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The First Cells II Evolution Biology 4974/5974 D. F. Tomback Biology 4974/5974 Evolution The First Cells II Figures and tables from M.W. Strickberger (2000) Evolution, 3 rd ed, Jones and Bartlett. Learning goals: know and understand • The key arguments for the “RNA World,” or RNA first hypothesis. • The genetic code: its triplet codon form, why it is universal, and why it is redundant. • Steps in the origin of anaerobic metabolism and early ‘photosynthesis.’ • The merger of photosystems I and II and release of molecular oxygen, followed by the evolution of aerobic metabolism. • The origin of eukaryotic cells through endosymbiosis and supporting evidence. • The oldest fossil cells. Early biochemical pathways Central dogma: Replication (DNA to DNA) Transcription (DNA to RNA) Translation (RNA to protein) • Which came first: proteins or nucleic acids and which nucleic acids? • How did metabolic pathways arise? From: de Duve (1995) 1 The First Cells II Evolution Biology 4974/5974 D. F. Tomback Properties of RNA: “RNA First” and the “RNA world” RNA as both template and catalyst • RNA can catalyze its own replication without protein enzymes; can bind ATP for energy. • RNA can make peptide bonds. • Introns in m-RNA and nuclear RNA are self-splicing. • RNA can cleave t-RNA precursors at the proper bond. • “Ribozymes” cleave phosphoester bonds of RNA. • RNA can catalyze the cleavage of an amide bond. • RNA silencing, through double-stranded RNA. • Self-cleaving ribozymes may regulate the expression of some genes. • RNA fragments join with coenzymes in many metabolic reactions(e.g., NAD, FAD). Basic argument: only a self-replicating molecule can build a functional unit. The universal genetic code • All organisms essentially share the same genetic code. • The genetic code is redundant. • What does that mean? • How did the code evolve? • Triplet code initially involved fewer amino acids? • The first two positions specify which amino acid. • The number of codons per amino acid is proportional to the frequency of the amino acid in proteins. Why is the genetic code universal? To code for 20 amino acids + stop code, at least 1,070 possibilities using 64 codons. Why this code? Proposed explanations (hypotheses): 1. Stereochemical affinity between either a codon or an anticodon and an amino acid: no evidence. 2. Amino acid-codon association arose by chance and perhaps several times. In a successful group of protocells, any major change would produce nonfunctional proteins. Thus, one code was favored and changes then were limited: frozen accident viewpoint. 2 The First Cells II Evolution Biology 4974/5974 D. F. Tomback The evolution of metabolism See Endboxes to Chapter 8 ATP (Adenosine Triphosphate): early breakthrough as an energy carrier. Anaerobic glycolysis Embden-Myerhoff glycolytic pathway. First metabolic pathway? (End Box 8.2) • Converts glucose (C6 H12O6) to 2 pyruvic acids, with a net yield of 2 ATPs • C6H12O6 + 2 ADP + 2 Pi + 2 NAD+ 2 C3H4O3 + 2 ATP + 2 NADH +2 H+ + 2 H2O Note: Retrograde evolution--Metabolic pathways evolved with depletion in the environment of required molecules. This exerts selection for synthesis of that molecule from a precursor. The pathway then gets longer and longer over time. Photosynthesis End Box 8.1 Cyclic photosynthesis (came first) • Yields 1 ATP for each round. • Nearly all photosynthesis systems depend on chlorophyll. • Bound to membrane of protocell. • This system could reduce CO2 to produce a carbon source. • Leads to the first autotrophs. Calvin Cycle • Synthesizes glucose from CO2 using energy. • Advantage: freed organisms from external carbon sources. • Anaerobic autotrophs Which came first: autotrophs or heterotrophs? (Hint: use the parsimony principle –Occam’s razor) Oxygen and aerobic metabolism Photosystems I and II merger • Likely that non-cyclic photosystems I and II merged together (from lateral gene transfer). • Found