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A5. Abiotic Synthesis of Genetic Polymers - Biology

A5.  Abiotic Synthesis of Genetic Polymers - Biology


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Abiological synthesis of polymer precursors is a long way from creating genetic polymers like RNA and DNA. This would make the nucleic acid less likely to cleave at the phosphodiester bond with the replacement of a nucleophilic 2' OH with an H, and make the genetic molecule more stable. Synthetics ssTNA can base pair with either RNA, DNA, or itself to form duplexes.

genetics.mgh.harvard.edu/szos...earch-pro.html

Other possible candidate include peptide nucleic acids (PNA). These can also form double stranded structures with DNA, RNA, or PNA single strands. They were initially designed to bind to dsDNA in the major grove forming a triple-stranded structure. Binding could alter DNA activity, possibly by inhibiting transcription, for example. The structure of a single-stranded PNA is shown. Note that the backbone, a polymer of N-(2-aminoethyl)glycine (AEG) which can be made in prebiotic soups, is not charged, making it easier to bind to dsDNA. AEG polymerizes at 100oC to form the backbone.

In addition to changing the backbone, additional bases other than A, C, T, G, and U can be accommodated into dsDNA and ssRNA molecules (Brenner, 2004)

In a recent extension, Pinheiro et al have shown that 6 different foreign backbone architectures can produce xeno-nucleic acids (XNAs) that can be replicated by engineered polymerases which make XNAs from a complementary DNA strand, and a polymerase that can make a complementary copy of DNA from an XNA. XNAs can also be evolved as aptamers to bind specific target molecules. The investigators replaced the deoxyribose and ribose backbone sugar with xenoanalogs (congeners) including 1,5-anhydrohexitol (HNAs), cyclohexene (CeNA), 2'-O,4'-C-methylene-b-D ribose (locked nucleic acids - LNA), L-arabinose (LNA), 2'-fluoro-L-arabinose (FANAs) and threose (TNAs) as shown in the figure below.

Figure: Xeno-nucleic acid sugar congeners

Polymers of these XNA can bind to complementary RNA and DNA and as such act as nuclease-resistant inhibitors of translation and transcription.

Von Kiedrowski, in an experiment similar to the self-replication of peptides described above, has shown that a single stranded 14 mer DNA strand, when immobilized on a surface, can serve as a template for the binding of complementary 7 mers and their conversion to 14 mers. When released by base, this process can occur with exponential growth of the complementary 14 mers. (von Kiedrowski Nature, 396, Nov 1998). Ferris has shown that if the clay montmorillonite is added to an aqueous solution of diadensosine pyrophosphate, polymerization occurs to produce 10 mers which are 85% linked in a 5' to 3' direction.

Contributors

  • Prof. Henry Jakubowski (College of St. Benedict/St. John's University)

Primitive Genetic Polymers

Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles𠅊 situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?

In contemporary life, nucleic acids provide the amino acid sequence information required for protein synthesis, while protein enzymes carry out the catalysis required for nucleic acid synthesis. This mutual dependence has been described as a 𠇌hicken-or-the-egg” dilemma concerning which came first. However, requiring that these biopolymers appeared strictly sequentially may be an overly restrictive preconception—nucleic acids and noncoded peptides may have arisen independently and only later become dependent on each other. Nevertheless, the requirements for the chemical emergence of life would appear simplified if one polymer was initially able to store and transfer information as well as perform selective chemical catalysis—two essential features of life.

The discovery of catalytic RNA molecules in the early 1980s (Kruger et al. 1982 Guerrier-Takada et al. 1983) created widespread interest in an earlier proposal (Woese 1967 Crick 1968 Orgel 1968) that nucleic acids were the first biopolymers of life, as nucleic acids transmit genetic information and could have once been responsible for catalyzing a wide range of reactions. The ever-increasing list of processes that involve RNA in contemporary life continues to strengthen this view (Mandal and Breaker 2004 Gesteland and Atkins 2006). Furthermore, the rule-based one-to-one pairing of complementary bases in a Watson-Crick duplex ( Fig.ਁ ) provides a robust mechanism for information transfer during replication that could have been operative from the advent of oligonucleotides. In contrast, there is no obvious and general mechanism by which the amino acid sequence of a polypeptide can be transferred to a new polypeptide as part of a replication process.

Two base-paired RNA dinucleotide steps with functional units discussed in the text annotated. In contemporary life, the nucleoside linker is phosphate, and the information unit is one of the canonical nucleobases (A, G, C, and U). The contemporary trifunctional moiety, ribose, is coupled via N,O-acetals to the informational unit and via phosphoesters to the nucleoside linker.

If we accept that nucleic acids must have appeared without the aid of coded proteins, we are still faced with the question of how the first nucleic acid molecules came to be. Broadly defined, there are two schools of thought regarding the origin of the earliest nucleic acids. In one school, it is proposed that abiotic chemical processes initially gave rise to nucleotides (i.e., phosphorylated nucleosides), which were then coupled together to yield polymers identical in chemical structure to contemporary RNA. In support of this model, Sutherland presents in his article current progress toward discovering possible chemical pathways for the prebiotic synthesis of RNA mononucleotides, as well as methods for their protein-free polymerization (Sutherland 2010).

A second school of thought, discussed in this article, considers RNA to be a product of evolution, and that a different RNA-like polymer (or proto-RNA) was used by the earliest forms of life. Just as the deoxyribose sugar of DNA was likely the product of Darwinian evolution (selected for the hydrolytic stability it provides this long-lived biopolymer), so, too, might the sugar, phosphate, and bases of RNA have been refined by evolution. In this scenario, a proto-RNA is more likely to have spontaneously formed than RNA, because a proto-RNA could have had more favorable chemical characteristics (e.g., greater availability of precursors and ease of assembly), but such a polymer was eventually replaced, through evolution, by RNA (potentially after several incremental changes), based on functional characteristics (e.g. nucleoside stability, versatility in forming catalytic structures). Thus, contemporary RNA may possess chemical traits that, although optimally suited for contemporary life, may have been ill-suited for the earliest biopolymers, with the converse being true for proto-RNA.


Introduction

Extreme environmental conditions can have a negative impact on plant growth. Much of this decline in production may be explained by abiotic stresses (i.e. unfavorable environmental conditions), which potentially result in cell or tissue damage and/or reduced growth. Considering current climate projections, it is of immense importance to understand the processes that underpin plant growth during changes in our environment ( Mickelbart et al., 2015). Traditionally, these conditions include temperature (either cold or heat), drought, osmotic, salinity, and other non-biotic environmental stresses ( Le Gall et al., 2015). In addition to these stresses, abiotic changes at non-stress levels (e.g. light and temperature fluctuations between day and night conditions) can also influence plant growth. Because of their sessile nature, plants must sense and respond to changes in their environment. One of the most common plant adaptations to environmental changes is differential regulation of growth, to grow either away from adverse conditions or towards more favourable conditions. Plant cells are surrounded by a protective and supportive polysaccharide-based plant cell wall that sustains differential growth during both cell division and cell expansion. Therefore, it is likely that cell wall changes are required for differential growth responses to changing environmental conditions.

Many studies have tracked gene expression patterns, protein levels, and metabolite changes in response to different abiotic conditions in a variety of plants (for example, see table 1 in Le Gall et al., 2015 Kosova et al., 2011). While these reports have generated important information to better understand plant cellular responses to abiotic stresses, we focus this review on potential mechanisms that control plant cell wall changes, in particular the cell wall component cellulose, at the genetic and cell biology levels in the model system Arabidopsis thaliana in response to abiotic stress.

Plant responses to abiotic stress

Different abiotic stresses lead to both general and specific influences on plant growth and development. For example, at elevated temperatures, many plants show altered architecture: in Arabidopsis, hypocotyls and petioles elongate to resemble the morphological response of shade avoidance ( Hua, 2009 Tian et al., 2009). Under high salinity conditions, damage to plants includes reduced leaf expansion, stomatal closure, and reduced photosynthesis, finally leading to biomass loss due to osmotic imbalance ( Zhang and Shi, 2013). In addition, overaccumulation of Na + can induce K + efflux, leading to toxic effects ( Mahajan and Tuteja, 2005 Maathuis et al., 2014). Combinations of abiotic stress can further interact to affect plant physiology ( Suzuki et al., 2014). Drought, salinity, and low temperature can lead to turgor loss via changes in osmotic conditions. Consequently, membranes may become disorganized, proteins may denature, and reactive oxygen species (ROS) can accumulate, leading to oxidative damage ( Krasensky and Jonak, 2012).

In addition to these physiological responses, many abiotic stress conditions induce production of abscisic acid (ABA), which is often referred to as the ‘stress hormone’. ABA functions as a key regulator in the activation of plant adaptation to drought and salinity ( Cutler et al., 2010 Golldack et al., 2014). ABA production and ABA signaling have also been implicated in temperature stress signaling and responses to changes in light conditions or carbon availability ( Ljung et al., 2015), and in non-stress physiological roles, such as stomatal regulation and seed dormancy ( Finkelstein, 2013). Other signals are likely also to play a role in plant responses to abiotic factors, but these are less well characterized ( Yoshida et al., 2014).

At the cellular level, ABA signaling perception and transduction pathways have been extensively reviewed elsewhere ( Cutler et al., 2010 Raghavendra et al., 2010 Finkelstein, 2013). Three different protein classes seem to constitute the core signaling components, namely Pyrabactin Resistance 1 (PYR)/Regulatory Components of ABA Receptors (RCARs), protein phosphatase 2C (PP2C) and PP2A family members, and SNF1-related protein kinase 2s (SnRK2s). However, a number of other proteins have also been implicated in ABA signaling ( Cutler et al., 2010). Other cellular responses include a short-term increase in cytosolic Ca 2+ , production of ROS ( Pei et al., 2000), and activation of kinase cascades and other signaling events. Similar to most other signal transduction pathways, ABA responses eventually lead to changes in gene expression patterns via several well-characterized regulatory elements. Microarray data have shown that many ABA-responsive genes are also differentially regulated during dehydration and salt tolerance. These include protein kinases and phosphatases, regulatory proteins, cell wall proteins, and enzymes that detoxify ROS however, the specific changes that occur in response to ABA can vary between organisms, tissues, and developmental stages ( Nemhauser et al., 2006 Cutler et al., 2010).

The plant cell wall

Plant cell walls are primarily composed of polysaccharides, but also include proteins and other compounds. Cell wall polysaccharides are grouped into three main classes, based on their chemistry: cellulose ( McFarlane et al., 2014), hemicelluloses ( Scheller and Ulvskov, 2010), and pectins ( Atmodjo et al., 2013). The composition of the cell wall can differ between species, organs, tissues, and even developmental stages ( Popper et al., 2011). However, in dicot primary cell walls (i.e. the walls of growing cells that can respond to environmental factors), cellulose is the primary component by weight and the main load-bearing structure ( Zablackis et al., 1995). Cellulose is synthesized at the plasma membrane–cell wall interface by cellulose synthase (CesA) enzymes. The CesAs are organized into a large, multiprotein complex, called the cellulose synthase complex (CSC). The organization of the CSC allows for co-ordinated synthesis of cellulose microfibrils, which are made up of many β-1,4-glucan chains. In the model plant, A. thaliana, cellulose synthesis requires at least three different plasma membrane-localized CesA proteins. CesA1, CesA3, and one of the CesA6-like proteins (CesA2, CesA5, CesA6, and CesA9) are required for cellulose synthesis in primary cell walls, which are actively growing. In contrast, CesA4, CesA7, and CesA8 are required for secondary cell wall synthesis ( McFarlane et al., 2014).

