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Cellular differentiation in the process of generation of the eukaryotic cell.

Primitive atmosphere of the earth did not contain oxygen gas (O2) when the proto-cells were generated successfully as the result of chemical evolution and then evolved. Therefore, they first had acquired anaerobic energy metabolism, fermentation. The cellular metabolisms have often been formed by reorganizing to combine or recombinate between pre-existing metabolisms and newly born bioreactions. Photosynthetic metabolism in eukaryotic chloroplast consists of an electron-transfer photosystem and a fermentative reductive pentose phosphate cycle. On the other hand, O2-respiration of eukaryotic mitochondrion is made of Embden-Meyerhof (EM) pathway and tricarboxylic acid cycle, which originate from a connection of fermentative metabolisms, and an electron-transfer respiratory chain, which has been derived from the photosystem. These metabolisms already are completed in some evolved prokaryotes, for example the cyanobacterium Chlorogloea fritschii and aerobic photosynthetic bacteria Rhodospirillum rubrum and Erythrobacter sp. Therefore, it can be reasonably presumed that the eukaryotic chloroplast and mitochondrion have once been formed as the result of metabolic (and genetic) differentiations in most evolved cyanobacterium. Symbiotic theory has explained the origin of eukaryotic cell as that in which the mitochondrion and chloroplast have been derived from endosymbionts of aerobic bacterium and cyanobacterium, respectively, and has mentioned as one of the most potent supportive evidences that amino acid sequences of the photosynthetic and O2 -respiratory enzymes show similarities to corresponding prokaryotic enzymes. However, as will be shown in this discussion, many examples have shown currently that prokaryotic sequences of informative molecules are conserved well not only in those of the mitochondrial and chloroplast molecules but also in the nuclear molecules. In fact, the similarities in sequence of informative molecules are preserved well among the organisms not only in phylogenetically close relationships but also under highly selective pressure, that is under a physiological constraint for the species in their habitats. Therefore, the similarities in amino acid sequences of proteins between the prokaryotes and the organelles are not necessarily direct evidence for their phylogenetical closeness: it gives still less evidence for a symbiotic relationship between the prokaryotes and the organelles. The metabolic compartmentalization of the membranes is an important tendency in cellular evolution to guarantee high specificity and rate of the metabolisms. It is suggested from the data that the intracellular membranes are not static but undergo dynamic turnover. Furthermore, these facts strongly support the Membrane Evolution Theory which was proposed by one of the authors in 1975.

Amino Acid Sequence↗
PubMed1984

The investigation of the HCN derivative diiminosuccinonitrile as a prebiotic condensing agent. The formation of phosphate esters.

Diiminosuccinonitrile (DISN) is formed readily by the Fe3+ oxidation of diaminomaleonitrile, a tetramer of HCN. DISN effects the phosphorylation of uridine in 13% yield to a mixture of the isomers of UMP when the reaction is performed in dimethylformamide solution. A 4% yield of the UMP isomers is obtained in neutral aqueous solution using 2 times the DISN concentration and 7 times the phosphate concentration used in DMF. DISN did not effect the conversion of adenosine to AMP or 5'-AMP to 5'-ADP in aqueous solution. The cyclization of 3'-AMP and 3'-UMP to the corresponding 2'-3'-cyclic phosphates proceeds in yields as high as 40-50% at 60 degrees C in pH 6 aqueous solutions in the presence of divalent metal ions. Lower yields of the cyclic phosphate are observed when 2'-AMP is the starting material. Substitution of acetate buffer for imidazole buffer results in a decrease in the yield of cyclic phosphate, the extent of which depends on the metal ion used in the reaction. No 3'5'-cyclic AMP was detected as a reaction product with either 5'-AMP or 3'-AMP as the starting material except for a 2.4% yield from 3'-AMP in the presence of Zn2+. BrCN effects the conversion of 3'-AMP to the 2'-3'-cyclic AMP in 37-65% yield depending on the divalent cation used as catalyst. A mechanism has been proposed for these cyclization reactions and their potential significance to the prebiotic synthesis of ribonucleic acid derivatives is discussed.

Adenosine↗
PubMed1986

Kinetics of the hydrolysis of guanosine 5'-phospho-2-methylimidazolide.

