The mechanisms of three protocellular functions have been studied using molecular modeling techniques. These functions are (1) the transport of ions across membranes, (2) the formation of photoactivated proton gradient that could drive chemical synthesis in the protocell, and (3) the organization of small peptides necessary for catalytic activity. In all these processes, membranes play an essential role. The transfer of ions across the barrier formed by protocellular walls is facilitated by the formation of deep, thinning defects in the membrane. Membranes also form a barrier to charged species that allows for retaining proton gradients. These gradients can be generated by a simple transmembrane proton pump consisting of a proton source and two acceptors. The directionality of the pump is ensured by a "gate-keeping" mechanism involving a water molecule, conformational change of the primary acceptor or tautomerization of a histidine. The pump can be formed by two transmembrane helices but not one helix. They provide surfaces at which organic molecules concentrate and small peptides can organize into ordered, amphiphilic structures. In general, valuable information about the origins and evolution of protocells can be obtained from the knowledge of physical and chemical principles that govern functioning of contemporary cells.