General Principles of Biochemistry of the Elements

I. Overview.- 1. Global Aspects of the Biochemistry of the Elements.- 1.1 Introduction.- 1.2 The Distribution and Bioutilization of the Elements.- 1.3 Biogeochemical Cycling of the Elements.- 1.3.1 Introduction.- 1.3.2 Cycles of Macronutrients.- 1.3.2.1 Carbon Cycle.- 1.3.2.2 Oxygen Cycle.- 1.3.2.3 Nitrogen Cycle.- 1.3.2.4 Sulfur Cycle.- 1.3.2.5 Phosphorus Cycle.- 1.3.2.6 Biogeochemical Cycles of Alkali and Alkaline Earth Metals.- 1.3.3 Biogeochemical Cycles of Some Trace Elements.- 1.3.3.1 Cycle of Iron.- 1.3.3.2 Cycle of Manganese.- 1.3.3.3 Cycles of Other Essential Trace Elements.- 1.3.4 Biogeochemical Cycles of Some Toxic Elements.- 1.3.4.1 Cycle of Mercury.- 1.3.4.2 Cycle of Arsenic.- 1.4 Historical Perspective on the Biochemistry of the Elements.- 1.4.1 Outline of a Possible Origin of Life.- 1.4.2 Outline of the Evolution of Life on the Primitive Earth.- 1.4.3 Environmental (Elemental) Constraints on the Origin and Evolution of Life.- 2. Some Basic Principles of the Biochemistry of the Elements.- 2.1 Basic Principles in Biological Selection of Elements.- 2.2 Some Relevant Inorganic Principles.- 2.2.1 Reduction Potential.- 2.2.1.1 General Formulations.- 2.2.1.2 Standard Reduction Potential: Determining Factors.- 2.2.1.3 pH Dependence, Eh-pH Diagram.- 2.2.2 Lewis Acidity.- 2.2.2.1 Charge-to-Radius Ratio (or Ionic Potential) and Effective Nuclear Charge.- 2.2.2.2 Acidity of a Complexed Metal Cation.- 2.2.3 Number of Electrons versus Structures.- 2.2.4 Constraints Imposed by Biomolecules.- II. Chemical Principles of the Biochemistry of the Elements.- 3. Oxidation—Reduction and Enzymes and Proteins.- 3.1 Introduction.- 3.2 Basic Fitness Rule as Applied to Oxidation-Reduction Reactions.- 3.2.1 Iron-Cytochromes and Iron-Sulfur Proteins.- 3.2.2 Other Redox Proteins Containing Iron.- 3.2.3 Similarity between Iron and Manganese.- 3.2.4 Blue-Copper Proteins and Enzymes.- 3.2.5 Nickel as a Possible Redox Center.- 3.3 Peculiarity of Molybdenum.- 3.3.1 Availability.- 3.3.2 Oxidation-Reduction and Other Characteristics of Molybdenum in Aqueous Medium.- 3.3.3 The Types of Oxidation-Reduction Reactions Catalyzed by Molybdenum Enzymes.- 3.3.4 Xanthine Oxidase and Aldehyde Oxidase.- 3.3.5 Sulfite Oxidase and Nitrate Reductase.- 3.3.6 Compatibility of Tungsten and Molybdenum.- 3.4 Manifestation of Evolutionary Adaptation.- 3.4.1 Iron-Sulfur Proteins.- 3.4.2 Heme Proteins.- 3.4.2.1 Porphyrins.- 3.4.2.2 Porphyrin-like Compounds.- 3.4.3 Blue-Copper Proteins and Enzymes.- 3.5 Oxidation-Reduction of Sulfur Compounds.- 3.5.1 Reduction of Sulfate.- 3.5.2 Oxidation-Reduction of Other Sulfur Compounds.- 3.6 Selenium, Its Oxidation-Reduction, and Enzymes Dependent on It.- 3.6.1 Glutathione Peroxidase.- 3.6.2 Glycine Reductase.- 3.6.3 Formate Dehydrogenase.- 3.6.4 Other Enzymes.- 4. Enzymes and Proteins in the Reactions of Oxygen and Oxygen Derivatives.- 4.1 Oxygen Carrying and Storing.- 4.1.1 Distribution.- 4.1.2 Application of Basic Fitness Rule.- 4.1.3 Genealogy of Proteins.- 4.1.4 The Active Site of Hemoglobin.- 4.1.5 The Active Sites of Hemerythrin and Hemocyanin.- 4.2 Superoxide Dismutase.- 4.3 Dioxygenase Reactions.- 4.3.1 Naive Views—Dioxygenase.