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Prebiotic chemistry

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https://www.readbyqxmd.com/read/27909555/effect-of-dual-type-oligosaccharides-on-constipation-in-loperamide-treated-rats
#1
Sung Hee Han, Ki Bae Hong, Eun Young Kim, So Hyun Ahn, Hyung Joo Suh
BACKGROUND/OBJECTIVES: Constipation is a condition that can result from intestinal deformation. Because humans have an upright posture, the effects of gravity can cause this shape deformation. Oligosaccharides are common prebiotics and their effects on bowel health are well known. However, studies of the physiological functionality of a product that contains both lactulose and galactooligosaccharides are insufficient. We investigated the constipation reduction effect of a dual-type oligosaccharide, Dual-Oligo, in loperamide-treated rats...
December 2016: Nutrition Research and Practice
https://www.readbyqxmd.com/read/27862722/evaporite-borate-containing-mineral-ensembles-make-phosphate-available-and-regiospecifically-phosphorylate-ribonucleosides-borate-as-a-multifaceted-problem-solver-in-prebiotic-chemistry
#2
Hyo-Joong Kim, Yoshihiro Furukawa, Takeshi Kakegawa, Andrei Bita, Romulus Scorei, Steven A Benner
RNA is currently thought to have been the first biopolymer to support Darwinian natural selection on Earth. However, the phosphate esters in RNA and its precursors, and the many sites at which phosphorylation might occur in ribonucleosides under conditions that make it possible, challenge prebiotic chemists. Moreover, free inorganic phosphate may have been scarce on early Earth owing to its sequestration by calcium in the unreactive mineral hydroxyapatite. Herein, it is shown that these problems can be mitigated by a particular geological environment that contains borate, magnesium, sulfate, calcium, and phosphate in evaporite deposits...
November 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27827919/taming-prebiotic-chemistry-the-role-of-heterogeneous-and-interfacial-catalysis-in-the-emergence-of-a-prebiotic-catalytic-information-polymer-system
#3
REVIEW
Pierre-Alain Monnard
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth...
November 4, 2016: Life
https://www.readbyqxmd.com/read/27802310/non-enzymatic-oligomerization-of-3-5-cyclic-amp
#4
Giovanna Costanzo, Samanta Pino, Anna Maria Timperio, Judit E Šponer, Jiří Šponer, Olga Nováková, Ondrej Šedo, Zbyněk Zdráhal, Ernesto Di Mauro
Recent studies illustrate that short oligonucleotide sequences can be easily produced from nucleotide precursors in a template-free non-enzymatic way under dehydrating conditions, i.e. using essentially dry materials. Here we report that 3',5' cyclic AMP may also serve as a substrate of the reaction, which proceeds under moderate conditions yet with a lower efficiency than the previously reported oligomerization of 3',5' cyclic GMP. Optimally the oligomerization requires (i) a temperature of 80°C, (ii) a neutral to alkaline environment and (iii) a time on the order of weeks...
2016: PloS One
https://www.readbyqxmd.com/read/27730379/influence-of-microhydration-on-the-structures-and-proton-induced-charge-transfer-in-rna-intermediates
#5
M C Bacchus-Montabonel, F Calvo
Solvation effects are of major interest in the context of radiation damage, due to their potential applications in cancer therapy. Reliable modeling of the solvent is, however, quite challenging, and numerous studies have been devoted to isolated biomolecules and stepwise-hydrated molecules in which the amount of solvent is controlled one molecule at a time. The influence of stepwise hydration on radiation damage is investigated here using the example of proton-induced charge transfer in two biomolecular targets...
November 2016: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27711447/pyrite-surface-environment-drives-molecular-adsorption-cystine-on-pyrite-100-investigated-by-x-ray-photoemission-spectroscopy-and-low-energy-electron-diffraction
#6
M Sanchez-Arenillas, E Mateo-Marti
We have demonstrated that the annealing process for cleaning pyrite surfaces is a critical parameter in promoting ordering on the surface and driving surface reactivity. Furthermore, we describe a spectroscopic surface characterization of the presence or absence of the surface ordering, as indicated by the Low Energy Electron Diffraction (LEED) pattern, as a function of the surface annealing process. Complementary X-ray photoemission spectroscopy (XPS) results provide evidence that longer annealing processes of over 3 hours repair the sulfur vacancies in the pyrite, making FeS species partially disappear in favor of FeS2 species...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27700137/carbon-monoxide-and-the-potential-for-prebiotic-chemistry-on-habitable-planets-around-main-sequence-m-stars
#7
J Manik Nava-Sedeño, Adrian Ortiz-Cervantes, Antígona Segura, Shawn D Domagal-Goldman
Lifeless planets with CO2 atmospheres produce CO by CO2 photolysis. On planets around M dwarfs, CO is a long-lived atmospheric compound, as long as UV emission due to the star's chromospheric activity lasts, and the sink of CO and O2 in seawater is small compared to its atmospheric production. Atmospheres containing reduced compounds, like CO, may undergo further energetic and chemical processing to give rise to organic compounds of potential importance for the origin of life. We calculated the yield of organic compounds from CO2-rich atmospheres of planets orbiting M dwarf stars, which were previously simulated by Domagal-Goldman et al...
