Up uPCpAp pLpCpUpCpApCpCp

And longer U-oligomers has been demonstrated with predominantly 3 '-5' and 2 '-5' linked products, respectively the different regioselectivities observed in these two papers result from their differing reaction set-ups. (ii) Template-Directed Polymerization on Mineral Surfaces Template-directed RNA polymerization (ImpA on poly(U) and ImpG on poly(C)) can be mediated by several minerals, e.g., by hydroxylapatite and attapulgite, a clay.24 One may reasonably assume that a template-directed...

Sources of Organic Molecules

The surface of Mars is dotted with impacts of meteoritic bodies. Moreover, the older are the surfaces, the more numerous are the impacts and more significant are their sizes. Consequently many bodies coming from the interplanetary medium have hit the surface of Mars, particularly at the beginning of its history.36,37,74 Currently, several hundred tons of objects coming from the interplanetary medium fall on the Earth's surface75-78 and also on the surface of Mars. Analyses oftheir molecular...

Some Historical Background and General Data

Discovered in 1655 by the Dutch astronomer Christiaan Huygens, the largest moon ofSaturn was much later named Titan by John Herschel in the nineteenth century. Observations of limb darkening around the disk of Titan by the Spanish astronomer Jos Comas-Sola in 1908 suggested the presence of an appreciable atmosphere around Titan. This hypothesis was taken seriously into consideration by the British astronomer James Jeans who calculated that a planetary body like Titan can keep a substantial part...

Theory for the Origin of Genes and Introns

It has been proposed that DNA evolved late only after the evolutionary stage of the Last Universal Common Ancestor (LUCA), i.e., only during the establishment of the main phyletic lines.13,14 Based on this proposal, LUCA would have an RNA genome. One ofthe hypotheses compatible with this evolutionary scenario maintains that LUCA possessed a genome made up of pieces of RNA and that one of the major mechanisms that led to the creation of gene products was trans-splicing. In other words, all the...

The Beginning of Life on Earth and the Genetic Code

Sequence analysis ofgenomes ofspecies from all three domains of life showed that primarily proteins related with energy processes and protein synthesis, transcription and replication can be considered to Corresponding Author Knud H. Nierhaus Max-Planck-Institut f r Molekulare Genetik, Ihnestrasse 73, AG Ribosomen, 14195 Berlin, Germany. Email nierhaus molgen.mpg.de Table 2.1. Approximate molecular composition of a bacterial cell. Adapted from reference 23. Approx. Number of Molecules Number of...

RNA Monomers

Although the synthesis of the different RNA monomers from prebiotic molecules is mostly beyond the scope of this chapter (see ref. 2), a quick summary ofresearch efforts on this topic is necessary. The implication of monomer syntheses (or the lack thereof) for the de novo emergence of an RNA World from prebiotic organic mixtures is essential for our discussion. RNA monomers, P-D-ribonucleotides, are rather complex molecules formed by three different types of molecules a nucleobase, a ribose and...

Ribozymes in Replication

The earliest forebears ofgenomes in a putative RNA World would likely have been simple ribozymes that could have replicated themselves from available materials. The earliest and simplest mechanism for replication would in turn likely have involved self-templated Corresponding Author Andrew D. Ellington Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology University of Texas at Austin, Austin, Texas 78712, USA. Email andy.ellington mail.utexas.edu Figure 11.1....

Vesicles and Other Compartments

The notion that compartments are basic structures of life existed in the literature long before the work of Maturana and Varela. Historically, the first models of compartments were the coacervates,10 that are microscopic droplets of proteins and sugars formed by self-assembly, which since they can adsorb small molecules and transform them in a sort of primitive metabolism were supposed to be the precursor of cells. A second attempt to model primitive compartments was made by Fox11 based on...

Europas Ocean

With a diameter of 3120 km, Europa is one of the four largest satellites of Jupiter, the so called Galilean satellites which were discovered by Galileo Galilei in 1610. With the grand tour of the Voyager mission in the outer solar system, a tremendous amount of new information has been obtained on the giant planets and their *Fran ois Raulin LISA, Universit s Paris 12 et Paris 7, CNRS, 61 Av. du G n ral de Gaulle, 94010, Cr teil, France. Email raulin lisa.univ-paris12.fr iron-nch Orr HE dlicati...

