Origin of Life Lectures PDF

Bottom-up approach Making clear the steps extending from the formation of Earth to the emergence of life The bottom-up” strategy starts with cosmochemical, plane-tological, geological, and any other useful source of evidence to reconstruct the ambient, chemical inventory and the proc...

Bottom-up approach Making clear the steps extending from the formation of Earth to the emergence of life The bottom-up” strategy starts with cosmochemical, plane-tological, geological, and any other useful source of evidence to reconstruct the ambient, chemical inventory and the processes involved in the origin of life. Top-down approach Studying first the fundamental genetic system of extant organisms and the subsequent emergence of life: all known organisms are compared in order to reconstruct the genetic and metabolic makeup of the What would be the minimal system to have a living system? There is need of different chemistries (probabily interefering with each other) to get all the sort of buidling block of the macromolecules  Hypotheses on the nature of LUCA and the position of viruses in the universal tree of life Patrick Forterre Institut Pasteur (Département de Microbiologie) Paris and Institut de Biologie Cellulaire Integrative, I2BC, Paris-Saclay, Gif sur Yvette Origin of life lectures Naples, October 22, 2024 All living organisms on Earth, cells and viruses, use the same macromolecules to carry information and the same genetic code ADN If all cellular organisms are evolutionarily related, they should share a last common ancestor LUCA origin of life Charles Darwin In 1996, the Last Common Ancestor to all present living organisms (except viruses) has been called LUCA at an international meeting organized at thefondation des Treilles The Last Universal Common (cellular) Ancestor Stanley Miller Christian De Duve  Did LUCA really existed or is it a concept? LUCA origin of life  The pattern of ribosomal proteins distribution between the three domains can be use to root the tree What is the most parsimonious rooting explaining the distribution of ribosomal proteins in the three domains ? 0 Lecompte et al., NAR. 2002 Comprehensive investigation of ribosomal genes in complete genomes from 66 different species allows us to address the distribution of r-proteins between and within the three primary domains The root in the « bacterial branch » is more parsimonious to explain the phylogenomic distribution pattern of ribosomal proteins BACTERIA ARCHAEA EUKARYA Ribosomal proteins are studied in the search for LUCA because they are universal, highly conserved, and essential for life. They are +2 integral to ribosomes, which perform protein synthesis (peptide bond formation), a core function present in all organisms. Their sequence and structural similarities across Bacteria, + 11 Archaea, and Eukarya suggest inheritance from a common ancestor. Ribosomal proteins are less prone to horizontal gene transfer, making them reliable indicators of vertical evolution. Additionally, their role in translation reveals + 23 proteins insights into LUCA’s biochemistry, including the + 33 proteins genetic code and molecular machinery. Their universality and evolutionary stability make ribosomal proteins ideal for tracing life’s shared 34 proteins LUCA ancestry.  Molecular phylogenesis: Evidence of evolution All cells, from bacterial to human, have in their DNA the instructions that regulate life processes and in turn, these instructions are converted into proteins. https://pdb101.rcsb.org/motm/206 http://www.phylogeny.fr/ Protein database The Protein Data Bank (PDB) is an archive for 3-D structure data of proteins and nucleic acids. These data, obtained mainly through X- ray crystallography or NMR, deposited by biochemists from all over the world, are in the public domain and are accessible free of charge. Homology: definition Two sequences are homologous if they share a common evolutionary ancestry. There are no degrees of homology; sequences are either homologous or not. Homologous proteins almost always share a significantly related three- dimensional structure. Myoglobin and beta globin have very similar structures, as determined by X‐ray crystallography.  