Coenzyme-A Technologies Inc. Body Image Product

The Evolutionary Origin of Cellular Metabolism

By: Nickolaos D. Skouras, Ph.D.

This paper grew out of an extensive study of the origin of carbon-based metabolism on a rocky planet with substantial quantities of water. It thus steers away from an unrealistically generalized view of life and points to the biota we know that has robustly maintained itself, with a core metabolism that is probably unchanged, on a fit planet for four billion years. My approach is congruent with Henderson’s attempt, in The Fitness of the Environment, to embed life in the geochemistry of the planet and in the physical and organic chemistry of the metabolic building blocks that are the essence of biological structure and function.

Global ecology, the vast overview, involves the input of carbon dioxide and reductants, which eventually emerge as hydrogen and the production of water and methane, or some other suitably reduced form of carbon. The atmosphere at the time of life’s origin had almost no free oxygen, a condition that persisted for the first two billion years of life.

The initial carbon dioxide and hydrogen presumably bubbled up from the magma where thermal processes separated the members of redox couples. This heating of the magma resulted primarily from fission of uranium and thorium and the decay of potassium 40. After some two billion years, photosynthesis took over and hydrogen was produced by the photolysis of water generating the free oxygen of the atmosphere. Thus the energy source for life shifted from the earth’s fission reactions to the sun’s fusion reactions. That the ecosystem adjusted to this change is in itself of great interest, showing the extreme robustness of core metabolism.

Species of largely anaerobic bacteria that are autotrophic and incorporate carbon dioxide through the reductive citric acid cycle, or a substantial portion of that cycle, were first discovered in 1966. In these bacteria energy enters through photons or redox couples leading to reductants such as NADH and pyrophosphates such as ATP. In the reductive TCA cycle, a lyase splits the citrate into acetyl CoA and oxaloacetate. A pathway of carbon dioxide incorporation leads from acetyl CoA to pyruvate to oxaloacetate. The two oxaloacetates continue around the reductive cycle, each picking up two more carbon dioxides and ending up as citrate. The reductive TCA cycle is thus network-autocatalytic and accumulates intermediates. The cycle in this form is unrelated to primary energy transduction but serves as a core engine of synthesis for all the fundamental metabolic building blocks. Thus:

All lipids come from acetyl CoA.

All sugars come from pyruvate.

Amino acids come from the keto acids pyruvate, oxaloacetate, and alpha keto glutarate.

Pyrimidines come from oxaloacetate.

Pyrroles come from succinate.

All other intermediates come from the compounds listed above.

The main features of the cycle are that it is network-autocatalytic (as distinguished from template-autocatalytic) and is the core of all biosynthesis. It has persisted for four billion years and remains the central metabolic essence of biology from cellular biology to global ecology. It survived the oxygen catastrophe, remaining the center of biosynthesis. It is the basic aspect of our search for laws of life.

Geochemical evidence and biochemical generalizations thus lead us to the following conjectures:

Reductive metabolism preceded oxidative metabolism.
Autotrophy preceded heterotrophy.
Chemoautotrophs preceded photoautotrophs.
The early reactions could have preceded cellularity, because the reactions involve molecules of the cycle interacting with environmental molecules that have an effectively constant concentration. This renders the reactions approximately first-order kinetically and obviates the need for spatial closure at the very beginning.

(Note that this view differs widely from a paradigm originated by Miller and Urey fifty years ago.)

We now proceed to our three central postulates:

I. The citric acid cycle was and is the core of biology.

II. Membrane-mediated energy transduction from redox couples to pyrophosphate is a unique form, given a requirement for phosphates in an anabolic pathway that generates membrane amphiphiles. The current transduction cycle is universal, and all three of its species (electrons, protons, and phosphodiester bonds) have unique relations to charge transport in an aqueous environment. Its form represents an intrinsic need for geometrically as well as chemically structured separation of potential energy in a reaction sequence otherwise determined by chemical structure.

III. All of biomass lies within a narrow band of hydrogen saturation of carbon, within a narrow range of Gibbs free energy of formation per carbon atom, and within a range characterized by a maximum of molecular complexity in terms of chain-extending and chain-terminating bonds.

These three postulates lead to a result we designate the “feed-down principle.” Biology is clearly hierarchical, leading from metabolism to structures to cellularity to prokaryotes to eukaryotes, etc. At the lower hierarchical levels, features are selected which feed down favorably to the metabolic core that is the sources of the building blocks from the cellular to the ecosystem level. This principle makes the core citric acid cycle the creative and generative center for all life. It is hard to envision any replaying of the tape that would not incorporate the citric acid cycle as the central construct. Given the feed-down principle, the cycle provides constraints on the entire hierarchical structure. Note that the molecules of the citric acid cycle are composed mostly of carbon, hydrogen, and oxygen. In addition, the reactions involve sulfyl hydryls and phosphates. The latter two facilitate the reactions of the cycle. Coming off the cycle, ketoacids react with ammonia to yield amino acids and pyrimidines. The introduction of nitrogen opens the way to informatic molecules: amino acids, nucleic acids, and other functional nitrogen heterocycles.

