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Williams & Da Silva, J. Chem. Ed. 2004 Research: Science and Education The Trinity of Life: The Genome, the Proteome, and the Mineral Chemical Elements R. J. P. Williams* Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom; *[email protected] J. J. R. Fraústo da Silva Department of Chemistry, Instituto Superior Técnico, Lisbon, Portugal The investigation of the nature of living organisms has There is then a trinity of linked variables in the evolu- been dominated recently by the study of the genome. The tion of organisms, the genome, the proteome, and the envi- main thrust has been to obtain and interpret linear sequences ronmental elements. Given their advantages we shall of DNA (or RNA) nucleotides, but it is clear that an under- concentrate on the metal elements and their changes both in standing of activity in cells can only come from the further, the environment and in cells. Thus we need a name for the now quantitative, analysis of gene products, RNAs, and pro- profiles of the metal contents of cells. In each compartment teins, but especially from the detailed description of the sec- we shall refer to the free metallome, the profile of free metal ond of these, the proteome, and the functions of its ion concentrations, [Mn+], and the total metallome, which components. There is, therefore, the need to recognize that includes concentrations of free and bound metal species (1). as well as the sequence we must know the structure, the lo- To see the connection between the origin and evolution of cal concentration in each compartment, and the activity of the metallomes of cells to the environment and its changes each protein. The activity of a biological polymer, RNA, or we give first a brief outline of the known or presumed initial a protein, or even of DNA, in vivo cannot be deduced even environment and its changes over time. 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 envi- ronment is a part of the living system. The cellular content Table 1. Available Element Concentrations in the Sea of elements is readily divided into a dependence on the con- As They Changed with Time Element As centrations of metal ions and their complexes and on simple Aerobic Simple Ion or Original Conditions/M nonmetal compounds. Three advantages stem from the study Conditions/M of the metal elements relative to that of nonmetal, organic, Species element distributions that is of C, H, N, O, S, or P: (a) there Na+ >10−1 >10−1 are fewer than 20 free chemical elements to discuss (Table K+ ~10−2 ~10−2 1), which are easily followed in cells; (b) quantitative analy- 2+ −2 −2 sis of metal ions, free and bound, is relatively simple experi- Mg ~10 >10 mentally, even in compartments; and (c) there is a direct Ca2+ ~10−3 ~10−3 connection to the environment since the elements, for ex- −7.5 −7.5 3− V0~1 ~10 (VO4 ) ample free ions, are usually not grossly changed in com- 2+ −7 −9 pounds. The connection to the environment leads from the Mn ~10 ~10 abundance and environmental availability of the elements and F0e ~1 −7 (Fe2+)0~1 −17 (Fe3+) therefore gives an independent variable to the possibilities of Co2+ <10−13 ~(10−11) evolution. Ni2+ <10−12 <10−9 An inquiry not just into element requirements in organ- 20 10 2 isms today but to an inspection of evolution linked to Earth’s C0u <1 − , Cu+ <10− , Cu + chemistry and its changes over 4 × 109 years is then a neces- Zn2+ <10−12 <10−8 sary part of the development of organisms. The nonmetals M0o <1 −10 (MoS 2−, Mo(OH) )0~1 −7 (MoO 2−) bound in small molecular species in cells, also circumscribed 4 6 4 −9 2− −9 2− by the state of the elements in the atmosphere and aqueous W0~1 (WS4 )0~1 (WO4 ) solutions, are less easily related to their chemical elements in H+ p)H ~7 pH 8 (sea the environment and their changes owing to the complexity −3 −2 2− S0~1 (H2S0) 1 (SO4 ) of the organic chemistry involved. Again these molecular spe- 2− −5 −5 cies are directly related to the need to produce genetic mate- HPO4 <10 <10 NOTE:sThe value for the original primitive conditions are estimate rial and proteins. Obviously the genome and the proteome −2 based on a pH of 8.0, an H2S concentration of ~10 M, and a CO2 and their evolution can also be followed but they are not di- pressure of one atmosphere. The concentrations in today’s aerobic rectly related to environmental chemicals though they are in- condition are taken from Cox (2). Those of the original environment are teractive with them. estimated as described in references (1, 3, 4). 