Studies of fluorescent protein-conjugated CesAs have revealed that they are localized to the plasma membrane, the Golgi apparatus, and small subcellular compartments called small CesA-containing compartments (SmaCCs) or microtubule-associated CesA compartments (MASCs) ( Paredez et al., 2006 Crowell et al., 2009 Gutierrez et al., 2009). According to current models of cellulose synthesis, the biochemical activity of the CesAs propels the CSC through the plasma membrane ( McFarlane et al., 2014), and this movement is related to the speed and direction of cellulose microfibril synthesis ( Paredez et al., 2006). Because of the close spatial relationship between the trajectories of CesAs and cortical microtubules, it is hypothezised that cellulose synthesis is guided by microtubules ( Baskin, 2001 Paredez et al., 2006). Indeed, several proteins have been identified that interact with both microtubules and CesAs, and that are required for normal levels of cellulose synthesis ( Bringmann et al., 2012 Li et al., 2012). Presumably, the intracellular CesAs (i.e. Golgi and SmaCC/MASC-localized CesAs) are inactive. These SmaCCS/MASCs may, together with the pH of the trans-Golgi network, control the delivery and recycling of CesAs to and from the plasma membrane ( Luo et al., 2015). Therefore, internalization of active, plasma membrane-localized CSCs might be one mechanism of regulating cellulose synthesis.

As the main load-bearing component of the cell wall in young, actively growing Arabidopsis tissues, cellulose is an important component of cell wall changes required for directional cell expansion in response to changing abiotic conditions. Other cell wall components, such as lignin ( Cano-Delgado et al., 2003 Moura et al., 2010) and matrix polysaccharides ( Sasidharan et al., 2011 Tenhaken, 2015), are clearly altered under biotic and abiotic stresses. Important changes to the cell wall can also be driven by biotic and developmental factors however, these have been reviewed elsewhere (Sanchez- Rodriguez et al., 2010 Hamann, 2012 Bellincampi et al., 2014).


Chapter 26 - The Tree of Life: An Introduction to Biological Diversity

  • The oldest known fossils are 3.5-billion-year-old stromatolites, rocklike structures composed of layers of cyanobacteria and sediment.
  • If bacterial communities existed 3.5 billion years ago, it seems reasonable that life originated much earlier, perhaps 3.9 billion years ago, when Earth first cooled to a temperature where liquid water could exist.

Prokaryotes dominated evolutionary history from 3.5 to 2.0 billion years ago.

  • The early protobionts must have used molecules present in the primitive soup for their growth and replication.
  • Eventually, organisms that could produce all their needed compounds from molecules in their environment replaced these protobionts.
    • A rich variety of autotrophs emerged, some of which could use light energy.
    • These organisms transformed the biosphere of the planet.
    • Representatives from both groups thrive in various environments today.

    Metabolism evolved in prokaryotes.

    • The chemiosmotic mechanism of ATP synthesis is common to all three domains—Bacteria, Archaea, and Eukarya.
      • This is evidence of a relatively early origin of chemiosmosis.
      • The cell would have to spend a large portion of its ATP to regulate internal pH by driving H+ pumps.
      • The first electron transport pumps may have coupled the oxidation of organic acids to the transport of H+ out of the cell.
      • Such anaerobic respiration persists in some present-day prokaryotes.
      • The metabolism of early versions of photosynthesis did not split water and liberate oxygen.
      • Some living prokaryotes display such nonoxygenic photosynthesis.
      • When oxygenic photosynthesis first evolved, the free oxygen it produced likely dissolved in the surrounding water until the seas and lakes became saturated with O2.
      • Additional O2 then reacted with dissolved iron to form the precipitate iron oxide.
      • These marine sediments were the source of banded iron formations, red layers of rock containing iron oxide that are a valuable source of iron ore today.
      • About 2.7 billion years ago, oxygen began accumulating in the atmosphere and terrestrial rocks with oxidized iron formed.
      • The increase in atmospheric oxygen likely doomed many prokaryote groups.
      • Some species survived in habitats that remained anaerobic, where their descendents survive as obligate anaerobes.

      Concept 26.4 Eukaryotic cells arose from symbioses and genetic exchanges between prokaryotes

      • Eukaryotic cells differ in many respects from the smaller cells of bacteria and archaea.
        • Even the simplest single-celled eukaryote is far more complex in structure than any prokaryote.
        • Other fossils that resemble simple, single-celled algae are slightly older (2.2 billion years) but may not be eukaryotic.
        • Traces of molecules similar to cholesterol are found in rocks dating back 2.7 billion years.
          • Such molecules are found only by aerobically respiring eukaryotic cells.
          • If confirmed, this would place the earliest eukaryotes at the same time as the oxygen revolution that changed the Earth’s environment so dramatically.
          • They have no cytoskeleton and are unable to change cell shape.
          • The first eukaryotes may have been predators of other cells.
          • Mitosis made it possible to reproduce the large eukaryotic genome.
          • Meiosis allowed sexual recombination of genes.
          • A process called endosymbiosis probably led to mitochondria and plastids (the general term for chloroplasts and related organelles).
          • The term endosymbiont is used for a cell that lives within a host cell.
          • A heterotrophic host could use nutrients released from photosynthesis.
          • An anaerobic host would have benefited from an aerobic endosymbiont.
          • The theory of serial endosymbiosis supposes that mitochondria evolved before plastids.
          • The inner membranes of both organelles have enzymes and transport systems that are homologous to those in the plasma membranes of modern prokaryotes.
          • Mitochondria and plastids replicate by a splitting process similar to prokaryotic binary fission.
          • Like prokaryotes, each organelle has a single, circular DNA molecule that is not associated with histone.
          • These organelles contain tRNAs, ribosomes, and other molecules needed to transcribe and translate their DNA into protein.
          • Ribosomes of mitochondria and plastids are similar to prokaryotic ribosomes in terms of size, nucleotide sequence, and sensitivity to antibiotics.
          • Comparisons of small-subunit ribosomal RNA from mitochondria, plastids, and various living prokaryotes suggest that a group of bacteria called the alpha proteobacteria are the closest relatives to mitochondria and that cyanobacteria are the closest relatives to plastids.
          • Some mitochondrial and plastic proteins are encoded by the organelle’s DNA, while others are encoded by nuclear genes.
          • Some proteins are combinations of polypeptides encoded by genes in both locations.
          • Some researchers have proposed that the nucleus itself evolved from an endosymbiont.
          • Nuclear genes with close relatives in both bacteria and archaea have been found.
          • These transfers may have taken place during the early evolution of life, or may have happened repeatedly until the present day.
          • The Golgi apparatus and the endoplasmic reticulum may have originated from infoldings of the plasma membrane.
          • The cytoskeletal proteins actin and tubulin have been found in bacteria, where they are involved in pinching off bacterial cells during cell division.
          • These bacterial proteins may provide information about the origin of the eukaryotic cytoskeleton.
          • However, the 9+2 microtubule apparatus of eukaryotic flagella and cilia has not been found in any prokaryotes.

          Concept 26.5 Multicellularity evolved several times in eukaryotes

          • A great range of eukaryotic unicellular forms evolved as the diversity of present-day “protists.”
          • Molecular clocks suggest that the common ancestor of multicellular eukaryotes lived 1.5 billion years ago.
            • The oldest known fossils of multicellular eukaryotes are 1.2 billion years old.
            • Recent fossil finds from China have produced a diversity of algae and animals from 570 million years ago, including beautifully preserved embryos.
            • According to the snowball Earth hypothesis, life would have been confined to deep-sea vents and hot springs or those few locations where enough ice melted for sunlight to penetrate the surface waters of the sea.
            • The first major diversification of multicellular eukaryotic organisms corresponds to the time of the thawing of snowball Earth.
            • Some cells in the colonies became specialized for different functions.
            • Such specialization can be seen in some prokaryotes.
            • For example, certain cells of the filamentous cyanobacterium Nostoc differentiate into nitrogen-fixing cells called heterocysts, which cannot replicate.
            • A multicellular eukaryote generally develops from a single cell, usually a zygote.
            • Cell division and cell differentiation help transform the single cell into a multicellular organism with many types of specialized cells.
            • With increasing cell specialization, specific groups of cells specialized in obtaining nutrients, sensing the environment, etc.
            • This division of function eventually led to the evolution of tissues, organs, and organ systems.

            Animal diversity exploded during the early Cambrian period.

            Plants, fungi, and animals colonized the land about 500 million years ago.

            • The colonization of land was one of the pivotal milestones in the history of life.
              • There is fossil evidence that cyanobacteria and other photosynthetic prokaryotes coated damp terrestrial surfaces well more than a billion years ago.
              • However, macroscopic life in the form of plants, fungi, and animals did not colonize land until about 500 million years ago, during the early Paleozoic era.
              • For example, plants evolved a waterproof coating of wax on their photosynthetic surfaces to slow the loss of water.
              • In the modern world, the roots of most plants are associated with fungi that aid in the absorption of water and nutrients from the soil.
                • The fungi obtain organic nutrients from the plant.
                • Terrestrial vertebrates, which include humans, are called tetrapods because of their four limbs.

                Earth’s continents drift across the planet’s surface on great plates of crust.

                • Earth’s continents drift across the planet’s surface on great plates of crust that float on the hot, underlying mantle.
                  • Plates may slide along the boundary of other plates, pulling apart or pushing against each other.
                  • Mountains and islands are built at plate boundaries or at weak points on the plates.
                  • About 250 million years ago, near the end of the Paleozoic era, all the continental landmasses came together into a supercontinent called Pangaea.
                  • Ocean basins deepened, sea level lowered, and shallow coastal seas drained.
                    • Many marine species living in shallow waters were driven extinct by the loss of habitat.
                    • As the continents drifted apart, each became a separate evolutionary arena with lineages of plants and animals that diverged from those on other continents.
                    • Australian flora and fauna contrast sharply from that of the rest of the world.
                      • Marsupial mammals fill ecological roles in Australia analogous to those filled by placental mammals on other continents.
                      • In Australia, marsupials diversified and the few early eutherians became extinct.
                      • On other continents, marsupials became extinct and eutherians diversified.

