enzymes attached to QDs and generate a hypothesis in regards to the unique architecture of the enzyme-nanoparticle (NP) construct that leads to increases in catalysis. We highlight work with phosphotiresterase (PTE) attached to two distinctly sized QDs in neutralizing a simulant nerve agent, as well as in other enzyme systems.