October 4, 2016: Astrobiology
https://www.readbyqxmd.com/read/27629398/bringing-prebiotic-nucleosides-and-nucleotides-down-to-earth
#8
Michele Fiore, Peter Strazewski
There may be more than one way leading to RNA: Recent discoveries in the synthesis of nucleoside and nucleotide precursors are described and put into the wider context of prebiotic systems chemistry. Mixing Butlerow's carbohydrate precursors with Traube's 5-formylaminopyrimidines has led to the formation of prebiotic purine nucleosides whereas the mixing of 5-phosphoribose with barbituric acid and melamine gave supramolecular fibers from stacks of Whitesides' rosettas.
September 15, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27624284/thermal-behavior-of-d-ribose-adsorbed-on-silica-effect-of-inorganic-salt-coadsorption-and-significance-for-prebiotic-chemistry
#9
Mariame Akouche, Maguy Jaber, Emilie-Laure Zins, Marie-Christine Maurel, Jean-Francois Lambert, Thomas Georgelin
Understanding ribose reactivity is a crucial step in the "RNA world" scenario because this molecule is a component of all extant nucleotides that make up RNA. In solution, ribose is unstable and susceptible to thermal destruction. We examined how ribose behaves upon thermal activation when adsorbed on silica, either alone or with the coadsorption of inorganic salts (MgCl2 , CaCl2 , SrCl2 , CuCl2 , FeCl2 , FeCl3 , ZnCl2 ). A combination of (13) C NMR, in situ IR, and TGA analyses revealed a variety of phenomena...
September 14, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27534830/mixed-anhydride-intermediates-in-the-reaction-of-5-4h-oxazolones-with-phosphate-esters-and-nucleotides
#10
Ziwei Liu, Lukas Rigger, Jean-Christophe Rossi, John D Sutherland, Robert Pascal
5(4H)-Oxazolones can be formed through the activation of acylated α-amino acids or of peptide C termini. They constitute potentially activated intermediates in the abiotic chemistry of peptides that preceded the origin of life or early stages of biology and are capable of yielding mixed carboxylic-phosphoric anhydrides upon reaction with phosphate esters and nucleotides. Here, we present the results of a study aimed at investigating the chemistry that can be built through this interaction. As a matter of fact, the formation of mixed anhydrides with mononucleotides and nucleic acid models is shown to take place at positions involving a mono-substituted phosphate group at the 3'- or 5'-terminus but not at the internal phosphodiester linkages...
October 10, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27518115/detection-of-macromolecular-fractions-in-hcn-polymers-using-electrophoretic-and-ultrafiltration-techniques
#11
Margarita R Marín-Yaseli, Cristina Cid, Ana I Yagüe, Marta Ruiz-Bermejo
Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers...
August 12, 2016: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/27472365/dry-wet-cycling-and-the-thermodynamics-and-kinetics-of-prebiotic-polymer-synthesis
#12
David S Ross, David Deamer
The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life's origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium Nm + Nn ↔ Nm+n + H₂O is endoergic by about 3...
July 26, 2016: Life
https://www.readbyqxmd.com/read/27467333/quantitation-of-%C3%AE-hydroxy-acids-in-complex-prebiotic-mixtures-via-liquid-chromatography-tandem-mass-spectrometry
#13
Eric T Parker, H James Cleaves, Jeffrey L Bada, Facundo M Fernández
RATIONALE: Spark discharge experiments, like those performed by Stanley Miller in the 1950s, generate complex, analytically challenging mixtures that contain biopolymer building blocks. Recently, α-amino acids and α-hydroxy acids (AHAs) were subjected to environmental cycling to form simple depsipeptides (peptides with both amide and ester linkages). The synthesis of AHAs under possible primordial environments must be examined to better understand this chemistry. METHODS: We report a direct, quantitative method for AHAs using ultrahigh-performance liquid chromatography and triple quadrupole mass spectrometry...
September 30, 2016: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/27464613/the-role-of-aqueous-aerosols-in-the-glyoxylate-scenario-an-experimental-approach
#14
Margarita R Marín-Yaseli, Elena González-Toril, Cristina Mompeán, Marta Ruiz-Bermejo
The origin of life is one of the fundamental questions in science. Eschenmoser proposed the "glyoxylate scenario", in which plausible abiotic synthesis pathways were suggested to be compatible with the constraints of prebiotic chemistry. In this proposal, the stem compound is HCN. In this work, we explore the "glyoxylate scenario" through several syntheses of HCN polymers, paying particular attention to the role of the aqueous aerosols, together with statistical methods, as a step to elucidate the synthetic problem of the origin of life...
