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Raggi, L, Bada JL, Lazcano A.  2016.  On the lack of evolutionary continuity between prebiotic peptides and extant enzymes. Physical Chemistry Chemical Physics. 18:20028-20032.   10.1039/c6cp00793g   AbstractWebsite

The significance of experiments that claim to simulate the properties of prebiotic small peptides and polypeptides as models of the polymers that may have preceded proteins is critically addressed. As discussed here, most of these experiments are based only on a small number of a larger set of amino acids that may have been present in the prebiotic environment, supported by both experimental simulations and the repertoire of organic compounds reported in carbonaceous chondrites. Model experiments with small peptides may offer some insights into the processes that contributed to generate the chemical environment leading to the emergence of informational oligomers, but not to the origin of proteins. The large body of circumstantial evidence indicating that catalytic RNA played a key role in the origin of protein synthesis during the early stages of cellular evolution implies that the emergence of the genetic code and of protein biosynthesis are no longer synonymous with the origin of life. Hence, reports on the abiotic synthesis of small catalytic peptides under potential prebiotic conditions do not provide information on the origin of triplet encoded protein biosynthesis, but in some cases may serve as models to understand the properties of the earliest proteins.

Parker, ET, Cleaves HJ, Callahan MP, Dworkin JP, Glavin DP, Lazcano A, Bada JL.  2011.  Prebiotic Synthesis of Methionine and Other Sulfur-Containing Organic Compounds on the Primitive Earth: A Contemporary Reassessment Based on an Unpublished 1958 Stanley Miller Experiment. Origins of Life and Evolution of Biospheres. 41:201-212.   10.1007/s11084-010-9228-8   AbstractWebsite

Original extracts from an unpublished 1958 experiment conducted by the late Stanley L. Miller were recently found and analyzed using modern state-of-the-art analytical methods. The extracts were produced by the action of an electric discharge on a mixture of methane (CH(4)), hydrogen sulfide (H(2)S), ammonia (NH(3)), and carbon dioxide (CO(2)). Racemic methionine was formed in significant yields, together with other sulfur-bearing organic compounds. The formation of methionine and other compounds from a model prebiotic atmosphere that contained H(2)S suggests that this type of synthesis is robust under reducing conditions, which may have existed either in the global primitive atmosphere or in localized volcanic environments on the early Earth. The presence of a wide array of sulfur-containing organic compounds produced by the decomposition of methionine and cysteine indicates that in addition to abiotic synthetic processes, degradation of organic compounds on the primordial Earth could have been important in diversifying the inventory of molecules of biochemical significance not readily formed from other abiotic reactions, or derived from extraterrestrial delivery.

Rivas, M, Becerra A, Pereto J, Bada JL, Lazcano A.  2011.  Metalloproteins and the Pyrite-based Origin of Life: A Critical Assessment. Origins of Life and Evolution of Biospheres. 41:347-356.   10.1007/s11084-011-9238-1   AbstractWebsite

We critically examine the proposal by W chtersh user (Prokaryotes 1: 275-283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787-1808, 2006b) that putative transition metal binding sites in protein components of the translation machinery of hyper-thermophiles provide evidence of a direct relationship with the FeS clusters of pyrite and thus indicate an autotrophic origin of life in volcanic environments. Analysis of completely sequenced cellular genomes of Bacteria, Archaea and Eucarya does not support the suggestion by W chtersh user (Prokaryotes 1: 275-283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787-1808, 2006b) that aminoacyl-tRNA synthetases and ribosomal proteins bear sequence signatures typical of strong covalent metal bonding whose absence in mesophilic species reveals a process of adaptation towards less extreme environments.

Bada, JL.  1998.  Biogeochemistry of organic nitrogen compounds. Nitrogen-Containing Macromolecules in the Bio- and Geosphere. 707( Stankiewicz BA, VanBergen PF, Eds.).:64-73., Washington: Amer Chemical Soc Abstract

Nitrogen containing organic compounds represent the second most abundant reservoir of nitrogen on the surface of the Earth. However, the organic compounds that make up this global nitrogen pool are not well characterized. Although amino acids and the nitrogenous bases of nucleic acids make up only a few percent of the total organic nitrogen reservoir, the geochemical reactions of these compounds have been extensively studied. Because hydrolysis reactions are rapid on the geologic time scale, both proteins and nucleic acids (DNA and RNA) are not preserved for more than 10(3) to 10(5) years in most environments. The racemization reaction of amino acids converts the L-amino acids present in the biosphere into a racemic mixture (D/L amino acid ratio = 1.0) in the geosphere in less than 10(6) years. Anhydrous conditions, such as those that may be associated with amber entombed insects, may retard both biopolymer hydrolysis and racemization. Condensation reactions between amino acids and sugars, including sugars at apurinic sites in nucleic acid fragments, likely result in the incorporation of these compounds into geopolymers such as humic acids. Although rearrangement reactions in geopolymers may scramble the original molecular structures, part of the global organic nitrogen inventory was originally derived from amino acids and nucleic acid bases.