Homology: Identity and similarity When two sequences are homologous, their amino acid or nucleotide sequences usually share significant identity. While homology is a qualitative inference (sequences are homologous or not), identity and similarity are quantities that describe the relatedness of sequences. The percent similarity of two protein sequences is the sum of both identical and similar matches. In the globin family for example, all the members are homologous but some have sequences that have diverged so greatly that they share no recognizable sequence identity (e.g., human beta globin and human neuroglobin share only 22% amino acid identity). In general, three‐dimensional structures diverge much more slowly than amino acid sequence identity between two proteins. Homology: Orthologs diverged after a speciation event and are presumed to have similar biological functions; example,human and rat myoglobins both transport oxygen in muscle cells. orthologs and Paralogs are homologous sequences that arose by a mechanism such as gene duplication. paralogs For example, human alpha 1 globin (NP_000549.1) is paralogous to alpha 2 globin (NP_000508.1); indeed, these two proteins share 100% amino acid identity  Phylogenetic trees Phylogenetic trees are branching diagrams that depict hypotheses of evolutionary relationships between extant and/or extinct organisms. In particular, they depict degrees of relationship among organisms, indicating that certain groups of organisms are more closely related to one another than they are to other groups.  Nomenclature Terminal taxa are connected by branches. The branches are the line segments that make up the tree. Branches come together at branching points called nodes. Each nodes represents a common ancestor shared by two or more terminal taxa. A taxon (plural taxa), or taxonomic unit, is a grouping of real organisms, morphologically and genetically distinguishable from others and recognizable as a systematic unit. Taxa are positioned within a hierarchical structure in scientific classification. Nodes: these are points on a phylogenetic tree where branching occurs. A node represents the end of the ancestral taxon and the point at which a new species separates from its predecessor. Branches: are the lines on a phylogenetic tree that represent ancestral and/or descendant lineages. Branches arising from nodes represent descendant species that separate from a common ancestor.  Nomenclature Molecular phylogeny is used to trace the evolutionary trees of relationships between organisms. These trees are based on nucleotide or protein sequence data. Trees, if properly designed, give information on distances and evolutionary times.  The Woese tree of life Bactéries Archées Eucaryotes LUCA The root in the « bacterial branch » is more parsimonious to explain the phylogenomic distribution pattern of ribosomal proteins BACTERIA ARCHAEA EUKARYA +2 + 11 + 23 proteins + 33 proteins 34 proteins LUCA Woese and Fox called the last universal ancestor of Archaebacteria, Eubacteria and Eukaryotes the progenote An organism in which the link between the genotype and the phenotype was not yet firmly established The progenote: a very primitive organism with an RNA genome An organism producing rather primitive proteins with very unfaithful translation Was LUCA a progenote ?  If the tree is rooted between Bacteria and Arkarya LUCA had probably much smaller ribosomes than modern organisms BACTERIA ARCHAEA EUKARYA 57 proteins 68 proteins 78 proteins + 23 proteins + 33 proteins LUCA 34 proteins  LUCA had probably no ATP synthase Mulkidjanian et al., Nature Rev Microbiol., 2007 ARCHAEA BACTERIA EUKARYA The crucial component of ATP synthase is not homologous in Bacteria and Archaea/Eukarya  The arkaryal and bacterial basal transcription factors are non homologous, suggesting non specific initiation of transcription in LUCA. B A E TBP Omega factors TFIIB TFB GreA GreB LUCA TFS Owing to the complete absence of any The elongation first hypothesis (Finn Werner) bona fide σ-factor homologues in archaea and eukaryotes, and of any TBP or TFIIB homologues in bacteria, it is unlikely that the RNAP of the LUCA initiated transcription aided by σ-like, TBP-like or TFIIB-like transcription factors. The molecular machineries for DNA replication are non homologous between Arkarya and Bacteria, suggesting that LUCA still had an RNA genome. B A PolD E Topo VI DnaA Cdc6 DicA MCM DnaB PriS DnaG PriL PolC PolB ssb RNA-based GINS RPA DnaN LUCA? Complex PCNA NAD ligase RFC Hu ATP ligase Histones  The transition from RNA to DNA genomes, that take place in an RNA-Cell, required the production by this cell of very complex enzymes RNR : Ribonucleotide reductase ThyA or ThyX : Thymidylate synthases RNR : Reverse transcriptase RNA U-DNA T-DNA RNR ThyA/X RT Hypothesis: DNA and DNA replication machineries first originated in viruses B A PolD E Topo VI DnaA Cdc6 DicA MCM DnaB PriS DnaG PriL PolC PolB ssb RNA-based GINS RPA DnaN LUCA? Complex PCNA NAD ligase RFC Hu ATP ligase Histones  Viruses encode many different molecular machineries for DNA replication, sometimes very divergent, sometimes even non homologous to the two cellular machineries Giant