In lieu of carbon-based primary metabolisms found in plants and animals, certain bacteria and archaea survive by catabolizing ammonia. These organisms are globally pervasive and control biogeochemical nitrogen cycle fluxes. A dearth of understanding persists regarding the underlying biochemistry of these nitrogen-based metabolisms due to the difficulties associated with culturing ammonia-oxidizing organisms. Nevertheless, copper is known to play a vital role in biological ammonia oxidation (BAO).This thesis explores the biochemistry of two of the most abundant copper proteins in the model ammonia-oxidizing bacterium, Nitrosomonas europaea. Molecular biology and structural biology techniques are employed to develop a heterologous technology for the isolation of an integral membrane protein complex, which is believed to catalyze the first step of BAO, ammonia monooxygenase (AMO). Additionally, an investigation into the in vivo function of nitrosocyanin (Ncya) is made. Spectroscopic techniques are utilized to assess the activity and electron transfer kinetics of Ncya. The results provide insight into Ncya function and challenge proposed hypotheses.