International Journal of Molecular Sciences

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Open AccessArticle

RNA Relics and Origin of Life

by Jacques Demongeot, Nicolas Glade, Andrés Moreira and Laurent Vial

Int. J. Mol. Sci. 2009, 10(8), 3420-3441; https://doi.org/10.3390/ijms10083420 - 31 Jul 2009

Cited by 22 | Viewed by 17103

Abstract

A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of [...] Read more.

A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 933 KiB

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Chirality Emergence in Thin Solid Films of Amino Acids by Polarized Light from Synchrotron Radiation and Free Electron Laser

by Jun-ichi Takahashi, Hiroyuki Shinojima, Michiko Seyama, Yuko Ueno, Takeo Kaneko, Kensei Kobayashi, Hajime Mita, Mashahiro Adachi, Masahito Hosaka and Masahiro Katoh

Int. J. Mol. Sci. 2009, 10(7), 3044-3064; https://doi.org/10.3390/ijms10073044 - 7 Jul 2009

Cited by 45 | Viewed by 13000

Abstract

One of the most attractive hypothesis for the origin of homochirality in terrestrial bioorganic compounds is that a kind of “chiral impulse” as an asymmetric excitation source induced asymmetric reactions on the surfaces of such materials such as meteorites or interstellar dusts prior [...] Read more.

One of the most attractive hypothesis for the origin of homochirality in terrestrial bioorganic compounds is that a kind of “chiral impulse” as an asymmetric excitation source induced asymmetric reactions on the surfaces of such materials such as meteorites or interstellar dusts prior to the existence of terrestrial life (Cosmic Scenario). To experimentally introduce chiral structure into racemic films of amino acids (alanine, phenylalanine, isovaline, etc.), we irradiated them with linearly polarized light (LPL) from synchrotron radiation and circularly polarized light (CPL) from a free electron laser. After the irradiation, we evaluated optical anisotropy by measuring the circular dichroism (CD) spectra and verified that new Cotton peaks appeared at almost the same peak position as those of the corresponding non-racemic amino acid films. With LPL irradiation, two-dimensional anisotropic structure expressed as linear dichroism and/or linear birefringence was introduced into the racemic films. With CPL irradiation, the signs of the Cotton peaks exhibit symmetrical structure corresponding to the direction of CPL rotation. This indicates that some kinds of chiral structure were introduced into the racemic film. The CD spectra after CPL irradiation suggest the chiral structure should be derived from not only preferential photolysis but also from photolysis-induced molecular structural change. These results suggest that circularly polarized light sources in space could be associated with the origin of terrestrial homochirality; that is, they would be effective asymmetric exciting sources introducing chiral structures into bio-organic molecules or complex organic compounds. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 323 KiB

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Organic Analysis of Peridotite Rocks from the Ashadze and Logatchev Hydrothermal Sites

by Marie-Paule Bassez, Yoshinori Takano and Naohiko Ohkouchi

Int. J. Mol. Sci. 2009, 10(7), 2986-2998; https://doi.org/10.3390/ijms10072986 - 3 Jul 2009

Cited by 16 | Viewed by 12126

Abstract

This article presents an experimental analysis of the organic content of two serpentinized peridotite rocks of the terrestrial upper mantle. The samples have been dredged on the floor of the Ashadze and Logatchev hydrothermal sites on the Mid-Atlantic Ridge. In this preliminary analysis, [...] Read more.

This article presents an experimental analysis of the organic content of two serpentinized peridotite rocks of the terrestrial upper mantle. The samples have been dredged on the floor of the Ashadze and Logatchev hydrothermal sites on the Mid-Atlantic Ridge. In this preliminary analysis, amino acids and long chain n-alkanes are identified. They are most probably of biological/microbial origin. Some peaks remain unidentified. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 248 KiB

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The Dimeric Proto-Ribosome: Structural Details and Possible Implications on the Origin of Life

by Ilana Agmon

Int. J. Mol. Sci. 2009, 10(7), 2921-2934; https://doi.org/10.3390/ijms10072921 - 30 Jun 2009

Cited by 61 | Viewed by 10705

Abstract

A symmetric pocket-like entity, composed of two L-shaped RNA units, encircles the peptide synthesis site within the contemporary ribosome. This entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide [...] Read more.

