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Chapter 16 The Origin of Life and Precambrian Evolution 3 Main Questions are being pursued about the origin of the Earth 1. What was the first living or primordial form? 2. Where did it come from? 3. What was the last common ancestor (cenancestor) of today's organisms and when did it live? What was the first living thing? What was the first living thing? • The origin of life has been under investigation (observational studies as well as experimentation) for almost 80 years. • The main problem lies in the question “which did life acquire first, proteins or nucleic acid?” What was first , RNA, DNA or Protein? • PROTEIN – can do complicated biological tasks but cannot propagate themselves • DNA – can propagate but cannot do any kind of biological work. Ribozymes • Ribozymes discovered in 1982 by Sidney Altman and Thomas Cech • Enzymes that could break and reform bonds that link nucleic acids into chains – Enzymes were not made of protein, but nucleic acid (RNA) • Dozens of naturally occurring ribozymes have now been discovered. Structure of Rybozymes • 30 to 1000 ribonucleotides long • Single stranded • Molecule folds back on itself many times to form a three dimensional structure. • This structure provides and active site that enables it to have catalytic activity. An RNA World? • RNA used to be thought of as DNA’s poor cousin. • With the discovery of Rybozymes many researches envision a time when life was based entirely on RNA – An RNA world. • RNA shows all of the following characteristics: – Catalytic ( biological work) – Information storage – Information transmission An RNA World ? • RNA simultaneously possesses a – Genotype – its primary sequence – Phenotype – its biological reactivity . ( by virtue of its ability to fold back on itself and form an active site.) Does RNA represent the first molecules of life? • Supportive evidence – RNA is an ancient molecule – Found in the most highly conserved information processing machinery – the ribosome. – It is the RNA in ribosomes that catalyze the formation of peptide bonds in translation. – Ribonucleoside triphosphates are the major component of energy molecules in cells – ATP, NAD, FAD Defining Life • One of the defining characteristics of life is the ability to evolve – Descent with modification requires • the ability to record and make alterations in heritable information (genotype). • The ability to distinguish valuable changes from detrimental ones (variation in phenotype). Shown to evolve in test tube experiments • Populations of catalytic RNA exhibit variation in nucleotide sequence. • This variation is heritable • Researchers have devised experiments in which sequence variation results in differences in survival • Exmple: Qb bacteriophage with replicase One important problem remains with RNA as first molecule of life • RNA cannot copy itself without the help of proteins. – Some research is being done to find RNA Ribozymes capable of synthesizing RNA. Some success so far. – RNA autoreplicase remains a Holy Grail for origins of life research. The question still remains • Where did the first RNAs come from? What was the early atmosphere like? • Quite a debate • Was it oxidizing, made up of mostly O2 and CO2 or • Reducing made of H2 , CH4 and NH3 • Or maybe intermediate. …or….. • Maybe the earliest organic molecules came from outer space via meteorites. – Murchison meteorite provide direct evidence that some organic molecules have survived the trip to earth from outer space (dozens of amino acids.) Miller and Urey 1953 • Miller and Urey used a highly reducing atmosphere and electric sparks to produce a mixture of organic molecules (including some amino acids) in just one week. But ancient atmosphere now believed to be more oxidizing • We now believe that the atmosphere was not so reducing being mostly CO2 instead of methane. • A CO2 dominating atmosphere has been shown to be able to produce aldehydes (needed to make ribose) from carbon dioxide The Oparin-Haldane Model A null model to be used to test hypotheses for the formation of the first molecules of life. 1. Simple building block molecules such as Cyanide, methane, carbon dioxide, ammonia need to be assembled into organic molecules such as amino acids and nucleotides. 2. Organic molecules need to be assembled into biological polymers 3. A combination of biological polymers is assembled into a self-replicating organism that feeds off of existing organic molecules How do we get from inorganics to the building blocks of life? • Juan Oro and others have showed adenine could be made form ammonia and cyanide. • Pyrimidines harder to synthesize • Ribose sugars can be made from formaldehyde • Problem is in the handedness that biological systems use is not faithfully produced by these reactions • Lots of questions remain Next problem is the assembly of biological molecules into polymers • James Ferris – showed that polymers could be formed from nucleotides and amino acids in a prebiotic soup. • Used a clay material on which the polymers were allowed to form. – Otherwise, hydrolysis in water would immediately destroy polymers as they were formed. • Clay also acts as a catalyst to join subunits together Early on the earth was not conducive to formation of stable organic molecules or “life” The extreme heat of the earth along with regular meteor impacts prevented life from forming earlier than about 4.4 to 3.8 bya The hot earth, volcanic activity, plate tectonics, and erosion have destroyed most evidence of the earliest life. • The first evidence that life existed dates back to 3.85 billion years ago. Evidence that life arose shortly after the environment allowed Formation of Cellular Life • Finding the Most Recent common Ancestor of all living things – the cenancestor • Use principle of parsimony (the simplest explanation with the fewest steps that can explain all of the evidence) • • • • • Shared features of all living things DNA – heritable info Proteins- how DNA is expressed Same 20 amino acids Use the same genetic code Cell is basic unit of life – Needed for compartmentalization so chemicals can be concentrated in the cell – Needed to link a genotype to a phenotype so traits can be passed on Long way from self-replicating RNA to cells • Sidney