Highlights•The mechanisms of proton transfer established in photochemical reactions in organic dyes are discussed in order to achieve deeper understanding of functioning of biochemical systems.•From this focus, the proton motions in biocatalysis, photobiocatalysis, operation of selective proton channels and systems of photosynthesis and cellular respiration are analyzed.•For explaining the formation of transmembrane proton gradients, a simple ‘proton lift’ concept is presented that may be the basis of further research and analysis.