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7/25/11 Evolution of life Molecular Evolution Early Evolution: The Building Blocks of Life Biogenesis - the development of life from preexisting life Abiogenesis - emergence of life from inanimate organic and inorganic molecules Dr. Erica Bree Rosenblum Life - an organismic state characterized by capacity for organization, metabolism, growth, adaptation, reaction to stimuli, and reproduction Evolution of life Evolution of life 4.5 3.6 b.y.a b.y.a “The duration was once considered too short for the emergence of something as complex as a living cell. Hence suggestions were made that germs of life may have come to earth from outer space…even on a spaceship sent out by some distant civilization” Inorganic materials to cellular life in a few hundred million years! 4.5 3.6 b.y.a b.y.a X Duve, Scientific American, 1995 There are now compelling explanations for how life originated on earth within a relatively short timeframe. today Formation of earth ~4.6 BYA - formation of our solar system Bombardment with interstellar debris for many million years Heat of some impacts enough to sterilize entire planet Take home message from first 1/2 billion years: Even if there were very early steps in origin of life they were likely wiped out. Probiotic chemistry Cosmic spaces contain carbon, hydrogen, oxygen, nitrogen, sulfur, silicon, etc. These small molecules can interact to form stable organic compounds. (Organic chemistry is just carbon chemistry.) Obviously not all organic compounds are alive. But carbon chemistry is the basis for life on earth. 1 7/25/11 Abiotic chemistry experiments Probiotic chemistry experiments Abiotic chemistry: aims to recreate in the lab the chemical events that lead to the early building blocks of life. Abiotic chemistry: aims to recreate in the lab the chemical events that lead to the early building blocks of life. 1828: Friedrich Wohler synthesized urea. 1953: Miller-Urey experiment Demonstration that organic compounds could be synthesized from inorganic materials without any “vital force”. Water, methane, ammonia and hydrogen sealed inside flasks - subject to heat and electricity (to simulate lightning through amtomspheric water vapor). Probiotic chemistry experiments Probiotic chemistry experiments Abiotic chemistry: aims to recreate in the lab the chemical events that lead to the early building blocks of life. After one week, nearly 15% of carbon was in organic compounds. DNA and RNA were not formed but sugars, lipids and some building blocks for nucleic acids were formed. 2% of carbon formed amino acids! What macromolecule came first? Abiotic chemistry: aims to recreate in the lab the chemical events that lead to the early building blocks of life. There is debate over whether: - experimental conditions were similar enough to primitive atmospheric conditions - experimental yields were too low to explain prebiotic processes But these and other more recent experiments demonstrate the feasibility of generating organic compounds from inorganic materials. What macromolecule came first? "At some point a particularly remarkable molecule was formed by accident. We will call it the Replicator. It may not have been the biggest or the most complex molecule around, but it had the extraordinary property of being able to create copies of itself." "At some point a particularly remarkable molecule was formed by accident. We will call it the Replicator. It may not have been the biggest or the most complex molecule around, but it had the extraordinary property of being able to create copies of itself." Richard Dawkins, The Selfish Gene Richard Dawkins, The Selfish Gene DNA RNA Proteins DNA Proteins information storage DNA processing protein production cell structure enzymatic activity Needed for protein construction Needed for DNA replication 2 7/25/11 X What macromolecule came first? Proteins? Proteins do not self-replicate. X What macromolecule came first? DNA? DNA is catalytically inert and does not directly participate in protein synthesis DNA RNA Proteins DNA RNA Proteins information storage DNA processing protein production cell structure enzymatic activity information storage DNA processing protein production cell structure enzymatic activity X What macromolecule came first? RNA? RNA can both STORE and PROCESS information X X What macromolecule came first? RNA? RNA solves the chicken and egg problem DNA RNA Proteins RNA information storage DNA processing protein production cell structure enzymatic activity DNA processing protein production X X Experimental RNA Evolution RNA can be selected for different catalytic activities in the lab, including key steps toward self. The RNA World Have not been able to recreate all these steps In 2006 Nobel Prize in both Chemistry and Medicine were awarded for discoveries related to RNA RNA “is swiftly emerging from the shadows of its betterknown cousin DNA” - Warren Leary “RNA world”: The hypothesis that RNA predated DNAbased life and may have been the first step in the evolution of cellular life Term coined by Walter Gilbert in 1986: hypothetical historical stage where: “RNA molecules and cofactors [were] a sufficient set of enzymes to carry out all the chemical reactions necessary for the first cellular structures”. 