Life is a non-equilibrium state and maintaining it thus requires a constant supply of external energy. To this end, organisms consume nutrients and convert the chemical energy into the universal energy carrier ATP. The energy conversion is achieved by the respiratory chain, which comprises multiple membrane-bound enzymes that convert the chemical energy into an electrochemical proton gradient, which is stored across a biological membrane. This proton gradient is, in turn, consumed by ATP synthase to produce ATP. On a molecular level, this is realized by a series of charge transfer processes, which are catalyzed by the respiratory chain complexes I-IV. These enzymes can also combine into larger assemblies, so-called supercomplexes, although their functional role remains highly debated.

In this thesis I will discuss the function of complexes I, III, and IV as well as the mycobacterial III₂IV₂ obligate supercomplex and the superoxide scavenger superoxide oxidase. To elucidate key functional aspects of these enzymes we have employed computational methods together with structural data and experimental measurements. Specifically, we have investigated the mechanism of complex I deactivation, as well as the proton transfer mechanics in its membrane domain. In complex IV, we have identified a mechanism by which steroid molecules can inhibit the enzyme, and describe how electric fields can selectively direct protons along specific pathways. Moreover, we have explored long-range charge transfer mechanisms in the unique mycobacterial III₂IV₂ supercomplex, and investigated the mechanism of the unique, membrane-bound superoxide scavenger superoxide oxidase. The combined results shed light on the molecular mechanisms that enable these enzymes to transduce energy.