Biological ammonia (NH3) oxidation, referred to as nitrification, is a critical part of the biogeochemical nitrogen cycle. Nitrification is mediated by both bacteria and archaea to ultimately oxidize NH3 to nitrite (NO2–), though there are also complete NH3-oxidizing (comammox) bacteria capable of oxidizing NH3 completely to nitrate (NO3–). In addition to these products, nitrification is also a major source of the by-products and environmental pollutants nitric oxide (NO), nitrous oxide (N2O) and nitrogen dioxide (NO2). Many steps of biological nitrification, including those leading to the production of these harmful products, are not currently clear; however, the work presented in this dissertation describes recent efforts and discoveries towards a complete understanding of the nitrification pathway. This process begins in both bacteria and archaea with the enzyme ammonia monooxygenase (AMO), which oxidizes NH3 to hydroxylamine (NH2OH). There exist two metal-binding sites in AMO of interest as these are highly conserved in AMOs and related enzymes. The true active site of this enzyme remains in debate, but here we show that both sites must remain intact for effective catalysis. In bacteria, the formed NH2OH is further oxidized to NO by the enzyme NH2OH oxidoreductase (HAO), though prior convention stated that HAO was able to oxidize NH2OH fully to NO2–. There exists another enzyme in NH3–oxidizing bacteria (AOB) known as cytochrome (cyt) P460 that can oxidize NH2OH to NO and N2O. Here we present structural and mechanistic studies that describe how the unusual P460 cofactor and surrounding amino acids allow for this catalysis. The recent discovery that the true product of HAO is NO and not NO2– presents a challenge to find the enzyme in AOB which can complete this oxidation to the final product NO2–. Here we present a potential candidate, nitrosocyanin (NC), and describe preliminary experiments on its interaction with NO.