A Thermodynamic Basis for Prebiotic Amino Acid Synthesis and the Nature of the First Genetic Code (original) (raw)
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Thermodynamic Basis for Prebiotic Amino Acid Synthesis and Constraints on the First Genetic Code
2010
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.
Abiotic synthesis of amino acids and self-crystallization under prebiotic conditions
Scientific Reports, 2014
Building on previous research on the origin and homochirality of life, this study focuses on analyses profiling important building blocks of life: the natural amino acids. The spark discharge variation of the iconic Miller experiment was performed with a reducing gas mixture of ammonia, methane, water and hydrogen. Amino acid analysis using liquid chromatography coupled with tandem mass spectrometry after pre-column derivatizaiton revealed the generation of several amino acids including those essential for life. Re-crystallization of the synthetic products and enantiomeric ratio analysis were subsequently performed. Results from liquid chromatography coupled with either fluorescent detector or tandem mass spectrometry after pre-column derivatization with chiral reagent revealed spontaneous and effective asymmetric resolution of serine and alanine. This work describes a useful analytical platform for investigation of hypotheses regarding the origin and homochirality of amino acids under prebiotic conditions. The formation of numerous amino acids in the electric discharge experiment and the occurrence of high enantiomeric ratios of amino acids in re-crystallization experiment give valuable implications for future studies in unraveling fundamental questions regarding origins and evolution of life.
The origins of amino acids in ancient terrestrial and extraterrestrial materials
Instruments, Methods, and Missions for Astrobiology XI, 2008
The earliest evidence for amino acids on Earth is in Precambrian sedimentary rocks with varied metamorphic histories. Igneous rocks rarely contain such compounds, exceptions being those introduced via the migration of fluids into fractures subsequent to crystallization. Martian meteorites are excellent examples of ancient igneous rocks that apparently contain amino acids associated with minerals precipitated in rock fractures. The challenge has been to determine whether the organic compounds present in ancient terrestrial and extraterrestrial materials are indigenous and, if so, are representative of past life or pre-biotic synthesis. A summary of what is known to date about amino acids in ancient terrestrial and extraterrestrial materials is presented. Alternative approaches for distinguishing their origin(s) are discussed.
2021
The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is to glimpse in which chemical scenarios the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as a homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades as nucleotides are complex though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named “Prebio...
Physical Chemistry Chemical Physics, 2011
It has always been a question of considerable scientific interest why amino acids (and other biomolecule building blocks) formed and accumulated in the prebiotic ocean. In this study, we suggest an answer to this question for the simplest amino acid, glycine. We have shown for the first time that classical equilibrium thermodynamics can explain the most likely selection of glycine (and the derivative of its dipeptide) in aqueous media, although glycine is not the lowest free energy structure among all (404) possible constitutional isomers. Species preceding glycine in the free energy order are either supramolecular complexes of small molecules or such molecules likely to dissociate and thus get back to the gas phase. Then, 2-hydroxyacetamide condensates yielding a thermodynamically favored derivative of glycine dipeptide providing an alternative way for peptide formation. It is remarkable that a simple equilibrium thermodynamic model can explain the accumulation of glycine and provide a reason for the importance of water in the formation process.
Rapid Communications in Mass Spectrometry, 2015
The search for the conditions which must have prevailed in the long-distant past during the conversion of inanimate matter into animate matter is a fascinating area of research and it continues to draw the attention of the scientific community. The initiation of life on this planet must have been preceded by the development of biomolecules, amongst which amino acids have unique importance. Formation of amino acids under a certain set of conditions is shown in the present experiments. METHODS: Solutions of ammonium carboxylates or the mixture of two such salts were prepared in 3:6.9:0.1 (v/v/v) acetonitrile/water/formic acid at a concentration of 50 μM. The studies were performed using a quadrupole timeof-flight (QqTOF) mass spectrometer. The formation of different amino acids was detected with high-resolution mass spectrometry. RESULTS: Here, we show the formation of amino acids when a solution of ammonium salts was injected into an electrospray ionization (ESI)-QqTOF-MS instrument. The ammonium salts were the source of NH 3 and CO 2 and H 2 O was available in the medium. It seems that the combination of NH 3 , CO 2 , and H 2 O leads to the formation of amino acids. CONCLUSIONS: Further to the literature reports of formation of amino acids under the reduced atmosphere represented by gases such as NH 3 , CH 4 , H 2 and H 2 O, here we demonstrate the formation of amino acids by the combination of NH 3 /NO 2 , CO 2 and water vapours in the ESI source of the mass spectrometer.
Modern and prebiotic amino acids support distinct structural profiles in proteins
Open Biology
The earliest proteins had to rely on amino acids available on early Earth before the biosynthetic pathways for more complex amino acids evolved. In extant proteins, a significant fraction of the ‘late’ amino acids (such as Arg, Lys, His, Cys, Trp and Tyr) belong to essential catalytic and structure-stabilizing residues. How (or if) early proteins could sustain an early biosphere has been a major puzzle. Here, we analysed two combinatorial protein libraries representing proxies of the available sequence space at two different evolutionary stages. The first is composed of the entire alphabet of 20 amino acids while the second one consists of only 10 residues (ASDGLIPTEV) representing a consensus view of plausibly available amino acids through prebiotic chemistry. We show that compact conformations resistant to proteolysis are surprisingly similarly abundant in both libraries. In addition, the early alphabet proteins are inherently more soluble and refoldable, independent of the genera...
Low-lying energy levels of amino acids and its implications for origin of life
Journal of Molecular Structure-theochem, 2005
A major challenge in understanding the origins of life is to elucidate how nature selects a small part of molecules from a large number of candidates as building blocks of life, e.g. amino acids and proteins. Inspired by the thermodynamic principle in protein-structure selection, we attempted to explore whether there exists a thermodynamic criterion to differentiate amino acids from their isomers. In this letter, the energies of 20 natural amino acid and corresponding isomers are calculated by quantum chemical methods. It is revealed that the energy levels of amino acids (especially small ones) are not distributed randomly but located at the bottom of the energy diagrams of their isomers, suggesting that thermodynamic factor plays an important role in selecting the basic building blocks of life. q
Prebiotic chemical kinetics imprint on positional codon usage
Journal of The Brazilian Chemical Society, 2010
Foram analisados mais de um milhão de exons pertecentes aos 3 domínios da vida, Eubacteria, Archea e Eukarya. Um número significante de primeiros codons com um excesso de bases idênticas nas suas duas primeiras posições foi encontrado nos genomas das Eubacterias e Archea. Este excesso tem uma freqüência muito menor nos genomas das Eukarya. Propõe-se que esta discrepância depende da cinética de crescimento dos oligoribotídeos na Terra primitiva, que foi diminuindo com o passar do tempo. Over one million exons across the three Domains of Life have been analyzed and a significant excess of first codons containing identical bases in their first two positions has been found in Eubacteria and Archaea genomes. This frequency is observed to be much lower in the genome of Eukarya. This discrepancy is proposed to depend on the kinetics of oligoribotide/oligoribotide-like growth in the primeval Earth, toned down during further evolution.