Photosynthesis converts solar energy into chemical energy to drive the biological processes of life on our planet. Photosystem I (PSI) is one of the two reaction centers of oxygenic photosynthesis in cyanobacteria and higher plants. PSI is a multisubunit membrane bound protein complex that catalyzes the photooxidation of plastocyanin in the thylakoid lumen and the photoreduction of ferredoxin in the cytoplasm. The PsaA/PsaB subunits form the heterodimeric core that harbors the primary electron donor P700 and acceptors A0, A1, and FX. Two electron acceptors, F A and FB, occupy PsaC one of three peripheral proteins bound to PSI. The secondary electron acceptor, A1, contains a phylloquinone, a molecule utilized only in PSI. The object of this dissertation is to probe phylloquinone biosynthesis and the bioenergetic aspects of phylloquinone, plastoquinone, and other naphthoquinones in the A1 site of PSI;To investigate phylloquinone's role in PSI, we substituted alternative naphthoquinones and plastoquinone into the A1 site to observe the physiological of the cells and energetic changes in PSI. Menaquinone biosynthetic genes have been identified in E. coli with the phylloquinone homologs elucidated from the Synechocystis sp. PCC 6803 genome. Four phylloquinone biosynthetic genes in Synechocystis have been mutationally disabled, menA, menB, menD, and menE, leading to a complete loss of phylloquinone in the cells. The plastoquinone containing mutant occupies the A1 site instead, allowing a reduced 2 electron transfer in PSI rate. The orientation and distance of the mutant A1 quinone to P700 is the same as wild type. Physiological changes in the mutants include decreased growth rate, oxygen evolution, and chlorophyll content. Addition of the direct product of naphthoate synthase (menB), 2-carboxy-1,4-naphthoquinone, restored phylloquinone content of the PSI complexes to the wild-type levels. Mutant cells also utilize free phylloquinone from the growth medium to displace plastoquinone in PSI. Addition of vitamin K3, 1,4-naphthoquinone, 2-hydroxy-1,4-naphthoquinone, or 1,2-naphthoquinone allowed the cells to synthesize phytylated naphthoquinones, which were inserted into the A1 site in a fraction of the PSI complexes. This dissertation determined the biosynthetic pathway of phylloquinone and alternative phytylated quinones in the A1 site are capable of electron transfer from A0 to FX.