The sugar model: catalysis by amines and amino acid products.

Entrez PubMed: "Ammonia and amines (including amino acids) were shown to catalyze the formation of sugars from formaldehyde and glycolaldehyde, and the subsequent conversion of sugars to carbonylcontaining products under the conditions studied (pH 5.5 and 50 degrees C). Sterically unhindered primary amines were better catalysts than ammonia, secondary amines, and sterically hindered primary amines (i.e. alpha-aminoisobutyric acid). Reactions catalyzed by primary amines initially consumed formaldehyde and glycolaldehyde about 15-20 times faster than an uncatalyzed control reaction. The amine-catalyzed reactions yielded aldotriose (glyceraldehyde), ketotriose (dihydroxyacetone), aldotetroses (erythrose and threose), ketotetrose (erythrulose), pyruvaldehyde, acetaldehyde, glyoxal, pyruvate, glyoxylate, and several unindentified carbonyl products. The concentrations of the carbonyl products, except pyruvate and ketotetrose, initially increased and then declined during the reaction, indicating their ultimate conversion to other products (like larger sugars or pyruvate). The uncatalyzed control reaction yielded no pyruvate or glyoxylate, and only trace amounts of pyruvaldehyde, acetaldehyde and glyoxal. In the presence of 15 mM catalytic primary amine, such as alanine, the rates of triose and pyruvaldehyde of synthesis were about 15-times and 1200-times faster, respectively, than the uncatalyzed reaction. Since previous studies established that alanine is synthesized from glycolaldehyde and formaldehyde via pyruvaldehyde as its direct precursor, the demonstration that the alanine catalyzes the conversion of glycolaldehyde and formaldehyde to pyruvaldehyde indicates that this synthetic pathway is capable of autocatalysis. The relevance of this synthetic process, named the Sugar Model, to the origin of life is discussed."

Weber AL. The sugar model: catalysis by amines and amino acid products. Orig Life Evol Biosph. 2001 Feb-Apr;31(1-2):71-86.

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Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions.

Entrez PubMed: "The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway."

Weber AL. Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions. Orig Life Evol Biosph. 2002 Aug;32(4):333-57.

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On the emergence of biological complexity: life as a kinetic state of matter.

Entrez PubMed: "A kinetic model that attempts to further clarify the nature of biological complexification is presented. Its essence: reactions of replicating systems and those of regular chemical systems follow different selection rules leading to different patterns of chemical behavior. For regular chemical systems selection is fundamentally thermodynamic, whereas for replicating chemical systems selection is effectively kinetic. Building on an extension of the kinetic stability, concept it is shown that complex replicators tend to be kinetically more stable than simple ones, leading to an on-going process of kinetically-directed complexification. The high kinetic stability of simple replicating assemblies such as phages, compared to the low kinetic stability of the assembly components, illustrates the complexification principle. The analysis suggests that living systems constitute a kinetic state of matter, as opposed to the traditional thermodynamic states that dominate the inanimate world, and reaffirms our view that life is a particular manifestation of replicative chemistry."

Pross A. On the emergence of biological complexity: life as a kinetic state of matter. Orig Life Evol Biosph. 2005 Apr;35(2):151-66.

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Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism.

Entrez PubMed: "The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates."

Weber AL. Orig Life Evol Biosph. 2004 Oct;34(5):473-95. Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism. Orig Life Evol Biosph. 2004 Oct;34(5):473-95.

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Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate.

Entrez PubMed: "Experiments exploring the potential catalytic role of iron sulfide at 250 degrees C and elevated pressures (50, 100, and 200 megapascals) revealed a facile, pressure-enhanced synthesis of organometallic phases formed through the reaction of alkyl thiols and carbon monoxide with iron sulfide. A suite of organometallic compounds were characterized with ultraviolet-visible and Raman spectroscopy. The natural synthesis of such compounds is anticipated in present-day and ancient environments wherever reduced hydrothermal fluids pass through iron sulfide-containing crust. Here, pyruvic acid was synthesized in the presence of such organometallic phases. These compounds could have provided the prebiotic Earth with critical biochemical functionality."
Cody GD, Boctor NZ, Filley TR, Hazen RM, Scott JH, Sharma A, Yoder HS Jr. Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science. 2000 Aug 25;289(5483):1337-40.
Comment in: Science. 2000 Aug 25;289(5483):1307-8.