An interesting generalization is the almost universal entry of nitrogen into covalently bonded biomolecules by the route of alpha keto glutarate and ammonia to glutamic acid and glutamic acid and ammonia to glutamine. All subsequent pathways to nitrogenous compounds involve glutamate or glutamine as the nitrogen donor. This result is sufficiently general that we might regard it as an ecological principle, a single chemical-flow pathway to all the nitrogen in the biosphere. This type of finding suggests a firm logic to the entire network of intermediary metabolism.

Returning to the energy flow, the primary free energy driving the biosphere comes from the overall reaction:

CO₂ + 4H₂ → CH₄ + 2 H₂O

The free energy of the products is appreciably lower than that of the reactants. The hydrogenation need not go to completion, and possible products might be acetate, ethanol or hydrocarbons. At an intermediate degree of hydrogenation, the products formed are components of the citric acid cycle or molecules of the character CH₂O(Nx). The citric acid cycle intermediates are in a fairly narrow band of energy of formation below carbon dioxide and hydrogen and above methane and water.

One feature of bioenergetic gradients of energy level can be seen in examining covalent bond energies of formation for two classes of bonds, those that terminate chains (C-H) and those that extend chains (C-C). Both the high-energy inputs (C=O) and (H-H) and the low-energy outputs (O-H) and (C-H) are completely dominated by chain- terminating bonds so only small molecules are present. At intermediate energies such as those represented in the citric acid cycle intermediates, there are an appreciable number of chain-extending bonds, thus leading to large molecules and a degree of complexification that is a result of the bioenergetics. Thus the energy range governed by the citric acid cycle is the range characterized by radical molecular complexity. This is the informatic domain of biochemistry.

A qualitatively new phenomenon enters when the synthesis products produced along the reactions pathways from the core feed down to have an effect on the core metabolism. Consider two examples. If the synthesized products are catalytic for core reactions, then the effects on the core are governed by the feed-down principle. Catalysts may be small molecules such as proline and and pyridoxal phosphate. Since the network is autocatalytic, aiding any reaction will aid all the reactions. In the second example, the synthesized molecules are capable of generating structure and compartmentalization. The synthesis of amphiphiles that give rise to vesicles is an example of reaction products that produce structures and shift the kinetics from first to second order.

As soon as reactions within a vesicle produce substantial amounts of polar molecules, the buildup of osmotic pressure threatens the integrity of the vesicle. The solution to this problem among the prokaryotes is the emergence of the wall, an extra vesicular meshwork that protects the vesicle from stress. Features of the wall in contemporary prokaryotes are:

It is effectively a single megamolecule engulfing the vesicle.
It is made of a repeating polymer of dimers of amino sugars orthogonal to connecting units of pentapeptides. Note that the building blocks are molecules close to the TCA core in the metabolic chart.
The synthesis of components within the vesicle and the assembly of these units external to the vesicle are at present enigmatic.
The wall has a strong feed-down effect.

Returning to the core metabolic network that seems universal among the autotrophs, we note certain features:

All reactions are anabolic.
The network substrates are a group of about 400 relatively small molecules.
Less than 100 of these molecules are at the termini of reaction pathways and make up the building blocks and functioning agents of biochemistry.
The network appears to be highly structured and organized.

The metabolic network in biology is analogous to the periodic table of the elements in chemistry. The latter results from a non-dynamical symmetry rule, the Pauli exclusion principle. It is not derivable from other principles of physics. The task ahead for theoretical biology is to formulate a principle to generate the universal chart of metabolism.

Having formulated an overall view of biology, we may turn to the question of why fine-tuning has not been central to theoretical biology. A viewpoint debate going on in physics has pitted the grand unified theorists against the complex matter theorists. Biology seems to lie in the domain of the complex matter theorists, and this is consistent with this presentation. We are reminded of the celebrated Feynman’s Lectures on Physics, in which he noted: "If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis (or the atomic fact or whatever you wish to call it) that all things are made of atoms- little particles that move about in perpetual motion, attracting each other when they are a little distance apart, but repelling when being squeezed into one another. In that one sentence, you will see, there is an enormous amount of information about the world, if just a little imagination and thinking are applied.” Biological thought begins with atoms, and in this discrete domain, fine-tuning has not been central.

By way of historical reference for this meeting, it is interesting to note the Jean Perrin’s classical book Les Atomes, establishing the unquestioned validity of the atomic hypotheses, was published in 1913, the same year as the Henderson book we are celebrating today.

I suggest that the relation between energy of formation and complexity is a kind of fine-tuning, but it has a different feel to it. It is as if the Pauli principle and the periodic table of the elements marks a distinction between particle physics and chemistry.

Molecular complexity generated by covalent bonding may mark a similar distinction between chemistry and biology.