A symmetric pocket-like entity, composed of two L-shaped RNA units, encircles the peptide synthesis site within the contemporary ribosome. This entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and elongation. This structural element, beyond offering the initial step in the evolution of translation, is hypothesized here to be linked to the origin of life. By catalyzing the production of random peptide chains, the proto-ribosome could have enabled the formation of primary enzymes, launching a process of co-evolution of the translation apparatus and the proteins, thus presenting an alternative to the RNA world hypothesis. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 1024 KiB

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Calculation of the Aqueous Thermodynamic Properties of Citric Acid Cycle Intermediates and Precursors and the Estimation of High Temperature and Pressure Equation of State Parameters

by Peter Dalla-Betta and Mitchell Schulte

Int. J. Mol. Sci. 2009, 10(6), 2809-2837; https://doi.org/10.3390/ijms10062809 - 22 Jun 2009

Cited by 13 | Viewed by 13600

Abstract

The citric acid cycle (CAC) is the central pathway of energy transfer for many organisms, and understanding the origin of this pathway may provide insight into the origins of metabolism. In order to assess the thermodynamics of this key pathway for microorganisms that [...] Read more.

The citric acid cycle (CAC) is the central pathway of energy transfer for many organisms, and understanding the origin of this pathway may provide insight into the origins of metabolism. In order to assess the thermodynamics of this key pathway for microorganisms that inhabit a wide variety of environments, especially those found in high temperature environments, we have calculated the properties and parameters for the revised Helgeson-Kirkham-Flowers equation of state for the major components of the CAC. While a significant amount of data is not available for many of the constituents of this fundamental pathway, methods exist that allow estimation of these missing data. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 458 KiB

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Amino Acid Synthesis in a Supercritical Carbon Dioxide - Water System

by Kouki Fujioka, Yasuhiro Futamura, Tomoo Shiohara, Akiyoshi Hoshino, Fumihide Kanaya, Yoshinobu Manome and Kenji Yamamoto

Int. J. Mol. Sci. 2009, 10(6), 2722-2732; https://doi.org/10.3390/ijms10062722 - 15 Jun 2009

Cited by 7 | Viewed by 13234

Abstract

Mars is a CO₂-abundant planet, whereas early Earth is thought to be also CO₂-abundant. In addition, water was also discovered on Mars in 2008. From the facts and theory, we assumed that soda fountains were present on both planets, [...] Read more.

Mars is a CO₂-abundant planet, whereas early Earth is thought to be also CO₂-abundant. In addition, water was also discovered on Mars in 2008. From the facts and theory, we assumed that soda fountains were present on both planets, and this affected amino acid synthesis. Here, using a supercritical CO₂/liquid H₂O (10:1) system which mimicked crust soda fountains, we demonstrate production of amino acids from hydroxylamine (nitrogen source) and keto acids (oxylic acid sources). In this research, several amino acids were detected with an amino acid analyzer. Moreover, alanine polymers were detected with LC-MS. Our research lights up a new pathway in the study of life’s origin. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 227 KiB

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Tryptophanase-Catalyzed L-Tryptophan Synthesis from D-Serine in the Presence of Diammonium Hydrogen Phosphate

by Akihiko Shimada, Haruka Ozaki, Takeshi Saito and Fujii Noriko

Int. J. Mol. Sci. 2009, 10(6), 2578-2590; https://doi.org/10.3390/ijms10062578 - 3 Jun 2009

Cited by 12 | Viewed by 12186

Abstract

Tryptophanase, an enzyme with extreme absolute stereospecificity for optically active stereoisomers, catalyzes the synthesis of L-tryptophan from L-serine and indole through a ?-substitution mechanism of the ping-pong type, and has no activity on D-serine. We previously reported that tryptophanase changed its stereospecificity to [...] Read more.