                      Concept 26.6 New information has revised our understanding of the tree of life

                      • In recent decades, molecular data have provided new insights into the evolutionary relationships of life’s diverse forms.
                      • The first taxonomic schemes divided organisms into plant and animal kingdoms.
                      • In 1969, R. H. Whittaker argued for a five-kingdom system: Monera, Protista, Plantae, Fungi, and Animalia.
                        • The five-kingdom system recognized that there are two fundamentally different types of cells: prokaryotic (the kingdom Monera) and eukaryotic (the other four kingdoms).
                        • Plants are autotrophic, making organic food by photosynthesis.
                        • Most fungi are decomposers with extracellular digestion and absorptive nutrition.
                        • Most animals ingest food and digest it within specialized cavities.
                        • Most protists are unicellular.
                        • However, some multicellular organisms, such as seaweeds, were included in Protista because of their relationships to specific unicellular protists.
                        • The five-kingdom system prevailed in biology for more than 20 years.
                        • These data led to the three-domain system of Bacteria, Archaea, and Eukarya as “superkingdoms.”
                        • Bacteria differ from Archaea in many key structural, biochemical, and physiological characteristics.
                        • Molecular systematics and cladistics have shown that the Protista is not monophyletic.
                        • Some of these organisms have been split among five or more new kingdoms.
                        • Others have been assigned to the Plantae, Fungi, or Animalia.
                        • New data, including the discovery of new groups, will lead to further taxonomic remodeling.
                        • Keep in mind that phylogenetic trees and taxonomic groupings are hypotheses that fit the best available data.

                        Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 26-1


                        Handbook of Biodegradable Polymers: Isolation, Synthesis, Characterization and Applications

                        Andreas Lendlein is Director of the Institute of Polymer Research at Helmholtz-Zentrum Geesthacht in Teltow, Germany, and serves on the Board of Directors of the Berlin-Brandenburg Center for Regenerative Therapies, Berlin. He is Professor for Materials in Life Sciences
                        at University of Potsdam and Professor in Chemistry at the Freie Universitat Berlin as well as member of the medical faculty of Charite University Medicine Berlin. His research interests in macromolecular chemistry and material science are polymer-based biomaterials with special emphasis given to multifunctional materials, stimuli-sensitive polymers, especially shape-memory polymers, and biomimetic polymers. Furthermore, he explores potential applications of such biomaterials in biofunctional implants, controlled drug delivery systems, and regenerative therapies. He completed his habilitation in Macromolecular Chemistry in 2002 at the RWTH Aachen University, worked as a visiting scientist at the Massachusetts Institute of Technology, and received his doctoral degree in Materials Science from Swiss Federal Institute of Technology (ETH) in Zurich in 1996. Andreas Lendlein received more than 20 awards for his scientific work, and his achievements as an entrepreneur including the BioFUTURE Award in 1998, the 2000 Hermann-Schnell Award and the World Technology Network Award in the category Health & Medicine in 2005. He has published more than 220 papers in journals and books, and is an inventor of more than 250 published patents and patent applications.

                        Adam Sisson received his PhD in Supramolecular Chemistry in 2005 under the guidance of Professor Anthony Davis at the University of Bristol, UK. Following this, he moved into the group of Professor Stefan Matile at the University of Geneva, Switzerland, to conduct postdoctoral
                        research in self-assembling nanomaterials. In 2007 he embarked upon research into polymeric nanogels as an Alexander von Humboldt Stiftung sponsored research fellow with Professor Rainer Haag at the Free University of Berlin, Germany. Since 2010 he is leading a Junior research group "Cell and Tissue Specific Materials" at the Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Geesthacht in Teltow, Germany. His research interests focus on studying and manipulating the interactions of synthetic materials with various
                        biological moieties in a range of applications.


                        Test Prep for AP® Courses

                        Consider these microbial mats, which grow over a hydrothermal vent. Determine which of the following pieces of evidence best supports the alternative scenario of early life formation, in which organic compounds on early Earth formed near submerged volcanoes.

                        1. Some prokaryotes that live near deep-sea vents today use hydrogen as an energy source.
                        2. Fossilized stromatolites that are 3.5 billion years old are found near deep-sea vents.
                        3. Extremophiles that exist today live in a variety of extreme environments, including those that are high in salinity.
                        4. The chemical composition of water around deep-sea vents is the same as it was on early Earth.
                        1. The lack of organic compounds without the sparks indicates that complex organic components are formed from less complex biotic components subjected to solar radiation.
                        2. The first trial of the experiment must have been done incorrectly.
                        3. Abiotic molecules can only develop into organic molecules in the presence of oxygen, so oxygen should be added.
                        4. Lightning, or some form of energy, is needed for the inorganic molecules in the atmosphere to interact with each other. This indicates that a similar energy source was present on early Earth that stimulated the interaction and development.
                        1. Analysis of the chemical composition of meteorites sometimes yields amino acids.
                        2. A hydrothermal vent in the Sea of Cortés releases hydrogen sulfide and iron sulfide.
                        3. Researchers dripped solutions of amino acids onto hot surfaces to produce amino acid polymers.
                        4. Some present-day prokaryotes live and reproduce in very extreme and unforgiving environments, such as the Arctic.

                        Which of the following cell types does Figure 22.10 illustrate?

                        1. Ribosomes are the sites of protein synthesis found in prokaryotic and eukaryotic cells. The cell wall is a protective layer, typical in prokaryotic cells and in some eukaryotes. Chromosomal DNA, the genetic material of the cell, is present in a nucleoid region in prokaryotes while enclosed in a nucleus in eukaryotes.
                        2. Ribosomes are the sites of protein synthesis found in prokaryotic and eukaryotic cells. The cell wall is a protective layer found in some prokaryotic and eukaryotic cells. Chromosomal DNA is the genetic material of the cell, enclosed in a nucleus in prokaryotes while present in a nucleoid region in eukaryotes.
                        3. Ribosomes are the sites of ATP production found in both prokaryotic and eukaryotic cells. The cell wall is a protective layer, typically found in prokaryotic cells and in some eukaryotes. Chromosomal DNA is present in a nucleoid region in both eukaryotes and prokaryotes. It is the genetic material of the cell.
                        4. Ribosomes are the sites of protein synthesis found in prokaryotic and eukaryotic cells. The cell wall is a protective layer, typically found in prokaryotic cells but not in eukaryotes. Chromosomal DNA, the genetic material of the cell, is present in the nucleus in prokaryotes, while it is enclosed in a nucleoid region in eukaryotes.
                        1. Genes for antibiotic resistance are transferred from the nonpathogenic bacterium to a pathogenic bacterium via transduction.
                        2. Genes for antibiotic resistance are transferred from the nonpathogenic bacterium to a pathogenic bacterium via transformation.
                        3. Genes for antibiotic resistance are transferred from the nonpathogenic bacterium to a pathogenic bacterium via conjugation.
                        4. Genes for antibiotic resistance are transferred from the nonpathogenic bacterium to a pathogenic bacterium via binary fission.
                        1. A population including individuals capable of conjugation would be more successful because all of its members would form recombinant cells having new gene combinations advantageous in a new environment.
                        2. A population including individuals capable of conjugation would be more successful because some members could form recombinant cells having new gene combinations advantageous in a new environment.
                        3. A population including individuals not capable of conjugation would be more successful because the members undergoing conjugation would form new recombinant cells having gene combinations lethal in the new environment.
                        4. A population including individuals not capable of conjugation would be more successful because conjugation will result in an increase in genetic diversity of the prokaryotic population, which will be disadvantageous in a new population.

                        Review the diagram, which summarizes results of an experiment using different preparations of E. coli grown either in the presence or the absence of the antibioitc ampicillin. Identify the plate or plates on which only ampicillin-resistant bacteria grow.

                        Evaluate the diagram, which summarizes the findings of an experiment with E.coli. Apply your understanding of the experiment and of bacterial genetic recombination to explain why there are fewer colonies on plate IV than on plate III.

                        1. All E.coli cells were not successfully transformed on plate IV.
                        2. The nutrient agar medium inhibited the growth of some bacteria on plate IV.
                        3. All E.coli cells were successfully transformed on plate IV.
                        4. The bacteria on plate III were naturally resistant to ampicillin.

                        Consider the identity of the labeled structures within a cell. Determine which of the structures allows you to positively identify the cell as a prokaryote.

                        1. Have metabolic pathways evolved separately in Bacteria and Archaea?
                        2. Should all methanogens be classed as Archaea in evolutionary phylogeny?
                        3. Have methanogens evolved to live in both moderate and extreme environments?
                        4. Did the methanogenic bacteria species also evolve as a strict anaerobe?
                        1. Do archaean methanogens differ from other Archaea structurally, and if so, in what way? Is one or more of these structural differences related to these methanogens’ ability to use H2 to oxidize CO2?
                        2. Do archaean methanogens differ from other Bacteria structurally, and if so, in what way? Is one or more of these structural differences related to these methagens’ ability to use CO2 to oxidize H2?
                        3. Do archaean methanogens differ from other Archaea structurally, and if so, in what way? Is one or more of these structural differences related to these methagens’ ability to use CO2 to oxidize H2?
                        4. Do archaean methanogens differ from other Archaea structurally, and if so, in what way? Is one or more of these structural differences related to these methagens’ ability to use H2O to oxidize H2?
                        1. chemoautotrophs, obligate anaerobes
                        2. chemoheterotrophs, faculative anaerobes
                        3. chemoheterotrophs, obligate anaerobes
                        1. The Strain 2 bacteria increased the availability of potassium in the soil, and this nutrient was needed and used by the seedlings in the soil. The Strain 1 bacteria decreased the availability of potassium in the soil.
                        2. The soil with Strain 1 bacteria must have had more potassium in comparison to soil with Strain 2 bacteria. The seedlings took up more potassium in Soil 1 than in 2 due to this difference.
                        3. The Strain 1 bacteria increased the availability of potassium in the soil, and this nutrient was needed and used by the seedlings in the soil. The Strain 2 bacteria decreased the availability of potassium in the soil.
                        4. The Strain 1 bacteria decreased the availability of potassium in the soil, and this nutrient was needed and used by the seedlings in the soil. The Strain 2 bacteria increased the availability of potassium in the soil.
                        1. The growth in Flask A will exceed that of Flask B.
                        2. The growth in Flask B will exceed that of Flask A.
                        3. The growth in each flask will be about equal.
                        4. There will be little to no growth in each flask.
                        1. The growth between flasks would differ because endospores formed 20 years ago would be more dormant compared to endospores formed 100 years ago, before the marsh was polluted.
                        2. The growth between flasks would differ because endospores formed 20 years ago would be less adapted to polluted conditions compared to endospores formed 100 years ago, before the marsh was polluted.
                        3. The growth between flasks would differ because endospores formed 20 years ago would be more adapted to polluted conditions compared to endospores formed 100 years ago, before the marsh was polluted.
                        4. The growth between flasks would differ because endospores formed 20 years ago would be less dormant compared to endospores formed 100 years ago, before the marsh was polluted.
                        1. The growth in Flask A will continuously exceed that of Flask B.
                        2. The growth in Flask B will continuously exceed that of Flask A.
                        3. The differences in growth between the two flasks will eventually decrease.
                        4. Eventually, there will be little to no growth in each flask.
                        1. Because the endospores formed 20 years ago would evolve resistance to the pollutant fairly quickly. The bacteria in Flask A would die, and the difference in population size of each flask would lessen.
                        2. Because the endospores formed 20 years ago would lose their resistance to the pollutant. The bacteria in Flask A would die, and the difference in population size of each flask would lessen.
                        3. Because the endospores formed 100 years ago, before the marsh was polluted, they would lose their resistance to the pollutant. The bacteria in Flask B would then grow more prolifically, and the difference in population size of each flask would lessen.
                        4. Because the endospores formed 100 years ago, before the marsh was polluted, they would evolve resistance to the pollutant fairly quickly. The bacteria in Flask B would then grow more prolifically, and the difference in population size of each flask would lessen.
                        1. By undergoing genetic recombination through conjugation, transduction, and transformation.
                        2. By undergoing reproduction through binary fission.
                        3. By undergoing genetic recombination through conjugation and transcription.
                        4. Reproduction among bacteria through any mechanism results in the spread of antibiotic resistance genes.
                        1. The wrong course of antibiotics was used on the patients, so the infection was never treated.
                        2. Not all of the bacteria were killed, and the remaining ones reproduced and brought back the symptoms of infection.
                        3. The antibiotics were not prescribed for a long enough time to treat the infection.
                        4. The patients with recurring infection had suffered issues with resistance that made them vulnerable to additional pathogens.
                        1. The diversity would not get altered and would remain the same.
                        2. Species abundance and relative distribution would likely increase.
                        3. Depending on the changes, species abundance and relative distribution may change.
                        4. Species abundance and relative distribution would likely decrease.
                        1. In some cases it is commensal and in others it is parasitic.
                        2. In some cases it is mutualistic and in others it is commensalistic.
                        3. It is almost always parasitic.
                        4. It is almost always mutualistic.

