Photoactive proteins have been studied as a fascinating link between chemistry and biology. The structured environment of the protein both drives specific photochemical reactions and converts the energy from photo-reactions, such as isomerizations, into biological function and signaling. This dissertation presents work that spectroscopically probes the link between energy dynamics and protein function and structure in the photosynthetic reaction center from R. sphaeroides, a synthetic light harvesting complex, and the bacteriophytochromes RpBphP2 from R. palustris and PaBphP from P. aeruginosa. In each of these three systems, chromophores are embedded inside a larger apo-protein. The immediate solvation environment around the chromophore is static compared to a solvent like water and cannot rearrange in response to absorption of light and subsequent change in electronic structure. To investigate the photochemistry itself, the protein’s influence on the reaction must be fully understood. Does the relationship between the protein and the chromophore drive the photochemistry by constraining the electrostatic environment? Using two-dimensional electronic spectroscopy (2D-ES), in which the absorption and emission energies of the system are mapped onto two axes, it is feasible to observe differences across an ensemble of complexes each in microscopically different conformations and untangle congested spectra. Chapter 2 presents a study in which the photochemistry and biological function of bacteriophytochromes are shown to persist through significant environmental fluctuations. In chapter 3, a synthetic light harvesting system based on the idea that the protein provides a scaffold for light harvesting is investigated. The system does exhibit noticeable excited state interactions, but does not display the coherent energy transfer characteristic of photosynthetic light harvesting complexes. Chapter 4 presents work that endeavor to perturb energy transfer in the photosynthetic reaction center in purple bacteria. Incredibly, the complex is able to retain ultrafast energy transfer despite highly disruptive mutations, and we provide evidence that the energy gaps between excitonic states are compensated by the vibrational modes of the bacteriochlorophyll molecules, meaning that the chromophore’s intricate vibrational structure in exploited for energy transfer. Finally, this dissertation concludes with proposals for future directions to investigate photochemistry in biology and biology with photochemistry.