We have studied the hydrolysis of guanosine 5'-phospho-2-methylimidazolide, 2-MeImpG, in aqueous buffered solutions of various pH's at 75 degrees C and 37 degrees C. At 75 degrees C and pH < or = 1.0, two kinetic processes were observed spectrophotometrically: the first and more rapid one is attributed to the hydrolysis of the phosphoimidazolide P-N bond; the second and much slower one, to the cleavage of the glycosidic bond. At 37 degrees C, pH 2.0, the spectrophotometrically determined rate constant of P-N bond hydrolysis was confirmed by using high pressure liquid chromatography, HPLC. With the latter technique it was possible to separate reactants and products and also to extend the pH-rate profile into the neutral region where rates are slower and, therefore, difficult to measure spectrophotometrically. The pH-rate profiles at both temperatures exhibit similar behavior. At pH < 2 the pseudo-first-order rate constant increases with decreasing pH; in the region 2 < pH < 7 there is a plateau followed by a decrease for pH > 7. These data are consistent with a reactivity order zwitterion > anion for P-N bond hydrolysis. It is noteworthy that P-N bond hydrolysis in phosphoimidazolides is very slow compared to other phosphoramidates. This may be one of the reasons why this compound showed extraordinary ability in forming long oligomers under template-directed conditions.

Evolution, Chemical↗
PubMed1992

An efficient lightning energy source on the early Earth.

Miller and Urey suggested in 1959 that lightning and corona on the early Earth could have been the most favorable sources of prebiotic synthesis. In 1991 Chyba and Sagan reviewed the presently prevailing data on electrical discharges on Earth and they raised questions as to whether the electrical sources of prebiotic synthesis were as favorable as was claimed. The proposal of the present paper is that localized lightning sources associated with Archaean volcanoes could have possessed considerable advantages for prebiotic synthesis over the previously suggested global sources.

Earth, Planet↗
PubMed1990

Polymerization of the cyclic pyrophosphates of nucleosides and their analogues.

When 2'-deoxythymidine-3',5'-cyclic diphosphate, or the cyclic pyrophosphates of the acyclic nucleoside analogues II and IV are heated to 65-85 degrees C in the presence of imidazole, oligomers with lengths up to 20-30 are formed in excellent yield. This reaction provides a useful source of oligomers for use as templates in aqueous condensation reactions. In the absence of evidence to the contrary, we assume that the oligomers are atactic. The potential significance of this reaction in prebiotic chemistry is discussed.

Diphosphates↗
PubMed1987

Oligoglyceric acid synthesis by autocondensation of glyceroyl thioester.

The autocondensation of the glyceroyl thioester S-glyceroyl-ethanethiol yielded oligoglyceric acid. The rates of autocondensation and hydrolysis of the thioester increased from pH 6.5 to pH 7.5 in 2,6-lutidine and imidazole buffers. Autocondensation and hydrolysis were much more rapid to imidazole buffers than in 2,6-lutidine buffers of the same pH. The efficiency of ester bond synthesis was about 20% for 40 mM S-glyceroyl-ethanethiol in 2,6-lutidine and imidazole buffers near neutral pH. The size and yield of the oligoglyceric acid products increased when the concentration of the thioester was increased. The relationship of these results to prebiotic polymer synthesis is discussed.

Energy Metabolism↗
PubMed1987

Oligomerization of 3'-amino-3'deoxyguanosine-5'phosphorimidazolidate on a d(CpCpCpCpC) template.

3'-Amino-3'-deoxyguanosine-5'-phosphorimidazolidate (ImpGNH2) oligomerizes more rapidly and regiospecifically than related nucleotide derivatives on a d(CpCpCpCpC) template. The greater nucleophilicity of the amino group leads to efficient oligomerization even when the structure of the double-helical complex formed by the template and the substrate is not optimal for reaction. The use of amine-containing analogues should permit us to develop models of potentially prebiotic polymerization reactions that cannot be studied easily using natural nucleotides.

Amines↗
PubMed1990

Prebiotic synthesis of histidyl-histidine.

Histidyl-histidine (His-His) has been synthesized in a yield of up to 14.4% under plausible prebiotic conditions using histidine (His), cyanamide, and 4-amino-5-imidazole carboxamide. A trace amount of His trimer was also detected. Because the imidazole group of His is involved in a number of important enzymatic reactions, and His-His has been shown to catalyze the prebiotic synthesis of glycyl-glycine, we expect this work will stimulate further studies on the catalytic activities of simple His-containing peptides in prebiotic reactions.

Aminoimidazole Carboxamide↗
PubMed1985

Alanine synthesis from glyceraldehyde and ammonium ion in aqueous solution.

Alanine is formed under anaerobic conditions from glyceraldehyde and ammonium ion in aqueous solutions of sodium phosphate (pH 7.0) or imidazole-imidazolium chloride (pH 7.0) at ambient temperature. In 500 mM imidazole (pH 7.0), alanine synthesis from 10 mM glyceraldehyde and 15 mM ammonium ion is roughly 6 times more rapid in the presence of 10 mM 3-mercaptopropionate (0.62% yield at 60 days) than in its absence (0.10% yield at 60 days). Likewise, the formation of alanine in 500 mM sodium phosphate (pH 7.0) from 5 mM glyceraldehyde and 10 mM ammonium ion is more rapid in the presence of 10 mM N-acetylcysteine than in its absence. In this reaction with N-acetylcysteine, the ratio of the yield of alanine to the yield of lactate is fairly constant. The yield of alanine is about 4.5% that of lactate. Alanine synthesis in the presence of thiol probably proceeds via alanyl thioester, which is produced by rearrangement of the imine of the hemithioacetal of pyruvaldehyde, a product of glyceraldehyde dehydration. The significance of this reaction for molecular evolution is discussed.