viruses Herpes T4 Baculovirus Bacteria Archaea Eukaryotes The « out of viruses » hypothesis for the origin of DNA RT ThyA RNA U-DNA T-DNA HMC-DNA RNR ThyA’ ThyX Was LUCA a progenote ? LUCA was not a “modern cell” Simpler ribosomes (30-40 proteins) No initiation factors for transcription No ATP synthases (fermentation first?) But..a membrane with protein pumps RNA genomes  RNA WORLD HYPOTESIS RNA can perform the roles of both a replicating information store (like DNA, genotype) and a catalysts (like protein enzymes, phenotype). RNA WORLD HYPOTESIS The RNA World is the conceptual idea that there was a period in the early history of life on Earth when RNA (or something chemically very similar) carried out most of the information processing and metabolic transformations needed for biology to emerge from chemistry.  ASSEMBLY OF AN INFORMATION BEARING POLYMER: AN RNA WORLD? Strong points: RNA has some catalytic properties (self-splicing introns, riboswithches, RNA ligases, RNA polymerase ribozyme can be selected in vitro and improved etc). RNA is capable of making proteins (Noller 1992): the peptidyl transferase center of the ribosome is a ribozyme. The synthesis of the nucleotides of DNA is carried out by building the corresponding RNA nucleotides first and then converting them to DNA nucleotides. Some biochemical processes use RNA (but not DNA) nucleotides (for instance ATP) or ribonucleotide coenzymes (NAD etc). as the main energy carrier and the cofactors used to assist a number of enzymes. Molecular fossil of an RNA based metabolism? Discovery that RNA could evolve in vitro over time in response to selection. This study gave rise to the field of in vitro evolution by demonstrating that RNA could behave in a Darwinian manner in the absence of cells (evolution of a self replicating molecule outside cell); (if RNA molecules are allowed to replicate in vitro, selection automatically screens out those mutant molecules that best combine stability and replicability — the molecular equivalent of darwinian survival and proliferation —under the adopted conditions) RNA has the ability to self-replicate: For a pure RNA world (i.e. one in which proteins play no role) there must have been an RNA catalyst (or ribozyme) capable of catalysing the replication of RNA  RNAs has several structural and functional attributes Ribozymes are widespread among almost all kingdoms of life: These findings support the hypothesis that catalytic RNA are relics of an ancient RNA world (Ribosome is a ribozyme since ribosomal RNA (rRNA) occupies the central core of the ribosome and catalyzes peptide bond formation during protein biosynthesis while the protein part of the ribosome plays a secondary role). Riboswitches are RNA motifs that, by binding a small molecule ligand, can exert regulatory control over the transcript in a cis-acting manner. Riboswitches are now recognized as important and widespread elements in the control of gene expression in numerous evolutionarily distant Bacteria, Archaea, Plantae, Fungi and Algae. microRNAs (miRNAs) a large family of small, approximately 21-nucleotide-long, non-coding RNAs, lends further support to the RNA world hypothesis. miRNAs are key post-transcriptional regulators of gene expression. In mammals, for instance, miRNAs were predicted to control the activity of approximately 30% of all protein-coding genes and were shown to participate in the regulation of almost every cellular process investigated so far Semi-self-sustained RNA systems, which can catalyze their own replication, provides additional evidence that RNA is capable of functions presently performed by proteins  From chemical evolution to biochemical evolution Links between steps II-III and III-IV are missing According to one hypothetical scenario, the first organisms were products of chemical evolution in four stages: 1. Abiotic synthesis of small organic molecules, such as amino acids and nucleotides. 2. Joining of small molecules (monomers) into biopolymers, including proteins and nucleic acids. 