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At least 991 records · Page 55Linked to original sources
PubMed2001

Can enantiomorphic crystals like quartz play a role in the origin of homochirality on earth?

This communication reviews the possible actions of enantiomorphic crystals on the surface of Earth as sources of homochirality of organic compounds. The discovery of asymmetric adsorption and asymmetric catalysis involving optically active quartz crystals has led some authors to conclude that this source of asymmetry played an important role as a source of homochirality in nature, a concept that later proved erroneous. Moreover, data regarding the preponderance in nature of l-quartz crystals have been used to confirm calculations of the parity violation energy difference (PVED) for l-quartz and, hence, to explain the prevalence of L-amino acids and D-sugars in living matter. As discussed here, quartz and other enantiomorphs such as sodium chlorate can produce chiral intermediates active in autocatalytical processes. Our most recent compilation of the literature, however, reveals that the distribution of d- and l-quartz crystals at the surface of the Earth when all possible locations are included is quite random. Although quartz can serve as an effective asymmetric inductor in autocatalytic processes, it cannot be the source of homochirality of living matter because of the random occurrence of the two types of enantiomorphs. The calculations of PVED values for quartz therefore lack a sound physical basis.

Crystallization↗
PubMed2003

Titan aerosol analogues: analysis of the nonvolatile tholins.

Laboratory experiments that produced tholins in a simulated Titan atmosphere were conducted. We report the first systematic analyses of these compounds using Fourier-transform ion cyclotron resonance mass spectrometry. The findings suggest surprising simplicity and nonrandomness in the mass distribution and regularity in species clusters. The degree of unsaturation generally increased with increasing molecular weight in a predictable fashion, and nitrogen is proposed as the dominant carrier of unsaturation. In detected compounds with a general formula of C(x)H(y)N(z), the carbon to nitrogen ratio (x/z) varied only slightly within a narrow limit, and decreased with increasing molecular weights. These compounds are of potential prebiotic interest since they sediment to the surface of Titan, and would dissolve readily in transient aqueous pools that might be generated from time to time by impacts and volcanic

Aerosols↗
PubMed2006

Was Earth ever infected by martian biota? Clues from radioresistant bacteria.

Here we propose that the radioresistance (tolerance to ionizing radiation) observed in several terrestrial bacteria has a martian origin. Multiple inconsistencies with the current view of radioresistance as an accidental side effect of tolerance to desiccation are discussed. Experiments carried out 25 years ago were reproduced to demonstrate that "ordinary" bacteria can develop high radioresistance ability after multiple cycles of exposure to high radiation dosages followed by cycles of recovery of the bacterial population. We argue that "natural" cycles of this kind could have taken place only on the martian surface, and we hypothesize that Mars microorganisms could have developed radioresistance in just several million years' time and, subsequently, have undergone transfer to Earth by way of martian meteorites. Our mechanism implies multiple and frequent exchanges of biota between Mars and Earth.

Bacteria↗
PubMedDate not supplied

Characterization of genetic markers for in vitro cell line identification of the marine sponge Axinella corrugata.

The marine sponge Axinella corrugata is being developed as a model organism for in vitro marine invertebrate research. Molecular genetics methods such as DNA fingerprinting [amplified fragment length polymorphism (AFLP) and single-stranded conformation polymorphism (SSCP)] and single-locus DNA sequence analyses were applied to this model to meet the primary objective of identifying positive A. corrugata-specific molecular markers that will aid in verifying cell identity in vitro and distinguish sponge cells from potential microbial contaminants. The extent of intra- and interspecific variation in these markers from geographically distinct samples of A. corrugata and closely related sponge taxa was also assessed. Two novel nuclear loci along with intervening transcribed spacer (ITS) regions of nuclear rRNA were characterized, although the latter appeared to better meet primary marker criteria, such as taxonomic specificity and high frequency of detection (via polymerase chain reaction [PCR]) from different individuals (n > 40) and cell cultures. Phylogenetic and phylogeographic analyses of ITS DNA sequences helped clarify taxonomies and also suggested species boundaries between and among western Atlantic and eastern Atlantic/Indian Ocean A. corrugata and Axinellidae samples. Patterns of genetic variation have important implications for the systematics, evolution, and chemical ecology of A. corrugata and related axinellids and are discussed.

Animals↗
PubMed1977

Wheat embryo mitochondrial 18S ribosomal RNA: evidence for its prokaryotic nature.