only in cyanobacteria and chloroplasts of eukaryotes. • Photosystem II dissociates water into electrons, protons, and releases oxygen • 2H2O 4e- + 4H+ + O2 3 The First Cells II Evolution Biology 4974/5974 D. F. Tomback Oxygen • Fossil prokaryotes, 3 to 3.5 billion years of age appear photosynthetic. • First trace of O2 about 2 - 2.3 billion years ago, shown by S isotopes. • O2 levels remained low (~1%) until about 2 billion years ago. • Upsurge in photosynthesis? • Low O2 in deep oceans until 580 mya. • Current O2 levels bout 21%. Des Marais (2000) Oxygen increase Increase in atmospheric oxygen rapidly about 2 billion years ago Evidence • Deposition of banded iron in oceans--sedimentary deposits of iron, possibly formed biologically (Fe2O3). • Remained low in deep ocean. Consequences • Oxidizing atmosphere. • Ozone layer—reduced energy. • Harmful to many organisms: extinctions? • Door opened for aerobic metabolism. Aerobic metabolism Higher oxygen levels paved the way for more efficient metabolism—aerobic: Krebs Cycle (citric acid cycle). • Initially anaerobic metabolism and two pathways. • Uses pyruvate from glycolysis, produces ATP, electrons, and H+. Electron transport system or oxidative phosphorylation • Passes electrons from the KC down respiratory chain. • Ultimately, O2 is reduced to 2 H2O. • Glycolysis + Krebs cycle + OP generates 38 ATPs— highly efficient. 4 The First Cells II Evolution Biology 4974/5974 D. F. Tomback Krebs cycle and electron transport chain Fig. EB3.1 Endosymbiosis theory First eukaryote from a symbiosis between an archaebacterium and a eubacterium, which produced a nuclear membrane. • Ancestral “eukaryote”: anaerobic with flexible cell walls. • Internal cytoskeleton with microtubules and actin filaments. • Allowed cells to change shape. • Could “prey” on prokaryotes. Steps in primary endosymbiosis: • Aerobic prokaryote became mitochondrion. • Cyanobacterium became a chloroplast, leading to photosynthesis. • Spirochete, became a flagellum • These symbionts over time became organelles. Secondary endosymbiosis: • Some eukaryotes acquired chloroplasts from other eukaryotes. Fig. 9.4 Paramecium bursaria with symbiotic algae. Evidence for endosymbiosis • Mitochondria and chloroplasts have their own DNA and ribosomes like prokaryotes. • The primitive amoeba Pelomyxa and other species have bacterial symbionts. • Mitochondrial genome of the freshwater protozoan Reclinomonas americana contains more genes than found in any mtDNA (Lang et al. 1997); symbiont is a rickettsia-like bacterium; other members of this group lack mitochondria. • Eventually, genes are transferred from the symbionts to the nucleus or are lost. 5 The First Cells II Evolution Biology 4974/5974 D. F. Tomback Horizontal gene transfer The incorporation of one organism’s genes into the nuclear DNA of another organism. • • • • • • Now known to be widespread. Between prokaryotes. Prokaryotes to eukaryotes. Between some eukaryotes. Continues today. 10% of genome of most single cells; one-third of genome of prokaryotes from HGT. • Mechanisms: via plasmids, intracellular symbionts, or parasites. The oldest fossil cells Fig. 8.3A: Stromatolites composed of calcium carbonate secreted by cyanobacteria are the oldest organisms known (3.5 By old) and the longest lasting. Fig. 8.2 Filamentous unicellular fossil found in stromatolite chert in the3.5 By-old Warrawoona formation in Western Australia. Study guide • What arguments support RNA evolving first? • What are explanations for why the genetic code is universal? What is meant by redundancy of the code? • Explain why heterotrophs probably evolved before autotrophs? • What were probably the main energy metabolic pathways of the a) first heterotrophs, b) first autotrophs? • What new metabolic pathway led to the rise in atmospheric oxygen? What pathways could then evolve? How did that affect energy metabolism? • What different forms of evidence support the endosymbiosis hypothesis? 6