Tryptophanase, an enzyme with extreme absolute stereospecificity for optically active stereoisomers, catalyzes the synthesis of L-tryptophan from L-serine and indole through a ?-substitution mechanism of the ping-pong type, and has no activity on D-serine. We previously reported that tryptophanase changed its stereospecificity to degrade D-tryptophan in highly concentrated diammonium hydrogen phosphate, (NH₄)₂HPO₄ solution. The present study provided the same stereospecific change seen in the D-tryptophan degradation reaction also occurs in tryptophan synthesis from D-serine. Tryptophanase became active to D-serine to synthesize L-tryptophan in the presence of diammonium hydrogen phosphate. This reaction has never been reported before. D-serine seems to undergo ?-replacement via an enzyme-bonded ?-aminoacylate intermediate to yield L-tryptophan. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 463 KiB

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To What Extent Is Water Responsible for the Maintenance of the Life for Warm-Blooded Organisms?

by Anatoliy I. Fisenko and Nikolay P. Malomuzh

Int. J. Mol. Sci. 2009, 10(5), 2383-2411; https://doi.org/10.3390/ijms10052383 - 22 May 2009

Cited by 21 | Viewed by 11757

Abstract

In this work, attention is mainly focused on those properties of water which are essentially changed in the physiological temperature range of warm-blooded organisms. Studying in detail the half-width of the diffusion peak in the quasi-elastic incoherent neutron scattering, the behavior of the [...] Read more.

In this work, attention is mainly focused on those properties of water which are essentially changed in the physiological temperature range of warm-blooded organisms. Studying in detail the half-width of the diffusion peak in the quasi-elastic incoherent neutron scattering, the behavior of the entropy and the kinematic shear viscosity, it is shown that the character of the translational and rotational thermal motions in water radically change near T_H ~ 315 K, which can be interpreted as the temperature of the smeared dynamic phase transition. These results for bulk pure water are completed by the analysis of the isothermic compressibility and the NMR-spectra for water-glycerol solutions. It was noted that the non-monotone temperature dependence of the isothermic compressibility (?_T) takes also place for the water-glycerol solutions until the concentration of glycerol does not exceed 30 mol%. At that, the minimum of ?_T shifts at left when the concentration increases. All these facts give us some reasons to assume that the properties of the intracellular and extracellularfluidsare close to ones for pure water. Namely therefore, we suppose that the upper temperature limit for the life of warm-blooded organisms [T_D = (315 ± 3) K] is tightly connected with the temperature of the dynamic phase transition in water. This supposition is equivalent to the assertion that the denaturation of proteins at T ? T_H is mainly provoked by the rebuilding of the H-bond network in the intracellular and extracellular fluids, which takes place at T ? T_H. A question why the heavy water cannot be a matrix for the intracellular and extracellular fluids is considered. The lower physiological pH limit for the life of warm-blooded organisms is discussed. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 400 KiB

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A Possible Mechanism for Evading Temperature Quantum Decoherence in Living Matter by Feshbach Resonance

by Nicola Poccia, Alessandro Ricci, Davide Innocenti and Antonio Bianconi

Int. J. Mol. Sci. 2009, 10(5), 2084-2106; https://doi.org/10.3390/ijms10052084 - 13 May 2009

Cited by 17 | Viewed by 12971

Abstract

A new possible scenario for the origin of the molecular collective behaviour associated with the emergence of living matter is presented. We propose that the transition from a non-living to a living cell could be mapped to a quantum transition to a coherent [...] Read more.

