November 20, 2009 Bioe 109 Fall 2009 Lecture 23 The origin of life

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1 November 20, 2009 Bioe 109 Fall 2009 Lecture 23 The origin of life - the question of when and how life originated on earth is perhaps the most profound and difficult question to answer. - the earth itself is approximately 4.55 billion years old. - the time at which life first appeared on earth keeps getting pushed further and further back in time. - we now think that life may have arisen about 3.8 billion years ago. - this creates a dilemma because it is unlikely that our planet could have sustained life over the first 500 million years. - this means that life must have evolved almost as soon conditions were favorable for it to occur (within a 200 million year window). - although this represents a considerable amount of time, the first forms of life we see in the fossil record are rather sophisticated (i.e., they are photosynthetic). - there are two additional problems is accounting for the origin of life on earth. - the first is the fact that even the simplest of cells we see today are enormously complicated. - furthermore, their ability to carry out the diversity of tasks necessary for their survival and reproduction is based on the enzymes - catalysts that speed up the rate of biochemical reactions several thousand fold without themselves being consumed. - how did primitive cells live and evolve without enzyme-catalyzed metabolism? - the second problem is that conditions on our planet when life evolved were substantially different than today. - in fact, there is still disagreement as to the precise composition of the early earth s atmosphere. - this complicates attempts to reconstruct the steps that lead to both the evolution of simple organic molecules and the evolution of the simplest proto-cells from these precursors. How do we define life? - what is life? - there is no consensus over the key defining features of living organisms. - however, most biologists would agree that the following criteria for defining life should be met: 1. It must be capable of reproducing. 2. It must possess a genotype and a phenotype. 3. It must possess a metabolism. 4. It must be capable of evolving. - in all of these criteria are accepted then viruses would not qualify as being alive because they do not possess genes encoding for energy-producing biochemical pathways.

2 Theories for the origin of life on earth. 1. Extraterrestrial theories. - an extraterrestrial theory for the origin of life on earth is older than you may think. - it dates back to the Swedish chemist Arrhenius proposed the theory of Panspermia in panspermia simply means germs everywhere. - this theory proposes that life originated elsewhere in the universe and drifted from planet to planet by pressure of starlight. - the earth was therefore seeded by germs - this is unlikely given the dangers of space travel on living matter (i.e., UV radiation) although microbes may have arrived under the protection of an icy envelope in a meteorite. - this theory does not have a particularly wide support - the conditions under which life (as we know it) originated seem rather restrictive. 2. The chemical theory - if an extraterrestrial origin for life is discounted, just one possibility remains. - life originated de novo from molecules produced abiogenically - i.e., not manufactured by organisms. - this is the chemical theory. - this theory proposes that life originated on earth following a period of chemical evolution under conditions when the earth s atmosphere contained no oxygen. - during this period, simple inorganic molecules reacted to form organic molecules like amino acids and sugars, which in turn formed more complex compounds like macromolecules. - organized replicating systems then protocells, then ultimately true cells evolved. - this theory is also called the Oparin-Haldane theory because it was conceived independently by the Russian biologist A.I. Oparin and the British geneticist J.B.S. Haldane in the 1920 s. - the basic theory involves a series of intermediate steps: inorganic molecules organic molecules biological polymers replicating systems protobionts true cells Step 1: inorganic molecules organic molecules

3 - were conditions favorable in this pre-biotic ocean for organic molecules to be formed from inorganic precursors? - two sources of evidence suggest that the answer to this question is yes. 1. Extraterrestrial evidence from meteorites - prebiotic chemical evolution should be reflected in extraterrestrial material like meteorites that reach the earth. - this is because if chemical evolution is likely to happen, the early earth should not have been alone in producing such compounds. - since the 19th century meteorites were known to contain organic compounds. - however, it was difficult to say unequivocally that the organic material discovered in meteorites originated elsewhere, or whether it represented contamination from terrestrial sources. - unambiguous evidence for extraterrestrial organic molecules was obtained in the early 1970 s when 2 meteorites were studied in great detail. - one of these was called the Murchison meteorite found near Murchison, Australia. - the Murchison meteorite was found to contain amino acids that were mixtures of D and L isomers. - this is a very important observation because all organisms on earth are composed of L isomers. - furthermore, over 70 different amino acids were discovered in the Murchison meteorite, many of which have never been seen before on earth. - this is obviously a significant finding because all organisms alive today possess proteins that are composed of only 20 amino acids - therefore, the organic compounds discovered in meteorites are consistent with the chemical theory. - the discovery of organic compounds in meteors not only supports a key component of the Chemical Theory but also suggests that this may have been a major source of such compounds during the early history of the earth. - this is because the earth was bombarded by substantial numbers of large meteors between 4.4 to 3.8 bya when the solar system was still forming. - substantial amounts of organic material may have been delivered to the earth from this source. 2. Laboratory experiments - what energy sources were available for pre-biotic chemistry? - the obvious source is the sun - but the crucial factor is not the amount of energy but rather the type of energy available. - only radiation with a wavelength below 200 nm can dissociate ammonia and water into free radicals that can initiate syntheses of larger compounds. - about 1.2% of UV radiation can do this, but this is still the main source. - the other source of energy is electric discharges. - the scenario for chemical evolution is for an anoxic, slightly reducing atmosphere is acted on by UV radiation and electric discharges.

