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PubMed1997

Emergence of template-and-sequence-directed (TSD) syntheses: II. A computer simulation model.

The initiation of the bio-geochemical scenario described in Part I serves in the present work as the basis for computer modeling, where the central process of the simulation algorithm. i.e., peptide-catalyzed oligomeric growth, is based on mass action equations. The computer model starts with a minimal system in which catalyzed growth processes of proto-RNA templates and small peptides take place, starting from their building blocks. The emerging populations of random oligomers also include a very small fraction of proto-tRNAs and a small fraction of catalytic peptides. Using simplifying assumptions regarding catalyzed proto-RNA template-replication, as well as selectivity of certain molecules and processes, the proportion of proto-tRNA in the proto-RNA molecular population increases rapidly; it is followed by TSD peptide synthesis, based on an ad hoc genetic code and specific peptide catalysts allocated for this synthesis. Consequently, a feedback system is initiated in which TSD peptides involved in the relevant catalytic reactions of the TSD syntheses also start to accumulate. The initial sporadic formation of TSD peptides is thus replaced gradually by cycles of positive feedback and autocatalysis characterized by accumulation of catalytic peptides and Proto-tRNAs and TSD-Reaction-Takeover. The model system which can be considered a 'toy model' can synthesize its templates and catalysts under a wide range of reaction parameters and initial concentrations, thus demonstrating a robustness which is essential for molecular evolution processes. The critical stage of the buildup of a molecular mechanism for the initiation of a minimal TSD reaction cycle has thus been described; because of the centrality of TSD reaction cycles in biology, it is assumed to be central also in the origin of life processes.

Adenosine Triphosphate↗
PubMed2004

Hydrogen bonding interactions of liposomes simulating cell-cell recognition. A review.

Amphiphiles bearing polar heads with the property to form hydrogen bond(s) exhibit unique organizational and aggregational behaviour. Thus appropriate amphiphilic molecules assemble and form liposomes, which further interact through hydrogen bonding with complementary molecules or liposomal counterparts affording larger and more elaborated aggregates. A number of examples are demonstrating the interaction mode of liposomes and of associated phenomena as related to the structural features of the supramolecular aggregates obtained. The recognition between cells incorporating recognizable amphiphiles in their membranes has shown similarities to the analogous interactions between liposomes. Thus molecular recognition between liposomes can be used in modeling recognitions occurring between cells. Designed experiments in this area can support the Lipid World Model proposed for the origin of life.

Hydrogen Bonding↗
PubMed1998

Selective amplification by auto- and cross-catalysis in a replicating peptide system.

Self-replication has been demonstrated in synthetic chemical systems based on oligonucleotides, peptides and complementary molecules without natural analogues. However, within a living cell virtually no molecule catalyses its own formation, and the search for chemical systems in which both auto- and cross-catalysis can occur has therefore attracted wide interest. One such system, consisting of two self-replicating peptides that catalyse each other's production, has been reported. Here we describe a four-component peptide system that is capable of auto- and cross-catalysis and allows for the selective amplification of one or more of the products by changing the reaction conditions. The ability of this system selectively to amplify one or more molecules in response to changes in environmental conditions such as pH or salt concentration supports the suggestions that self-replicating peptides may have played a role in the origin of life.

Amino Acid Sequence↗
PubMed2003

The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence.

The existence of a correlation between the optimal growth temperature of various organisms and a thermophily index (based on the propensity of amino acids to enter more frequently into the proteins of thermophiles/hyperthermophiles) allows inferences to be made on the mesophilic or thermophilic nature of the last universal common ancestor (LUCA). By reconstructing the ancestral sequences of the various ancestors using methods based on maximum likelihood and maximum parsimony, these sequences can be attributed to the mesophiles or (hyper)thermophiles and the following conclusions can be drawn. (1) There is no evidence that the LUCA might have been a mesophile and observations seem to imply that the LUCA was a thermophile or a hyperthermophile; (2) The ancestors of the Archaea and Bacteria domains seem to be (hyper)thermophiles while that of the Eukarya domain turns out to be a mesophile. These conclusions are independent of both (i) where the root is located on the topology of the universal tree (based on that of the small subunit ribosomal RNA) and (ii) the presence of hyperthermophile bacteria near the node of the Bacteria domain ancestor. These conclusions are easier to interpret in the light of the hypotheses that see the origin of life taking place at a high temperature.

Animals↗
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↗
PubMed1999

Enhanced photolysis of nucleic acid monomers by pyrophosphate in the simulated primitive soup.