3 7/25/11 2009 Nature The pro-RNA World Have not been able to recreate all these steps 2009 Science Important distinction: “RNA Early” NOT necessarily “RNA first”. Take home message: There is strong evidence that RNA came before DNA and proteins. However, there were likely stages between the formation of the first organic compounds and the origin of RNA. More research needed to understand transition from probiotic chemistry to pro-RNA world. The pro-RNA World The RNA World Have not been able to recreate all these steps Likely stages in the pro-RNA world: - development of pathway that turned raw organic material into RNA - development of RNA replication With the origin of RNA replication, Darwinian evolution was possible. - inevitable replication mistakes generated variation. - variants which replicated faster or were more stable had an advantage - development of RNA-dependent protein synthesis Take home message: A simple Darwinian process involving variation, competition, selection, and differential survival could explain early molecular evolution. Evolution of molecular cooperation Darwinian evolution continued to generate the other macromolecules and to generate more complex enzymedependent metabolism Evolution of molecular cooperation RNA world implies existence of genetic code before DNA. DNA most likely evolved from RNA. All major macromolecules (RNA, DNA, proteins) existed by ~ 3.5 bya 4 7/25/11 Evolution of molecular cooperation There is a possibility that DNA evolved from RNA more than once! Thymidylate synthases catalyze dTMPs (necessary for DNA synthesis), and there are 2 unrelated thymidylate synthases in prokaryotic lineages. There are 2 unrelated sets of DNA replication proteins in different prokaryotic lineages Evolution of molecular cooperation Nearly all extant organisms have DNA-based genomes. Why did DNA-based (instead of RNA-based) genomes win? - DNA is mutationally less vulnerable than RNA. [e.g., RNA doesn’t correct the very common mutation from C->U] - This chemical advantage lead to more reliable production of progeny genotypes. Summary of early life First unambiguous fossils of cellular life Summary of early life: By 3.2 B.Y.A. first unambiguous fossils RNA based genomes Origin of ribosome, proteins, genetic code Filamentous organisms around hydrothermal vents Origin of DNA based genomes Membranes before or after DNA? Origin of cell membranes Timing of early diversification? Diversification of cellular life Tree of life Tree of life First billion years of life dominated by prokaryotes First billion years of life dominated by prokaryotes Simple cells without membraneenclosed organelles. Simple cells without membraneenclosed organelles. Two prokaryotic domains evolved independently from ancient common ancestor: - Bacteria - Archaea Two prokaryotic domains evolved independently from ancient common ancestor: - Bacteria - Archaea 5 7/25/11 Tree of life Tree of life 2.7 B.Y.A. First evidence of Eukaryotes cells with membrane-enclosed organelles and nucleus. Phenomenal prokaryotic diversity. Bacteria form much of earth’s biomass. 40 million bacterial cells in gram of soil. 10 times more bacterial cells than human cells in human body! Tree of life Rooting the tree of life “Three domain system” - Bacteria - Archaea - Eukaryotes For early evolution, there is evidence for a “ring of life” instead of a “tree of life”: Eukaryotic genes involved in: - information processing (transcription and translation) cluster with archaea - housekeeping (metabolism) cluster with eubacteria Eukaryote origin may be Archaea-Bacteria chimera. Ring of Life Bacteria Eukaryotes Genomic re-patterning in Eukaryotes Archea Evolution of genome complexity Due to a simple fusion or a more gradual horizontal transfer? This was a LONG time ago so there are still debates about this. - Genome size expansion - Chromosome linearity (from a circular ancestral genome) - Transcript processing - Intragenic spacers (introns) - Mobile genetic elements 6 7/25/11 Eukaryotic explosion Tree of life Land plants ~ 0.4 B.Y.A Another billion years pass.. Flowering plants ~ 0.14 B.Y.A By 0.55 M.Y.A Multicellular animals appear This is followed by the Cambrian explosion Mammals ~ 0.10 B.Y.A Humans ~ 0.002 B.Y.A Nearly ALL animal phyla appear within about 10 million years! A geological perspective on life on earth 4.5 bya earth 3.6 bya life mammals evolve 2.7 bya eukaryotes earth forms eukaryotes arrive Summary 0.02 bya mammals Humans have been on earth for < 0.0001% of its history! life begins 7