We present a catalog of sequences of oligonucleotides produced by T1 ribonuclease digestion of 32P-labeled small-ribosomal-subunit RNA ("18S rRNA) isolated from purified wheat embryo mitochondria. This catalog is compared to catalogs published for prokaryotic and chloroplast 16S rRNAs and to preliminary results for wheat cytosol 18S rRNA. These comparisons indicate that: (1) wheat mitochondrial 18S rRNA is clearly prokaryotic in nature, showing significantly more sequence homology with 16S rRNAs than can be expected to arise by chance (p less than 0.000001); (2) shared oligonucleotide sequences include an especially high proportion of those identified as conserved in the evolution of prokaryotic rRNAs; and (3) wheat embryo mitochondrial and cytosol 18S rRNAs retain no more, and perhaps less, than the minimum sequence homology detectable by this sensitive method. These results argue in favor of an endosymbiotic origin for mitochondria.

Base Sequence↗
PubMed1985

Amino acid sequence of a ferredoxin from thermoacidophilic archaebacterium, Sulfolobus acidocaldarius. Presence of an N6-monomethyllysine and phyletic consideration of archaebacteria.

The amino acid sequence of a ferredoxin from a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius, was determined by a combination of various conventional methods to be as follows: Gly-Ile-Asp-Pro-Tyr-Arg-Thr-His-Lys-Pro-Val-Val-Gly-Asp-Ser-Ser-Gly-His- Lys-Ile -Tyr-Gly-Pro-Val-Glu-Ser-Pro-Lys(Me)-Val-Leu-Gly-Val-His-Gly-Thr-Ile-Val -Gly-Va l-Asp-Phe-Asp-Leu-Cys-Ile-Ala-Asp-Gly-Ser-Cys-Ile-Thr-Ala-Cys-Pro-Val-As n-Val-P he-Gln-Trp-Tyr-Glu-Thr-Pro-Gly-His-Pro-Ala-Ser-Glu-Lys-Lys-Ala-Asp-Pro-V al-Asn- Glu-Gln-Ala-Cys-Ile-Phe-Cys-Met-Ala-Cys-Val-Asn-Val-Cys-Pro-Val-Ala-Ala- Ile-Asp -Val-Lys-Pro-Pro. It was composed of 103 amino acid residues giving a molecular weight of 10,908 excluding Fe and S atoms. This ferredoxin contained an N6-monomethyllysine residue at position 29 which was determined by a comparison of the elution profile of the acid hydrolysates of the protein and peptides on an amino acid analyzer with three methyl derivatives of lysine and also by field desorption mass spectrometry of a purified peptide. The ferredoxin has only 7 cysteine residues, which probably participate in constructing the Fe-S clusters of this ferredoxin, indicating the presence of a unique chelate structure. Comparison of this ferredoxin with other archaebacterial ferredoxins indicated that the archaebacteria might have multiple origins in an evolutionary tree.

Amino Acid Sequence↗
PubMed1994

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

A method has been developed to detect pairs of positions with correlated mutations in protein multiple sequence alignments. The method is based on reconstruction of the phylogenetic tree for a set of sequences and statistical analysis of the distribution of mutations in the branches of the tree. The database of homology-derived protein structures (HSSP) is used as the source of multiple sequence alignments for proteins of known three-dimensional structure. We analyse pairs of positions with correlated mutations in 67 protein families and show quantitatively that the presence of such positions is a typical feature of protein families. A significant but weak tendency is observed for correlated residue pairs to be close in the three-dimensional structure. With further improvements, methods of this type may be useful for the prediction of residue--residue contacts and subsequent prediction of protein structure using distance geometry algorithms. In conclusion, we suggest a new experimental approach to protein structure determination in which selection of functional mutants after random mutagenesis and analysis of correlated mutations provide sufficient proximity constraints for calculation of the protein fold.

Amino Acid Sequence↗
PubMed2003

Contingency and determinism.

Contingency versus determinism is an old, classic issue in the history of science, and certain trends of contemporary science literature appear to be bringing it to the foreground again.

Biological Evolution↗
PubMed1980

The structure of beta-lactamases.

The beta-lactamases are widely distributed in both Gram-positive and Gram-negative bacteria. They all inactivate penicillins and cephalosporins by opening the beta-lactam ring. Many varieties of the enzyme can be distinguished on the basis of their catalytic and molecular properties, but only amino acid sequence determination gives information upon which a molecular phylogeny can be based. The present evidence suggests that the beta-lactamases have a polyphyletic origin. All the beta-lactamases of currently known amino acid sequence belong to one homology group, here called class A enzymes. Class B consists of the mechanistically distinct Bacillus cereus beta-lactamase II, which preliminary partial sequence analysis suggests to be structurally unrelated to the class A enzymes. It is predicted that sequence analysis will show that further classes will need to be created to account for particular beta-lactamases of distinctive molecular and mechanistic properties.

Amino Acid Sequence↗
PubMed1981

Evolution of glycolytic enzymes.