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Iron-sulfur world

Wächtershäuser, in the iron-sulfur world theory, postulates that an early form of metabolism predated genetics. By metabolism, Wächtershäuser refered to a cycle of chemical reactions that produce energy in a form that can be harnessed by other processes. Wächtershäuser's idea was that a primitive metabolic cycle could produce increasingly complex compounds.

A key concept within the iron-sulfur theory was that this early chemistry of life occurred on mineral surfaces, such as iron pyrites, near deep submarine hydrothermal vents. This was an anerobic, hyperthermic (near 100^oC), high pressure environment. Acetic acid plays a special role in Wächtershäuser's theory because acetic acid is part of the citric acid cycle that is fundamental to cellular metabolism.

Discussing the origin of life. [Science. 2002] PMID: 12400544
Origin of life. Some like it hot, but not the first biomolecules. [Science. 2002] PMID: 12065824
Origin of life. II. From prebiotic replicators to protocells. [Arch Sci Compte Rendu Seances Soc. 1999] PMID: 14677551
The role of accuracy for early stages of the origin of life. [Orig Life Evol Biosph. 1995] PMID: 11536674
Electroweak enantioselection and the origin of life. [Orig Life Evol Biosph. 1995] PMID: 11536670
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Critique of the hypothesis: Two-dimensional life? [Proc Natl Acad Sci U S A. 1991]
A model [Wachtershauser, G. (1988) Microbiol. Rev. 52, 452-484], according to which life started in the form of a monomolecular layer of interacting anionic metabolites electrostatically bound to a positively charged surface, is examined critically. The model raises a number of thermodynamic and kinetic difficulties.
de Duve C, Miller SL. Two-Dimensional Life? (Free Full Text pdf) Proc Natl Acad Sci U S A. 1991 Nov;88:10014-7.

Polymerization on the rocks: theoretical introduction. [Orig Life Evol Biosph. 1998] PMID: 9611763
The reactions of methanimine and cyanogen with carbon monoxide in prebiotic molecular evolution on earth. [Orig Life Evol Biosph. 2001] PMID: 11770257
Gunter Wachtershauser profile. Between a rock and a hard place. [Science. 2002] PMID: 11896256
The REH theory of protein and nucleic acid divergence: a retrospective update. [J Mol Evol. 1978] PMID: 722809
Reaction sequence of iron sulfide minerals in bacteria and their use as biomarkers
Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. [Science. 2000] PMID: 10958777
A sulfurous start for protein synthesis? [Science. 1998] PMID: 9714669
Prebiotic chemistry. Where smokers rule. [Science. 1997] PMID: 9132945
See
Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives. [Biochemistry. 2004] PMID: 15035610
The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front. [J Geol Soc London. 1997] PMID: 11541234
Ammonia formation by the reduction of nitrite/nitrate by FeS: ammonia formation under acidic conditions. [Orig Life Evol Biosph. 2005] PMID: 16228644
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Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life. [Science. 1998] PMID: 9685253
Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. [Science. 1997] : modified: "In experiments modeling the reactions of the reductive acetyl-coenzyme A pathway at hydrothermal temperatures, it was found that an aqueous slurry of coprecipitated NiS and FeS converted CO and CH3SH into the activated thioester CH3-CO-SCH3, which hydrolyzed to acetic acid. In the presence of aniline, acetanilide was formed. When NiS-FeS was modified with catalytic amounts of selenium, acetic acid and CH3SH were formed from CO and H2S alone. The reaction can be considered as the primordial initiation reaction for a chemoautotrophic origin of life."
Huber C, Wachtershauser G. Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. Science. 1997 Apr 11;276(5310):245-7. Comment in: Science. 1997 Apr 11;276(5310):222..

More from Wächtershäuser:
Review : Before enzymes and templates: theory of surface metabolism. Microbiol Rev. 1988 Dec;52(4):452-84.