Acetylcysteine↗
PubMed1987

Efficient near ultraviolet light induced formation of hydrogen by ferrous hydroxide.

The formation of hydrogen on irradiating ferrous ion in aqueous solution or suspension was studied over a wide range of pH. In addition to the known reaction in acid solution which decreases in yield with increasing pH and required far UV light, there is an efficient reaction occurring between pH 6 and 9 which utilizes near UV light. The latter reaction is an approximately linear function of both the concentration of ferrous ion and the light intensity. The quantum yield of hydrogen from the suspension of Fe(OH)2 at pH 7.2 is very high: > or = 0.3. The quantum yield decreases by a factor of five at 1 mole percent of ferric ions. To explain these observations it is proposed that an intermediate formed on excitation of the Fe(OH)2 polymer is further reduced by a neighboring Fe(+2) to form H2. These results support the work of Braterman et al. (1983) which claimed that the near UV driven photooxidation of ferrous ions could be responsible for formation of the Banded Iron Formations on the early earth. The efficient photoreaction observed in the present work could also serve as a source of active reducing equivalents to reduce CO2 and thus provide a solution to a dilemma in the arguments on the role of reduced carbon in the origin of life.

Carbon Dioxide↗
PubMed1987

Kinetic analysis of the template effect in ribooligoguanylate elongation.

We have undertaken a complete kinetic analysis of the template-directed oligoguanylate synthesis originated in Orgel's laboratory (Inoue and Orgel, 1982). The reaction of guanosine 5'-phospho-2-methylimidazolide, 2-MelmpG, with ribooligoguanylates all 3'-5' linked, designated n3 with n = 7-12, was studied in the presence/absence of the complementary template polycytidylic acid, poly(C). Conditions were chosen where poly(C) and 2-MelmpG are in large excess over the oligoguanylate. In the absence of the template at 37 degrees C the reaction leads to three isomeric oligomers that are elongated by one monomer unit. They are the 3'-5' linked, (n + 1)3, the 2'-5' linked, (n + 1)2, and the pyrophosphate product, (n + 1)p, formed in an approximate ratio 1:2:5. In the presence of the template the reaction is 20-fold faster and yields products n + 1, n + 2, n + 3 etc. as long as 2-MelmpG is available. Most importantly the formation of the natural, 3'-5' linked isomer, is enhanced selectively by 140-fold at 37 degrees C. Qualitative observations allow the conclusion that this enhancement is temperature dependent and increases with decreasing temperature. For example, at 1 degree C only the 3'-5' linked isomers were detected. Initial rates for the disappearance of the n3 oligoguanylate were determined at 1, 23, and 37 degrees C. It was found that the pseudo-first order rate constant for oligoguanylate elongation was linearly proportional to the 2-MelmpG concentration. This implies that the reaction complex poly(C).n3.2-MelmpG does not accumulate under the reaction conditions, a conclusion which is also supported by infrared data (Miles and Frazier, 1982). The implication of the above results with respect to chemical evolution is that lower temperatures, i.e., close to freezing, enhance the regioselectivity of these template-directed reactions and that one way to improve replication models may be sought in finding conditions that favor stable reaction complexes.

Adenine Nucleotides↗
PubMed1989

Some acyclic analogues of nucleotides and their template-directed reactions.

Bismonophosphoimidazolides of acyclic analogues of guanosine IV and adenosine V were synthesized. They undergo oligomerization in the presence of complementary polynucleotide templates. Details of their synthesis and their subsequent template- and nontemplate-directed reactions are described, and their possible relevance to the origin of life is discussed.

Adenosine↗
PubMed2001

Calculation of radiation-induced DNA damage from photons and tritium beta-particles. Part I: Model formulation and basic results.

