While membrane-associated proteins make up a substantial percentage of total cellular proteins, a much smaller fraction of known X-ray and NMR protein structures are derived from membrane proteins, Alternative approaches to understanding structure, function, and mechanism in membrane-associated enzymes are clearly needed. Vibrational FT-IR spectroscopy offers a method by which high-resolution structural and dynamic information can be obtained about this class of proteins. Reaction-induced FT-IR spectroscopy is an implementation of vibrational spectroscopy, in which the difference spectrum associated with a perturbative stimulus is recorded. This approach simplifies the spectrum and monitors the structural changes directly involved in the functional transition. In this article, we describe reaction-induced FT-IR studies of the photosynthetic and transport proteins, photosystem II, photosystem I, and lactose permease. In oxygenic plant photosynthesis, photosystem II and I convert Light energy to chemical energy. In secondary active transport, the permease converts an electrochemical gradient into the energy required to move lactose into the cell. Reaction-induced FT-IR spectra acquired from these proteins can identify intermediates in the reaction mechanism. Vibrational bands in spectra acquired from photosystem II, photosystem I, and the permease are assigned by a combination of site-directed mutagenesis, isotopic labeling, and kinetic techniques. This article summarizes our recent progress in the study of photosynthetic and transport proteins with reaction-induced PT-IR spectroscopy.