- 4.3.2 An Alternative View—Dioxygenase.- 4.3.3 Further Discussion on Dioxygenases.- 4.3.4 Heme-Containing Dioxygenases.- 4.3.5 Dihydroxylases.- 4.4 Monooxygenase Reactions (Plus Peroxidases and Catalase).- 4.4.1 Cytochrome P-450-Dependent Enzymes.- 4.4.2 Monooxygenases Dependent on Nonheme Iron.- 4.4.3 Monooxygenases Containing Copper.- 4.5 Oxidases Effecting Reduction of Oxygen to Water.- 4.5.1 Cytochrome c Oxidase.- 4.5.2 Blue-Copper Oxidases.- 4.5.3 Tyrosinase-Catecholase Activity.- 4.6 The Reverse of Oxidase Reactions—Decomposition of Water.- 4.7 Oxidases That Produce Hydrogen Peroxide.- 4.8 Summary I—Basic Fitness of Iron and Copper (and Manganese).- 4.9 Summary II—Differential Functions of Heme Proteins: Evolutionary Adaptation.- 5. Enzymes in Acid—Base Reactions.- 5.1 General Mechanisms of Rate Enhancement by Enzymes.- 5.2 Proteinases and Peptidases: Metalloenzymes and Metal-Free Enzymes.- 5.2.1 Mechanisms of Metal-Free Proteinases.- 5.2.2 Mechanisms of Metalloenzymes.- 5.2.3 Need for a Metal Cation.- 5.2.4 Consideration of the “Superacid” Theory.- 5.2.5 Other Mechanisms.- 5.3 Metalloenzymes Other Than Proteinases and Peptidases.- 5.3.1 Zn(II) [Co(II)] Enzymes.- 5.3.1.1 Aldolase.- 5.3.1.2 Carbonic Anhydrase.- 5.3.1.3 DNA Polymerases.- 5.3.1.4 Transcarboxylase and Pyruvate Carboxylase.- 5.3.1.5 Summary.- 5.3.2 Iron-Dependent Enzymes.- 5.3.2.1 Serine Dehydratase and Lysine 2,3-Mutase.- 5.3.2.2 Aconitase (Aconitate Dehyratase).- 5.3.2.3 Other Iron-Dependent Enzymes.- 5.3.3 Enzymes Dependent on Other Metals.- 5.3.4 Concluding Remarks.- 5.4 Metal Activation.- 5.4.1 Hydrolysis of ATP by Metal Ions.- 5.4.2 Some Pertinent Characteristics of Metal Cations.- 5.4.3 Kinases.- 5.4.4 Hydrolysis of Phosphate Ester Bonds.- 5.5 Other Metalloenzymes.- 6. Structural Functions.- 6.1 Effects on Molecular Structures.- 6.1.1 Effects on Protein Structures.- 6.1.2 Effects on Polynucleotides.- 6.2 Effects on Intermolecular Interactions.- 6.2.1 Interactions with Polysaccharides and Their Derivatives.- 6.2.2 Interactions with Lipids, Phospholipids, and Membranes.- 6.3 Inorganic Substances in Macrostructures (Biomineralization).- 6.3.1 Silica as the Frustule of Diatoms.- 6.3.2 Silica in Other Organisms.- 6.3.3 Formation of Calcium Carbonate Shell in Molluscs.- 6.3.4 Formation of Bone/Cartilage/Dentin.- 7. Miscellaneous Topics.- 7.1 Nitrogen Fixation.- 7.1.1 The Basic Fitness of Molybdenum for Nitrogen Fixation.- 7.1.2 Alternative Views.- 7.2 Vitamin B12 and B12 Coenzymes.- 7.2.1 B12, B12 Coenzymes—Their Chemistry and Reactions.- 7.2.2 Enzymes Dependent on B12 Coenzyme.- 7.2.3 The Basic Fitness of Cobalt.- 7.3 Chromium.- 7.3.1 GTF.- 7.3.2 Other Possible Functions of Chromium.- 7.4 Vanadium.- 7.4.1 Possible Oxidation–Reduction Functions.- 7.4.1.1 Vanadium in Ascidians.- 7.4.1.2 Other Oxidation–Reduction Effects.- 7.4.2 Other Effects.- 7.5 Tin.- 7.6 Intracellular Ca(II).- 7.6.1 General Discussion of the Signal Transduction and Its Manifestation.- 7.6.2 Examples of the Action of Intracellular Ca(II).- 7.6.2.1 Epinephrine’s Action on Glycogenolysis in Muscle Cells.- 7.6.2.2 Muscle (Skeletal or Smooth) Contraction.- 7.6.2.3 Release of a Neurotransmitter.- 7.6.3 Why Ca(II)?.- III. Chemical Principles of Transport of the Elements.