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                          • Book title: Biology for AP® Courses
                          • Publication date: Mar 8, 2018
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                          Future perspectives

                          Extracellular polymers that are produced by bacterial pathogens are major virulence factors. Thus, inhibition of their biosynthesis pathways represents a strategy for the treatment of bacterial infections. Owing to rising rates of antimicrobial resistance, the development of novel strategies to fight bacterial infections is in high demand. Insights into the synthesis, secretion and regulation of biopolymers will disclose new and specific targets suitable for drug discovery for example, for targets that weaken bacterial defences against the host immune defences or antimicrobial treatment (Fig. 5).

                          Polymers that are produced by non-pathogenic bacteria are considered safe materials for a range of applications. Despite great advances in the design of cell factories for enhanced biopolymer production as well as production of tailored biopolymers, challenges remain. Because of a plethora of interacting components and multiple feedback loops in complex biological systems, rational engineering of novel GRAS-certified cell factories and biopolymers remains challenging. It is important to reduce this complexity through systems biology to better inform genome-scale metabolic models, metabolic network modelling and computational simulations of large data sets that feed into synthetic biology approaches. This work will provide the foundation for efficient bioengineering strategies and accurate predictions for cell factory and bioprocess development.

                          In this Review, we have highlighted the advances in understanding the roles of bacterial biopolymers in pathogenesis and their current and potential applications as bio-based materials. We hope that this Review will guide both drug discovery programmes and the development of new bio-based materials by outlining strategies to overcome pitfalls and challenges associated with biopolymers as virulence factors and as innovative bio-based materials.


                          Abstract

                          In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection. Unfortunately, the presence of manganese ions in the transcription mixture leads to the misincorporation of tGTP nucleotides opposite dG residues in the templating strand, which are detected as G-to-C transversions when the TNA is reverse transcribed back into DNA. Here we report the synthesis and fidelity of TNA replication using 7-deaza-7-modified guanosine base analogues in the DNA template and incoming TNA nucleoside triphosphate. Our findings reveal that tGTP misincorporation occurs via a Hoogsteen base pair in which the incoming tGTP residue adopts a syn conformation with respect to the sugar. Substitution of tGTP for 7-deaza-7-phenyl tGTP enabled the synthesis of TNA polymers with >99% overall fidelity. A TNA library containing the 7-deaza-7-phenyl guanine analogue was used to evolve a biologically stable TNA aptamer that binds to HIV reverse transcriptase with low nanomolar affinity.


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                          An Astrobiology Strategy for the Exploration of Mars (2007)

                          Life as we know it (i.e., terran life, as discussed in Chapter 1) is based on organic chemistry and is constructed of carbonaceous compounds. These organic materials are pervasive in Earth&rsquos crust and constitute an extensive chemical and isotopic record of past life that far exceeds what is recorded by visible fossils. 1 The ubiquity of coal, organic-rich black shales, and petroleum hydrocarbons, for example, is one manifestation of life&rsquos activities that extends deep into the geological record and can be used to observe past biological activity and events. 2 In fact, biogenic organic matter is so ubiquitous and overwhelming in its abundance that it is exceedingly difficult to identify organic compounds and organic matter of unambiguously nonbiological origin. The notable exceptions are organic compounds in meteorites and synthetics. 3

                          Experience with studies of terrestrial materials suggests that of all the various life-detection techniques available, analysis of carbon chemistry is the first among equals. Imaging and other life-detection techniques are important and will always be part and parcel of planetary exploration, but few would assert that any single methodology provides a more robust way to find extraterrestrial life than organic analysis. Accordingly, the prime emphasis here is on chemical methods for life detection. However, organic analysis alone is insufficient to detect life. The results from an ensemble of all of the relevant methodologies, combined with considerations of geological and environmental plausibility, will likely provide the best evidence for the presence or absence of life in a sample.

                          Although all of the assumed characteristics of hypothetical martian life forms discussed in Chapter 1 can inform and guide the overall search for biosignatures, the assumption concerning the key role likely to be played by organic chemistry will prove to be particularly important. This assumption implies that martian organisms would produce and use a wide range of small molecules and organic polymers that could serve as chemical biosignatures in their intact or fragmentary states. But to apply this knowledge for remote sensing experiments on Mars or other planetary bodies, astrobologists need to distinguish reliably between biological molecules and those that are nonbiological in origin. The following discussion identifies specific features that distinguish abiotic compounds from compounds or patterns produced by present-day life on Earth. To address the past geocentric focus, the discussion

                          considers some generic features that could not be generated abiologically and that would be the foundation of a sound approach to the recognition of nonterran life.

                          ABIOTIC CHEMISTRY

                          Abiotic chemistry, both organic and inorganic, provides important information about the pathways that might have led toward an origin of life. Unfortunately, there is in origin-of-life scenarios no consensus about the synthesis of organics on early Earth or elsewhere, and so astrobiologists cannot search for a specific chemistry. Among the models suggested as possibly relevant for the origin of life are atmospheric electric discharges, as proposed by Miller and Urey, 4 which have been shown to synthesize a range of organic compounds, including amino acids, from mixtures of methane, ammonia, and water. Discharge experiments yield few organic compounds when carried out in the kinds of oxidized gas mixtures of carbon dioxide thought to have predominated on early Mars. Additional processes that might have contributed to the inventory of organic compounds on early Mars include those associated with the transient effects of bolide impacts 5 and, more importantly, a variety of mineral-catalyzed chemical reactions including water-rock reactions (e.g., serpentinization) and Strecker, Fischer-Tropsch, and FeS-driven organic synthesis. 6 Water-rock reactions produce copious amounts of hydrogen that could lead to the subsurface formation of hydrocarbons from carbon dioxide and have also been shown to reduce nitrogen to ammonia, 7 both of which could make their way to planetary surfaces. Strecker synthesis is the reaction of ammonia, hydrogen cyanide, and aldehydes to give amino acids and related products. Fischer-Tropsch chemistry is the mineral-catalyzed high-temperature reaction of carbon monoxide and hydrogen to give hydrocarbons. FeS-driven organic synthesis, first proposed by Wächtershäuser, 8 , 9 has been experimentally demonstrated for only a relatively limited set of syntheses.

                          It is safe to assume that organic compounds that might have contributed to the prebiotic potential of the planet could have been synthesized elsewhere in the solar system or in interstellar space and then carried to the surface of Mars via carbonaceous chondrites and interplanetary dust particles. Since there is no consensus about the past history of prebiotic processes on Mars, it is more constructive to first consider the availability of the elements that constitute organic matter.

                          Carbon. C is found as gaseous carbon dioxide in the martian atmosphere, as carbon dioxide ice, and as carbonate minerals. Carbonates have been found in small amounts in martian meteorites but have not been detected in significant quantities by orbital remote sensing techniques or in chemical analyses of the martian regolith by landers.

                          Hydrogen. H is present as water ice and vapor and in hydrated minerals, and may be present within the crust as liquid water. The high D/H ratios of martian water show that Mars has lost a fraction of its water to space from the upper atmosphere. Because of the low atmospheric pressure, liquid water is not stable at the surface of modern Mars. The polar ice caps are thought to contain significant quantities of water ice, and the Gamma Ray Spectrometer on the Mars Odyssey spacecraft has detected significant quantities of subsurface hydrogen, presumably in the form of water ice. 10 Thus, the abundance of hydrogen would not have hindered life on Mars at any time in its history.

                          Nitrogen. N is poorly retained by the inner planets owing to its volatility and stability as N2 and also to the relative instability and solubility of its involatile forms. Currently, 2.7 percent of the martian atmosphere is nitrogen. Although nitrogen is crucial for life, it may be rare on Mars. 11 The observed ratio of 15 N/ 14 N suggests that a large fraction of the planet&rsquos nitrogen inventory has been lost to space. No measurements have yet identified nitrogen stored in surface or subsurface minerals.

                          Oxygen. O is present in H2O and CO2, in oxides and sulfate minerals on the highly oxidized surface, and in silicates and other minerals within the crust.

                          Phosphorus. Phosphate minerals are actually more abundant in meteorites than in most igneous rocks on Earth. Volatile compounds of phosphorus (phosphorus pentoxide and phosphine) are rare, making phosphate minerals more valuable as sources of phosphorus for organisms than other biotic elements with common volatile forms.

                          Sulfur. S is very abundant as sulfates at the martian surface, and sulfides are common accessory minerals in martian meteorites and, presumably, the martian crust. Isotopic measurements suggest that sulfur species are also present in the martian atmosphere. 12

                          Other metals. Metal ions such as are required by biological systems&mdashMg, Ca, Na, K, and transition elements&mdashare abundant in martian surface rocks and, presumably, in subsurface rocks as well.

                          TERRAN BIOSIGNATURES AND POTENTIAL MARTIAN BIOSIGNATURES

                          Molecular Biosignatures

                          The carbon chemistry of terran organisms is well understood. Researchers have detailed knowledge of the metabolic and reproductive machinery of many living organisms and can recognize the residual chemicals long after life has expired. Chemistry provides many tools for identifying extant and fossil carbon-based life on Earth and, potentially, throughout the universe.

