Arthur L. Weber

The peptide-catalyzed stereospecific synthesis of tetroses: a possible model for prebiotic molecular evolution.

Using a water-based prebiotic model of sugar synthesis involving glycolaldehyde self-condensation, we demonstrate that homochiral l-dipeptide catalysts lead to the stereospecific syntheses of tetroses. The asymmetric effect is largest for erythrose, which may reach a d-enantiomeric excess of >80% with l-Val-l-Val catalyst. Based on results obtained with various peptides, we propose a possible catalytic-reaction intermediate, consisting of an imidazolidinone ring formed between the two nitrogen atoms of the peptide catalyst and the C1 of one glycolaldehyde molecule. The study was motivated by the premise that exogenous material, such as the nonracemic amino acids found in meteorites, could have participated in the terrestrial evolution of molecular asymmetry by stereospecific catalysis. Because peptides might have formed readily on the early Earth, it is possible that their catalytic contribution was relevant in the prebiotic processes that preceded the onset of life.

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

Ammonia and amines (including amino acids) were shown tocatalyze the formation of sugars from formaldehyde andglycolaldehyde, and the subsequent conversion of sugars tocarbonyl-containing products under the conditions studied (pH5.5 and 50°C). Sterically unhindered primary amineswere better catalysts than ammonia, secondary amines, andsterically hindered primary amines (i.e.α-aminoisobutyric acid). Reactions catalyzed by primaryamines initially consumed formaldehyde and glycolaldehyde about15–20 times faster than an uncatalyzed control reaction. Theamine-catalyzed reactions yielded aldotriose (glyceraldehyde),ketotriose (dihydroxyacetone), aldotetroses (erythrose andthreose), ketotetrose (erythrulose), pyruvaldehyde, acetaldehyde,glyoxal, pyruvate, glyoxylate, and several unindentifiedcarbonyl products. The concentrations of the carbonyl products,except pyruvate and ketotetrose, initially increased and thendeclined during the reaction, indicating their ultimateconversion to other products (like larger sugars or pyruvate).The uncatalyzed control reaction yielded no pyruvate orglyoxylate, and only trace amounts of pyruvaldehyde, acetaldehyde and glyoxal. In the presence of 15 mM catalyticprimary amine, such as alanine, the rates of triose andpyruvaldehyde of synthesis were about 15-times and 1200-timesfaster, respectively, than the uncatalyzed reaction. Sinceprevious studies established that alanine is synthesized fromglycolaldehyde and formaldehyde via pyruvaldehyde as its directprecursor, the demonstration that the alanine catalyzes theconversion of glycolaldehyde and formaldehyde to pyruvaldehydeindicates that this synthetic pathway is capable ofautocatalysis. The relevance of this synthetic process, namedthe Sugar Model, to the origin of life is discussed.

PREBIOTIC AMINO ACID THIOESTER SYNTHESIS: THIOL-DEPENDENT AMINO ACID SYNTHESIS FROM FORMOSE SUBSTRATES (FORMALDEHYDE AND GLYCOLALDEHYDE) AND AMMONIA

Formaldehyde and glycolaldehyde (substrates of the formose autocatalytic cycle) were shown to react with ammonia yielding alanine and homoserine under mild aqueous conditions in the presence of thiol catalysts. Since similar reactions carried out without ammonia yielded α-hydroxy acid thioesters (Weber, 1984a, b), the thiol-dependent synthesis of alanine and homoserine is presumed to occur via amino acid thioesters – intermediates capable of forming peptides (Weber and Orgel 1979). A pH 5.2 solution of 20 mM formaldehyde, 20 mM glycolaldehyde, 20 mM ammonium chloride, 23 mM 3-mercaptopropionic acid, and 23 mM acetic acid that reacted for 35 days at 40°C yielded (based on initial formaldehyde) 1.8% alanine and 0.08% homoserine. In the absence of thiol catalyst, the synthesis of alanine and homoserine was negligible. Alanine synthesis required both formaldehyde and glycolaldehyde, but homoserine synthesis required only glycolaldehyde. At 25 days the efficiency of alanine synthesis calculated from the ratio of alanine synthesized to formaldehyde reacted was 2.1%, and the yield (based on initial formaldehyde) of triose and tetrose intermediates involved in alanine and homoserine synthesis was 0.3 and 2.1%, respectively. Alanine synthesis was also seen in similar reactions containing only 10 mM each of aldehyde substrates, ammonia, and thiol. The prebiotic significance of these reactions that use the formose reaction to generate sugar intermediates that are converted to reactive amino acid thioesters is discussed.

Stereoselective Syntheses of Pentose Sugars Under Realistic Prebiotic Conditions

Glycolaldehyde and dl-glyceraldehyde reacted in a water-buffered solution under mildly acidic conditions and in the presence of chiral dipeptide catalysts produced pentose sugars whose configuration is affected by the chirality of the catalyst. The chiral effect was found to vary between catalysts and to be largest for di-valine. Lyxose, arabinose, ribose and xylose are formed in different amounts, whose relative proportions do not change significantly with the varying of conditions. With LL-peptide catalysts, ribose was the only pentose sugar to have a significant D-enantiomeric excess (ee) (≤44%), lyxose displayed an L-ee of ≤66%, arabinose a smaller L-ee of ≤8%, and xylose was about racemic. These data expand our previous findings for tetrose sugars and further substantiate the suggestion that interactions between simple molecules of prebiotic relevance on the early Earth might have included the transfer of chiral asymmetry and advanced molecular evolution.