A new possible scenario for the origin of the molecular collective behaviour associated with the emergence of living matter is presented. We propose that the transition from a non-living to a living cell could be mapped to a quantum transition to a coherent entanglement of condensates, like in a multigap BCS superconductor. Here the decoherence-evading qualities at high temperature are based on the Feshbach resonance that has been recently proposed as the driving mechanism for high T_c superconductors. Finally we discuss how the proximity to a particular critical point is relevant to the emergence of coherence in the living cell. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 271 KiB

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Concept of Sustained Ordering and an ATP-related Mechanism of Life’s Origin

by Erik M. Galimov

Int. J. Mol. Sci. 2009, 10(5), 2019-2030; https://doi.org/10.3390/ijms10052019 - 6 May 2009

Cited by 16 | Viewed by 10185

Abstract

This paper shows that the steadystate of a system of conjugated reactions, which are characterized by disproportionation of entropy and proceed in the domain of linear interactions, is an attractor of ordering. Such systems are primed to produce ordering, and life is a [...] Read more.

This paper shows that the steadystate of a system of conjugated reactions, which are characterized by disproportionation of entropy and proceed in the domain of linear interactions, is an attractor of ordering. Such systems are primed to produce ordering, and life is a specific manifestation of the sustained ordering inherent to the chemistry of carbon. The adenosine triphospate (ATP) molecule has properties which makes ATP hydrolysis to be most appropriate to form such a system in primitive world. Hence, ATP is suggested to play a key role in prebiological evolution. Principles of the origin and evolution of life following from the concept of ordering are stated. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 503 KiB

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Localization of D-?-Aspartyl Residue-Containing Proteins in Various Tissues

by Ryota Motoie, Noriko Fujii, Shigeru Tsunoda, Kenji Nagata, Tadashi Shimo-oka, Tadatoshi Kinouchi, Norihiko Fujii, Takeshi Saito and Koji Ono

Int. J. Mol. Sci. 2009, 10(5), 1999-2009; https://doi.org/10.3390/ijms10051999 - 29 Apr 2009

Cited by 22 | Viewed by 11055

Abstract

Prior to the emergence of life, it is believed that only L-amino acids were selected for formation of protein and that D-amino acids were eliminated on the primitive Earth. Whilst homochirality is essential for life, the occurrence of proteins containing D-?-aspartyl (Asp) residues [...] Read more.

Prior to the emergence of life, it is believed that only L-amino acids were selected for formation of protein and that D-amino acids were eliminated on the primitive Earth. Whilst homochirality is essential for life, the occurrence of proteins containing D-?-aspartyl (Asp) residues in various tissues from elderly subjects has been reported recently. Here, we demonstrate the presence of a D-?-Asp-containing protein in the cardiac muscle of heart, blood vessels of the lung, chief cells of the stomach, longitudinal and circular muscle of the stomach, small intestine and large intestine. Since the D-?-Asp residue occurs through a succinimide intermediate, this isomer may potentially be generated in proteins more easily than initially thought. Formation of the D-?-Asp residue in proteins may be related to stress. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 115 KiB

Open AccessArticle

Coenzyme Autocatalytic Network on the Surface of Oil Microspheres as a Model for the Origin of Life

by Alexei A. Sharov

Int. J. Mol. Sci. 2009, 10(4), 1838-1852; https://doi.org/10.3390/ijms10041838 - 22 Apr 2009

Cited by 22 | Viewed by 11312

Abstract

Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecules. I suggest that coenzyme-like molecules (CLMs) performed hereditary functions before the emergence of nucleic acids. Autocatalytic CLMs modified (encoded) surface properties of hydrocarbon microspheres, to which they were anchored, [...] Read more.

Coenzymes are often considered as remnants of primordial metabolism, but not as hereditary molecules. I suggest that coenzyme-like molecules (CLMs) performed hereditary functions before the emergence of nucleic acids. Autocatalytic CLMs modified (encoded) surface properties of hydrocarbon microspheres, to which they were anchored, and these changes enhanced autocatalysis and propagation of CLMs. Heredity started from a single kind of self-reproducing CLM, and then evolved into more complex coenzyme autocatalytic networks containing multiple kinds of CLMs. Polymerization of CLMs on the surface of microspheres and development of template-based synthesis is a potential evolutionary path towards the emergence of nucleic acids. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 714 KiB