In our simulation of the photochemistry of the primitive soup, it was found that yield of chromophore loss of some nucleic acid bases, nucleosides and nucleotides [NA] undergoing ultraviolet radiation by medium pressure mercury lamp [MPML] was enhanced by pyrophosphate and triphosphate whether O2 is present or not. The yield of chromophore loss of guanosine, uracil, 5 CMP, and the derivatives of adenine and thymine was observed to rise with the increase of molar concentration of pyrophosphate in N2-saturated systems. In air-saturated samples, increase in yield of chromophore loss was observed when the concentration of pyrophosphate reaches 5 x 10(-4) M, relative yield of chromophore loss (CL(rel)) coming to maximum in the range from 0.01 to 0.1 M, followed by a slight decline with the further increase of pyrophosphate concentration. The enhancement of photolysis of NA by pyrophosphate was due to the interaction between NA and pyrophosphate radicals photoionized by UV quanta of wavelength less than about 210 nm in the emission spectrum of a MPML. The relevance of this phenomenon to the origin of life has been discussed as well.

Diphosphates↗
PubMedDate not supplied

The sugar model: catalysis by amines and amino acid products.

Ammonia and amines (including amino acids) were shown to catalyze the formation of sugars from formaldehyde and glycolaldehyde, and the subsequent conversion of sugars to carbonylcontaining products under the conditions studied (pH 5.5 and 50 degrees C). Sterically unhindered primary amines were better catalysts than ammonia, secondary amines, and sterically hindered primary amines (i.e. alpha-aminoisobutyric acid). Reactions catalyzed by primary amines initially consumed formaldehyde and glycolaldehyde about 15-20 times faster than an uncatalyzed control reaction. The amine-catalyzed reactions yielded aldotriose (glyceraldehyde), ketotriose (dihydroxyacetone), aldotetroses (erythrose and threose), ketotetrose (erythrulose), pyruvaldehyde, acetaldehyde, glyoxal, pyruvate, glyoxylate, and several unindentified carbonyl products. The concentrations of the carbonyl products, except pyruvate and ketotetrose, initially increased and then declined during the reaction, indicating their ultimate conversion to other products (like larger sugars or pyruvate). The uncatalyzed control reaction yielded no pyruvate or glyoxylate, and only trace amounts of pyruvaldehyde, acetaldehyde and glyoxal. In the presence of 15 mM catalytic primary amine, such as alanine, the rates of triose and pyruvaldehyde of synthesis were about 15-times and 1200-times faster, respectively, than the uncatalyzed reaction. Since previous studies established that alanine is synthesized from glycolaldehyde and formaldehyde via pyruvaldehyde as its direct precursor, the demonstration that the alanine catalyzes the conversion of glycolaldehyde and formaldehyde to pyruvaldehyde indicates that this synthetic pathway is capable of autocatalysis. The relevance of this synthetic process, named the Sugar Model, to the origin of life is discussed.

Acetaldehyde↗
PubMed1992

Chemical studies on the existence of extraterrestrial life.

Although the search for extraterrestrial intelligence has not produced any direct evidence of extraterrestrial life, the emergence of life on Earth, which appears to be controlled by universal laws of physics and chemistry, must have been repeated elsewhere in the universe. The experimental approaches in our laboratory to understand the origin of life on the Earth are summarized in an attempt to obtain a better insight into the chemical basis of extraterrestrial life.

Amino Acids↗
PubMed1992

The use of mineral crystals as bio-markers in the search for life on Mars.

Photographs that depict presumed fluvial features on the martian surface have led geologists to hypothesize that water flowed across the early martian terrain. From this, it has been further hypothesized that the surface and atmospheric conditions on early Mars were similar to those on early Earth. Because the oldest fossil evidence of life on Earth dates back to this early period, at least 3.5 billion years ago, the possibility exists that the early Martian environment could have also been conducive to the origin of life. To investigate this possibility, universal signatures or bio-markers indicative of past (or present) biological activity must be identified for use in the search for life on Mars. Several potentially applicable biomarkers have been identified and include: organics (e.g., specific classes of lipids and hopanes), suites of specific inorganic and organic compounds, as well as the isotopic ratios of C, N, and S. Unfortunately, all of these bio-markers may be of biologic or abiotic origin; these origins are often difficult to distinguish. Thus, the discovery of any one of these compounds alone is not a bio-marker. Because minerals produced under biologic control have distinctive crystallographies, morphologies, and isotopic ratios that distinguishable from abiotically produced minerals with the same chemical composition, and are stable through geologic time, we propose the use of minerals resulting from biologically controlled mineralization processes as bio-markers.

Atmosphere↗
PubMed1985

[The meaning of the genetic code: reconstruction of the stage of prebiologic evolution].

According to a certain order in sets of the two first codon bases, 20 common amino acids can be divided into 5 families each containing 4 amino acids; the corresponding order in the distribution of codon bases can be easily detected, if common amino acids are distributed for the numbers of hydrogen atoms per molecule (Sukhodolets, 1980). In the present paper, the order in the distribution of codon bases is explained on the basis of the hypothesis claiming the prebiological existence of crystalline associates composed of amino acids and bases as free molecules. In these heterogeneous crystalline associates amino acids were analogs to the base douplets and the arrangement of molecules followed a certain rule, namely: 40 protons per molecular complex forming a standard structural compartment. It is proposed that the crystalline associates existed as lyotropic liquid crystals with hydrocarbons as solvent. The genetical code allows to discover two different original crystallization types for bases and amino acids. Therefore, the life possibly originates from combining in the same structure different crystallization patterns, which resulted in formation of a finite crystalline associate.