RNA Constituents

Prebiotic evolution, as concluded by Orgel, in all likelihood went through an RNA World The demonstration that ribosomalpeptidesynthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World.6 Accordingly extensive research has been directed to the plausible abiotic syntheses of the constituents of RNA. The synthesis ofadenine from hydrogen cyanide by Oro initiated the prebiotic chemistry of nucleic acids.22 Refluxing of ammonium cyanide forms the HCN...

Habitability of Titan

Indeed, although Titan's surface is too cold and the energy available in its environments is not abundant enough to provide conditions of habitability, the subsurface ocean may be suitable for life. As suggested by Fortes24 the possible mean temperature ofthe ocean (260 K and even 300 K in the vicinity of cryovolcanic hotspots), is not an obstacle to the development of living systems. The same is true for the pressure and pH parameters. At a depth of 200 km, the expected pressure in Titan's...

Archean Atmosphere and Climate

The Earths rock record really begins at 3.8 Ga. The period prior to that, which we have been discussing so far, is called the Hadean Era. The period between 3.8 Ga and 2.5 Ga is called the Archean Era. It is still poorly understood compared to more recent time periods however, there are rocks of Archean age on all 7 continents and there is a vast literature describing what those rocks tell us about the Archean atmosphere and climate. We shall not, in this briefchapter, attempt to summarize all...

Introduction

In a prebiotic World, organisms as we currently know them did not exist, but the molecules that carried information and performed catalysis would have arisen during this period of biochemical evolution. Comparative analysis of modern organisms suggests that most biological information is stored in the form of nucleic acids (DNA and RNA), while proteins carry out most catalysis. But was this always the case Obviously, catalysts that enabled the synthesis and decoding of the hereditary material...

Consequences for Potential Biological Activity

All the necessary conditions for the appearance and maintenance of biological activity were thus established on the surface of Mars during the first 700 million years of its history. Although the spontaneous chemical reactions which led to the birth of the first living organisms on Earth are not known and the establishment of Earth-like conditions does not necessarily lead to the appearance of Life, it appears justified to ask, faced with the presence ofEarth-like environmental conditions on...

Optimized Energy Consumption for Protein Synthesis

The synthesis of new proteins is, as we mentioned above, an extremely energy demanding process. Adding up the energy required for (i) the synthesis of a codon, which is the nucleic acid information unit for an amino acid, (ii) the charging reaction of a tRNA by its synthetase with the correct (cognate) amino acid and (iii) the subsequent incorporation of this amino acid into the nascent peptide chain, a total of 10 energy-rich bonds need to be sacrificed. In this context an energy-rich bond...

Theorem of the Polyphyletic Origin of tRNA Genes

The arguments regarding the tRNA split genes of N. equitans can be summarized in a theorem on the nonmonophyletic origin of tRNA genes If the half genes ofN. equitans tRNAs represent the plesiomorphic form of tRNA genes, then the mere observation ofthe existence of such genes in an organism implies that the hypothesis of the monophyletic origin of tRNA is false and the polyphyletic origin oftRNA genes is true. The proofofthis theorem is straightforward. Ifthe monophyletic hypothesis is true,...

Defining Moment of Life

If one is to name the longest running riddle, this one must rank high. All humans pass through life once, cherish it and are always fascinated by it. This fascination is precious common ground for humanity, cutting across all barriers of time, geography and language. For prebiotic evolution, solving the riddle is sheer necessity, for it is impossible to know when prebiotic ends and biotic begins without knowing what biotic means. Some definitions of life go back many decades 63 FG Hopkins in...

Carbonaceous Chondrites and Their Organic Content

Meteorite Organic Macro Mlecule

Carbonaceous chondrite (CC) meteorites are a subgroup of the stony meteorites that take their name from round glassy inclusions, named chondrules and the distinction ofcontaining organic carbon in various percent abundances (about 1-4 ). CC have a primitive elemental composition that is similar to that of the Sun as well as that of the Cosmos overall, since the Sun is a rather average star. They have the appearance ofaggregate rocks (Fig. 6.2), i.e., ofmate-rial packed together without signs of...

Theories Formulated to Explain the Origin of Introns

Three theories have been suggested to explain the origin of introns 4-6 A. The introns late theory suggests that introns and the spliceosome, the cell organelle that splices out the intron from the gene transcript to yield the mature mRNA, first originated in the eukaryotic lineages and, since then, have accumulated in the genomes of eukaryotes.2,5 Sources of new introns include reverse splicing and the insertion of transposable elements.5 B. The introns early theory proposes that the...

