Lecture 18 - Origin of Life on Earth

Lecture 18 - Origin of Life on Earth - 1 Lecture 18 - The...

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Unformatted text preview: 1 Lecture 18 - The Origin of Life on Earth The Big Question in Evolution: How did life originate? Three questions: what IS "life on Earth", when did it originate, and (by far the most difficult), HOW did life come into being? I: What is life (on Earth, or elsewhere)? We can use the methodology of phylogenetics (i.e., parsimony) to infer the properties of the MRCA (most recent common ancestor) of all life on Earth. By parsimony, we infer the phenotype of the MRCA: 1) stored information in DNA. Or did it...? 2) translated that information into protein, using the canonical genetic code, via RNA intermediates, by means of ribosomes 3) had a cell membrane. Or did it...? - It would appear that the MRCA was not too different from certain extant bacteria - Even the simplest cellular organism is almost unimaginably complex - Does this evidence mean the FIRST life on earth was essentially bacteria-like? Q: What IS life? Old argument of philosophers of biology 1. Self-reproducing 2. Respond to environmental stimuli 3. Capable of evolving (i.e., heritable mutation) II: When did life on Earth evolve? - A brief history of time: Big Bang ~ 15 BYA, solar system accretes ~ 4.5 BYA. ~4 BYA, earth has cooled and cosmic bombardment has abated enough to support life. ~3.7 BYA the chemical signature of life appears. * Rocks from Greenland that are dated at ~ 3.7 BYA contain graphite globules that have a carbon isotope (12C/13C) ratio that is characteristic of biological processes. The oldest fossil cells are ~3.4 billion years old, found in rocks in SA - Were these fossil cells in the lineage of the MRCA? Can't say. But we can say with some confidence that cellular organisms were present AT LEAST 3.4 BYA, which puts the appearance of life on Earth farther back than that. III. The (hypothesized) Origin of Life - A little thought leads to the conclusion that life must have evolved from a molecule that could replicate itself from unambiguously non-living precursor raw materials. 2 - 1920s, Oparin and Haldane independently suggested that the primordial atmosphere was reducing (oxygen-free), and that with appropriate energy (e.g., lightning, UV) that organic compounds could be synthesized. Both envisaged associations of hydrophobic molecules in free solution. - In the 50s, Miller and Urey (and others) demonstrated that the organic precursors of biological polymers (e.g., amino acids) could form from inorganic precursors under putative "original conditions", e.g., reducing (oxygen-poor) atmosphere. * A historical problem was that the molecules known to have biological activity, i.e., catalytic ability, were proteins, but there was no known mechanism by which proteins could store the information necessary for self-replication. * Conversely, nucleic acids are known to store information, but there was no known mechanism by which they could perform biological work. - In the early '80s, Cech and Altman independently discovered RNA enzymes ("ribozymes") that could catalyze chemical reactions. * Cech's group discovered a segment of ribosomal RNA in Tetrahymena that was a self-splicing intron, i.e., it catalyzed its own removal from the transcribed RNA. * There are now many known examples of ribozymes. e.g., the catalytic function of the ribosome is thought to be at least in part a function of its RNA component. Another e.g., the snRNA element of the spliceosome. * It has also been shown that DNA can have catalytic properties * A partial list of enzymatic functions that can be performed by ribozymes include: - The discovery of ribozymes led to speculation about an "RNA world" that preceded the current DNA world (now widely accepted, doesn't mean it's true). 