3. Origin of self-replicating molecules that eventually made inheritance possible 4. Packaging of these molecules into “protobionts” droplets with membranes that maintained  A step forward….towards polymerization of macromolecules Condensation and polymerization of these organic precursor molecules requires some mechanisms to promote their concentration. Macromolecules are found in biology (DNA, RNA, proteins) and lipids are all polymers and form via condensation reactions. There is need of a fluctuating environment which is sometimes wet and sometimes dry – a wet period so that the components mix and interact and then a dry period so that water is removed and these components can form a polymer,”.. Minerals and geochemical environments: the silica minerals [email protected]  The simple crystal structure of clays consists of layers of corner-linked SiO4 tetrahedra bound to layers of edge-linked Al2O6 octahedra Overlayng sheets bind to each other like “a deck of cards” by van der Waals forces and interlayer cations. Clays often incorporate Mg2+, Fe2+, and Fe3+ in place of Al3+ in the octahedral layers and Al3+ for Si4+ in the tetra- hedral layers. Due to the relative arrangement between cations and anions within the crystal lattice of clay minerals, negative charges are arranged along the surface of the clay particle, while positive charges are arranged along the edge. This charge distribution controls the interaction of the particle with water molecules and ions in it. In addition, this distribution controls the structure of the clays. The interaction between clay particles and water also depends, of course, on the arrangement of electrical charge in the dipoles that make up the water molecules. Minerals=Clays: types and chemical structure NO isomorphic Si4+ –> Al3+ + X2++ Si4+ –> Al3+ + X2++ substitution Si4+ –> Al3++ Si4+ –> Mg2+–> Al3+ + interstratum Na+, interstratum Na+, → NO inter cations interstratum K+ Mg2+ K+, Rb+, Cs+ + Ca2+, K+, Rb+, Cs+ + Ca2+, Mg2+ Mg2+ Al4 [Si4O10(OH)8] KAl4 [AlSi7O20(OH)4] (Mg,Fe)12- pAl2p/3[Si (Mg8O 20(OH) 0.75)Mg616] [Al1.5Si6.5O20(OH)4] nH2O (Na,Ca)0.33(Al,Mg)2(Si4O10)(OH)2 · nH2O [email protected]  Minerals=Clays: geochemical environments in the emergence of protocells Intercalation = penetration of organic molecules into the interlayer space of clay minerals. Washing with water or heating lead to desorbing Arrangement of alkylammonium ions in the interlayer space of smectites Water molecules in the interlayer space of smectites and vermiculites can be displaced by many polar organic molecules. The interlayer cations can be exchanged by various types of organic cations. It depends on hydrogen bonds, ion–dipole interaction, co- ordination bonds, acid–base reactions, charge-transfer, and van der Waals forces. Most elements are left off by reduction (Fe+3 to Fe+2) and the reduction break down the minerals [email protected]  COMMUNITY CLAY Life can be embedded into a solid substance (clay) and that the early clays could have played an important role in prebiotic synthesis acting as "chemical factories" for processing simple organic building blocks into the more complex molecules from which the first life arose. Clay minerals might play a role in chemical evolution because of their to take up, protect (from UV radiation), concentrate and catalyze the polymerization of organic molecules These surfaces might not only have concentrated these organic compounds together, but also helped arrange them into organized patterns much like our genes do now. After a while, organic molecules evolved to the point where they learned to replicate without the crystals clay (genetic take over).  sheet Minerals=Clays: features Assembly deformation assembly Translation Hydrated minerals (OH group in the structure more abundant that Assembly spaces Si) Cl, F, NH4 presence, also C (Cuadros, 2017) Montmorillonite swelling Particle anisotropy Several surfaces: external basal (planar)and edge surfaces (interlayer) Surface can be modified (by adsorption,ion exchange or grafting) Properties: plasticity, hardening on drying or firing. Hydrophobic–Hydrophilic Colloid forms Pores: Channeled structures and wide surface that favor mineral-fluids Aggregation and spaces interaction [email protected]  Typical structure of Montmorillonite Two outside sheets, called tetrahedral sheets, contain silicon ions tetrahedrally coordinated to oxygens. The middle sheet, called the octahedral sheet, is made up of aluminum ions surrounded by oxygens in octahedral coordination. Some of the Si4+ ions in the tetrahedral sheet are replaced by Fe3+, and some of the Al3+ ions in - **Montmorillonite** is a type of clay mineral that the octahedral sheet are replaced has a **layered structure**. It consists of three main sheets: by Mg2+ ions: excess of negative - **Tetrahedral sheets (top and bottom)**: These contain silicon ions (Si4+) that are bonded to oxygen ions in a charges **tetrahedral arrangement**. This means each silicon ion is surrounded by four oxygen atoms forming a pyramid-like structure. - **Octahedral sheet (middle)**: This sheet contains aluminum ions (Al3+) surrounded by oxygen atoms in an **octahedral arrangement**. Here, aluminum is bonded to six oxygen atoms, creating a six-sided shape (octahedron). - **Ion substitution and charge**: - Some of the **Si4+** ions in the tetrahedral sheet can be replaced by **Fe3+** (iron ions), and some **Al3+** ions in the octahedral sheet can be replaced by **Mg2+** (magnesium ions). - This substitution causes a **negative charge** in the structure, because Fe3+ and Mg2+ have fewer positive charges than the ions they replace. These negative charges balance out by attracting **positively charged ions** in the spaces between the sheets. Particles of montmorillonite consist of irregular platelets that stack on top of each other when dry. When water - **Structure behavior**: is added the metal ions in the interlayer become hydrated, which expands the distance between the platelets. - When montmorillonite is **dry**, its platelets (flat pieces) stack on top of each other. - When **water** is added, the metal ions between the layers get **hydrated** (water molecules attach), which **expands the distance** between the platelets.  STATE OF TRANSITION AND ENERGY OF ACTIVATION Transition state theory Free energy diagram extended to include the transition state (‡) through which the molecules must pass to go from S to P and vice versa. The transition state is the highest point of the curve, when the molecule can decay to S or become P The molecules in the transition state do not correspond to a stable chemical species, but represent a transitory molecular moment in which the breaking/formation of a bond, a charge, etc. they are transitory. altezza The difference between the energy levels of the basal state and the transition state is the activation energy (G‡) necessary to align the reacting groups, form transient charges, reorganize the bond and percorso everything necessary to promote the reaction ### Activation Energy and Transition State Theory A high activation energy corresponds to This is about **how reactions happen** and what energy is involved: a low reaction rate! - **Transition State Theory**: - In a chemical reaction, the reactants (starting molecules) need to pass through a **transition state** to become products. - The **transition state** is a high-energy point where the bonds are breaking and forming, but it’s not a stable molecule. - The **activation energy (deltaG)** is the amount of energy needed to reach this transition state. The higher the activation energy, the **slower** the reaction because molecules need more energy to get to the transition state.  Catalysts are chemical compounds that increase the rate of a reaction by lowering the activation energy required to reach the transition state. Unlike reactants, a catalyst is not consumed as part of the reaction process. The process of speeding up a reaction by using a catalyst is known as catalysis. Types of catalysis Acid-base catalysis (transfer of protons from an acid or acceptance of protons from a base) Covalent catalysis(transient formation of a covalent bond between the enzyme and the substrate Catalysis by metals(they promote the correct orientation of the substrates, mediate redox reactions and stabilize/shield opposite charges) -- **Catalysts** - **Catalysts**: are substances that **lower the activation energy**, making reactions happen faster. Catalysts are not used up in the reaction, meaning they are available to help with many reactions. ### Types of Catalysis - **Acid-base catalysis**: Involves transferring **protons (H+)** to or from a molecule. - **Covalent catalysis**: The catalyst temporarily forms a **covalent bond** with the molecule being reacted. - **Catalysis by metals**: Metals can help align molecules properly and sometimes help with **electron transfers** (redox reactions). ### Collision Theory and Activation Energy - **Collision theory** explains that molecules need to **collide** with enough energy and in the right orientation for a reaction to happen. - Increasing temperature or reactant concentration increases the chances of collisions happening. - If molecules collide with **too little energy** or in the **wrong orientation**, the reaction won’t happen. - **Energy profile of a reaction**: Activation energy - When a reaction happens, the energy goes up to the **transition state** (high energy) and then drops down to form the **products**. Collision theory: agitated by thermal motion, the molecules of the reactants collide relentlessly. Increasing the concentration of the reactants and/or the temperature of the ility system, raises the probability of collision events Valitutti, Falasca, Amadio Lineamenti di chimica © Zanichelli editore 2019  Activation energy For the reaction to take place (effective collisions): a certain number of collisions must occur between the molecules of the reactants the collisions must occur with appropriate orientation the particles must have sufficient kinetic energy. Energy trend during