- 8. Chemistry of Uptake—Thermodynamic and Kinetic Factors in Passive Transport.- 8.1 Introduction.- 8.2 Thermodynamic Considerations of Uptake of Metal Ions.- 8.2.1 From Seawater.- 8.2.2 From Gut Lumen or Soil.- 8.2.3 From Circulating System to Individual Cells.- 8.3 Kinetic Factors in Uptake of Metal Ions.- 8.4 Uptake of Anions—Thermodynamic Factors.- 8.4.1 Ionic Radius.- 8.4.2 Thermodynamics of Anion Uptake.- 8.4.3 Other Factors in Anion Uptake.- 9. lonophores, Channels, Transfer Proteins, and Storage Proteins.- 9.1 Ionophores.- 9.1.1 Ionophores for Proton.- 9.1.2 Cation Ionophores.- 9.1.3 Ionophores for Iron—Siderophores.- 9.1.3.1 Catechol-Type Siderophores.- 9.1.3.2 Hydroxamate-Type Siderophores.- 9.1.3.3 Other Siderophores.- 9.2 Channels.- 9.2.1 Channels for Cations.- 9.2.1.1 Na Channels.- 9.2.1.2 K Channels.- 9.2.1.3 Ca Channels.- 9.2.2 Channel-Forming Antibiotics.- 9.3 (Serum) Transfer Proteins for Inorganic Compounds.- 9.3.1 Fe(III) Transfer Proteins—Transferrin.- 9.3.2 (Serum) Transfer Proteins for Other Metal Ions.- 9.4 Calcium-Binding Proteins.- 9.4.1 Some General Features of Calcium-Binding Proteins.- 9.4.2 Examples.- 9.4.2.1 Parvalbumin.- 9.4.2.2 Troponin-C.- 9.4.2.3 Calmodulin.- 9.4.2.4 Other Calcium-Binding Proteins.- 9.5 Storage Proteins and Other Binding Proteins.- 9.5.1 Storage Proteins for Iron.- 9.5.2 Storage and Other Binding Proteins for Other Elements.- 10. Active Transport.- 10.1 Introduction.- 10.2 General Features of Active Transport.- 10.3 ATPases and Cation Translocations.- 10.3.1 Sodium Pump—Na/K-ATPase.- 10.3.2 Calcium Pump—Ca/Mg-ATPase (of Sarcoplasmic Reticulum).- 10.3.3 Mitochondrial H+-ATPase (Proton Pump) and Chloroplast H+-ATPase.- 10.3.3.1 Introduction.- 10.3.3.2 Mitochondrial H+-ATPase.- 10.3.3.3 Chloroplast H+-ATPase.- 10.3.4 A Summary Discussion of Cation-Translocating ATPases.- 10.4 Proton Pump Coupled with Electron Transfer Processes, and Other Proton Pumps.- 10.4.1 Mitochondrial System.- 10.4.2 Chloroplast System.- 10.4.3 Bacteriorhodopsin.- 10.5 Other Modes of Active Transport.- 10.6 Active Transport of Other Cationic Elements.- 10.7 Active Transport of Anions.- IV. Biological Aspects I—Metabolism of the Elements.- 11. Metabolism of Elements by Bacteria, Fungi, Algae, and Plants.- 11.1 Bacteria.- 11.1.1 Gram-Positive Bacteria.- 11.1.1.1 Iron.- 11.1.1.2 Other Elements.- 11.1.2 Gram-Negative Bacteria.- 11.1.2.1 Iron.- 11.1.2.2 Other Elements.- 11.2 Fungi (Yeast, Mold, Mushroom).- 11.2.1 Iron.- 11.2.2 Other Elements.- 11.3 Algae.- 11.4 Lichen and Moss.- 11.5 Binding of Metal Ions to Polysaccharides and Derivatives.- 11.6 Plants.- 11.6.1 Absorption from Roots.- 11.6.2 Absorption by Other Tissues.- 11.6.3 Long-Distance Transport in Plants.- 12. Metabolism of Elements in Mammals and Vertebrates.- 12.1 Metabolism of Iron.- 12.1.1 Absorption of Iron.- 12.1.1.1 Carrier-Mediated Transport at Intestinal Lumen–Mucosal Cell Border.- 12.1.1.2 Intracellular Iron Carriers in Mucosal Cells.- 12.1.1.3 Passive Transport.- 12.1.2 Transport in Blood Vessels.- 12.1.3 Hemoglobin Production.- 12.1.4 Catabolism of Hemoglobin.- 12.2 Metabolism of Copper.- 12.2.1 Distribution and Functions.- 12.2.2 Absorption and Transport of Copper.- 12.2.3 Copper in Liver.- 12.3 Metabolism of Zinc.