A possible primordial peptide cycle. [Science. 2003] PMID: 12920291
A sulfurous start for protein synthesis? [Science. 1998] PMID: 9714669
Origin of life. Life as we don't know it. [Science. 2000] PMID: 10979855
Organic sulfur compounds resulting from the interaction of iron sulfide, hydrogen sulfide and carbon dioxide in an anaerobic aqueous environment. [Orig Life Evol Biosph. 1996] PMID: 11536750
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Historical perspective: the problem of the origin of life in the context of developments in biology. [Orig Life Evol Biosph. 1988] PMID: 3285284
Evolution of the first metabolic cycles. [Proc Natl Acad Sci U S A. 1990] PMID: 2296579
Life in a ligand sphere. [Proc Natl Acad Sci U S A. 1994] PMID: 8183902
Between history and physics. [J Mol Evol. 1982] PMID: 6178836
Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. [J Mol Evol. 2001] PMID: 11675615
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Investigation of the prebiotic synthesis of amino acids and RNA bases from CO2 using FeS/H2S as a reducing agent. [Proc Natl Acad Sci U S A. 1995] PMID: 8524872
[FeS/FeS2], a redox system for the origin of life (some experiments on the pyrite-hypothesis). [Orig Life Evol Biosph. 1994] PMID: 11536658
Energetics and kinetics of the prebiotic synthesis of simple organic acids and amino acids with the FeS-H2S/FeS2 redox couple as reductant. [Orig Life Evol Biosph. 1999] PMID: 10077866
Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions. [Science. 1997] PMID: 9092471
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The origin of life and its methodological challenge. [J Theor Biol. 1997] PMID: 9299293
Evolution of the first metabolic cycles. [Proc Natl Acad Sci U S A. 1990] PMID: 2296579
A model for the origin of life. [J Mol Evol. 1982] PMID: 7120429
On the origin of metabolic pathways. [J Mol Evol. 1999] PMID: 10486000
Noisy clues to the origin of life. [Proc Biol Sci. 2002] PMID: 12495484
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The iron-sulphur proteins: evolution of a ubiquitous protein from model systems to higher organisms. [Orig Life. 1974] PMID: 4416334
Chemical evolution. [Nature. 1971] PMID: 4923113
Chemical evolution. [Am Sci. 1975] PMID: 1115436
Ambiguity in the interpretation of abiotic syntheses. [Orig Life. 1975] PMID: 1153186
Life's beginnings--origin

Photoelectrochemical power, chemical energy and catalytic activity for organic evolution on natural pyrite interfaces. [Orig Life Evol Biosph. 2003] PMID: 12967264
Reaction sequence of iron sulfide minerals in bacteria and their use as biomarkers. [Science. 1998] PMID: 9572727
Asymmetric adsorption by quartz: a model for the prebiotic origin of optical activity. [Orig Life. 1975] PMID: 171608
No soup for starters? Autotrophy and the origins of metabolism. [Trends Biochem Sci. 1995] PMID: 7482696
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A theoretical approach to the link between oxidoreductions and pyrite formation in the early stage of evolution. [Biochim Biophys Acta. 2002] PMID: 11997130
The origin of intermediary metabolism. [Proc Natl Acad Sci U S A. 2000] PMID: 10859347
The origin of life and its methodological challenge. [J Theor Biol. 1997] PMID: 9299293
Formation of amide bonds without a condensation agent and implications for origin of life. [Nature. 1994] PMID: 8159243
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The chemical basis of membrane bioenergetics.
All organisms rely on chemiosmotic membrane systems for energy transduction; the great variety of participating proteins and pathways can be reduced to a few universal principles of operation. This chemical basis of bioenergetics is reviewed with respect to the origin and early evolution of life. For several of the cofactors which play important roles in bioenergetic reactions, plausible prebiotic sources have been proposed, and it seems likely that these cofactors were present before elaborate protein structures. In particular, the hydrophobic quinones require only a membrane-enclosed compartment to yield a minimum chemiosmotic system, since they can couple electron transport and proton translocation in a simple way. It is argued that the central features of modern bioenergetics, such as the coupling of redox reactions and ion translocation at the cytoplasmic membrane, probably are ancient features which arose early during the process of biogenesis. The notion of a thermophile root of the universal phylogenetic tree has been discussed controversially, nevertheless, thermophiles are interesting model organisms for reconstructing the origin of chemiosmotic systems, since they are often acidophiles and anaerobic respirers exploiting iron-sulfur chemistry. This perspective can help to explain the prominent role of iron-sulfur proteins in extant biochemistry as well as the origin of both respiration and proton extrusion within the context of a possible origin of life in the vicinity of hot vents.
Berry S. The chemical basis of membrane bioenergetics. J Mol Evol. 2002 May;54(5):595-613.

More abstracts on membrane bioenergetics on PubMed:
Evolution of membrane bioenergetics. [J Supramol Struct. 1980] PMID: 6453255
Chemiosmotic systems in bioenergetics: H(+)-cycles and Na(+)-cycles. [Biosci Rep. 1991] PMID: 1668527
Bioenergetics of the Archaea. [Microbiol Mol Biol Rev. 1999] PMID: 10477309
Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. [J Mol Evol. 2001] PMID: 11675615
The first cellular bioenergetic process: primitive generation of a proton-motive force. [J Mol Evol. 1991] PMID: 1663558

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Entropy and charge in molecular evolution--the case of phosphate.