4 - the most famous experiment attempting to replicate the synthesis of chemicals in the early atmosphere was performed by Stanley Miller at the University of Chicago in Miller sealed water in 200 ml vessels, removed the air, added hydrogen, methane, ammonia, and water vapor. - the water was boiled and an electric discharge was passed through the chamber for a week. - after this time, the water turned red due to the synthesis of organic compounds. - in the mixture were 10 of the 20 amino acids that occur in proteins, fatty acids, purines, pyrimidines, aldehydes and sugars. - there was one problem with this experiment - it didn t mimic the early atmosphere in that it was too strongly reducing. - more recent work by Miller to address this problem produced the wrong things - nitrous and nitric acids instead of organic compounds. - some of these problems have been solved by adding dissolved iron to the reaction soup - this iron was likely to present as clays in the early ocean. Step 2: inorganic molecules biological polymers - more recently, experiments have attempted to synthesize polymers of nucleic acids and proteins on the surfaces of clays. - clays have the appealing property that they readily absorb organic molecules and can join them together and shield them from hydrolysis (that would occur in solution). - the clay mineral montmorillonite has been used to synthesize polynucleotides up to 40 nucleotides long. - a mixture of two minerals - illite and hydroxylapatite - have been used to synthesize polypeptides up to 55 amino acids long. - therefore, the formation of polymers of organic molecules appears feasible. Step 3: biological polymers replicating systems - the next step of the chemical theory presents the most serious difficulties. - the acquisition of the capacity to self-replicate is undeniably the point at which non-living matter came to life. - no one really knows how this could have happened. - Cairns-Smith and his colleagues have proposed that the first self-replicating proto-organisms were the clay minerals themselves. - it is proposed that these clay crystals may have the capacity to replicate simply by growing layer by layer, as these minerals have a tendency to do. - if some interaction developed between the clay minerals and the biological polymers on them resulted in enhanced stability, or the capacity to replicate more faithfully, or grow more rapidly, then the clay-polymer hybrid would have had a stronger selective advantage over others. - this is an important point because the process of natural selection could have operated on entities in that gray area between life and non-life in an analogous fashion to how it operates today in the organic world.

5 - natural selection could have, and probably did have, an important role to play in the evolution of the first proto-cells. - according to this model of Cairns-Smith there would have been a genetic takeover of the replicating function of these clay-polymer hybrids. - it is clear that the first self-replicator was RNA and not DNA. - what is the evidence that RNA preceded DNA? The RNA world - there is now growing evidence that the early world may have been RNA-based. - this was first hinted at by the discovery in 1982 that RNA molecules can possess catalytic activity. - these ribozymes thus may have preceded proteins as the first catalytic molecules. - over two dozen ribozymes have now been characterized. - more recent studies that are described in the textbook show that, in vitro, RNA too can evolve. - a number of labs now routinely employ selection experiments on ribozymes in which the trait selected is the capacity to perform a different chemical reaction, or increase in the efficiency by which it catalyzes an existing function. - starting from a variable RNA population, catalytic activity has been found to be a trait capable of evolving quite rapidly. - a growing number of catalytic reactions have been performed by ribozymes, including aminoacyl transfer, carbon-carbon bond formation, and peptide bond formation. - there is still one problem, however - replication. - all selection experiments performed to date have helped the RNA population replicate itself. - without the capacity for self-replication, we are missing one of the most components for life. - experiments again have shown that ribozymes can be selected that catalyze the formation of phosphoester bonds - i.e., make growing strands of RNA. - however, the capacity to make RNA molecules is limited and much work needs to be done. - additional evidence suggesting that RNA preceded DNA comes from the fact that: 1. RNA is involved in DNA replication. 2. RNA plays a major role in protein synthesis. 3. Ribonucleoside triphosphates (ATP, GTP) are the energy currency of cells. 4. Deoxyribonucleotides are synthesized from RNA precursors. - it is still along way from a self-replicating RNA molecule to the simplest living cells. - we can identify a number of advantages that the DNA world has over the RNA world. - one of the most significant advantages provided by DNA is that it is much more stable than RNA. - in double-stranded form, DNA becomes even more stable and can withstand high temperatures and spontaneous breakdown by acids or bases. Step 4. Replicating systems protocells