the reaction (energy profile). Valitutti, Falasca, Amadio Lineamenti di chimica © Zanichelli editore 2019  Classify catalysts as either heterogeneous or homogeneous depending on whether they occupy the same phase as the reaction mixture ### Homogeneous vs. Heterogeneous Catalysts - **Homogeneous catalysts**: These are in the same phase (solid, liquid, or gas) as the reactants. For example, enzymes are homogeneous catalysts in **biological reactions**. - **Heterogeneous catalysts**: These are in a different phase from the reactants, often solid catalysts in liquid or gas reactions. For example, in the petroleum industry, solid catalysts speed up reactions. in **RNA formation** by catalyzing reactions that link nucleotides (building blocks of RNA). - When **activated nucleotides** bind to clay surfaces, they form longer RNA chains. The rate at which these chains grow depends on the **type of nucleotides** and how they are oriented on the clay.  Enzymatic catalysis are examples of ### Enzyme Catalysis (Homogeneous Catalysis) **active sites**. homogeneous catalysis - **Enzymes** are biological catalysts (usually proteins) that speed up biochemical reactions. They work by **binding** reactants (called **substrates**) at specific - Enzymes lower the activation energy by **stabilizing** the transition state and **orienting** the substrates properly for the reaction. Homogeneous - **Specificity ofcatalysis enzymes**:involves thehighly Enzymes are introduction ofsubstrates. specific to their an aqueous phase They only catalyst bind well into to certain an aqueous molecules and help solution in reactions of reactants. involving those specific molecules. Enzymes are **chemoselective**, **regioselective**, and **stereoselective**, meaning they can choose specific chemical groups, positions on molecules, or shapes of molecules to work with. Enzymes are a special class of catalyst that can accelerate biochemical reactions. Enzymes are proteins that bind reactants, or substrates, in regions called active sites. Upon binding, conformational changes in enzymes result in stabilization of the transition state complex, lowering the activation energy of a reaction. An advantage of homogeneous catalysis is that the catalyst mixes into the reaction mixture, allowing a very high degree of interaction between catalyst and reactant molecules.  ENTROPIC REDUCTION OF S: PROXIMITY AND ORIENTATION INDUCED BY BINDING TO S 1. Reduction in the relative motions of substrates that must react with each other: Entropic reduction produced by proximity and orientation This is one of the major contributions to catalysis as it promotes productive collisions between two molecules. ### Entropic Reduction in Catalysis - **Entropic reduction** refers to the **reduction in freedom of movement** of substrates as they are bound to the enzyme. This helps them **align correctly** for the reaction and **promotes productive collisions**. - **For example**: When two molecules need to react, if they are randomly moving, they might not collide in the right way. Binding them to a catalyst reduces their random movement (entropy), making the correct collision more likely. Reactions between an ester and a carboxyl group to produce anhydrides. The rate increases by reducing the entropic degrees of freedom of the reactants.  SPECIFICITA’ DEGLI ENZIMI The functional groups of E that are able to form optimal interactions in the transition state with a given substrate will not bind as well to a different substrate, and E will show towards the latter less specificity Enzymes have a very high degree of specificity with respect to the identity chemical identity of the reactants (substrates) and the products of the reactions catalyzed by them. Gli enzimi sono chemioselettivi, regioselettivi e stereoselettivi.  Classify catalysts as either heterogeneous or homogeneous depending on whether they occupy the same phase as the reaction mixture Generally, heterogeneous catalysts are solid compounds that are added to liquid or gas reaction mixtures The reason such catalysts are able to speed up a reaction has to do with collision theory. According to collision theory, reactant molecules must collide with proper orientation. A catalyst essentially acts like a “traffic cop,” aligning molecules in just the right way so that it’s easier for them to combine and react. N.B- limitation of heterogeneous catalysis has to do with the available surface area of the catalyst ### Catalysis by Clays - **Clays** like **montmorillonite** can also act as catalysts. They often contain **metal ions** like Fe3+ and Mg2+, which can donate or accept electrons, aiding in redox reactions. - **Clay minerals** can catalyze acid-base reactions (proton transfer) and can also interact with **organic molecules** to promote various organic reactions by **binding molecules** in their layers.  