For a long time the chemical reactions controlling bioluminescence were not understood. The structures to be tested on were unknown to potential investigators and the technology undeveloped (Chan et al. 2008). In recent years a lot of light has been shed on the subject, figuratively speaking.
“Chemiluminescence is observed when a chemical reaction results in the formation of an excited state of a product molecule. This product may emit light, if fluorescent, or may transfer the energy to any suitable acceptor present.” (Herring & Morin JG 1978).
Chemiluminescence is an exothermic reaction unlike fluorescence and phosphorescence which often deal with absorption. These chemiluminescent processes are controlled by luciferins (Figure 2, click image to view large), believed to be the evolutionary starting point for light-producing systems. Luciferins are simple molecules, raised to a higher, less stable, energy level via an oxidation reaction; once excited, the process by which the molecules return to a stable state generates light energy as a by-product (Rees et al. 1998). These reactions are aided by species-specific specialized catalysing enzymes, these can be either Luciferases or photoproteins (Haddock et al. 2010).
It has been suggested that bioluminescence evolved accidentally as a by-product of oxygen-detoxifying reactions as Coelenterazine (Figure 2), a luciferin present in most marine groups, is a very effective antioxidant (Rees et al. 1998). Coelenterazine has been found in non-bioluminescent organisms as well, supporting the argument it has a use beyond generating light and it is also the most commonly occurring luciferin. It is possible, once organisms migrated down through the water column and beyond the photic zone the oxygen-detoxifying mechanism became obsolete and natural selection was free to select for improvements to bioluminescence (Rees et al. 1998).
The sites of these reactions are known as Photocytes; large concentrations of these Photocytes, particularly in specialized glands or tissues, are known as Photophores (Clarke 1963).