                          At the most basic level, researchers can examine the elemental composition of bulk organic matter preserved on Mars or in returned Mars samples as an indicator of biogenicity. On Earth, all organisms are composed largely of the six elements&mdashC, H, N, O, P, and S&mdashwhose abundances are discussed above and in Chapter 2. Their proportions vary between organisms and ecosystems. 13 Mechanisms and pathways involved in preservation can change these ratios for example, N and P decline significantly during fossilization. Nevertheless, the discovery in a Mars sediment sample of organic matter with significant abundances of N, O, P, and S would indicate a similarity to biological material on Earth. The relative scarcity of N (see previous section) combined with the key role it plays in biological processes suggests that organic nitrogen compounds would be an important potential biosignature. 14

                          Organic geochemists coined the term &ldquobiological marker compound&rdquo or &ldquobiomarker&rdquo to describe individual organic compounds that serve as molecular biosignatures. 15 &ndash 17 Biomarkers comprise a spectrum of biomolecules spanning those that are present in living systems (biomarkers for extant life), structurally-related fossil derivatives that have been preserved in sediments (biomarkers for past life), or complex chemicals that have generic traits characteristic of biology but for which no precursor organism is known (sometimes called orphan biomarkers). The last set could include molecules derived from unrecognized terran life (present or past) or extraterrestrial life.

                          Biomolecules commonly show a huge diversity of chemical structures. However, unambiguous identification of something as chemically complex and biology-specific as DNA, a protein, a phospholipid, a steroid, or even a select set of small molecules would be difficult to refute as a successful life-detection experiment. Such a set of select small molecules might include some of the 20 protein amino acids in large excess over their nonprotein counterparts, some sugars, or a select group of fatty acids such as might be found in the polar lipids of contemporary organisms. While nucleic acids, proteins, carbohydrates, and intermediary metabolites are essential components of life, and obviously potential molecular biosignatures, compounds in these classes are rapidly recycled by other living systems and are chemically fragile. On Earth, they are not known for their ability to survive intact over geological timescales.

                          Lipids and structural biopolymers are biologically essential classes of compounds renowned for their stability under harsh environmental conditions. 18 Hydrocarbons, for example, are a class of lipid known to be stable on Earth over billion-year timescales. 19 , 20 Furthermore, their chemical structures can be as diagnostic for biology as those of amino acids or other biomolecules. Thermodynamic arguments suggest that the lower temperatures on Mars would aid in the preservation of hydrocarbons. The specific empirical evidence for this comes from observations of petroleum deposits on Earth: high-temperature reservoirs show enhanced hydrocarbon cracking (i.e., more gas and gasoline-grade hydrocarbons) compared to equivalent low-temperature reservoirs.

                          Several important molecular biosignatures result from the propensity of molecules containing just a few carbon atoms to exist in different chemical and structural configurations, known as isomers. In other words, isomers are molecules having the same number of atoms of each element (i.e., their chemical formulas are the same), but exhibiting different connectivities between, and/or spatial arrangements of, their constituent atoms. In the simplest of cases, isomers of the same compound might be chemically identical but differ in their ability to rotate polarized light (e.g., the chirality of amino acids, as described in Box 3.1). In more complex examples, the connectivity and

                          spatial arrangements of atoms in organic molecules might give rise to compounds with very different chemical and physical characteristics (e.g., the diastereoisomers and structural isomers described in Boxes 3.2 and 3.3, respectively). All of these properties can unambiguously indicate biological origins because living systems frequently make use of just one of the multiple isomers that can exist for any given molecule. 21 , 22

                          Another important set of molecular biosignatures can be identified, based on the observation that all known organisms utilize a universal subset of small metabolites as generic building blocks for constructing biomass and more complex biomolecules. 23 The 20 amino acids of proteins, the four nucleotides of DNA, and the acetate precursor of most lipids are prime examples of generic building blocks. This simple fact, so fundamental to life on Earth, leads to patterns in the molecules of life and in the molecular remains of past life. This is in stark contrast to organic compounds produced in abiotic processes, which have structures and distributions with distinctly different patterns more likely to reflect thermodynamic controls. For any class of organic compounds, biosynthesis results in recurring patterns, readily recognizable to organic chemists. Detection of particular patterns (e.g., biomolecules with a preference for even or odd numbers of carbon atoms, as described in Box 3.4) and recurring themes (e.g., families of related molecules with a limited subset of all the possible numbers of carbon atoms, as described in Box 3.5) in small to moderate-sized organic molecules could lead to the validation of biosignatures for both terran and, possibly, nonterran life.

                          Taken together, these various chemical characteristics have led researchers to identify the following generic molecular biosignatures for carbon-based life:

                          Diastereoisomeric preference (see Box 3.2),

                          Structural isomer preference (see Box 3.3),

                          Repeating structural subunits or atomic ratios (see Box 3.4), and

                          Uneven distribution patterns or clusters of structurally related compounds (see Box 3.5).

                          In summary, any family of organic molecules common to Earthly life (e.g., lipids) if discovered on Mars would be important biological markers. However, at a more basic level, patterns of carbon number, or limited isomer distributions, or, isotopic composition (see next section), consistent with synthesis from small, repeating precursor molecules may point the way to the detection of extraterrestrial life be it terran or non-terran in its biological architecture.

                          Isotopic Biosignatures

                          The elements that are most important in organic chemistry all have multiple isotopes. The isotopic patterns of these elements and, increasingly, of transition metals can constitute biosignatures in terran samples. This is the case because kinetically controlled isotopic fractionations are common in biology and can be significant and dominant over equilibrium fractionation. Although geological processes fractionate these isotopes, biological processes tend to produce different, and sometimes diagnostic, effects. For example, enzymes involved in carbon fixation, methanogenesis, methane oxidation, sulfate reduction, and denitrification impose significant fractionations between precursor and product for carbon, hydrogen, sulfur, and nitrogen. Depletions or enrichments of certain isotopes from expected values can be used as biosignatures. However, such fractionations can reveal biological activity only if all the various components of a system are available for measurement and open system behavior has operated.

                          No fractionations will be observed if all of a precursor is converted to a product, regardless of whether equilibrium or kinetic fractionations operate. Furthermore, for an isotopic biosignature to be sound, the components of the system must be preserved intact without subsequent fractionation by physical or chemical processes. A myth commonly perpetuated is that a C-isotopic signature in organic carbon compounds of &minus20&permil to &minus80&permil is diagnostic of biology irrespective of any other factor. The 13 C-composition in organic compounds can be a biosignature only if the isotopic composition of the precursor carbon source is also known and, importantly, if the pedigree of the materials is also consistent with biological processes. These issues have made biological interpretations of

                          An important property of carbon compounds is that the same atoms can bond to each other in the same manner while assuming different configurations in space. The different three-dimensional arrangements of organic molecules having the same chemical and structural formulas can lead to a number of important properties relevant to the study of biomarkers. One of these properties is chirality. That is, some molecules have their component atoms arranged in two different spatial configurations that are mirror images of each other. If the mirror images are not superimposable one upon the other, then the molecule is said to be chiral and its two structural forms are called enantiomers (Figure 3.1.1).

                          The vast preponderance of biologically formed chiral compounds are synthesized exclusively as one or the other enantiomer for example, right-handed sugars and left-handed amino acids are the norm in biological systems. This phenomenon is known as homochirality. Some organisms, bacteria for example, may synthesize the same chiral compound in different enantiomeric forms. Once the organism dies, and its biochemicals are released into the environment, their chiral purity may or may not persist depending on the relative stability of the chemical bonds in the enantiomers. Various natural chemical processes can lead to racemization, the formation of mixtures of the two enantiomers. Although racemization may result in loss or corruption of a biological signature, the rate at which it happens can also have a practical application, such as in the dating of fossil organic matter using the degree of amino acid racemization. Amino acids with a slight chiral excess of, presumably, abiotic origin occur in meteorites. 1 , 2 Nevertheless, biology is the most likely source of compounds that occur purely or predominantly as one enantiomer.

                          Enantiomeric excess can be detected in a number of ways. Chiral compounds are optically active. That is, they rotate the plane of polarized light passing through them when in solution. Direct observation of optical activity is cumbersome. Biochemical detection of enantiomeric excess is possible, but the methodologies are generally specific to individual compounds or compound types. The most widely applicable and sensitive techniques involve indirect measurement through gas chromatography or gas chromatography-mass spectrometry.

                          1 J.R. Cronin and S. Pizzarello, &ldquoEnantiomeric Excesses in Meteoritic Amino Acids,&rdquo Science 275:951-955, 1997.

                          2 M.H. Engel and S.A. Macko, eds., Organic Geochemistry Principles and Applications, Plenum Press, New York, 1993.

                          FIGURE 3.1.1 The atoms in the &alpha-amino acid alanine can assume two different configurations in three-dimensional space. The two forms, L-alanine and D-alanine, are called enantiomers because they are non-superimposable mirror images of each other. Abiotic processes produce equal mixtures of both L and D enantiomers, but terran life preferentially uses the L or D form. For example, most organisms on Earth make exclusive use of the L form of &alpha-amino acids. Chemical bonds oriented out of and into the plane of the page are shown as solid or dashed wedges, respectively. Courtesy of Roger E. Summons, Massachusetts Institute of Technology.

                          Diastereomeric Preference

                          Diastereomeric preference is another manifestation of the ability of atoms in certain molecules to assume different orientations in space. If the two spatial arrangements of atoms are not mirror images of each other, then the different molecular forms are known as diastereomers or diastereoisomers (Figure 3.2.1). Unlike enantiomers, diastereoisomers have different physical and chemical properties and can be separated by chromatography or other processes that exploit subtle differences in polarity. Simple sugars are good examples of diastereoisomers and the more complex the molecule, the more possibilities there are to form diastereomers. Thus, for example, the steroid cholesterol (see Figure 3.2.2) can exist in 256 different structural configurations, but living systems make use of only one of them. 1

                          1 K.E. Peters, J.M. Moldowan, and C.C. Walters, The Biomarker Guide, Cambridge University Press, 2004.

                          FIGURE 3.2.1 The ability of atoms in organic molecules to assume multiple configurations in three-dimensional space is demonstrated by these three forms of tartaric acid. Structures A and B and A and C are superimposable mirror images of each other and so are termed diastereomers. Structures B and C are non-superimposable mirror images of each other and are, thus, enantiomers (see Box 3.1). Courtesy of Roger E. Summons, Massachusetts Institute of Technology.

                          FIGURE 3.2.2 Structure of cholesterol with its eight asymmetric carbon atoms identified with their position number. Theoretically, this compound could exist in as many as 256 (2 8 ) possible stereoisomers, and yet biosynthesis produces only the one illustrated.

                          carbon, nitrogen, or sulfur isotopic data in Archean sediments, for example, subject to debate. 24 &ndash 27 Although not likely to yield unambiguous biosignatures in the near future, isotopic analyses of martian sediments and atmospheric gases will be important for discerning their evolution and for establishing comparative data, as they do on Earth. Identification of a suite of supporting isotopic data in a reaction pathway, and its environmental context, is the most effective approach to identifying an isotopic biosignature. Elucidation of the isotopic systematics of

                          Structural Isomers

                          The propensity of carbon compounds to exist with multiple ring systems and unsaturations means that the generic organic compound CpHqNrOsPtSu, can assume an enormous variety of possible structures, known as structural isomers. 1 Despite the potential for variety, researchers observe that naturally synthesized biochemicals fall into patterns, and the number of known compounds is but a small subset of what is chemically feasible. Moreover, the biomolecule may be the thermodynamically least favored structure within a set of possible isomers if this aspect enhances its functional capacity.