Open AccessArticle

Non-Enzymatic Template-Directed Recombination of RNAs

by Sergey Y. Nechaev, Alexei V. Lutay, Valentin V. Vlassov and Marina A. Zenkova

Int. J. Mol. Sci. 2009, 10(4), 1788-1807; https://doi.org/10.3390/ijms10041788 - 21 Apr 2009

Cited by 11 | Viewed by 12263

Abstract

RNA non-enzymatic recombination reactions are of great interest within the hypothesis of the "RNA world", which argues that at some stage of prebiotic life development proteins were not yet engaged in biochemical reactions and RNA carried out both the information storage task and [...] Read more.

RNA non-enzymatic recombination reactions are of great interest within the hypothesis of the "RNA world", which argues that at some stage of prebiotic life development proteins were not yet engaged in biochemical reactions and RNA carried out both the information storage task and the full range of catalytic roles necessary in primitive self-replicating systems. Here we report on the study of recombination reaction occuring between two 96 nucleotides (nts) fragments of RNAs under physiological conditions and governed by a short oligodeoxyribonucleotide template, partially complementary to sequences within each of the RNAs. Analysis of recombination products shows that ligation is predominantly template-directed, and occurs within the complementary complex with the template in "butt-to-butt" manner, in 1- or 3- nts bulges or in 2-3 nts internal loops. Minor recombination products formed in the template-independent manner are detected as well. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 187 KiB

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Origin of Homochirality in Biosystems

by Søren Toxvaerd

Int. J. Mol. Sci. 2009, 10(3), 1290-1299; https://doi.org/10.3390/ijms10031290 - 18 Mar 2009

Cited by 36 | Viewed by 12358

Abstract

Experimental data for a series of central and simple molecules in biosystems show that some amino acids and a simple sugar molecule have a chiral discrimination in favor of homochirality. Models for segregation of racemic mixtures of chiral amphiphiles and lipophiles in aqueous [...] Read more.

Experimental data for a series of central and simple molecules in biosystems show that some amino acids and a simple sugar molecule have a chiral discrimination in favor of homochirality. Models for segregation of racemic mixtures of chiral amphiphiles and lipophiles in aqueous solutions show that the amphiphiles with an active isomerization kinetics can perform a spontaneous break of symmetry during the segregation and self-assembly to homochiral matter. Based on this observation it is argued that biomolecules with a sufficiently strong chiral discrimination could be the origin of homochirality in biological systems. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 651 KiB

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Formation versus Hydrolysis of the Peptide Bond from a Quantum-mechanical Viewpoint: The Role of Mineral Surfaces and Implications for the Origin of Life

by Albert Rimola, Piero Ugliengo and Mariona Sodupe

Int. J. Mol. Sci. 2009, 10(3), 746-760; https://doi.org/10.3390/ijms10030746 - 26 Feb 2009

Cited by 28 | Viewed by 14999

Abstract

The condensation (polymerization by water elimination) of molecular building blocks to yield the first active biopolymers (e.g. of amino acids to form peptides) during primitive Earth is an intriguing question that nowadays still remains open since these processes are thermodynamically disfavoured in [...] Read more.

The condensation (polymerization by water elimination) of molecular building blocks to yield the first active biopolymers (e.g. of amino acids to form peptides) during primitive Earth is an intriguing question that nowadays still remains open since these processes are thermodynamically disfavoured in highly dilute water solutions. In the present contribution, formation and hydrolysis of glycine oligopeptides occurring on a cluster model of sanidine feldspar (001) surface have been simulated by quantum mechanical methods. Results indicate that the catalytic interplay between Lewis and Brønsted sites both present at the sanidine surface, in cooperation with the London forces acting between the biomolecules and the inorganic surface, plays a crucial role to: i) favour the condensation of glycine to yield oligopeptides as reaction products; ii) inhibit the hydrolysis of the newly formed oligopeptides. Both facts suggest that mineral surfaces may have helped in catalyzing, stabilizing and protecting from hydration the oligopeptides formed in the prebiotic era. Full article

