In this work we have performed a computer analysis of the electron and proton transport in cyanobacteria cells using a mathematical model of light-dependent stages of photosynthesis, taking into account key stages of pH-dependent regulation of electron transport on both acceptor and donor sites of photosystem 1 (PS1). The comparison of theoretical and experimental data proves that the model adequately describes the multiphase kinetics of photoinduced redox transformations of P-700 (primary electron donor in PS1). Our computer simulation describes an impact of variations of the atmosphere gases (CO2 and O-2) on the induction events in cyanobacteria (P-700 photooxidation, generation of transmembrane Delta pH), which strongly depends on pre-illumination conditions (aerobic or anaerobic atmosphere). It has been shown that the variation of CO2 concentration in the cell interior may noticeably affect the kinetics of electron transport, acidification of lumen, and ATP synthesis. The contribution of alternative pathways of the electron transport (cyclic electron transport around PS1 and outflow of electrons to O-2) to the operation of cyanobacteria photosynthetic apparatus was analyzed. At the initial stage of induction period, cyclic electron fluxes around PS1 ("short" and "long" pathways) contribute substantially to photosynthetic electron transport. These fluxes, however, attenuate with the light-induced activation of the Calvin-Benson cycle reactions. In the meantime, efflux of electrons from PS1 to O-2 (or to another metabolic chains) increases with the oxygen accumulation in the medium. Effects of ferredoxin oxidation by hydrogenase, catalyzing formation of H-2, on the kinetics of P-700 photooxidation and distribution of electron fluxes on the acceptor side of PS1 has been modeled.