Bioinorganic Chemistry

A Survey


  • Ei-Ichiro Ochiai

Written by a preeminent teacher and scientist in the field, this book provides specialists, students, and general readers with an understanding of the basic chemistry of interactions of inorganic substances with biological systems at the molecular level. The author presents bioinorganic concepts in context and brings a distinct chemistry perspective to the subject.
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Lecturers and students studying bioinorganic chemistry in inorganic, natural-products chemistry, and biochemistry programs *


Book information

  • Published: July 2008
  • ISBN: 978-0-12-088756-9

Table of Contents

Chapt. 0. Basics of Bio/ecosystems and Biochemistry, and Other Basic Concepts 0.1.Biosphere (Ecosystem)0.1.1. Components of the biosphere-Living organisms0.1.2. Bodily structure of living organisms0.2. Cells, the Basic Functional Units of Living Organisms0.3. Basic Biochemicals Essential to Life0.3.1. Carbohydrates0.3.1.1. Monosasccharides0.3.1.2. Polysaccharides and derivatives0.3.2. Lipids0.3.2.1. Fats and phospholipids0.3.2.2. Steroids0.3.3. Proteins and amino acids0.3.3.1. Structures0.3.3.2. Reactions – formation and hydrolysis of protein0.3.4. Nucleotides, vitamins (coenzymes) and others0.3.4.1. Coenzymes0.3.4.2. Nucleotides0.3.4.3. Other vitamins0.3.4.4. Hormone, neurotransmitters and others0.3.5. DNA/RNA (Polynucleotide) Structures0.3.5.2. Reactions0.4. Types of Biochemical Reactions0.4.1. Reactions of acid-base type0.4.2. Reactions of oxidation-reduction type0.4.2.1. The idea of oxidation state0.4.2.2. The oxidation state of “C” in organic compounds and recognition of oxidation-reduction reactions0.4.2.3. Other kinds of oxidation-reduction reactions0.4.3. Free radical reactions0.5. Transition State Theory of Reaction, and Enzyme Kinetics0.5.1. Energy profile and transition state theory of reaction0.5.2. Enzyme Kinetics0.5.3. Enzyme reaction mechanismChapt. 1. Distribution of Elements1.1. Distribution of Elements in Earth Crust/Sea Water/Organisms1.2. The Engines to Drive the Biochemical Cycling of the Elements1.3. The Geochemical Cycling of Elements – Contribution by Biosphere1.4. Historical Change in the Biogeochemical Cycling of ElementsChapt. 2. Biological Necessity for and the Behaviors of Inorganic Elements 2.1. Introduction 2.2..Inorganic Elements in Biological Systems 2.2.1. Inorganic elements involved at molecular level 2.2.2. Inorganic elements involved at cellular level 2.2.3. Inorganic elements involved at physiological level 2.2.4. Biological systems involved in the metabolism of inorganic elements 2.3. Why have Organisms Chosen Specific Elements for their Specific Needs Basic Rules 2.4. Behaviors of Inorganic Elements-1-Fundamentals of Coordination Chemistry 2.4.1. Coordination compounds or metal complexes 2.4.2. Ligand field theory-how the predominant structure is determined 2.4.3. Thermodynamic tendency to form coordination compounds 2.4.4. Chelate effects 2.4.5. Ligand substitution reactions 2.4.6. Oxidation-reduction and reduction potential 2.4.7. Kinetic factors including long-range electron transference 2.5. Behaviors of Inorganic Elements-2-Organometallic Chemistry 2.5.1. Metal carbonyls and 18 electron rule 2.5.2. Other organometallic compounds 2.5.3. Some special types of reactions involving organometallic compoundsChapt. 3. How Do Enzymes Work? 3.1. Enzymatic Enhancement of Reaction Rate – General Considerations 3.1.1. “Transition state” theory 3.1.2. The “Dynamic” effects 3.1.3. A Composite theory 3.2. Metalloenzymes and Metal-Activated Enzymes/ProteinsChapt. 