Fox found that mixtures of polyamino acids in water or salt solutions spontaneously form microspheres The geological record provides signs of when life formed • Oldest fossils come from Apex chert in Western Australia • Simple cells growing in short filaments believed to be cyanobacteria • Probably already fairly high up on the evolutionary tree Due to incomplete fossil record, no way to know if these are ancestors of all living things or if they died out Need other methods to determine ancestral cell lineages Searching for a universal phylogeny • First tried to construct a phylogeny based on morphology but • Prokaryotes lack sufficient structural diversity to allow morphological comparisons for a phylogeny · • Also not enough detail in the fossil record The END Latest techniques read sequences in proteins or DNA structure • Use relative similarity of sequences to infer their relationships • More similar sequences go on neighboring branches, less similar on more distant branches Goal is to make an evolutionary tree for all living things • • • • Need a gene that is present in all organisms subject to strong stabilizing section function has remained the same in all organisms • Example gene which codes for the RNA in small ribosomal subunit studied by Carl Woese • Today used as a resource for building whole-life Basis for proposed changes in the classification system • 5 kingdom system of Whittaker bears little resemblance to actual evolutionary relationships • Prokaryotes on 2 of 3 main branches • Bacteria – includes most of the well-known prokaryotes • Archea Archea • First named archaebacteria • but shown to be more closely related to the eukaryotes than to the bacteria so now called Archea • live in physically harsh environments – hyperthermophiles – anaerobic methane producers • halophiles Very difficult to grow in lab cultures Now have 3 domains above the kingdom level Bacteria Archea Eucarya • Animalia. Plantae and Fungi kingdoms are still in pretty good shape, requiring only minor revision Protista needs to be closely looked at and broken up. The Earliest Life • Evidence indicates that the most recent common ancestor of all living things was highly evolved and biologically sophisticated A fly in the ointment Horizontal Gene Transfer • Using genes to estimate phylogeny gives different results. Lateral gene transfer • Scientists working on a universal phylogeny .... – Are finding examples of lateral gene transfer at a rapid pace – Believe that early in life’s history lateral transfer of genes was rampant – Think that phylogenies being built do not reflect the organisms phylogeny but only the phylogeny of the genes being used to construct those phylogenies For example phylogenies like this one in figure 6.18 on page 641 These scientists believe that this is more representative of what early history looked like. Recent studies have shown that... • Bacteria are showing lateral gene transfer at an astonishing rate. • Two strains of E. coli believed to be closely related strains show one strain, O157:H7, which causes food poisoning has 1,387 genes not found in the non-virulent K-12 strain. • On the other hand K-12 has 528 genes not found in O157:H7. • Another study showed that 18% of E. coli genes were acquired by lateral gene transfer. How do we root the estimated phylogeny of all living things • Look for the cenancestor or Most recent common ancestor by using parsimony • Need to make inferences about certain fundamental cellular traits • Map character state changes onto phylogenies • If a trait occurs in all three domains it belonged to the cenancestor . …. or …. • If it occurs in two of the domains but not the 3rd , we can infer that the trait occurred in the most recent common ancestor and was lost in one of the lineages. • Otherwise the trait would have had to arise 2 or 3 different times which is much less likely because it would require more evolutionary transitions. More evidence is being gathered all the time on the Archea • Increased information is expected from comparing whole genome sequences. This will allow the comparison of a great number of genes. Much of the new information seems to indicate that there may not have been just one single common ancestor Evidence shows that there has been lateral transfer of genes between organisms, perhaps at a very high rate early on in evolution of life Figure 14.14 Phylogenies like those shown in the text may actually only reflect the evolution of genes being looked at When did life begin • The earliest possible date is between 4.4 and 3.85 billion years ago • Based in estimated universal phylogeny • geological data • paleontological data From prokaryote to Eukaryote, Origin of organelles • Evolution from common ancestors to the Bacteria and Archea appears to have occurred slowly and by a process of gradual refinement • Eucarya differ from Bacteria and Archea in much more dramatic ways • More complicated genomes • introns ( noncoding DNA regions) • organelles • multicellularity – tissues Evolution of organelles • All evidence points to evidence that mitochondria and chloroplasts at least arose as endosymbionts – superficially resemble simple bacteria – contain DNA – The Genes in their DNA fits with the phylogeny of the bacteria rather than the eukarya – mitochondria are closely related to the purple bacteria – Chloroplasts are closely related to the Organelle genomes • Chloroplast and mitochondrial DNA is much more highly conserved than nuclear DNA • Mitochondrial DNA is very different in fungi , plants, and animals • Chloroplasts and mitochondria contain only a fraction of the DNA in a bacterial cell. • Abundant evidence exists that chloroplasts and mitochondria transferred genes to the nucleus early on in their evolution A few interesting facts about organelle DNA • RuBPCase (used in the Calvin cycle of photosynthesis) has two subunits; one is coded for by chloroplast DNA, the other in the nuclear DNA • A gene which codes for a translation factor is found in chloroplast DNA in green algae but in the nucleus in flowering plants • The cox 2 gene (used in aerobic respiration) is found in mitochondria of most plants but in mung beans it is found only in the nucleus and in legumes it is in both nucleus and mitochondria. The End first second