                          Structural isomers are readily separated using chromatography. In many, but not all cases, their mass spectra are also distinctive. As with other forms of isomerism, combinatorial instruments such as gas chromatographs-mass spectrometers and liquid chromatographs-mass spectrometers provide the most sensitive and diagnostic tools for trace analysis.

                          1 E.L. Eliel, S.H. Wilen, and L.N. Mander, Stereochemistry of Organic Compounds, Wiley, New York, 1994.

                          the C-cycle on Earth has been underway for more than 50 years, and much remains to be understood. 28 , 29 An added complication for studies of Mars is the unknown degree to which nonbiological atmospheric processes fractionate isotopes.

                          An example of an isotopic biomarker that might be used in the search for life on Mars is the 18 O/ 16 O ratio in phosphates. 30 Phosphorus in the form of phosphates (PO4 3&ndash ) is utilized in genetic material and cell membranes, and as a cofactor and energy-transporting molecule in terran biology. On Earth, the ultimate source of PO4 3&ndash is apatite that is dissolved, biologically processed, and redeposited as various sedimentary PO4 3&ndash phases and as biogenic calcium phosphate deposits (phosphorites). Biologically processed PO4 3&ndash on Earth has a strong biotic O-isotopic signature that is highly evolved from abiotic apatite baseline values. On Mars, evolution of the 18 O/ 16 O ratios in phosphates from this abiotic baseline could be used as a biomarker. Furthermore, the 18 O/ 16 O ratio of PO4 3&ndash records temperature and high-temperature exchange reactions with water, also making PO4 3&ndash a potential indicator of past hydrothermal activity on Mars. 31

                          An additional example of an isotopic effect concerns the tendency in biological processes for large molecules to be synthesized by the repeated addition of subunits of two or five carbon atoms (see Box 3.4). The lipid building blocks acetate (C2) and isopentenyl pyrolphosphate (C5) are, for example, isotopically inhomogeneous. Acetate provides one of the best examples because it shows very significant differences in the 13 C contents of its methyl and carboxyl carbons. 32 The most overt consequences are isotopic ordering in fatty acids and a major isotopic difference between acetogenic and polyisoprenoid lipids. In a single organism, the isotopic differences between acetogenic and polyisoprenoid lipids depend on how many of the polyisoprenoid carbon atoms arise from acetate versus carbohydrate metabolism. 33

                          Morphological Biosignatures

                          Morphological biosignatures represent the class of objects that can be interpreted as indicative of life based on their size, shape distribution, and provenance. Features of interest occur at both the macroscopic (e.g., stromatolites and microbially induced sedimentary structures) and the microscopic (e.g., microfossils) scale. If they were discovered on Mars, macroscale morphological features such as stromatolites, although being the subject of some contention as a definitive indicator of biogenicity, 34 would prove to be highly desirable targets for further study and/or sample return. 35 &ndash 37

                          Subunits and Building Blocks of Complex Organic Molecules

                          Virtually all biomolecules are constructed from a limited number of generic subunits or building blocks, the best-known examples being proteins and nucleic acids. Lipids, which are formed from only two basic building blocks, are polymers of either acetate or isopentenyldiphosphate precursors. The final products lack a hydrolyzable functionality (e.g., peptide linkages) at the point where subunits join, and, unlike other proteins and nucleic acids, lipids cannot be depolymerized.

                          A classic example of lipids are those that are found in membrane lipid bilayers of bacteria and eukarya and are made up of fatty acids esterified to glycerol. The most common fatty acids are all-acetate products and thus have even carbon numbers (e.g., C14, C16, C18, and C20). Odd-carbon-numbered members, generally synthesized from a non-acetyl starter, exist but are less abundant. Extension of fatty acid chain length proceeds by the addition of further acetate units. Terminating and modifying reactions such as desaturation, reduction, or decarboxylation yield common intermediate-molecular-weight series of products such as the plant and algal waxes made up of even-numbered alcohols (e.g., C26, C28, C30, C32) and odd-numbered hydrocarbons (e.g., C25, C27, C29, C31).

                          An additional illustration of the building-block principle is displayed by the terpenoids. These polymers of &Delta3-isopentenyldiphosphate have somewhat more complex origins and much more complex structures (Figure 3.4.1). As a result of isoprenoid biosynthesis and its evolution over geological time, terran life contains an enormous array of complex molecules related through their C5 architecture. The multiplicity of isoprenoid biosynthetic pathways, their distribution across different phylogenetic groups, their requirement, or otherwise, for molecular oxygen, and the types of post-synthesis modification are generally held to provide a powerful biosignature of evolutionary origins. For example, the molecules resulting from the pathway shown in Figure 3.4.1 are highly diagnostic of biosynthesis because, individually, they exhibit many features of biosynthesis (e.g., carbon number, chirality, and subsets of isomers).

                          Crocetane, 2,6,10-trimethyl-7-(3-methylbutyl)-dodecane, squalene, and biphytane are irregularly branched compounds, whereas phytane, labdane, and kaurane are regular and are constructed from four head-tail linked isoprene units. These compounds also illustrate how different structures can be diagnostic for specific physiologies (phytol and farnesol for photosynthesis, phytane for various archaea, crocetane for methanotrophy) or specific organisms (2,6,10-trimethyl-7-(3-methylbutyl)-dodecane for diatoms biphytane for crenarchaeota labdane and kaurane for conifers).

                          1 G. Ourisson and P. Albrecht, &ldquoHopanoids. 1. Geohopanoids: The Most Abundant Natural Products on Earth?,&rdquo Accounts of Chemical Research 25:398-402, 1992.

                          Cameras and spectral imagers on previous, continuing, and planned life-detection missions to Mars are capable of identifying structures and objects ranging from the macroscopic to the minuscule that, on Earth, are considered visible signatures for past or present biological activity. Such objects and structures include intact microbes, metazoa and metaphytes, stromatolites, microbial mats, and other large-scale structures composed of aggregates of cells, as well as component parts of multicellular organisms such as cysts, pollen, embryos, organs, and so on. On Earth, these objects are pervasive in surface environments and in the deep subsurface and leave no doubt about how abundant and tenacious life is. Researchers can also, to a degree, visually identify in Earth&rsquos sediments a rich fossil life extending in age to more than 2 billion years. So far, no such visible &ldquobiological&rdquo objects have been convincingly identified on Mars or in martian meteorites. If life exists, or existed in the past, on Mars or other

                          FIGURE 3.4.1 Structures of some regular, irregular, and cyclic C2O (diterpenoid) and C3O (triterpenopid), and C4O (tetraterpenoid) hydrocarbons that have been identified in sediments and that illustrate a variety of biosynthetic patterns based on repeating five-carbon subunits (after J.M. Hayes, &ldquoFractionation of Carbon and Hydrogen Isotopes in Biosynthetic Processes,&rdquo Reviews in Mineralogy and Geochemistry 43: 225-277, 2001).

                          planetary bodies, the evidence has not been forthcoming. In many respects, the search for martian life mirrors the search for the earliest life on Earth and faces similar obstacles. Attempting to reconstruct terran life&rsquos history back into deep time, researchers are confronted by the problem of a record made increasingly cryptic by the geochemical and geological processes that continually re-surface Earth and modify the rock record.

                          Poor preservation and ambiguity about what constitutes a biosignature have confounded the search for visible evidence of early microbial life on Earth 38 &ndash 45 and in the martian meteorite ALH 84001 in particular. 46 Related reports, and some of the controversies stemming from them, teach researchers that drawing an inference of biogenicity based on morphology is fraught with difficulties. If the feature being observed is demonstrably syngenetic with the host rock and displays a limited size (length and width) distribution, shows evidence of cellular

                          Clusters and Uneven Distribution Patterns of Structurally Related Compounds

                          The biosynthesis of large organic molecules from smaller molecules, as discussed in Box 3.4, leads to wider consequences, evidence of which can, in principle, be used as biomarkers. The synthesis of lipids by organisms, for example, from C2 or C5 building blocks creates clusters of compounds that differ by n C2 (acetogenic lipids) or n C5 (polyisoprenoids) units, where n is a positive interger. In a typical sample of terrestrial lipids, researchers find, for example, a predominance of even-carbon-numbered fatty acids odd-carbon-numbered hydrocarbons in leaf wax C15, C20, and C25 acyclic isoprenoids C20 and C30 cyclic terpenoids including steroids and C40 carotenoids. Subsets of these traits are even identifiable in highly altered or processed materials such as petroleum, where n-alkanes may exhibit preferences for odd-over-even or even-over-odd carbon numbers. Clusters of carbon numbers have the potential to be biosignatures because they indicate biosynthesis from universal building blocks.

                          In addition to obvious patterns of related compounds differing by two or five carbon atoms, the action of repeated addition of C2 or C5 subunits leads to an additional important biosignature. Functional biochemicals, such as lipids, have a tendency to show clusterings of related compounds at discrete molecular weight ranges. Examples of clusters seen include the following:

                          C15-C17 and C25-C33, respectively, for hydrocarbons associated with, for example, bacteria and plants

                          C26-C30 for the sterols associated with most eukaryotes

                          C30 for the triterpenoids associated with plants and bacteria and

                          C20, C25, C30, and C40 for lipids associated with archaea.

                          An additional biomarker related to clustering and isotopic fractionation is described in the subsection &ldquoIsotopic Biosignatures.&rdquo

                          A factor complicating the use of these biosignatures is the fact that most samples of biologically produced organic matter come from organisms that exist in complex ecosystems. The volatile components of a microbial mat, for example, will show compound classes with carbon numbers distributed roughly as described above and in Box 3.4. Similarly, the lipids in biofilms from hydrothermal vents display an uneven-carbon-number distribution. 1 The geological record is replete with additional examples. 2 Moreover, the C25-C30 fraction might contain more material than the C15-C20 fraction. This &ldquolumpiness&rdquo is in stark contrast to what is seen in assemblages of molecules made abiotically. 3 , 4 The Fischer-Tropsch process used to synthesize hydrocarbons, for example, creates molecules with an exponential distribution of sizes, with C1 > C2 > C3 > C4, and so on, falling away to almost zero by C30. Similarly, the amino acids seen in meteorites exhibit more C1 than C2 than C3 than C4 and so on. 5 - 8

                          1 L.L. Jahnke, W. Eder, R. Huber, J.M. Hope, K.U. Hinrichs, J.M. Hayes, D.J. Des Marais, S.L. Cady, and R.E. Summons, &ldquoSignature Lipids and Stable Carbon Isotope Analyses of Octopus Spring Hyperthermophilic Communities Compared to those of Aquificales Representatives,&rdquo Applied and Environmental Microbiology 67:5179-5189, 2001.

                          2 K.E. Peters, J.M. Moldowan, and C.C. Walters, The Biomarker Guide, Cambridge University Press, Cambridge, U.K., 2004.

                          3 See, for example, B. Sherwood Lollar, T.D. Westgate, J.A. Ward, G.F. Slater, and G. Lacrampe-Couloume, &ldquoAbiogenic Formation of Alkanes in the Earth&rsquos Crust as a Minor Source for Global Hydrocarbon Reservoirs,&rdquo Nature 416:522-524, 2002.