The requirements for glycolysis are examined in relation to other essential metabolic processes in the most primitive organisms. The construction of more complex enzymes from primitive domain building blocks is assessed with respect to glycolytic enzymes. Special attention is given to the evolution of the NAD binding domain in dehydrogenases and the related, frequently observed nucleotide binding domain. An attempt is made to differentiate between convergence and divergence of frequently observed domains. Consideration is given to the structure-function relation of these domains and the development of quaternary structure in later stages of evolution. Some attention is also given to the evolution of the structural adaptation to extreme environments as a means of differentiating between essential functions and specific modifications.

Animals↗
PubMed2006

The prebiotic molecules observed in the interstellar gas.

Over 130 molecules have been identified in the interstellar gas and circumstellar shells, the largest among them is a carbon chain with 13 atoms and molecular weight of 147 (twice that of the simplest amino acid glycine). The high reliability of astronomical identifications, as well as the fairly accurate quantitative analysis which can often be achieved, is emphasized. Glycine itself has been claimed, but a recent analysis indicates that few, if any, of the astronomical radio lines attributed to glycine are actually from that molecule. Polycyclic aromatic hydrocarbons (PAHs) have long been proposed as the source of the unidentified infrared bands between 3 and 16 microm, but no single PAH has been identified in space, partly because PAHs generally have weak or non-existent radio spectra. A remarkable exception is the non-planar corannulene molecule (C20H10) that has a strong radio spectrum; in the rich molecular cloud TMC-1, it is found that less than 10-5 of the carbon is contained in this molecule, suggesting that PAHs are not the dominant large molecules in the interstellar gas, as has been claimed. Owing to inherent spectroscopic limitations, determining the structures of the large molecules in space may require capture of the dust grains, which are continually entering the outer Solar System.

Evolution, Chemical↗
PubMed2006

Physical conditions on the early Earth.

The formation of the Earth as a planet was a large stochastic process in which the rapid assembly of asteroidal-to-Mars-sized bodies was followed by a more extended period of growth through collisions of these objects, facilitated by the gravitational perturbations associated with Jupiter. The Earth's inventory of water and organic molecules may have come from diverse sources, not more than 10% roughly from comets, the rest from asteroidal precursors to chondritic bodies and possibly objects near Earth's orbit for which no representative class of meteorites exists today in laboratory collections. The final assembly of the Earth included a catastrophic impact with a Mars-sized body, ejecting mantle and crustal material to form the Moon, and also devolatilizing part of the Earth. A magma ocean and steam atmosphere (possibly with silica vapour) existed briefly in this period, but terrestrial surface waters were below the critical point within 100 million years after Earth's formation, and liquid water existed continuously on the surface within a few hundred million years. Organic material delivered by comets and asteroids would have survived, in part, this violent early period, but frequent impacts of remaining debris probably prevented the continuous habitability of the Earth for one to several hundred million years. Planetary analogues to or records of this early time when life began include Io (heat flow), Titan (organic chemistry) and Venus (remnant early granites).

Biological Evolution↗
PubMed2006

Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life.

Large deposits of montmorillonite are present on the Earth today and it is believed to have been present at the time of the origin of life and has recently been detected on Mars. It is formed by aqueous weathering of volcanic ash. It catalyses the formation of oligomers of RNA that contain monomer units from 2 to 30-50. Oligomers of this length are formed because this catalyst controls the structure of the oligomers formed and does not generate all possible isomers. Evidence of sequence-, regio- and homochiral selectivity in these oligomers has been obtained. Postulates on the role of selective versus specific catalysts on the origins of life are discussed. An introduction to the origin of life is given with an emphasis on reaction conditions based on the recent data obtained from zircons 4.0-4.5Ga.

Amino Acids↗
PubMed2006

Conditions for the emergence of life on the early Earth: summary and reflections.

This review attempts to situate the emergence of life on the early Earth within the scientific issues of the operational and mechanistic description of life, the conditions and constraints of prebiotic chemistry, together with bottom-up molecular fabrication and biomolecular nanofabrication and top-down miniaturization approaches to the origin of terrestrial life.

Earth, Planet↗
PubMed2006

Transcription and translation in an RNA world.

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). If such a replicase makes a reverse complementary copy of any sequence (including itself), in a simple RNA world, there is no mechanism to prevent self-hybridization. It is proposed that this can be avoided through the synthesis of a parallel complementary copy. The logical consequences of this are pursued and developed in a computer simulation, where the behaviour of the parallel copy is compared to the conventional reverse complementary copy. It is found that the parallel copy is more efficient at higher temperatures (up to 90 degrees C). A model for the ribopolymerase, based on the core of the large subunit (LSU) of the ribosome, is described. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have 'poisoned' the ribopolymerase by cross-reacting with the nucleoside-triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes, it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of aminoacylated tRNA-like products. Using base-pairing interactions, some of these molecules might cross-link two ribopolymerases, giving rise to a precursor of the modern ribosome. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors.

Evolution, Chemical↗