6 - one interesting possibility for how these simple proto-cells evolved came from experiments by Sidney Fox at the University of Florida in the 1950 s. - Fox showed that heating mixtures of amino acids and then allowing them to cool it is possible to form protein-like polymers called proteinoids. - when cooled these proteinoids can produce protein microspheres. - these proteinoid microspheres may represent a model for early protocells. - several features of these microspheres may have favored the arisal of early proto-cells, notably the capacity of these microspheres to protect and concentrate organic material in a favorable microenvironment. - more recently, experiments have shown that lipids, or mixtures of lipids and proteins can form spontaneously in solution. - these liposomes have a lipid bilayer similar to that seen in living cells. - because the bilayer is semi-permeable, liposomes can undergo swelling or contraction if exposed to varying salt solutions. - they also have been found under some conditions to develop a membrane potential and to bud off smaller liposomes or engulf others. - liposomes can also uptake substrates from their surroundings. - if an RNA-protein based metabolism was established in primitive protobionts, natural selection could have again entered the picture to favor microspheres over others if they possessed a replicative advantage. Step 5. Protobionts true cells - this last step would involve an increase in the biochemical sophistication of the protobionts and the evolution of DNA as the repository of the genetic information. - DNA has a number of advantages of RNA (notably its greater stability) and this would have freed the RNA to greater catalytic efficiencies (since it was freed from having to serve both functions). What is the evidence for prokaryotic life 3.5 to 4 bya? Two sources: 1. stromatolites. - these are bun-shaped structures living in shallow tropical seas made by cyanobacteria. - Pre-Cambrian stromatolites are very abundant 3.5 bya and were though to be extinct. - however, stromatolites identical in appearance to these ancient fossils have recently been discovered. - the most famous occur in the Hamelin pool, Shark Bay in western Australia. 2. early photosynthesis from C isotope ratios.

7 - isotopic ratios of 13 C to 12 C indicate that autotrophic bacteria fixing carbon via the Calvin cycle for at least 3.5 by CO 2 is preferentially fixed in photosynthesis than the heavier 13 CO 2. - therefore, organic matter produced by photosynthesis has a higher ratio of 12 C to 13 C than the pool of inorganic carbon. - Greenland samples, dating to 3.8 bya, indicate carbon fixation. - if oxygen was being produced at this time, what came of it? - the earth s atmosphere did not become enriched in oxygen until 2 bya? - it is accepted by many paleontologists that reduced iron acted as an oxygen sink, forming a signature of banded ironstone in sediments between 2 and 2.5 bya. - it wasn t until the oxidizing of iron was complete that oxygen would begin to accumulate in the atmosphere. - the current guess as to when this occurred is around 1.8 to 2.2 bya. The origin and early evolution of the eukaryotes - recently, there have been a number of new hypotheses proposed for the early evolution of eukaryotes. - all have developed from insights provided from complete genomes of various Archea, Bacteria, Eucarya, and various viruses. 1. The universal gene-exchange pool hypothesis - this hypothesis was proposed by Carl Woese, who was the initial discoverer of the Archaea and the first to assemble a universal tree of life (based on ribosomal RNA gene sequences). - Woese realized that significant conflict existed between the branching patterns provided by different genes. - to explain this conflict, Woese has proposed that the Archaea, Bacteria, and Eucarya evolved only after extensive lateral gene transfer ceased. - this hypothesis predicts that initially there weren t distinct vertically propagating lineages but rather a communal pool of organisms swapping genes horizontally. - this hypothesis downplays the importance of natural selection and has been extremely controversial. 2. The ring of life hypothesis - this hypothesis posits that Eucarya evolved from a fusion of a bacterium and an archean. - the evidence for this comes from complete genome data that indicates some eukaryote genes are similar to Bacteria while others are more closely related to Archaea. - this hypothesis is not supported by evidence suggesting that the bacterial and archaeal genes present in eukaryotes arose at different times from different lineages, nor can it account for the hundreds of proteins unique to eukaryotes. 3. The chronocyte hypothesis

8 - this hypothesis was proposed by Russ Doolittle. - Doolittle proposed that an early chronocyte lineage evolved that possessed a cytoskeleton and the ability to consume other microbes by phagocytosis. - this chronocyte lineage engulfed an archaean that became an endosymbiont - the endosymbiont eventually become the nucleus. - no living chronocyte has been found. - however, recently Hartman and Fedorov (2004) identified 347 unique genes in eukarotes, many of which are involved in building the cytoskeleton and inner membranes. 4. The three viruses, three domains hypothesis - this controversial hypothesis was proposed recently by Patrick Forterre. - Forterre proposed that DNA-based viruses evolved to counter their host s defenses (these were RNA-based). - this would have been a highly successful strategy and DNA-based viruses could have invaded RNA-based lineages. - Forterre proposes that the host s RNA genes were reverse-transcribed into DNA and incorporated into three new lineages. - some support for this hypothesis has been provided by the phylogenetic distributions of DNAdependent RNA polymerases (see Fig on page 679). - however, this hypothesis is the most controversial proposed to date.