                          4 See, for example, M. Allen, B. Sherwood-Lollar, B. Runnegar, D.Z. Oehler, J.R. Lyons, C.E. Manning, and M.E. Summers, &ldquoIs Mars Alive?,&rdquo Eos 87:433 and 439, 2006.

                          5 M.A. Sephton, &ldquoOrganic Compounds in Carbonaceous Meteorites,&rdquo Natural Products Reports 19:292-311, 2002.

                          6 M.A. Sephton, C.T. Pillinger, and I. Gilmour, &ldquoAromatic Moieties in Meteoritic Macromolecular Materials: Analyses by Hydrous Pyrolysis and 13 C of Individual Compounds,&rdquo Geochimica et Cosmochimica Acta 64:321-328, 2000.

                          7 M.A. Sephton, C.T. Pillinger, and I. Gilmour &ldquoPyrolysis-Gas Chromatography&ndashIsotope Ratio Mass Spectrometry of Macromolecular Material in Meteorites,&rdquo Planetary Space Science 47:181-187, 2001.

                          8 M.A. Sephton, G.D. Love, J.S. Watson, A.B. Verchovsky, I.P. Wright, C.E. Snape, and I. Gilmour, &ldquoHydropyrolysis of Insoluble Carbonaceous Matter in the Murchison Meteorite: New Insights into Its Macromolecular Structure.&rdquo Geochimica et Cosmochimica Acta 68:1385-1393, 2004.

                          degradation, or is part of a discernable population that occurs in discrete phases within the samples on Earth that are relevant to the context of the sample, then further investigation is warranted. 47 The debates on early life and ALH 84001 (see Chapter 2) have shown that morphology must be combined with both chemistry and context to enable unambiguous detection of life. However, morphology is extremely valuable for detecting targets of interest for further investigation, particularly macroscopic structures such as stromatolites, microbial mats, and other large-scale aggregates created by communities of microorganisms.

                          Mineralogical and Inorganic Chemical Biosignatures

                          The mineralogy and chemistry of Earth materials can constitute a biosignature in some systems where organisms either accelerate or inhibit reactions that are thermodynamically possible. In addition, organisms can change the chemistry of rocks, fluids, and gases through the processes of secretion, assimilation, and electron transfer, sometimes creating mineralogical or chemical gradients that differ from those that would be established in an abiotic environment. Although there are a few examples of mineralogical biosignatures on Earth that unambiguously identify a biotic origin (e.g., coccoliths and diatoms), these are not likely to be applicable to Mars. 48 Most other types of inorganic chemical biosignatures can provide only indirect evidence of the presence of life and would thus most likely constitute supporting evidence accompanying other more diagnostic criteria. Examples of inorganic biosignatures are discussed below.

                          Biota can affect the identity of phases manifested in the rock record. For example, some bacteria transform mackinawite to greigite (sulfides), 49 and some fungi promote the formation of weddellite (Ca oxalate) in soils. These effects are related to the biological ability to nucleate minerals onto organic templates, or to the production of organic ligands that solubilize elements, affect growth mechanisms, or precipitate as salts. The inclusion of organic molecules or micronutrient impurities in mineral precipitates could also conceivably be indicative of biological activity.

                          Physical properties of minerals might also yield indirect, albeit ambiguous, evidence of biological processes. For example, the size distribution of precipitates might indirectly suggest a biotic origin, given that many mineralogical by-products of metabolism are nanocrystalline because they are formed under conditions of high oversaturation. 50 Surface etching or crystal habit, which can be affected by biological exudates or biofilm formation, might also be indirect indicators of biota. Biological phenomena can also be inferred in some cases from the characteristics of aggregations of minerals. Of possible interest for Mars is aggregation characteristic of Fe minerals precipitated by bacteria. For example, both the size distribution and the aggregation of magnetite crystals have been posited as biosignatures, 51 , 52 although these characteristics have also been attributed to abiotic processes, 53 thus pointing out the ambiguous nature of mineralogical properties as biosignatures.

                          Gradients in the concentration of elements recorded in Earth materials can also be diagnostic of biological phenomena. A well-known manifestation of elemental gradients driven by biological processes is certain soil horizons in which the exudation of organic complexants mobilizes elements and produces patterns indicative of the presence of biota. 54 The formation of gradients in the concentration of elements at the meter scale in soil horizons and at the micron scale on mineral surfaces or in endolithic communities might thus be important. 55 &ndash 57 The assimilation of trace elements at a low concentration by microorganisms or the sequestration of toxic elements into biologically mediated precipitates could also create distributions of trace elements that record the prior presence of biota in regolith or sedimentary environments.

                          Anomalies in the concentration of phosphorus have also been suggested as possible biomarkers that could be used in the search for life on Mars. 58 Phosphorus as PO4 3&ndash is utilized in a wide variety of biological processes and material. The ultimate source of PO4 3&ndash on Earth is igneous apatite, which is biologically processed and redeposited as biogenic calcium phosphates (phosphorites). On Earth, PO4 3&ndash is adsorbed strongly to iron- and aluminum-oxides and oxyhydroxides under aqueous conditions. Phosphorus phases found in martian soils, sedimentary environments, and in association with the abundant iron oxides on Mars might be a good target in a search for phosphorus as a biosignature. Additionally, patterns of phosphorous concentration could be used to guide the search for potential PO4 3&ndash biosignatures and other kinds of fossils.

                          Based on such considerations, past and present approaches to Mars astrobiological exploration have heavily emphasized instrument packages capable of detecting the chemical signatures of life, especially carbon compounds, isotopic signatures, and various other products of metabolism. The 2001 workshop on biosignatures organized by the NASA Biomarker Task Force established comprehensive objectives for developing a better understanding of biosignatures. Unfortunately, though, the results of the task group&rsquos deliberations were never published in full. 59 Because they represent an important starting point for future discussions, those objectives are reproduced in Appendix C.

                          REFERENCES

                          1. J.J. Brocks and R.E. Summons, &ldquoSedimentary Hydrocarbons, Biomarkers for Early Life,&rdquo pp. 65-115 in Treatise in Geochemistry (H.D. Holland and K. Turekian, eds.), 2003 K.E. Peters, J.M. Moldowan, and C.C. Walters, The Biomarker Guide, Cambridge University Press, Cambridge, 2004.

                          2. See, for example, A.H. Knoll, R.E. Summons, J.R. Waldbauer and J.E. Zumberge, &ldquoSuccessions in Biological Primary Productivity in the Oceans&rdquo in The Evolution of Photosynthetic Organisms in the Oceans (P. Falkwoski and A.H. Knoll eds), in press K.E. Peters, J.M. Moldowan and C.C Walters, The Biomarker Guide, Cambridge University Press, Cambridge, 2004.

                          3. See, for example, A.I. Rushdi and B.R.T. Simoneit, &ldquoLipid Formation by Aqueous Fischer-Tropsch-Type Synthesis over a Temperature Range of 100 to 400°C,&rdquo Origins of Life and Evolution of Biospheres 31:103-118, 2004 J.D. Pasteris and B. Wopenka, &ldquoLaser&ndashRaman Spectroscoy (Communication Arising): Images of the Earth&rsquos Earliest Fossils?&rdquo Nature 420:476-477, 2002 B. Sherwood Lollar, T.D. Westgate, J.A. Ward, G.F. Slater, and G. Lacrampe-Couloume, &ldquoAbiogenic Formation of Alkanes in the Earth&rsquos Crust as a Minor Source for Global Hydrocarbon Reservoirs,&rdquo Nature 416:522-524, 2002 T.M. McCollom, and J.S. Seewald, &ldquoCarbon Isotope Composition of Organic Compounds Produced by Abiotic Synthesis under Hydrothermal Conditions,&rdquo Earth and Planetary Science Letters 243:74-84, 2006.

                          4. S.L. Miller, &ldquoProduction of Some Organic Compounds under Possible Primitive Earth Conditions, Journal of the American Chemical Society 7:2351, 1955.

                          5. J.A. Kasting, &ldquoBolide Impacts and the Oxidation State of Carbon in the Earth&rsquos Early Atmosphere,&rdquo Origins of Life and Evolution of the Biosphere 20:199-231, 1990.

                          6. See, for example, R.M. Hazen &ldquoLife&rsquos Rocky Start,&rdquo Scientific American 284(4):76-85, 2001.

                          7. J.A. Brandes, N.Z. Boctor, G.D. Cody, B.A. Cooper, R.M. Hazen, and H.S. Yoder, &ldquoAbiotic Nitrogen Reduction on the Early Earth,&rdquo Nature 395:365-367, 1998.

                          8. G. Wächtershäuser, &ldquoBefore Enzymes and Templates: Theory of Surface Metabolism,&rdquo Microbiology Review 52:452-484, 1988.

                          9. G. Wächtershäuser, &ldquoEvolution of the First Metabolic Cycles,&rdquo Proceedings of the National Academy of Sciences 87:200-204, 1990.

                          10. W.V. Boynton, W.C. Feldman, S.W. Squyres, T.H. Prettyman, J. Brückner, L.G. Evans, R.C. Reedy, R. Starr, J.R. Arnold, D.M. Drake, P.A.J. Englert, A.E. Metzger, I. Mitrofanov, J.I. Trombka, C. d&rsquoUston, H. Wänke, O. Gasnault, D.K. Hamara, D.M. Janes, R.L. Marcialis, S. Maurice, I. Mikheeva, G.J. Taylor, R. Tokar, and C. Shinohara, &ldquoDistribution of Hydrogen in the Near Surface of Mars: Evidence for Subsurface Ice Deposits,&rdquo Science 297:81-85, 2002.

                          11. D.G. Capone, R. Popa, B. Flood, K.H. Nealson, &ldquoGeochemistry. Follow the Nitrogen,&rdquo. Science 312:708-709, 2006.

                          12. J. Farquhar, J. Savarino, T.L. Jackson, M.H. Thiemens, &ldquoEvidence of Atmospheric Sulphur in the Martian Regolith from Sulphur Isotopes in Meteorites,&rdquo Nature 404:50-52, 2000.

                          13. P.G. Falkowski and C.S. Davis, &ldquoNatural Proportions,&rdquo Nature 431:131, 2004.

                          14. D.G. Capone, R. Popa, B. Flood, K.H. Nealson, &ldquoGeochemistry. Follow the Nitrogen,&rdquo. Science 312:708-709, 2006.

                          15. G. Eglinton and M. Calvin &ldquoChemical Fossils,&rdquo Scientific American 261:32-43, 1967.

                          16. M.H. Engel and S.A. Macko, eds., Organic Geochemistry Principles and Applications, Plenum Press, New York, 1993.

                          17. K.E. Peters, J.M. Moldowan, and C.C. Walters,. The Biomarker Guide, Cambridge University Press, Cambridge, 2004.

                          18. M.H. Engel and S.A. Macko, eds., Organic Geochemistry Principles and Applications, Plenum Press, New York, 1993.

                          19. J.J. Brocks and R.E. Summons, &ldquoSedimentary Hydrocarbons, Biomarkers for Early Life,&rdquo pp. 65-115 in Treatise in Geochemistry (H.D. Holland and K. Turekian, eds.), 2003.

