The Transition to LifeThe Transition to LifeChemical Evolution Biological EvolutionInteracting Chemicals Reproduction of Organisms Natural Selection?Based on Simplest Life Now:Need:1. Nucleic Acids Replicatable Information2. Proteins Enzymes (Catalysts)3. Lipids Membranes (Enclosure)4. Carbohydrates Energy Storage(Pigments) (Energy Conversion)Too much to ask of chemical evolution⇒ Protolife?Protolife2. Protein ProtolifeProtein Self Replication?3. Nucleic Acid ProtolifeRNA Self Catalysis?Genetic Code1. “Virus” Free living but equivalent incomplexityProtein + Nucleic Acid + Supply by Environment4. Something ElseMineralsClay LayersMineral - MoleculePyriteThioestersGenetic Takeover? RNA DNAProtein-Based Protolife1. Proteinoid microspheres - Sidney FoxAmino Acids + Dry Heat Proteinoids(Hot Tidepool?) H2O (Tide) MicrospheresProtocellsProtolife? (Look like life)Can Add Proteinoid GrowSplit Divide “Reproduce”Bud BudForm Chains Like BacteriaBut “Reproduction” not exactLater incorporate Nucleic AcidsProteinoid Cells GenesProblem: How to incorporate Nucleic acids?Nucleic Acid Based ProtolifeRNA Genes Protein CellsSelf-replicating RNA moleculesExperiment by Sol SpiegelmanRNA from Qβ Virus - parasite on bacteriaInjects RNA - Bacterium makes replicase Enzyme to Replicate RNARNA multiplies, using activated nucleotides inBacterium new virusesIn Test Tube: Template RNA, Replicase,Activated Nucleotides (ATP, CTP, GTP, UTP)⇒ RNA copied without machinery of cellVariation: No template RNAReplicase made RNA from nucleotides ProteinManfred Eigen - further experiments with RNAin test tube:Mutant RNA strands competeDegrade to smallest (~ 200 nucleotides)RNA that replicase could recognize(Monster - Selfish RNA)RNA can do self-catalysis in some cases Could this have led to self replication?Eigen scenario1. A replicating RNA molecule forms bychance (random replicator - not a gene)ribozyme (catalyst, made of RNA)2. Family of similar RNA’s develops(quasispecies)3. Connection to proteins(quasispecies specialize to make parts ofprotein)4. Complex interactions (hypercycles)5. Use lipids to make protocells6. Competition leads to biological evolutionProblems with Nucleic Acid First Scenario1. Hard to get monomers2. Unlikely to link correctly3. Need existing proteins and lipids4. Hypercycles subject to instabilitiesN = size of molecular populationIf N small If N largePopulation Collapse Selfish RNA Short CircuitIf B D Short Circuit⇒ Only narrow range of sizes worksA BD CThe Origin of the Genetic Code• We need more than either protein or RNAprotolife• Need interaction via genetic code• Need translation• Consider first a scenario by R. ShapiroShapiro’s FableThe case for the “chicken”Protein first ⇒ replication problem“interpreters” aminoacyl tRNA synthetasesMatch tRNA &Amino acidsCould an earlier version have copied proteins directly?tRNAProto-interpreter1. Early Evolution: Start with 4-6 amino acidtypes, gradually add moreenzymes increase in size and catalytic power2. First use of phosphate as energy? (ATP) or sugar-phosphate chains for construction (Teichoic acids in membranes of some bacteria)(partial Qβ replicase)3. Bases added for structureSupport for protein synthesis ribosome4. Begin to copy RNA(Full Qβ replicase)Natural selection better ribosome5. Specialized, Short RNA aided attachment ofamino acids to proteins; became tRNA6. Then mRNA - to align tRNA’snow a separate genetic system that evolves7. DNA developed from RNAShapiro dates last step to prokaryote -eukaryotesplit (different ways of storing DNA info)Tests:1. Synthesize in lab? Not possible yet.2. Molecular archaeology - vestigial ability ofinterpreters to recognize amino acids inproteins3. Survivors of protein era? prions?Support for the “chicken”1. 1988 discovery that interpreter does notuse tRNA codon to recognize correct tRNA(in some cases) ~ 1/2- instead a single base pair at the other endof tRNA⇒ simpler, older code second genetic code⇒ connection of interpreter and tRNA more primitive than current code2. Dyson modeling of molecular “populations”Transition from disorder to order(non-life) (life)Finds number of monomer types likely to be9 - 11 (ok if used ~ 1/2 of modern proteins)But nucleotides (only 4) - not enoughFavors protein firstThe Egg Strikes BackOther work shows some RNA can catalyzeNon-RNA reactions1. RNA in ribosome appears to be whatcatalyzes peptide bond formationNoller, et al. 1992, Science, 256, 14162. RNA “ribozyme” catalyzes reactionsbetween amino acids and tRNAs First “interpreter” may have been RNAPiccirilli, et al. 1992, Science, 256, 1420Origin of the Genetic CodeCrucial step in any theoryAllows communicationNucleic Acids ProteinsEarly versions probably coded fewer aminoacids - less specificSome evidence for RNY and G - C more stable ⇒ 4 codons GGC glycineGCC alanineGAC aspartic acidGUC valineOthers added laterCommon inMiller Ureyand MeteoritesPurinePyrimidineEitherEvolution of Genetic CodeGaining specificityIf early tRNAs carries more than 1 kind ofamino acide.g.tRNAGlycine or alanineGlycineMutationCGGGCCmRNACCGGGCmRNAEvidence that code has evolvedFreeland, et al. Tested 106 other codesOnly one better at minimizing bad effects ofmutations⇒ Natural SelectionStill EvolvingSome organisms have slightly different codes inmitochondria or in nucleusOther Ideas• Neither the chicken nor the egg came first• Transitional forms that were later discardedOr was it the “egkin”?Some experiments with peptide nucleic acid(PNA).PNA: Peptide backbone with basesCan act as template for polymerization of RNAFrom activated nucleotides(Böhler, et al., Nature, 376, 578 & comments by Piccirilli, pg. 548 17 Aug. 1995PNA could be simpler to form under prebiotic conditionsMain point is that a simpler thing (not necessarily PNA)could have preceded RNAMembranes• Membranes provide enclosure– Also fundamental for metabolism• Membranes never arise from scratch– Always passed down and added to– All derived from ancestral cell• T. Cavalier-Smith proposes membranes– Plus nucleic acid formed “ob-cell”– Merger of 2 ob-cells formed first cellThioester World1. Need precursor to RNA world2. Need energy conversionProtometabolismBackground:C. deDuveIn Vital DustOHOHOCOHOHOCEsterHydroxyl +
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