Split Genes and Other Characteristics of Nanoarchaeum equitans

Nanoarchaeum equitans, a particularly unusual hyperther-mophilic archaeon, was isolated from a submarine hot vent and subsequently characterised. It is a parasite of another archaeon and displays a number of truly exceptional characteristics, e.g., its ribosomal RNA sequence does not contain the typical oligomeric sequences found in other Archaea. On the basis of the uniqueness of its rRNA sequence, N. equitans has been classified as the first representative of a new phylum of Archaea, the...

Heterotrophic Origin

Autotrophy First There are two schools of thought on whether the first cell was a heterotroph feeding on organic compounds available from environmental sources, or an autotroph using only CO2 and one-carbon compounds from the environment to synthesize all other organic compounds in-house (Fig. 1.3). Prebiotic evolution began with membranes, replicators and metabolites and proceeded to the Last Universal Common Ancestor, or LUCA, from which all extant life descended....

Conclusions

Since the discovery ofcatalytic RNAs in the early 1980s, directed evolution experiments have provided experimental validations of theoretical constructs of early evolution. Evolved ribozymes have been shown to catalyze many of the reactions that exist in modern metabolism, ultimately lending support to the existence of RNA as an template and catalyst during the transition from prebiotic chemistries to cellular biochemistries. Most importantly, directed evolution experiments demonstrate that...

Conclusion and Further Directions

True RNA amplification by non-enzymatic polymerization, a cornerstone process for the RNA World, remains elusive. However, considerable progress has been made in understanding how RNA fragments could have arisen given a pool of activated monomers and subsequently replicated. Studies have shown that several methodological approaches can support these reactions and yield 30- to 50-mer molecules whose length is compatible with catalytic activity. Furthermore, the replication ofan RNA strand can...

Proteins

Based on fossils, palaeontology has unearthed a magnificent panorama of organisms that populated planet Earth during the fossil-bearing periods starting in the Cambrian period. Further back into the the Precambrian 600 million years ago, the Ediacara fauna discovered near Adelaide in Australia, for example, comprise shell-less specimens of jelly-fish and segmented worms. Still further back in time, fossil microorganisms could be recognized microscopically from their relatively uniform imprints...

Old Debate Young Science

Few human cultures do not ponder the question of the origin of life and try to come up with an answer. The scientific culture is no exception and the search for an explanation has spanned centuries. Up to the end ofthe 17th Century, there was no reason to question the occurrence of spontaneous generation as an explanation of departures from like begetting like in biological reproduction, exemplified by the origin ofparasitic worms such as the fluke inside the human body. This view was...

Autopoieis and the Logic of Cellular Life

Cell's life is the starting point for the development ofautopoiesis (from Greek auto self, poiesis production), introduced in the Seventies by the two Chilean biologists Humberto R. Maturana and Francisco J. Varela.2,3,7 Autopoiesis does not concern the origins of life, but answers instead to the question what is life , analyzing the living organism as it is here and now. In this sense, autopoiesis is a descriptive theory based on phenomenology and starts from the recognition that the main...

RNA Polymerization or Self Condensation of RNA Monomers

To qualify as prebiotically plausible, any RNA polymerization process should likely occur in an aqueous environment or at least be supplied with its reacting species from an aqueous medium, in the presence of a complex mixture of monomers at low initial concentrations, and in the presence of metal-ion catalysts either as dissolved ions or on solid mineral surfaces. Furthermore, the polymerization rates must be higher than the decomposition rates of the polymeric products. This Figure 10.3....

Hypotheses on the Origin of Terrestrial Homochirality

How did this homochirality originate Was homochirality indispensable to the origin and or development of life Was it first widespread or limited These are all Astrobiological questions that have been debated since the time of Pasteur and parallel in mystery those concerning the origin of life. Both biotic and abiotic theories have been put forward.3 Biotic theories propose that life formed from achiral and or racemic molecules and that chiral selection developed and evolved through time, while...

The LUCA Genome

The uncovering of cytochrome deficiency at the LUCA stage based on the ancient six genomes of Mka, Mth, Mja, Pfu, Pab and Pho suggests the use ofthese genomes to define the LUCA genome genes that are present in all of these six genomes may be regarded at first approximation to be constituent genes of the LUCA genome. However, because the Mka-Mth-Mja group and the Pab-Pfu-Pho group have dissimilar modes of energy metabolism, the genes common to the two groups would lack the specific energy...