3 - The critical missing evidence is that no one has yet contrived a ribozyme with selfreplicating properties ("RNA autoreplicase"). The best anyone has come to date is a ribozyme that can link up to 20 nucleotides into an RNA polymer (ca. 2007). - A bigger problem is: Where did the self-replicating RNA come from? RNA doesn't just spontaneously assemble. Recent model of Koonin and Martin, built on model of Russell. Common features of all life on Earth: universal ("canonical") genetic code, homologous transcriptional/translational machinery, chirality of sugars (L) and amino acids (D). - All cells are surrounded by membranes and genomes encode >500 proteins. But, onset of life could not have been a single leap from disorganized chemicals to fullfledged cells. Process must have been a series of gradual steps, although perhaps rapid in geological time. Salient point: modern biochemistry could not have evolved in free solution. Current barrier to diffusion is cell membrane/cell wall. Thus, it is assumed that some sort of compartmentalization is necessary for the chemistry of life. BUT, Archaea and Eubacteria have membranes that consist of unrelated lipids (Archaea use isoprene ethers, Eubacteria use fatty acid esters) and the biosynthesis pathways of membrane biogenesis are not homologous. Cell walls of Archaea and Eubacteria are also very different and synthesis is not homologous. Inference #1: MRCA (=LUCA, Last Universal Common Ancestor) was NOT a free-living cell, did NOT have a cell membrane. NOTE: the inference by "parsimony" that the MRCA had a cell membrane assumes that "cell membrane" is the same character state in all taxa) Inference #2: MRCA existed within geologically formed compartments. A likely candidate: Iron sulfide (FeS) at warm (<90º C) hydrothermal spring. Such have been found at ancient hydrothermal sites, and simulated in the lab. FeS (and Fe-Ni-S) is known to catalyze a variety of biochemical reactions. Source of chemical energy provided by exergonic reaction between hydrothermal H2 and marine CO2 to produce reduced carbon compounds. Further, much of the DNA replication machinery (DNA polymerase, primase, helicase) is not homologous in Archaea and Eubacteria. Inference #3: MRCA had a modern system of transcription and translation but lacked a double-stranded replicating DNA genome - rather it probably had an RNA-based replication system. 4 However, other elements of the DNA replication machinery are homologous in all prokaryotes (sliding clamp, clamp-loader ATPase, DNA ligase), which leads to Inference #4: MRCA had a retrovirus-like replication cycle. Because RNA is unstable, MRCA might have been a set of co-inherited RNA fragments, each of which encoded one or a few proteins. NOTE: the previous inference by "parsimony" that the MRCA had a DNA-based information processing system assumes homology of the replication machinery Selection would operate among compartments in a FeS "colony". Selection would directly favor self-replicating elements, but "altruistic" elements that encoded (say) translation components or nucleic acid binding protein would be selected for their ability to enhance their own replication potential as well as of other elements, recombinants would be favored. So-called "selfish cooperatives"; replicative success = "fitness". At some point further evolution would require the association between the set of genetic elements and a replicable translation system, i.e., a ribosome. The original function of the ribosome is subject to debate (maybe not translation), but the MRCA clearly had an essentially modern ribosome. Larger, more stable information storage would be favored for co-transmission of beneficial combinations of genetic elements. Because of the instability of RNA, K&M argue that escape from the FeS compartment world would have not been possible before the origin of large DNA genomes, particularly because accurate cell-division machinery is necessary for free-living cells and is a complex undertaking. A key problem: the "Eigen-threshhold" (figure 1 from W&K): If the product of the error rate and the information capacity (i.e., mutation rate x genome size) is < 1 per replication cycle, most of the progeny will be exact copies of the parent and the system will be sustainable. If uxg > 1, most of the progeny will differ from the parent and the system will not be sustainable. Remember two distinct membrane lipid biosynthesis, might have evolved on distinct populations of the growing DNA genomes. It has been argued that the complex molecular nature of the MRCA required prior evolution of a membrane bounded system, partly because certain membrane associated enzymes such as the signal recognition particle and proton ATPase are conserved in Archaebacteria and Eubacteria. K&M draw the distinction between a "hydrophobic layer" and a "biogenic membrane", the former of which could arise geochemically in the conditions supposed (e.g., medium-chain hydrocarbons). ...
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This note was uploaded on 06/08/2011 for the course PCB 4674 taught by Professor Baer during the Fall '08 term at University of Florida.

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