(This article belongs to the Special Issue Origin of Life)

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Review

Jump to: Research

0 pages, 2482 KiB

Open AccessReview

Precambrian Lunar Volcanic Protolife

by Jack Green

Int. J. Mol. Sci. 2009, 10(6), 2681-2721; https://doi.org/10.3390/ijms10062681 - 11 Jun 2009

Cited by 2 | Viewed by 13400

Abstract

Five representative terrestrial analogs of lunar craters are detailed relevant to Precambrian fumarolic activity. Fumarolic fluids contain the ingredients for protolife. Energy sources to derive formaldehyde, amino acids and related compounds could be by flow charging, charge separation and volcanic shock. With no [...] Read more.

Five representative terrestrial analogs of lunar craters are detailed relevant to Precambrian fumarolic activity. Fumarolic fluids contain the ingredients for protolife. Energy sources to derive formaldehyde, amino acids and related compounds could be by flow charging, charge separation and volcanic shock. With no photodecomposition in shadow, most fumarolic fluids at 40 K would persist over geologically long time periods. Relatively abundant tungsten would permit creation of critical enzymes, Fischer-Tropsch reactions could form polycyclic aromatic hydrocarbons and soluble volcanic polyphosphates would enable assembly of nucleic acids. Fumarolic stimuli factors are described. Orbital and lander sensors specific to protolife exploration including combined Raman/laser-induced breakdown spectrocsopy are evaluated. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 129 KiB

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The Eukaryotic Cell Originated in the Integration and Redistribution of Hyperstructures from Communities of Prokaryotic Cells Based on Molecular Complementarity

by Vic Norris and Robert Root-Bernstein

Int. J. Mol. Sci. 2009, 10(6), 2611-2632; https://doi.org/10.3390/ijms10062611 - 4 Jun 2009

Cited by 12 | Viewed by 12328

Abstract

In the “ecosystems-first” approach to the origins of life, networks of non-covalent assemblies of molecules (composomes), rather than individual protocells, evolved under the constraints of molecular complementarity. Composomes evolved into the hyperstructures of modern bacteria. We extend the ecosystems-first approach to explain the [...] Read more.

In the “ecosystems-first” approach to the origins of life, networks of non-covalent assemblies of molecules (composomes), rather than individual protocells, evolved under the constraints of molecular complementarity. Composomes evolved into the hyperstructures of modern bacteria. We extend the ecosystems-first approach to explain the origin of eukaryotic cells through the integration of mixed populations of bacteria. We suggest that mutualism and symbiosis resulted in cellular mergers entailing the loss of redundant hyperstructures, the uncoupling of transcription and translation, and the emergence of introns and multiple chromosomes. Molecular complementarity also facilitated integration of bacterial hyperstructures to perform cytoskeletal and movement functions. Full article

(This article belongs to the Special Issue Origin of Life)

0 pages, 333 KiB

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Elementary Reactions and Their Role in Gas-Phase Prebiotic Chemistry

by Nadia Balucani

Int. J. Mol. Sci. 2009, 10(5), 2304-2335; https://doi.org/10.3390/ijms10052304 - 19 May 2009

Cited by 93 | Viewed by 17081

Abstract

The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided [...] Read more.

The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 161 KiB

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On the Free Energy That Drove Primordial Anabolism

by Michael Kaufmann

Int. J. Mol. Sci. 2009, 10(4), 1853-1871; https://doi.org/10.3390/ijms10041853 - 22 Apr 2009

Cited by 17 | Viewed by 13883

Abstract

A key problem in understanding the origin of life is to explain the mechanism(s) that led to the spontaneous assembly of molecular building blocks that ultimately resulted in the appearance of macromolecular structures as they are known in modern biochemistry today. An indispensable [...] Read more.

