Carbon-based nanomaterials of different dimensions (1–3D, tubes, bundles, films, papers and sponges, graphene sheets) have been created and their characteristic properties have been discussed intensively in the literature. Due to their unique advantageous, tunable properties these materials became promising candidates in new generations of applications in many research laboratories and, recently, in industries as well. Protein-based bio-nanocomposites are referred to as materials of the future, which may serve as conceptual revolution in the development of integrated optical devices, e.g. optical switches, microimaging systems, sensors, telecommunication technologies or energy harvesting and biosensor applications. In our experiments, we designed various carbon-based nanomaterials either doped or not doped with nitrogen or sulfur during catalytic chemical vapor deposition synthesis. Radio- and isotope analytical studies have shown that the used starting materials, precursors and carriers have a strong influence on the geometry and physico-/chemical characteristics of the carbon nanotubes produced. After determining the 14C isotope constitution 53 m/m% balance was found in the reaction center protein/carbon nanotubes complex in a sensitive way that was prepared in our laboratory. The result is essential in determining the yield of conversion of light energy to chemical potential in this bio-hybrid system.