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General Principles of Biochemistry of the Elements - Ei-Ichiro Ochiai

General Principles of Biochemistry of the Elements

Paperback

Published: 22nd March 2012
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The present book might be regarded as a sequel to my previous work, Bioinorganic Chemistry: An Introduction (Allyn and Bacon, 1977). The latter is essentially a collection of chemical and physical data pertinent to an understanding of the biological functions of the various elements and the proteins dependent on them. The ten years since its publication have seen an enormous increase in research activity in this area, hence of research papers. A number of monographs and review series on specific topics have also appeared, including the volumes in the series of which the present volume is a part. Nevertheless, a gap has developed between the flood of information available at a detailed level (papers and reviews) and a general description of the underlying principles of biofunctions of the elements as presently conceived. It is hoped that this book will help bridge this gap and at the same time provide an overview of the entire Biochemistry of the Elements series. Specifically, the work attempts to focus on "why" questions, especially, "Why has an element been chosen by organisms for a specific biofunction?" and "Why does an element behave the way it does in biological systems?" It therefore complements my 1977 book and, together with Laboratory Introduction to Bio-Inorganic Chemistry (E. -I. Ochiai and D. R. Williams, Macmillan, 1979), completes a trilogy on the topic of bioinorganic chemistry. This book consists of five parts. Two chapters constitute Part I.

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.

ISBN: 9781468453737
ISBN-10: 1468453734
Series: Biochemistry of the Elements
Audience: Professional
Format: Paperback
Language: English
Number Of Pages: 484
Published: 22nd March 2012
Dimensions (cm): 22.9 x 15.2  x 2.4
Weight (kg): 0.64