A key problem in understanding the origin of life is to explain the mechanism(s) that led to the spontaneous assembly of molecular building blocks that ultimately resulted in the appearance of macromolecular structures as they are known in modern biochemistry today. An indispensable thermodynamic prerequisite for such a primordial anabolism is the mechanistic coupling to processes that supplied the free energy required. Here I review different sources of free energy and discuss the potential of each form having been involved in the very first anabolic reactions that were fundamental to increase molecular complexity and thus were essential for life. Full article

(This article belongs to the Special Issue Origin of Life)

0 pages, 240 KiB

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Pseudo-Replication of [GADV]-Proteins and Origin of Life

by Kenji Ikehara

Int. J. Mol. Sci. 2009, 10(4), 1525-1537; https://doi.org/10.3390/ijms10041525 - 2 Apr 2009

Cited by 31 | Viewed by 16102

Abstract

The RNA world hypothesis on the origin of life is generally considered as the key to solve the “chicken and egg dilemma” concerning the evolution of genes and proteins as observed in the modern organisms. This hypothesis, however, contains several serious weak points. [...] Read more.

The RNA world hypothesis on the origin of life is generally considered as the key to solve the “chicken and egg dilemma” concerning the evolution of genes and proteins as observed in the modern organisms. This hypothesis, however, contains several serious weak points. We have a counterproposal called [GADV]-protein world hypothesis, abbreviated as GADV hypothesis, in which we have suggested that life originated from a [GADV]-protein world, which comprised proteins composed of four amino acids: Gly [G], Ala [A], Asp [D], and Val [V]. A new concept “pseudo-replication” is crucial for the description of the emergence of life. The new hypothesis not only plausibly explains how life originated from the initial chaotic protein world, but also how genes, genetic code, and proteins co-evolved. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 49 KiB

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Molecules, Water, and Radiant Energy: New Clues for the Origin of Life

by Gerald H. Pollack, Xavier Figueroa and Qing Zhao

Int. J. Mol. Sci. 2009, 10(4), 1419-1429; https://doi.org/10.3390/ijms10041419 - 27 Mar 2009

Cited by 52 | Viewed by 15711

Abstract

We here examine the putative first step in the origin of life: the coalescence of dispersed molecules into a more condensed, organized state. Fresh evidence implies that the driving energy for this coalescence may come in a manner more direct than previously thought. [...] Read more.

We here examine the putative first step in the origin of life: the coalescence of dispersed molecules into a more condensed, organized state. Fresh evidence implies that the driving energy for this coalescence may come in a manner more direct than previously thought. The sun’s radiant energy separates charge in water, and this free charge demonstrably induces condensation. This condensation mechanism puts water as a central protagonist in life rather than as an incidental participant, and thereby helps explain why life requires water. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 101 KiB

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Model Protocells from Single-Chain Lipids

by Sheref S. Mansy

Int. J. Mol. Sci. 2009, 10(3), 835-843; https://doi.org/10.3390/ijms10030835 - 2 Mar 2009

Cited by 43 | Viewed by 14931

Abstract

Significant progress has been made in the construction of laboratory models of protocells. Most frequently the developed vesicle systems utilize single-chain lipids rather than the double-chain lipids typically found in biological membranes. Although single-chain lipids yield less robust vesicles, their dynamic characteristics are [...] Read more.

Significant progress has been made in the construction of laboratory models of protocells. Most frequently the developed vesicle systems utilize single-chain lipids rather than the double-chain lipids typically found in biological membranes. Although single-chain lipids yield less robust vesicles, their dynamic characteristics are highly exploitable for protocellular functions. Herein the advantages of using single-chain lipids in the construction of protocells are discussed. Full article

(This article belongs to the Special Issue Origin of Life)

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0 pages, 399 KiB

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The Capabilities of Chaos and Complexity

by David L. Abel

Int. J. Mol. Sci. 2009, 10(1), 247-291; https://doi.org/10.3390/ijms10010247 - 9 Jan 2009

Cited by 26 | Viewed by 33175

Abstract

To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and [...] Read more.

To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization? Full article

(This article belongs to the Special Issue Origin of Life)

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