August 26, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27443234/the-abiotic-chemistry-of-thiolated-acetate-derivatives-and-the-origin-of-life
#15
Kuhan Chandru, Alexis Gilbert, Christopher Butch, Masashi Aono, H James Cleaves
Thioesters and thioacetic acid (TAA) have been invoked as key reagents for the origin of life as activated forms of acetate analogous to acetyl-CoA. These species could have served as high-energy group-transfer reagents and allowed carbon insertions to form higher molecular weight compounds such as pyruvate. The apparent antiquity of the Wood-Ljungdahl CO2 fixation pathway and its presence in organisms which inhabit hydrothermal (HT) environments has also led to suggestions that there may be a connection between the abiotic chemistry of compounds similar to TAA and the origins of metabolism...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27386550/prebiotic-chemicals-amino-acid-and-phosphorus-in-the-coma-of-comet-67p-churyumov-gerasimenko
#16
Kathrin Altwegg, Hans Balsiger, Akiva Bar-Nun, Jean-Jacques Berthelier, Andre Bieler, Peter Bochsler, Christelle Briois, Ursina Calmonte, Michael R Combi, Hervé Cottin, Johan De Keyser, Frederik Dhooghe, Bjorn Fiethe, Stephen A Fuselier, Sébastien Gasc, Tamas I Gombosi, Kenneth C Hansen, Myrtha Haessig, Annette Jäckel, Ernest Kopp, Axel Korth, Lena Le Roy, Urs Mall, Bernard Marty, Olivier Mousis, Tobias Owen, Henri Rème, Martin Rubin, Thierry Sémon, Chia-Yu Tzou, James Hunter Waite, Peter Wurz
The importance of comets for the origin of life on Earth has been advocated for many decades. Amino acids are key ingredients in chemistry, leading to life as we know it. Many primitive meteorites contain amino acids, and it is generally believed that these are formed by aqueous alterations. In the collector aerogel and foil samples of the Stardust mission after the flyby at comet Wild 2, the simplest form of amino acids, glycine, has been found together with precursor molecules methylamine and ethylamine. Because of contamination issues of the samples, a cometary origin was deduced from the (13)C isotopic signature...
May 2016: Science Advances
https://www.readbyqxmd.com/read/27382167/polymorphism-and-electronic-structure-of-polyimine-and-its-potential-significance-for-prebiotic-chemistry-on-titan
#17
Martin Rahm, Jonathan I Lunine, David A Usher, David Shalloway
The chemistry of hydrogen cyanide (HCN) is believed to be central to the origin of life question. Contradictions between Cassini-Huygens mission measurements of the atmosphere and the surface of Saturn's moon Titan suggest that HCN-based polymers may have formed on the surface from products of atmospheric chemistry. This makes Titan a valuable "natural laboratory" for exploring potential nonterrestrial forms of prebiotic chemistry. We have used theoretical calculations to investigate the chain conformations of polyimine (pI), a polymer identified as one major component of polymerized HCN in laboratory experiments...
July 19, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27351102/nonenzymatic-copying-of-rna-templates-containing-all-four-letters-is-catalyzed-by-activated-oligonucleotides
#18
Noam Prywes, J Craig Blain, Francesca Del Frate, Jack W Szostak
The nonenzymatic replication of RNA is a potential transitional stage between the prebiotic chemistry of nucleotide synthesis and the canonical RNA world in which RNA enzymes (ribozymes) catalyze replication of the RNA genomes of primordial cells. However, the plausibility of nonenzymatic RNA replication is undercut by the lack of a protocell-compatible chemical system capable of copying RNA templates containing all four nucleotides. We show that short 5'-activated oligonucleotides act as catalysts that accelerate primer extension, and allow for the one-pot copying of mixed sequence RNA templates...
2016: ELife
https://www.readbyqxmd.com/read/27257242/origin-of-life-beyond-prebiotic-chemistry
#19
Leroy Cronin, Sara Imari Walker
No abstract text is available yet for this article.
June 3, 2016: Science
https://www.readbyqxmd.com/read/27247410/enantiomer-excesses-of-rare-and-common-sugar-derivatives-in-carbonaceous-meteorites
#20
George Cooper, Andro C Rios
Biological polymers such as nucleic acids and proteins are constructed of only one-the d or l-of the two possible nonsuperimposable mirror images (enantiomers) of selected organic compounds. However, before the advent of life, it is generally assumed that chemical reactions produced 50:50 (racemic) mixtures of enantiomers, as evidenced by common abiotic laboratory syntheses. Carbonaceous meteorites contain clues to prebiotic chemistry because they preserve a record of some of the Solar System's earliest (∼4...
June 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
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