Typical structure of Montmorillonite Two outside sheets, called tetrahedral sheets, contain silicon ions tetrahedrally coordinated to oxygens. The middle sheet, called the octahedral sheet, is made up of aluminum ions surrounded by oxygens in octahedral coordination. Some of the Si4+ ions in the tetrahedral sheet are replaced by Fe3+, and some of the Al3+ ions in the octahedral sheet are replaced by Mg2+ ions: excess of negative charges Particles of montmorillonite consist of irregular platelets that stack on top of each other when dry. When water is added the metal ions in the interlayer become hydrated, which expands the distance between the platelets.  Clay minerals derive from weathering of Volcanic ash around the volcanic source The crystal structure of clays consists of layers of SiO4 tetrahedra bound to layers of AlO6 octahedra. These sheets bind to each other like “a deck of cards” by van der Waals forces and interlayer cations. Clays often incorporate Mg2+, Fe2+, and Fe3+ in place of Al3+ in the octahedral layers and Al3+ for Si4+ in the tetrahedral layers (replacement of a higher valent element with a lower valent one, generating negatively charged sites where substitution occurs) Most clay minerals absorb organic compounds binding them in the interlayers, and the clay expands to accommodate them. In some instances, the organics form complexes with the interlayer cation.  Catalytic properties of clay ### Clay Catalysis and Prebiotic Chemistry - **Prebiotic chemistry** refers to chemical reactions that might have happened before life began on Earth. - **Clays** might have played a role in **RNA formation** by catalyzing reactions that link nucleotides (building blocks of RNA). - When **activated nucleotides** bind to clay surfaces, they form longer RNA chains. The rate at which these chains grow depends on the **type of nucleotides** and how they are oriented on the clay. Clay minerals are well known to mediate redox reactions— the donation and acceptance of electrons, especially from iron in the clay lattice or interlayer Some clays promote acid-catalyzed reactions, because hydrogen ions readily exchange with other cations in montmorillonite. This ion exchange generates strongly acidic clay that catalyzes a wide variety of reactions initiated by the donation of a proton to the organic substrate. The positively charged organic molecule then undergoes elimination, addition, or rearrangement reactions. Clays also have the ability to accelerate organic reactions through the action of bound metal cations since the restricted movement and orientations of the metal complexes and the reacting substrates in the interlayer have led to greater reactivity of the bound organic molecule.  CLAYS AND THE PREBIOTIC SYNTHESIS OF RNA OLIGOMERS Activated monomers bind more strongly than the unactivated nucleotides (they have one less negative charge) especially under acidic conditions ((basic purine and pyrimidine rings are protonated). Activated purine nucleotides with their larger aromatic ring structures bind more strongly than pyrimidine nucleotides— (van der Waals forces allow stronger adsorption of these molecules onto clays) RNA oligomer formation is sequence selective (most dimers have a purine nucleotide at their 5’-end. ) Clay-catalyzed RNA elongation depends strongly on the specific bases exposed at the 3’-end of the strand. Pyrimidine nucleotides elongate at a significantly slower rate than purine nucleotides. Clay catalysis of a mixture of D and L nucleotides results in the formation of dimers that are predominantly D-D or L-L, as opposed to mixed D-L (Joshi et al. 2000). Daily addition of activated nucleotides to a 10-mer primer that had adsorbed on the montmorillonite, the primer elongated by adding as many as 40 monomers units over a two weeks period of time CLAYS AND THE PREBIOTIC SYNTHESIS OF RNA OLIGOMERS Activated monomers were added daily to 32pdA(pdA)8pA bound to montmorillonite, leading to the formation of 10-, 20-, 30- and 40-mers with 70% of 3’-5’ linkages) SiO4 silicon–oxygen tetrahedra,  Clay mineral particles on the beach undergo repeated drying and wetting, being dried at low tide, and wetted at high tide. This condition would favor polymerization of the clay-associated organic molecules. Using kaolinite and bentonite as the clay minerals, and glycine as the organic species, Lahav et al. (1978) obtained measurable amounts of glycine oligomers up to the 5-mer. Ferris et al. obtained about 50-mers of glutamic acid by incubating (activated) glutamic acid with illite.