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Stoichiometric Network Analysis: Studies on Chemical Coordinative Reactions Within Biological Material

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Chemical Evolution

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Abstract

SNA, introduced in the 1970s by Canadian chemist Bruce Clarke and derived from matrix stability analysis, can be used to identify feedback structures in chemical and other reaction networks which are due to autocatalysis. Autocatalysis in turn is a type of feedback which resembles the chemical processes underlying cell-budding or whole-organism reproduction: first and rather continuously absorb certain kinds of matter from some reservoir and process them in a complicated chemical network to finally obtain more of the compounds constructing this network which in case of living organisms is actively kept together by the outer linings of the organism is both about biological reproduction and autocatalysis in “humble” chemical systems like acid-catalyzed oxidations releasing more protons in protic solvents. As effective feedback relies on certain network topologies and limited presence of competing reactions in either case, SNA can provide certain statements on limiting conditions which must be obeyed to keep chemical entities involved in biochemistry as reproduction takes place on and on and evolution goes on. It can be shown that these criteria essentially limit the number of essential elements while powerful yet rare and selective possible catalysts like PGMs or rhenium are as efficiently excluded from bioinorganic chemistry as abundant elements which could run just few biorelevant transformations (most notable, Al and Ti).

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Notes

  1. 1.

    In SNA theory, one distinguishes among strong cycles (autocatalytic reaction order > combined orders of reactions which remove or inactivate parts of autocatalyst), critical cycles (autocatalytic reaction = combined orders of reactions which remove or inactivate parts of autocatalyst) and weak cycles (autocatalytic reaction < combined orders of reactions which remove or inactivate parts of autocatalyst).

    The latter are called weak as autocatalysis, and accordingly replication cannot be sustained in these conditions; according, neither oscillations nor bistability or selection among competitors would be (“successfully”) observable. This may happen in entire ecosystems when too many resources are consumed (e.g. by man interfering [excess fishery, wood logging], washout of nutrients, massive predation in key levels of a trophic pyramid with the resources not being resupplied by excretion when the latter takes place elsewhere [sinking below some halocline, excretion of piscivorous birds or mammals far off a lake or river]).

  2. 2.

    Yet compare Movile cave biodiversity to that seen in some usual soil mesofauna.

  3. 3.

    The terminal approach towards equilibrium occurs in a linear manner even with oscillator systems. Yet “normal” animals and fungi (except for anaerobic metabolism) use assemblies of food and oxidant initially rather far from equilibrium, and, as far as fungi are concerned, catalyst/substrate/oxidant systems may come very close, if not identical to, actual chemical oscillators (namely Mn2+/3+/malate or some amino acid or malonate or phenol/H2O2 except for a second oxidant added (IO3 − in [Briggs-Rauscher-kind] oscillators, or MnO4 − if you prefer Mn-related autocatalysis) and the pH of operation being not that acidic (that is, 3–4 rather than ≈ 1) in wood degradation.

  4. 4.

    Even symbiotic photoautotroph-heterotroph assemblies like lichens (alga or cyanobacterium/fungus), stony coral polyps (coelenterate animal/alga) or chemoautotroph-heterotroph endosymbiotic systems (clams or worms in black-smoker habitats) do (and, for the latter must [S demand]) continuously exchange matter with the environment restraining from constructing closed-loop cycles for anything falling short of fast growth. Hence a coral reef depletes its environs from phyto- and small zooplankton (and Ca2+, Sr2+, HCO3 − ions, of course) while photosynthesis does provide just a part of organic carbon and way too less dioxygen even to cover demands of the polyps, let alone the fishes, crustaceans and so on inhabiting the reef. Therefore symbiosis will not stabilize it towards external perturbations but multiply the risks (it can stand some predation of polyps by Chaetodon and parrot fishes and mechanical destruction by storm waves but declines when the water gets too warm for zooxanthelle survival or too acidic for actively maintaining the carbonate backbones).

  5. 5.

    Fränzle (2010).

  6. 6.

    Concerning catalytic features of nucleic acids (so-called ribozymes), please distinguish between (rather slow) spontaneous reproduction of RNA (which is usually effected by adding some protein-based enzyme) and its catalytic activity which commonly means “cutting out” (resecting) some part of the RNA chain which latter implies that, although the reaction is promoted by RNA, it is not autocatalytic but autodestructive. Self-replicating peptides, on the other hand, cause other enzyme reactions besides of making copies of their own.

  7. 7.

    Even when starting chemical evolution experiments with CH4- or C2H6-rich mixtures rather than COx/H2, yields of all glycine, glycolic, oxalic and lactic acids (besides of HCOOH) are larger than those of acetic or propionic acids (Dickerson 1978); thus there is a strong trend towards introduction of groups into carboxylate side-chains which commonly increase strength of coordinative binding of metal ions.

  8. 8.

    Note that commonly in complexes of amino acids, also such ones which carry ligand-active functional groups, it is the terminal carboxylate and the α-amino group which bind the metal ion while in peptides binding by suitable side-chains prevails. Thus, bulky substituents like 2-propyl (valine), 2-butyl (isoleucine) or benzyl (phenylalanine) will have a bigger impact on M-peptide interactions than on the simple M-AA complexes. Although there are cases of linkage isomerism in amino acids such as cysteine (thiolate + amine- vs. carboxylate + amine binding to Co(III)) or arginine, they are rare and unlikely to influence the pathway of chemical evolution. Thus, bulky substituents like 2-propyl (valine), 2-butyl (isoleucine) or benzyl groups (phenylalanine) bound to C2 of glycine will have a bigger impact on M-peptide interactions than on the simple M-AA complexes.

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Authors and Affiliations

  1. Environmental Institute of Scientific Networks (EISN), Haren, Germany

    Bernd Markert & Simone Wünschmann

  2. International Graduate School Zittau, Zittau, Germany

    Stefan Fränzle

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  1. Bernd Markert
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Markert, B., Fränzle, S., Wünschmann, S. (2015). Stoichiometric Network Analysis: Studies on Chemical Coordinative Reactions Within Biological Material. In: Chemical Evolution. Springer, Cham. https://doi.org/10.1007/978-3-319-14355-2_4

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