- 12.3.1 Distribution and Functions.- 12.3.2 Metabolism of Zinc.- 12.4 Metabolism of Other Trace Elements-Cobalt, Manganese, Molybdenum, and Others.- 12.4.1 Cobalt.- 12.4.1.1 Functions.- 12.4.1.2 Metabolism.- 12.4.2 Manganese.- 12.4.2.1 Distribution and Functions.- 12.4.2.2 Metabolism.- 12.4.3 Molybdenum.- 12.4.4 Chromium.- 12.4.5 Nickel.- 12.4.6 Vanadium.- 12.5 Metabolism of Major Inorganic Elements.- 12.5.1 Sodium and Potassium.- 12.5.2 Magnesium.- 12.5.3 Calcium.- V. Biological Aspects II—Toxicity of and Defense against the Elements.- 13. Oxygen—Its Toxicity and Defense against It.- 13.1 Toxicity of Oxygen and Its Derivatives.- 13.1.1 Dioxygen in the Ground State.- 13.1.2 Superoxide Radical, Hydroxyl Radical, and Hydrogen Peroxide.- 13.1.3 Singlet Oxygen.- 13.1.4 Killing of Microorganisms by Phagocytic Cells.- 13.1.5 Peroxidation, Aging, Carcinogenicity, and Inflammation.- 13.1.6 Inhibition of Enzymes by Oxygen and Its Derivatives.- 13.2 Defense Mechanisms against Oxygen Toxicity.- 13.2.1 Superoxide Dismutase.- 13.2.2 Catalase and Peroxidases.- 13.2.3 Radical Inhibitors, Antioxidants, Singlet Oxygen Quenchers.- 13.2.4 Protection of Nitrogenase from Oxygen.- 14. Toxicity of Heavy Metals.- 14.1 Chemical Bases of Toxicity of Heavy Metals.- 14.2 Metabolism and Physiological Consequences of Toxic Effects of Heavy Metals.- 14.2.1 In Algae and Plants.- 14.2.2 In Invertebrates and Fish.- 14.2.3 Copper in Mammals (Including Humans).- 14.2.3.1 Chronic Toxicity.- 14.2.3.2 Wilson’s Disease.- 14.2.4 Cadmium in Mammals.- 14.2.4.1 Metabolism.- 14.2.4.2 Toxicity.- 14.2.4.3 Other Effects.- 14.2.5 Lead in Mammals.- 14.2.5.1 Metabolism.- 14.2.5.2 Toxicity-Clinical Symptoms.- 14.2.5.3 Other Effects at the Cellular Level.- 14.2.6 Mercury in Mammals.- 14.2.6.1 Metabolism.- 14.2.6.2 Toxicity.- 14.3 Adaptation-Avoidance-Defense-Resistance-Tolerance.- 14.3.1 General Comments.- 14.3.2 Defense in Bacteria and Fungi.- 14.3.2.1 In Bacteria.- 14.3.2.2 In Fungi.- 14.3.3 Defense in Plants.- 14.3.4 Defense in Invertebrates and Fish.- 14.3.5 Defense in Mammals.- 14.3.5.1 General Comments.- 14.3.5.2 Metallothionein.- 14.3.5.3 Lead Inclusion Body.- 14.3.5.4 Other Compartmentation Mechanisms.- 14.3.5.5 Heavy Metal–Selenium Antagonism.- Note: The So-Called ppm.- 15. Toxicity of Other Elements.- 15.1 Selenium.- 15.1.1 Characteristic Features of the Chemistry and Metabolism of Selenium.- 15.1.2 Selenium Deficiency in Animals.- 15.1.2.1 Pathological States Related to Lack of Glutathione Peroxidase.- 15.1.2.2 Pathological States Related to Lack of Se2?-Dependent Proteins.- 15.1.3 Toxicity of and Defense against Selenium.- 15.1.3.1 In Plants.- 15.1.3.2 In Animals.- 15.1.3.3 Interactions with Other Elements.- 15.2 Arsenic.- 15.2.1 Characteristic Features of the Chemistry of Arsenic.- 15.2.2 Toxicity of and Defense against Arsenic.- 15.2.2.1 In Bacteria, Plants, and Invertebrates.- 15.2.2.2 In Animals—Cellular Mechanisms of Toxicity.- 15.3 Beryllium.- 15.3.1 Chemistry and Metabolism.- 15.3.2 Toxicity.- 15.4 Aluminum.- 15.4.1 Chemistry and Metabolism.- 15.4.2 Toxicity in Animals.- 15.4.3 Toxicity in Organisms Other Than Animals.- 15.5 Transition Metals.- 15.5.1 Vanadium.- 15.5.2 Chromium.- 15.5.3 Manganese.- 15.5.4 Nickel.- References.