The Trinity of Life: The Genome, the Proteome, and the Mineral Chemical Elements

738 Journal of Chemical Education • Vol. 81 No. 5 May 2004 • www.JCE.DivCHED.org The investigation of the nature of living organisms has been dominated recently by the study of the genome. The main thrust has been to obtain and interpret linear sequences of DNA (or RNA) nucleotides, but it is clear that an understanding of activity in cells can only come from the further, now quantitative, analysis of gene products, RNAs, and proteins, but especially from the detailed description of the second of these, the proteome, and the functions of its components. There is, therefore, the need to recognize that as well as the sequence we must know the structure, the local concentration in each compartment, and the activity of each protein. The activity of a biological polymer, RNA, or a protein, or even of DNA, in vivo cannot be deduced even then, since activity is a property of the whole cellular system and is therefore critically dependent on the concentrations of small molecules, the metallome, and ions as well as of these large organic molecules in each compartment. Many of the small molecule and ion variables are related to the element contents of the environment so that the environment is a part of the living system. The cellular content of elements is readily divided into a dependence on the concentrations of metal ions and their complexes and on simple nonmetal compounds. Three advantages stem from the study of the metal elements relative to that of nonmetal, organic, element distributions that is of C, H, N, O, S, or P: (a) there are fewer than 20 free chemical elements to discuss (Table 1), which are easily followed in cells; (b) quantitative analysis of metal ions, free and bound, is relatively simple experimentally, even in compartments; and (c) there is a direct connection to the environment since the elements, for example free ions, are usually not grossly changed in compounds. The connection to the environment leads from the abundance and environmental availability of the elements and therefore gives an independent variable to the possibilities of evolution. An inquiry not just into element requirements in organisms today but to an inspection of evolution linked to Earth’s chemistry and its changes over 4 × 109 years is then a necessary part of the development of organisms. The nonmetals bound in small molecular species in cells, also circumscribed by the state of the elements in the atmosphere and aqueous solutions, are less easily related to their chemical elements in the environment and their changes owing to the complexity of the organic chemistry involved. Again these molecular species are directly related to the need to produce genetic material and proteins. Obviously the genome and the proteome and their evolution can also be followed but they are not directly related to environmental chemicals though they are interactive with them. There is then a trinity of linked variables in the evolution of organisms, the genome, the proteome, and the environmental elements. Given their advantages we shall concentrate on the metal elements and their changes both in the environment and in cells. Thus we need a name for the profiles of the metal contents of cells. In each compartment we shall refer to the free metallome, the profile of free metal ion concentrations, [Mn+], and the total metallome, which includes concentrations of free and bound metal species (1). To see the connection between the origin and evolution of the metallomes of cells to the environment and its changes we give first a brief outline of the known or presumed initial environment and its changes over time. The Trinity of Life: The Genome, the Proteome, and the Mineral Chemical Elements