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

The thermodynamics of organic chemistry under mildaqueous conditions was examined in order to begin to understand itsinfluence on the structure and operation of metabolism and itsantecedents. Free energies (ΔG) were estimated for four types ofreactions of biochemical importance – carbon-carbon bond cleavage andsynthesis, hydrogen transfer between carbon groups, dehydration ofalcohol groups, and aldo-keto isomerization. The energies werecalculated 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 groupclasses (i.e., carboxylic acids, carbonyl groups, alcohols, andhydrocarbons), the transfer of the shared electron-pair to the morereduced carbon group is energetically favored over transfer to themore oxidized carbon group, and (2) that the energy of carbon-carbonbond transformation is primarily determined by the functional groupclass of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the sharedelectron-pair during cleavage, or that accepts the incipient sharedelectron-pair during synthesis). In contrast, the energy of hydrogentransfer between carbon groups is determined by the functional groupclass of both the hydrogen-donor group and the hydrogen-acceptorgroup. From these and other observations we concluded that thechemistry involved in the origin of metabolism (and to a lesser degreemodern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readilydissipated in a few energetically favorable irreversible reactions;(2) the energy dominance of a few transformation half-reactions thatdetermines whether carbon-carbon bond transformation (cleavage orsynthesis) is energetically favorable (ΔG < –3.5 kcal/mol), reversible(ΔG between ±3.5 kcal/mol), or unfavorable (ΔG > +3.5 kcal/mol);and (3) the dependence of carbon group transformation energy on thefunctional group class (i.e., oxidation state) of participatinggroups that in turn is contingent on prior reactions and precursors inthe synthetic pathway.

The Sugar Model: Autocatalytic Activity of the Triose- Ammonia Reaction

Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose–ammonia reaction product on the kinetics of a second identical triose–ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate of formation of pyruvaldehyde, the product of triose dehydration. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of autocatalytic molecules.

Sugars as the optimal biosynthetic carbon substrate of aqueous life throughout the universe.

Our previous analysis of the energetics ofmetabolism showed that both the biosynthesis of aminoacids and lipids from sugars, and the fermentation oforganic substrates, were energetically driven byelectron transfer reactions resulting in carbon redoxdisproportionation (Weber, 1997). Redoxdisproportionation – the spontaneous (energeticallyfavorable) direction of carbon group transformation inbiosynthesis – is brought about and driven by theenergetically downhill transfer of electron pairs frommore oxidized carbon groups (with lower half-cellreduction potentials) to more reduced carbon groups(with higher half-cell reduction potentials). In thisreport, we compare the redox and kinetic properties ofcarbon groups in order to evaluate the relativebiosynthetic capability of organic substrates, and toidentify the optimal biosubstrate. This analysisrevealed that sugars (monocarbonyl alditols) are theoptimal biosynthetic substrate because they containthe maximum number of biosynthetically useful highenergy electrons/carbon atom while still containing asingle carbonyl group needed to kinetically facilitatetheir conversion to useful biosynthetic intermediates. This conclusion applies to aqueous life throughout theUniverse because it is based on invariant aqueouscarbon chemistry – primarily, the universal reductionpotentials of carbon groups.

Growth of Organic Microspherules in Sugar-Ammonia Reactions

Reaction of small sugars of less than four carbons with ammonia in water yielded organic microspherules generally less than ten microns in size. The time course of microspherule growth was examined for the D-erythrose-ammonia reaction that yielded microspherules attached to the glass walls of containers. Measurements were made of the elemental composition and infrared spectrum of the microspherule material. These viscose semi-solid microspherules are viewed as possible containers for prebiotic catalytic processes relevant to the origin of life.

KINETICS OF ORGANIC TRANSFORMATIONS UNDER MILD AQUEOUS CONDITIONS: IMPLICATIONS FOR THE ORIGIN OF LIFE AND ITS METABOLISM

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 °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 α- or β-positioned carbonyl group were the most reactive. Compounds with an α- or β-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 1024-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.

Energy from Redox Disproportionation of Sugar Carbon Drives Biotic and Abiotic Synthesis

Abstract. To identify the energy source that drives the biosynthesis of amino acids, lipids, and nucleotides from glucose, we calculated the free energy change due to redox disproportionation of the substrate carbon of (1) 26-carbon fermentation reactions and (2) the biosynthesis of amino acids and lipids of E. coli from glucose. The free energy (cal/mmol of carbon) of these reactions was plotted as a function of the degree of redox disproportionation of carbon (disproportionative electron transfers (mmol)/mmol of carbon). The zero intercept and proportionality between energy yield and degree of redox disporportionation exhibited by this plot demonstrate that redox disproportionation is the principal energy source of these redox reactions (slope of linear fit =−10.4 cal/mmol of disproportionative electron transfers). The energy and disproportionation values of E. coli amino acid and lipid biosynthesis from glucose lie near this linear curve fit with redox disproportionation accounting for 84% and 96% (and ATP only 6% and 1%) of the total energy of amino acid and lipid biosynthesis, respectively. These observations establish that redox disproportionation of carbon, and not ATP, is the primary energy source driving amino acid and lipid biosynthesis from glucose. In contrast, we found that nucleotide biosynthesis involves very little redox disproportionation, and consequently depends almost entirely on ATP for energy. The function of sugar redox disproportionation as the major source of free energy for the biosynthesis of amino acids and lipids suggests that sugar disproportionation played a central role in the origin of metabolism, and probably the origin of life.n