4. Reactions of Acid-Base Type and Functions of Metal Cations 4.1. General Considerations 4.1.1. Different types (definitions) of acid-base 4.1.2. Enzymes catalyzing reactions of acid-base type 4.1.3. Acidity scale and acid character of metal cations – prominence of Zn(II) and Mg(II) 4.1.4. Kinetic factors 4.1.5. The enhancement of reaction by amino acid residues in protein 4.2. Mg(II)-dependent Enzymes 4.2.1. Rubisco (Ribulose1,5-bisphosphate carboxylase/oxygenase) 4.2.1. Pyruvate kinase 4.3. Zn(II)-dependent Enzymes 4.3.1. Carbonic anhydrase 4.3.2. Thermolysin, carboxypeptidase A and others 4.3.3. Leucine amonopeptidase 4.3.4. Alkaline phosphatase and purple-acid phosphatase 4.3.5. Alcohol dehydrogenase 4.4. Other Cation-dependent Enzymes 4.4.1. Aconitase, an iron-sulfur enzyme, and others 4.4.2. Arginase – a Mn enzyme 4.4.3. Urease and other Ni-enzymes 4.5. Structural Effects of Metal Ions 4.6. Metal Ions and Polynucleic Acids (DNA and RNA) 4.6.1. General characteristics of interactions of metal ions with polynucleotides Effects on structures Catalytic metal ions in DNA polymerases and nucleases 4.6.2. Gene regulation and metal ions 4.6.2. RibozymesChapt. 5. Reactions of Oxidation-Reduction Type including Electron Transfer Processes 5.1. General Consideration 5.1.1. Reduction potential Heme proteins and enzymes Iron-sulfur proteins Copper proteins Molybdenum proteins/tungsten proteins 5.1.2. Kinetic factors – electron transfer between and in protein(s) 5.2. Iron Enzymes and Proteins 5.2.1. Cytochromes and iron-sulfur electron transfer proteins 5.2.2. Nitrate reductase and nitric oxide reductase 5.2.3. Horse radish peroxidase (HRP), catalase and cytochrome c peroxidase 5.2.4. Hydrogenase 5.3. Copper Enzymes and Proteins 5.3.1. Blue copper proteins 5.3.2. Blue oxidases 5.3.3. Cytochrome c oxidase 5.3.4. Nitrite reductase and nitrous oxide reductase 5.3.5. Amine oxidases 5.3.6. Superoxide dismutase 5.4. Molybdenum Enzymes and Tungsten Enzymes 5.4.1. Xanthine oxidase and aldehyde oxidase 5.4.2. Sulfite oxidase and nitrate reductase (assimilatory) 5.4.3. DMSO reductase and nitrate reductase (respiratory) 5.4.4. Tungsten enzymes 5.5. Manganese Oxidoreductases 5.5.1. Manganese catalase 5.5.2. Water oxidase 5.6. Ni-containing Redox Enzymes 5.6.1. Ni-Fe (Se) hydrogenase 5.6.2. Carbon monoxide dehydrogenase (CODH) 5.6.3. Acetyl CoA synthase (ACS) 5.6.4. Methyl-coenzyme M reductaseChapt. 6. Oxygen-Carrying Processes and Oxygenation Reactions 6.1. Chemistry of Oxygen, Dioxygen and Related Entities 6.1.1. The electronic structures 6.1.2. Basic reactions of O and O2 6.1.3. Reactions of ground states of O and O2 6.1.4. Interactions of ground state O2 with compounds of transition metals 6.1.5. Reactions of oxygen derivatives 6.2. Reversible O2 Binding – Oxygen Carriers – 6.3. Monoosygenases 6.3.1. Monoyxgenases dependent on cytochrome P-450 6.3.2. Non-heme mononuclear iron monooxygenases 6.3.3. Non-heme dinuclear iron monooxygenase 6.3.4. Copper monooxygenases 6.4. Dioxygenases 6.5. Prostaglandin Endoperoxide SynthaseChapt. 7. Metal-Involving Free Radical Reactions 7.1. A Survey of Biologically Relevant Free Radicals 7.2. Why Radcials 7.3. Reactivities of Free Radicals 7.4. B12-Coenzyme (Adenosylcobalamin) Dependent Enzyme 7.4.1. Mutases, diol dehydratase and ethanolamine ammonia lyase 7.4.2. Ribonucelotide reductase (cobalamin dependent) 7.5. S-Adenosyl Methionine (SAM) Dependent Enzymes 7.6. Iron-Dependent Ribonucleotide Reductases 7.7. Galactose Oxidase 7.8. Other ExamplesChapt. 8. Nitrogen Fixation 8.1. Nitrogen Metabolism 8.2. Chemistry of N2 Reduction 8.3. Mo-dependent Nitrogenases 8.4. Other NitrogenasesChapt. 