A Biochemical Phylogeny of the Protists

Preface1 Introduction 1.1 What Are the Protists? 1.2 Why Are the Protists Interesting? 1.3 Systematics, Taxonomy, and Phylogeny 1.4 Why a Biochemical Phylogeny?2 Biochemistry and Evolution 2.1 The Nature of Biochemical Data and the Central Dogma 2.2 Data Weighting and the Central Dogma 2.3 Prebiotic Processes and "Biochemical Predestination" 2.4 Darwinian and Non-Darwinian Evolution 2.5 Biochemistry and Morphology 2.6 Ontogeny and Phylogeny 2.7 A Note on the Biochemical Method3 Phylogenetics 3.1 Phylogenetic Trees 3.2 Choice of Experimental Organisms 3.3 The Endosymbiotic Theory of Organelle Evolution4 Nucleic Acids 4.1 Evolution of the Genetic Code 4.2 DNA: Structure and Composition 4.3 RNA: Structures and Composition 4.4 Ribosomes5 Proteins Part I: General Considerations 5.1 Polypeptides, Proteins, and Enzymes 5.2 Phylogeny and the Structure of Enzymes: General and Theoretical Considerations 5.3 Enzyme Aggregates 5.4 Evolution of Biosynthetic Pathways 5.5 Evolution of Metabolic Energy Production 5.6 Biochemical Methods in the Phylogenetic Study of Proteins Part II: Heme Proteins, Metalloproteins, and Histones 5.7 Cytochromes 5.8 Heme Proteins Other than Cytochromes 5.9 Phycobiliproteins 5.10 Ferredoxins 5.11 Metalloproteins Other than Ferredoxins 5.12 Histones6 Proteins: Enzymes 6.1 Embden-Meyerhof-Parnas Glycolysis 6.2 Pentose Phosphate Pathway 6.3 Tricarboxylic Acid Cycle 6.4 Hatch-Slack Pathway 6.5 Glycolate Oxidation 6.6 Calvin Cycle 6.7 Polysaccharide Biosynthetic Enzymes 6.8 Fatty Acid Synthases 6.9 Lysine Biosynthetic Pathways 6.10 Ornithine Biosynthesis and the Ornithine-Citrulline Cycle 6.11 Isoleucine Biosynthesis Pathways 6.12 Tryptophan Biosynthesis and the Polyaromatie Biosynthetic Pathway 6.13 Glutamate Dehydrogenases 6.14 Lactate and Malate Dehydrogenases 6.15 Nitrate Reductases7 Metabolites: I 7.1 Monosaccharides and Oligosaccharides 7.2 Polysaccharides 7.3 Amino Acid Distribution8 Metabolites: II 8.1 Acetate-Derived Biosynthetic Pathways 8.2 Fatty Acids 8.3 Lipids 8.4 Acetylenic Compounds 8.5 Compounds Derived from Shikimic Acid 8.6 Other Routes to Aromatic Compounds9 Metabolites: III 9.1 The Mevalonic Acid Pathway: Isoprenoids 9.2 Phytol, Geranylgeraniol, and Farnesol 9.3 Quinones 9.4 Carotenoids 9.5 Sterols10 Metabolites: IV 10.1 The δ-Aminolevulinic Acid Pathway 10.2 Chlorophylls 10.3 Photosynthesis11 Miscellaneous Simple Molecules 11.1 Sulfate Reduction 11.2 Nitrogen Utilization 11.3 Carbon Monoxide Production 11.4 Mineral Nutrition and Vitamin Requirements12 A Biochemical Phylogeny 12.1 Other Phylogenies in the Literature 12.2 A Biochemical Phylogeny 12.3 Comparison of These Phylogenies13 Conclusions and Speculations 13.1 Reflections on the Biochemical Phylogeny 13.2 Time Course of Evolution 13.3 Important Unresolved QuestionsAppendixBibliographyTaxonomic IndexSubject Index