Entropy and charge in molecular evolution--the case of phosphate. : "Biopoesis, the creation of life, implies molecular evolution from simple components, randomly distributed and in a dilute state, to form highly organized, concentrated systems capable of metabolism, replication and mutation. This chain of events must involve environmental processes that can locally lower entropy in several steps; by specific selection from an indiscriminate mixture, by concentration from dilute solution, and in the case of the mineral-induced processes, by particular effectiveness in ordering and selective reaction, directed toward formation of functional biomolecules. Numerous circumstances provide support for the notion that negatively charged molecules were functionally required and geochemically available for biopoesis. Sulfite ion may have been important in bisulfite complex formation with simple aldehydes, facilitating the initial concentration by sorption of aldehydes in positively charged surface active minerals. Borate ion may have played a similar, albeit less investigated role in forming charged sugar complexes. Among anionic species, oligophosphate ions and charged phosphate esters are likely to have been of even more wide ranging importance, reflected in the continued need for phosphate in a proposed RNA world, and extending its central role to evolved biochemistry. Phosphorylation is shown to result in selective concentration by surface sorption of compounds, otherwise too dilute to support condensation reactions. It provides protection against rapid hydrolysis of sugars and, by selective concentration, induces the oligomerization of aldehydes. As a manifestation of life arisen, phosphate already appears in an organic context in the oldest preserved sedimentary record."

Arrhenius G, Sales B, Mojzsis S, Lee T. Entropy and charge in molecular evolution--the case of phosphate. J Theor Biol. 1997 Aug 21;187(4):503-22.

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Ammonia formation by the reduction of nitrite/nitrate by fes: ammonia formation under acidic conditions.

Entrez PubMed: "One issue for the origin of life under a non-reducing atmosphere is the availability of the reduced nitrogen necessary for amino acids, nucleic acids, etc. One possible source of this nitrogen is the formation of ammonia from the reduction of nitrates and nitrites produced by the shock heating of the atmosphere and subsequent chemistry. Ferrous ions will reduce these species to ammonium, but not under acidic conditions. We wish to report results on the reduction of nitrite and nitrate by another source of iron (II), ferrous sulfide, FeS. FeS reduces nitrite to ammonia at lower pHs than the corresponding reduction by aqueous Fe(+ 2). The reduction follows a first order decay, in nitrite concentration, with a half-life of about 150 min (room temperature, CO(2), pH 6.25). The highest product yield of ammonia measured was 53%. Under CO(2), the product yield decreases from pH 5.0 to pH 6.9. The increasing concentration of bicarbonate, at higher pH, interferes with the reaction. Comparing experiments under N(2) CO(2) shows the interference of bicarbonate. The reaction proceeds well in the presence of such species as chloride, sulfate, and phosphate, though the yield drops significantly with phosphate. FeS also reduces nitrate and, unlike with Fe(+ 2), the reduction shows more reproducibility. Again, the product yield decreases with increasing pH, from 7% at pH 4.7 to 0% at pH 6.9. It appears that nitrate is much more sensitive to the presence of added species, perhaps not competing as well for binding sites on the FeS surface. This may be the cause of the lack of reproducibility of nitrate reduction by Fe(+ 2) (which also can be sensitive to binding by certain species)."

Summers DP. Orig Life Evol Biosph. 2005 Aug;35(4):299-312. Ammonia formation by the reduction of nitrite/nitrate by fes: ammonia formation under acidic conditions.

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What Is Life and How Do We Search for It in Other Worlds?

PLoS Biology: What Is Life and How Do We Search for It in Other Worlds?: "The obvious diversity of life on Earth overlies a fundamental biochemical and genetic similarity. The three main polymers of biology-the nucleic acids, the proteins, and the polysaccarides�are built from 20 amino acids, five nucleotide bases, and a few sugars, respectively. Together with lipids and fatty acids, these are the main constituents of biomass: the hardware of life (Lehninger 1975, p 21). The DNA and RNA software of life is also common, indicating shared descent (Woese 1987). But with only one example of life�life on Earth�it is not all that surprising that we do not have a fundamental understanding of what life is. We don't know which features of Earth life are essential and which are just accidents of history."

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