Transfer RNA

With the search for LUCA based on protein paralogs troubled by artifacts, other biopolymers have to be looked to for sequence information. DNA and ribosomal RNAs are not useful in this regard because there is no DNA or rRNA paralog in cells. This leaves only the tRNAs. A limitation with tRNA sequences has always been that they are too short, containing only about 75 bases, some of which are only semi-variant. Thus the amount of sequence information from any particular tRNA sequence is small....

Ribozymes and Cofactors

Ribozyme Prebiotic

One of the acknowledged benefits of using proteins as catalysts is that the available chemical diversity of the amino acid side chains is much greater than that of the four canonical ribonucleotides. Amino acids enable reactions such as proton exchange near neutral pH (histidine), thiol chemistry (cysteine) and nucleophilic attack (serine). Amino acids also have divergent physicochemical properties and include positively charged moieties (histidine, lysine, arginine) and hydrophobic groups...

Laboratory Work

For a better insight into the most complex and less volatile material, one can also turn to experimental laboratory work. The principle ofsuch experiments is the following from observations of the most abundant species in comae and in the interstellar medium, one can infer the probable composition ofthe nucleus ices. A gaseous sample ofthe key species is deposited under vacuum on a cold substrate and irradiated during or after deposition by UV photons or charged particles. Condensed ices are...

RNA Peptidation

While the evolutionary advantage of switching from ribozymes to enzymes could be straightforward, the switch had to be implemented in compliance with two basic requirements. First, the formation of proteins must strictly obey instructions from the RNA genes, so that the wisdom already accumulated in the RNA sequences through evolution would not be wasted. The system could not afford to twice invent the genes. It followed that a dictionary, or code, had to be developed to translate RNA language...

Coevolution Theory

The coevolution theory (CET) describes the mechanisms that brought about the entry of biosynthetically-derived Phase 2 amino acids into a code initially encoding only the environmentally-derived Phase 1 amino acids and the transfer of codons from Phase 1 to Phase 2 amino acids The structure ofthe codon system is primarily an imprint of theprebioticpathways ofamino-acidformation, which remain recognizable in the enzymicpathways of amino-acid biosynthesis. Consequently the evolution ofthe genetic...

Conclusion

The universal genetic code was constructed in two phases. A predecessor code for environmentally derived Phase 1 amino acids underwent expansion to include biosynthetically derived Phase 2 amino acids. In the process the Phase 2 product amino acids received codons from their Phase 1 precursors. This expansion, by breaking up the original codon domains of the precursors, created a strangely structured code with seemingly irrational features such as the unequal allocations of one to six codons to...

Pathway to the Cell

The study of prebiotic evolution is defined by basic questions that need to be resolved before the emergence of a living cell can be outlined. Besides the questions examined in other chapters of this book, the present chapter addresses the following questions I. Was catalysis essential to life right from the start II. What were the energy requirements for prebiotic evolution III. Which came first membranes, replication or metabolism IV. Which came first heterotrophy or autotrophy Life requires...

Contents

1.1 Old Debate, Young 1.2 The Astrobiological 1.3 Pathway to the 1.4 Heterotrophic 1.5 Defining Moment of 2. The Minimal Markus Pech and Knud H. Nierhaus 2.1. 2.2 Chemical Components of a 2.3 Prokaryotic and Eukaryotic Cells 10 2.4 The Beginning of Life on Earth and the Genetic 2.5 Possibilities of Simplifying the Existing Bacterial Translational Apparatus 14 2.6 Optimized Energy Consumption 3. Planetary Astrobiology The Outer Solar System 18 3.1 Planetary Astrobiology, Habitability and the...

Specific References

The spontaneous generation controversy from Descartes to Oparin. John Hopkins Univ Press 1977. 7. Raulin-Cerceau F. Historical review of the origin of life and astrobiology. In Seckbach J, ed. Origins, Genesis, Evolution and Diversity of Life. Kluwer Academic Publishers, 2004 17-33. 8. Oparin AI translated by Morgulis S . The Origin of Life. MacMillan 1938 109-195. 9. Bada JL, Lazcano A. Prebiotic soup revisiting the Miller experiment. Science 2003 300 745-746. 10. Franck S, von...