Amino Acid Sequence↗
PubMed1989

Thermal synthesis and hydrolysis of polyglyceric acid.

Polyglyceric acid was synthesized by thermal condensation of glyceric acid at 80 degrees in the presence and absence of two mole percent of sulfuric acid catalyst. The acid catalyst accelerated the polymerization over 100-fold and made possible the synthesis of insoluble polymers of both L- and DL-glyceric acid by heating for less than 1 day. Racemization of L-glyceric acid yielded less than 1% D-glyceric acid in condensations carried out at 80 degrees C with catalyst for 1 day and without catalyst for 12 days. The condensation of L-glyceric acid yielded an insoluble polymer much more readily than condensation of DL-glyceric acid. Studies of the hydrolysis of poly-DL-glyceric acid revealed that it was considerably more stable under mild acidic conditions compared to neutral pH. The relationship of this study to the origin of life is discussed.

Evolution, Chemical↗
PubMed1999

A case for routine screening of coronary artery origins during echocardiography: fortuitous discovery of a life-threatening coronary anomaly.

Anomalous origin of the left main coronary artery from the right sinus of Valsalva with retropulmonary course is a rare congenital abnormality. It is associated with a high incidence of sudden cardiac death, particularly among young, athletic individuals. Many of these individuals do not have symptoms before sudden death, and the diagnosis is usually made at postmortem examination. We present a case of a 15-year-old boy who was evaluated for a systolic click with routine 2-dimensional echocardiography. The anomalous coronary artery was serendipitously identified, allowing surgical intervention. Coronary artery origin and proximal course should be visualized on routine echocardiography in the pediatric population.

Adolescent↗
PubMed2001

Aging: overview.

Aging is a universal process that began with the origination of life about 3.5 billion years ago. Accumulation of the diverse deleterious changes produced by aging throughout the cells and tissues progressively impairs function and can eventually cause death. Aging changes can be attributed to development, genetic defects, the environment, disease, and an inborn process--the aging process. The chance of death at a given age serves as a measure of the average number of aging changes accumulated by persons of that age, that is, of physiologic age, and the rate of change of this measure as the rate of aging. Chances for death are decreased by improvements in general living conditions. As a result, during the past two millennia average life expectancy at birth (ALE-B), determined by the chances for death, of humans has risen from 30 years, in ancient Rome, to almost 80 years today in the developed countries. Chances for death in the developed countries are now near limiting values and ALE-Bs are approaching plateau values that are 6-9 years less than the potential maximum of about 85 years. Chances for death are now largely determined by the inherent aging process after age 28. Only 1.1% of female cohorts in Sweden die before this age; the remainder die off at an exponentially increasing rate with advancing age. The inherent aging process limits ALE-B to around 85 years, and the maximum life span (MLS) to about 122 years. Past efforts to increase ALE-B did not require an understanding of aging. Such knowledge will be necessary in the future to significantly increase ALE-B and MLS, and to satisfactorily ameliorate the medical, economic, and social problems associated with advancing age. The many theories advanced to account for aging should be used, to the extent it is feasible, to help with these important practical problems, including applications of the free radical theory of aging. Past measures evolved by societies to ensure adequate care for older individuals are rapidly becoming inadequate because of changes in life style, the growing percentage of older people, declining fertility rates, and the diminishing size of the work forces to provide for the elderly. Measures are being advanced to help with this problem. Prospects are bright for further increases in the span of functional life and improvements in the lives of the elderly.

Adult↗
PubMedDate not supplied

[RNA world and its evolution].

The early idea of A. N. Belozersky on the precedence of RNA in the origin of life on Earth is developed. Basing on the present knowledge of functional omnipotence of RNA, the author considers three novel mechanisms that could play a critical role in the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, discovered by A.B. Chetverin, which could result in elongation of primary short oligoribonucleotides and generation of sequence variants for subsequent selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist solid surfaces, in the absence of membranes and any other coats; (3) systematic exponential enrichment of RNA population in functionally "the best" molecules by means of alternately dissolving the colonies upon flooding and forming new ones upon drying a pool ("primordial natural SELEX").

Esterification↗
PubMed2001

Bioastrophysical aspects of low energy ion irradiation of frozen anthracene containing water.

The origin of life on Earth remains a fascinating mystery in spite of many theories existing on this subject. However, it seems that simple prebiotic molecules could play an essential role in the formation of more complex organisms. In our experiment, we synthesized a class of these molecules (quinones) bombarding frozen anthracene containing water with low energy hydrogen ions. This experiment roughly simulated the astrophysical conditions which one can find in the solar system. Thus, we can hypothesize that prebiotic molecules could be created by interaction of the solar wind with interplanetary dust grains. The delivery of these molecules to early Earth may have contributed to the generation of life on our planet.

Anthracenes↗