Radiation-induced damage in nucleosomal DNA was modelled by Monte Carlo means. An atomistic representation of DNA with a first hydration shell was used. DNA single- and double-strand break (SSB and DSB) yields were calculated for 137Cs photons, x-rays and tritium beta-particles. Monte Carlo-generated electron tracks for liquid water were used to model energy deposition. Chemical evolution of a track and interactions between species and DNA following water radiolysis were modelled in an encounter-controlled manner. The effects of varying the scavenging capacity of the environment, the extent of DNA protection by histones and the setting of a threshold for direct energy depositions on DNA break yields were all systematically studied. DSB complexity was assessed in terms of DNA breaks and base damage accompanying a DSB. Model parameters were adjusted to make predictions consistent with experimental data on DSB yields and yield modification by a variety of factors including changing DNA conformation and incorporation of scavengers. An embedded model of nucleosomal DNA by histones was required to explain experimentally observed modification of DSB yield by removal of bound histones. Complex DSB, defined as DSB accompanied by an additional strand breakage, exhibited high association with base damage. It is shown that hydroxyl radical interactions with bases are a major contributor to DSB complexity. On average there were 1.15 and 2.69 OH-base interactions accompanying simple and complex DSB, respectively for 137Cs. Over 80% of complex DSB had at least one OH-base interaction associated with a DNA break.

Beta Particles↗
PubMed2006

Prebiotic homochirality as a critical phenomenon.

The development of prebiotic homochirality on early-Earth or another planetary platform may be viewed as a critical phenomenon. It is shown, in the context of spatio-temporal polymerization reaction networks, that environmental effects--be they temperature surges or other external disruptions--may destroy any net chirality previously produced. In order to understand the emergence of prebiotic homochirality it is important to model the coupling of polymerization reaction networks to different planetary environments.

Evolution, Chemical↗
PubMed2006

Looking for the primordial genetic honeycomb.

All life forms on Earth share the same biological program based on the DNA/RNA genomes and proteins. The genetic information, recorded in the nucleotide sequence of the DNA and RNA molecule, supplies the language of life which is transferred through the different generations, thus ensuring the perpetuation of genetic information on Earth. The presence of a genetic system is absolutely essential to life. Thus, the appearance in an ancestral era of a nucleic acid-like polymer able to undergo Darwinian evolution indicates the beginning of life on our planet. The building of primordial genetic molecules, whatever they were, required the presence of a protected environment, allowing the synthesis and concentration of precursors (nucleotides), their joining into larger molecules (polynucleotides), the protection of forming polymers against degradation (i.e. by cosmic and UV radiation), thus ensuring their persistence in a changing environment, and the expression of the "biological" potential of the molecule (its capacity to self-replicate and evolve). Determining how these steps occurred and how the primordial genetic molecules originated on Earth is a very difficult problem that still must be resolved. It has long been proposed that surface chemistry, i.e. on clay minerals, could have played a crucial role in the prebiotic formation of molecules basic to life. In the present work, we discuss results obtained in different fields that strengthen the hypothesis of a clay-surface-mediated origin of genetic material.

Aluminum Silicates↗
PubMed1994

Mantle hydrocarbons: abiotic or biotic?

Analyses of 227 rocks from fifty localities throughout the world showed that mantle derived rocks such as tectonized peridotites in ophiolite sequences (tectonites) arid peridotite xenoliths in alkali basalts contain heavier hydrocarbons (n-alkanes), whereas igneous rocks produced by magmas such as gabbro arid granite lack them. The occurrence of hydrocarbons indicates that they were not derived either from laboratory contamination or from held contamination; these compounds found in the mantle-derived rocks are called here "mantle hydrocarbons." The existence of hydrocarbons correlates with petrogenesis. For example, peridotite cumulates produced by magmatic differentiation lack hydrocarbons whereas peridotite xenoliths derived from the mantle contain them. Gas chromatographic-mass spectrometric records of the mantle hydrocarbons resemble those of aliphatics in meteorites and in petroleum. Features of the hydrocarbons are that (a) the mantle hydrocarbons reside mainly along grain boundaries and in fluid inclusions of minerals; (b) heavier isoprenoids such as pristane and phytane are present; and (c) delta 13C of the mantle hydrocarbons is uniform (about -27%). Possible origins for the mantle hydrocarbons are as follows. (1) They were in organically synthesized by Fischer-Tropsch type reaction in the mantle. (2) They were delivered by meteorites and comets to the early Earth. (3) They were recycled by subduction. The mantle hydrocarbons in the cases of (1) and (2) are abiogenic and those in (3) are mainly biogenic. It appears that hydrocarbons may survive high pressures and temperatures in the mantle, but they are decomposed into lighter hydrocarbon gases such as CH4 at lower pressures when magmas intrude into the crust; consequently, peridotite cumulates do not contain heavier hydrocarbons but possess hydrocarbon gases up to C4H10.

Carbon Isotopes↗
PubMed1996

Water erosion on Mars and its biologic implications.

The Martian surface shows abundant evidence of water erosion. Liquid water is unstable under present climatic conditions but conditions may have been different in the past. The planet has been volcanically active throughout its history. The combination of water and volcanism must have commonly resulted in hydrothermal environments similar to those in which grow the most primitive terrestrial life-forms.

Atmosphere↗