738 Journal of Chemical Education • Vol. 81 No. 5 May 2004 • www.JCE.DivCHED.org Research: Science and Education The Environment during Evolution though much of Mg and Ca also formed somewhat insoluble precipitates, such as carbonates. Formation of these carbon- Prior to the beginning of life, say 4 × 109 years ago, the ates presumably limited the content of these two ions in the ᎑3 atmosphere was reducing as a result of the dominant univer- sea. The initial presence of H2S (probably around 10 M) sal abundance of hydrogen over oxygen. The most common caused a drastic limitation on the availability of other ele- nonmetal elements were therefore present mostly as hydrides, ments, especially of trace metals and increasingly in the tran- for example, oxygen (H2O), sulfur (H2S), and selenium sition metal series, owing to the formation of sparingly soluble (H2Se), some carbon (CH4) though most of it was CO or sulfides, so that the concentrations of divalent elements fell 2+ CO2, and perhaps some nitrogen (NH3). Of the other abun- dramatically from that of Mn (Table 1). The availability of dant nonmetals, silicon and phosphorus were present as sili- free ions, calculated from the pH and their solubility prod- cate and phosphate in rocks and in solution while chlorine ucts, fall close to the Irving–Williams order (1) was reduced to chloride (HCl), which dissolved easily in wa- Mn2+ < Fe2+ < Co2+ < Ni2+ << Cu2+ (Cu+) > Zn2+ ter. The HCl was neutralized by reaction with basic metal minerals and much Na, and some K, Mg, and Ca were liber- The quantity of Zn in the sea must have been very low and ated into the sea. The amount of HCl seems to have been that of Cu negligible while there would have been around limiting in these reactions, hence it was the abundance of Cl 10᎑7 M Mn2+ and 10᎑7 M iron as Fe2+ (Table 1). Note, how- relative to that of other elements that decided the nature of ever, that it is difficult to know the availability of iron sul- the sea to this day. As a result of these neutralization reac- fide clusters that probably formed in the prevalent conditions tions the pH of the sea settled to a value close to 8 through and are somewhat water soluble. There would also have been buffering by carbonate, phosphate, and the mixed oxides very little molybdenum (largely precipitated as MoS2) but present. The reduced atmospheric and neutral aqueous solu- more tungsten, which is not so easily reduced from the W(VI) tion chemistry of the nonmetals did not greatly influence the state to the insoluble WS2, and almost certainly more vana- state of the most common metals, sodium, potassium, mag- dium than molybdenum since it would have been present in nesium, and calcium, which give simple ions in solution, more soluble species (5). Figure 1. A diagnostic illustration of the succession of oxidation–reduction potentials showing the changes of oxidation state of different elements from an H2 to an O2 atmosphere. We consider that Earth’s surface environment changed consecutively in the direction of the arrows over the period of 4 x 109 years. Nonmetals are on the left, metals on the right (1). www.JCE.DivCHED.org • Vol. 81 No. 5 May 2004 • Journal of Chemical Education 739 Research: Science and Education The dramatic but slow changes following the oxidation plants. It is generally agreed that cellular life started from such of the elements over the following 3 × 109 years as a result of anaerobic prokaryotes, cells with one central compartment the increase in O2 in the atmosphere are shown in Table 1 and an outer membrane (Figure 3), to greater and greater and Figure 1 and have been detailed elsewhere (1, 2). Here compartmental complexity (see Figure 7). we note first that the major nonmetals became CO2 (C), H2O 2᎑ 2᎑ (H), N2 (N), SO4 (S), and SeO4 (Se), but there was little The Primitive Cell Cytoplasm change in Cl᎑, Si(OH) , or HPO 2᎑. As sulfide was oxidized 4 4 The fact that the basic and major synthetic organic to sulfate in the sea, the availability of cobalt and nickel, but chemistry of all cells, the production of nucleotides, proteins, much more strikingly and more recently that of zinc and of fats, and polysaccharides is reductive and is a unique feature copper, inevitably and slowly increased, as did that of mo- ᎑ ᎑ of all organisms means that there had to be maintained re- lybdenum (MoO 2 ) and vanadium (VO 3 ).
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