9. Other Essential Elements 9.1. Introduction 9.2. Biochemistry of Nitrogen Compounds 9.3. Biochemistry of Phosphorus 9.4. Biochemistry of Sulfur Compounds 9.4.1. Cellular processes 9.4.2. Marine biogeochemical cycling 9.5. Selenium 9.5.1. Chemistry of selenium as compared to that of sulfur 9.5.2. Glutathione and selenium – glutathione peroxidase 9.5.3. Thioredoxin reductase 9.5.4. Other selenium containing proteins/enzymes 9.6. Boron 9.7. Silicon 9.7.1. Chemistry of silicon 9.7.2. Frustules of diatoms 9.7.3. Spicules in sponge 9.7.4. Other biological functions of silicon 9.8. Vanadium 9.8.1. Vanadins 9.8.2. Amavadin 9.8.3. Haloperoxidases 9.9. Chromium 9.10. Halogens and the Like 9.10.1. Formation of volatile halocarbons in macroalgae 9.10.2. HOX formation in mammals and others Formation of HOX by fungal chlorperoxidase Formation of HOX and others by mammalian peroxidases Chapt. 10. Metal-related Physiology 10.1. Metabolism of Metallic Elements 10.1.1. Iron metabolism (in human) Ferric reductase Divalent metal transporter (DMT1) Ferroxidase Transferrin (Tf) and transerrin receptor (TfR) Ferritin Ferroportin (Fpn)/hepcidin Regulation of ferritin and transferrin Iron metabolism in bacteria, fungi and plants 10.1.2. Copper metabolism An outline of copper metabolism in mammals Copper metabolism in bacteria and plants 10.1.3. Zinc metabolism In mammals in E. coli 10.1.4. A Mg(II) transporter 10.2. Physiological Processes Played by Metallic Elements 10.2.1. Na/K-ATPase and Ca-ATPase Mechanism Ion selectivity in metal ion transporters and channels – a general discussion 10.2.2. Ca(II) – second messenger, and other functions Control of cytoplasmic Ca(II) concentration10.2.2.2. Basic mechanisms of Ca(II)-physiology10.2.2.3. Synaptotagmin – as an example of physiology mediated by Ca(II) Why calcium(II)? 10.2.3. ZEN 10.2.4. Sensors for small molecules Oxygen sensors CO-sensors NO-sensors H2 sensors Redox sensors 10.2.5. Plant hormone, ethylene and copper 10.2.6. Magnetic navigation 10.2.7. Radiation shields 10.3. Biological Skeletons (Biominerals) 10.3.1. Calcium carbonate 10.3.2. Calcium oxalate 10.3.3. Calcium phosphateChapt. 11. Environmental Bioinorganic Chemistry 11.1. General Considerations 11.2. Toxicity of Inorganic Compounds 11.2.1. Abundance and toxicity 11.2.2. Toxicity of reactive oxygen species, and defense mechanisms 11.3. Molecular Mechanisms of Toxicity of Inorganic Compounds 11.3.1. Discrimination of elements by organisms – general considerations 11.3.2. Oxidative stress and metals and As – general effects 11.3.3. Individual element’s (acute) toxicity Cd(II) and Hg(II) Pb(II) Organometallic compounds Orgnotin compounds Be(II), Al(III) Tl(I) Cr Ni(II) ANIONS 11.3.4. Alzheimer’s disease and metals 11.4. Biological Defenses against Toxicity 11.4.1. Biological defense against mercury 11.4.2. Metallothioneins and phytochelatins Metallothioneins Copper-thionein Phytochelatins Use of sulfide 11.4.3. Defense against lead 11.4.4. Biotransformation of arsenic 11.5. Bioremediaion of Metals 11.5.1. Biosorption by brown algae and by microbial surfactants 11.5.2. Phytoremediation (phytoextraction of metals from soil) 11.5.3. Phytoextraction by microalgae (remediation of polluted water) 11.5.4. Other types of bioremediationChapt. 12 Medical Applications of Inorganic Compounds: Medicinal Inorganic Chemistry 12.1. Introduction 12.2. Cancer Therapy 12.2.1. Platinum compounds 12.2.2. Bleomycin 12.2.3. Radioactive pharmaceuticals 12.3. Gold Compounds for Rheumatoid Arthritis 12.4. Vanadium Compounds for Diabetes 12.5. Lithium Compounds for Psychiatric Disorders 12.6. Other Potential Drugs Containing Inorganic Compounds 12.7. Daignostic (Imaging) Agents 12.7.1. Gd(III)-containing agents for MRI 12.7.2. 99mTc-radioactive diagnostic pharmaceuticals