There are large gaps surrounding our understanding of secondary organic aerosols (SOA), which represent a significant fraction of fine particulate matter globally. One of the most difficult aspects of SOA to characterize is the molecular composition, because it is both complex and dynamic. However, the composition of SOA determines to a large extent the impact SOA has on climate, atmospheric chemistry, and human health. The main focus of this dissertation is the detailed composition analysis of SOA generated from important biogenic precursors and the characterization of chemistry induced by their simulated interaction with clouds, anthropogenic pollutants, and solar radiation. In particular, the gas- and aerosol-phase compounds associated with SOA from isoprene, the most abundant volatile organic compound emitted from the biosphere, are studied with the advanced technique of high-resolution mass spectrometry (HR MS). Many SOA compounds, particularly nitrogen-containing organics, are reported for the first time. Spectroscopy tools like UV-Vis, FT-IR and NMR are also used to characterize optical properties and molecular structures of SOA compounds. A secondary focus of this dissertation is to describe brown carbon formation from the ammonium- and amino acid-mediated aging of limonene SOA. Brown carbon changes the optical properties of SOA, but the sources are poorly understood. The experiments presented in this dissertation aim to elucidate the previously unknown precursors, kinetics and products of the reaction. The molecular detail gained from the HR-MS and spectroscopic analyses provides tremendous insight into the formation mechanism and further atmospheric reactions of SOA.