                          20. K.E. Peters, J.M. Moldowan, and C.C. Walters,. The Biomarker Guide, Cambridge University Press, Cambridge, 2004.

                          21. K.E. Peters, J.M. Moldowan, and C.C. Walters, The Biomarker Guide, Cambridge University Press, Cambridge, 2004.

                          22. E.L. Eliel, S.H. Wilen, and L.N. Mander, Stereochemistry of Organic Compounds, Wiley, New York, 1994.

                          23. See, for example, N.A. Campbell and J.B. Reece, Biology (7th edition), Benjamin Cummings, 2004.

                          24. See, for example, S.J. Mojzsis, G. Arrhenius, K.D. McKeegan, T.M. Harrison, A.P. Nutman, and C.R. Friend, &ldquoEvidence for Life on Earth Before 3,800 Million Years Ago,&rdquo Nature 384:55-59, 1996.

                          25. M.A. van Zuilen, K. Mathew, B. Wopenka, A. Lepland, K. Marti, and G. Arrhenius, &ldquoNitrogen and Argon Isotopic Signatures in Graphite from the 3.8-Ga-old Isua Supracrustal Belt, Southern West Greenland,&rdquo Geochimica et Cosmochimica Acta 69:1241-1252, 2005.

                          26. Y. Ueno, H. Yurimoto, H. Yoshioka, T. Komiya, and S. Maruyama, &ldquoIon Microprobe Analysis of Graphite from ca. 3.8 Ga Metasediments, Isua Supracrustal Belt, West Greenland: Relationship between Metamorphism and Carbon Isotopic Composition,&rdquo Geochimica et Cosmochimica Acta 66:1257-1268, 2002.

                          27. Y. Shen, R. Buick and D.E. Canfield &ldquoIsotopic Evidence for Microbial Sulphate Reduction in the Early Archaean Era,&rdquo Nature 410:77-81, 2001.

                          28. H. Craig, &ldquoThe Geochemistry of the Stable Carbon Isotopes of Carbon,&rdquo Geochimica et Cosmochimica Acta 3:53-92, 1953.

                          29. J.M. Hayes and J.R. Waldbauer, &ldquoThe Carbon Cycle and Associated Redox Processes through Time,&rdquo Philosophical Transactions of the Royal Society B: Biological Science 361:931-950, 2006.

                          30. R.E. Blake, J.C. Alt, and A.M. Martini, &ldquoOxygen Isotope Ratios of PO4 &ndash : An Inorganic Indicator of Enzymatic Activity and P Metabolism and a New Biomarker in the Search for Life,&rdquo Proceedings of the National Academy of Sciences, Astrobiology Special Feature 98:2148-2153, 2001.

                          31. R.E. Blake, J.C. Alt, and A.M. Martini, &ldquoOxygen Isotope Ratios of PO4 &ndash : An Inorganic Indicator of Enzymatic Activity and P Metabolism and a New Biomarker in the Search for Life,&rdquo Proceedings of the National Academy of Sciences, Astrobiology Special Feature 98:2148-2153, 2001.

                          32. J.M. Hayes, &ldquoFractionation of Carbon and Hydrogen Isotopes in Biosynthetic Processes,&rdquo Reviews in Mineralogy and Geochemistry 43:225-277, 2001.

                          33. J.M. Hayes, &ldquoFractionation of Carbon and Hydrogen Isotopes in Biosynthetic Processes,&rdquo Reviews in Mineralogy and Geochemistry 43:225-277, 2001.

                          34. J.M. Garcia-Ruiz, S.T. Hyde, A.M. Carnerup, A.G. Christy, M.J. Van Kranendonk, and N.J. Welham, &ldquoSelf-Assembled Silica-Carbonate Structures and Detection of Ancient Microfossils,&rdquo Science 302:1194-1197, 2003.

                          35. H.J. Hofmann, K. Grey, A.H. Hickman, and R. Thorpe, &ldquoOrigin of 3.45 Ga Coniform Stromatolites in Warrawoona Group, Western Australia,&rdquo Geological Society of America Bulletin 111:1256-1262, 1999.

                          36. S.L. Cady, J.D. Farmer, J.P. Grotzinger, J.W. Schopf, and A. Steele, &ldquoMorphological Biosignatures and the Search for Life on Mars,&rdquo Astrobiology 3:351-368, 2003.

                          37. A.C. Allwood, M.R. Walter, B.S. Kamber, C.P. Marshall, and I.W. Burch, &ldquoStromatolite Reef from the Early Archaean Era of Australia,&rdquo Nature 441:714-718, 2006.

                          38. See, for example, D.R. Lowe, &ldquoAbiological Origin of Described Stromatolites Older than 3.2 Ga,&rdquo Geology 22:387-390, 1994.

                          39. J.P. Grotzinger and A.H. Knoll, &ldquoStromatolites in Precambrian Carbonates Evolutionary Mileposts or Environmental Dipsticks,&rdquo Annual Reviews of Earth and Planetary Sciences 27:313-358, 1999.

                          40. H.J. Hofmann, K. Grey, A.H. Hickman, and R. Thorpe, &ldquoOrigin of 3.45 Ga Coniform Stromatolites in Warrawoona. Group, Western Australia.&rdquo Geological Society of America Bulletin 111:1256-1262, 1999.

                          41. M.D. Brasier, O.R. Green, A.P. Jephcoat, A.K. Kleppe, M.J. Van Kranendonk, J.F. Lindsay, A. Steele, and N.V. Grassineau, &ldquoQuestioning the Evidence for Earth&rsquos Oldest Fossils,&rdquo Nature 416:76-81, 2002.

                          42. J.W. Schopf, &ldquoMicrofossils of the Early Archaean Apex Chert: New Evidence of the Antiquity of Life,&rdquo Science 260:640-646, 1993.

                          43. J.W. Schopf, &ldquoAre the Oldest Fossils Cyanobacteria?,&rdquo pp. 23-61 in Evolution of Microbial Life Society for General Microbiology Symposium 54 (D. McL. Roberts, P. Sharp, G. Alderson, and M. Collins, eds.), Cambridge University Press, Cambridge, 1996.

                          44. J.W. Schopf, A.B. Kudryavtsev, D.G. Agresti, T.J. Wdowiak, and A.D. Czaja, &ldquoLaser Raman Imagery of Earth&rsquos Earliest Fossils,&rdquo Nature 416:73-76, 2002. J.M. Garcia-Ruiz, S.T. Hyde, A.M. Carnerup, V. Christy, M.J. Van Kranendonk, and N.J. Welham, &ldquoSelf-Assembled Silica-Carbonate Structures and Detection of Ancient Microfossils,&rdquo Science 302:1194-1197, 2003.

                          45. S.M. Awramik and K. Grey, &ldquoStromatolites: Biogenicity, Biosignatures, and Bioconfusion,&rdquo pp. 227-235 in Astrobiology and Planetary Missions (R. B. Hoover, G.V. Levin, A.Y. Rozanov, G.R. Gladstone, eds.), Proceedings of the SPIE, Volume 5906, 2005.

                          46. D.S. McKay, E.K. Gibson, Jr., K.L. Thomas-Keprt, H. Vali, C.S. Romanek, S.J. Clemett, X.D.F. Chillier, C.R. Maechling, and R.N. Zare, &ldquoSearch for Past Life on Mars: Possible Relic Biogenic Activity in Martian Meteorite ALH 84001,&rdquo Science 273:924-930, 1996.

                          47. J.W. Schopf, &ldquoThe Oldest Fossils and What they Mean,&rdquo pp. 29-63 in J.W. Schopf (ed.), Major Events in the History of Life, Jones and Bartlett Publishers, Boston, Mass., 1992.

                          48. J.F. Banfield, J.W. Moreau, C.S. Chan, S.A. Welch, and B. Little, &ldquoMineralogical Biosignatures and the Search for Life on Mars,&rdquo Astrobiology 1:447-465, 2001.

                          49. M.B. McNeil and B. Little, &ldquoMackinawite Formation during Microbial Corrosion,&rdquo Journal of Corrosion 46:599-600, 1990.

                          50. J.F. Banfield, J.W. Moreau, C.S. Chan, S.A. Welch, and B. Little, &ldquoMineralogical Biosignatures and the Search for Life on Mars,&rdquo Astrobiology 1:447-465, 2001.

                          51. K.L Thomas-Keprta, D.A. Bazylinski, J.L. Kirschvink, S.J. Clemett, D.S. McKay, S.J. Wentworth, H. Vali, E.K. Gibson, and C.S. Romanek, &ldquoElongated Prismatic Magnetite Crystals in ALH 84001 Carbonate Globules: Potential Martian Magnetofossils,&rdquo Geochimica et Cosmochimica Acta 64:4049-4081, 2000.

                          52. K.L. Thomas-Keprta, S.J. Clemett, D.A. Bazylinski, J.L. Kirschvink, D.S. McKay, S.J. Wentworth, H. Vali, E.K. Gibson, Jr., M.F. McKay, and C.S. Romanek, &ldquoTruncated Hexa-Octahedral Magnetite Crystals in ALH 84001: Presumptive Biosignatures,&rdquo Proceedings of the National Academy of Sciences 98:2164-2169, 2001.

                          53. See, for example, A.H. Treiman, &ldquoSubmicron Magnetite Grains and Carbon Compounds in Martian Meteorite ALH 84001: Inorganic, Abiotic Formation by Shock and Thermal Metamorphism,&rdquo Astrobiology 3:369-392, 2003.

                          54. A. Neaman, J. Chorover, and S.L. Brantley, &ldquoElement Mobility Patterns Record Organic Ligands in Soils on Early Earth,&rdquo Geology 33(2):117-120, 2005.

                          55. B. Kalinowski, L. Liermann, S.L. Brantley, A. Barnes, and C.G. Pantano, &ldquoX Ray Photoelectron Evidence for Bacteria-Enhanced Dissolution of Hornblende,&rdquo Geochimica et Cosmochimica Acta 64:1331-1343, 2000.

                          56. A. Neaman, J. Chorover, and S.L. Brantley, &ldquoElement Mobility Patterns Record Organic Ligands in Soils on Early Earth,&rdquo Geology 33(2):117-120, 2005.

                          57. H.J. Sun and E.I. Friedmann, &ldquoGrowth on Geological Time Scales in the Antarctic Cryptoendolithic Microbial Community,&rdquo Geomicrobiology Journal 16:193-202, 1999.

                          58. G. Weckwerth and M. Schidlowski, &ldquoPhosphorus as a Potential Guide in the Search for Extinct Life on Mars,&rdquo Advances in Space Research 15:185-191, 1995.

                          59. Michael Meyer, NASA Science Mission Directorate, personal communication, 2006.


                          Watch the video: Polymers and their synthesis and breakdown (February 2023).