A major challenge for the future understanding of the roots of human health is to link the physics and the physiology of the mitochondrion. Ubiquinone is a key component of the mitochondrion, which connects electron tunnelling, proton translocation and energy conversion, and the molecular diffusion of reducing power. Of equal importance is its interaction with molecular oxygen and superoxide generation, whether it is adventitious and damaging or regulated. This special issue intends to build on the exciting science presented and discussed at the meeting entitled “Quinone Binding and Catalysis” held in 2008 as a satellite to the 15th European Bioenergetics Conference (EBEC) in Dublin, Ireland. The topics of the articles range from fundamental characterisation of biological quinones and their function through the characterisation of their binding sites and finally cover the mechanism of individual electron transfer complexes of cellular respiration and photosynthesis with an emphasis on current advances in methodology.