Bioinorganic Chemistry (eBook)

Front Cover 1
Bioinorganic Chemistry: A Survey 4
Copyright Page 5
Contents 6
Preface 14
Introduction: Basics of Bio/Ecosystems and Biochemistry, and Other Basic Concepts 18
Biosphere (Ecosystem) 18
Components of the Biosphere—Living Organisms 18
Bodily Structures of Living Organisms 20
Cells, the Basic Functional Units of Living Organisms 20
Biochemical Compounds Essential to Life 21
Carbohydrates 22
Monosaccharides 22
Polysaccharides and Derivatives 24
Lipids 25
Fats and Phospholipids 26
Steroids 27
Proteins and Amino Acids 27
Structures 27
Reactions—Formation and Hydrolysis of Protein 33
Vitamins (Coenzymes), Nucleotides, and Others 34
Coenzymes 34
Nucleotides 35
Other Vitamins 36
DNA/RNA (Polynucleotide) 36
Structures 36
Reactions 40
Types of Biochemical Reactions 41
Reactions of Acid-Base Type 41
Reactions of Oxidation-Reduction Type 42
The Idea of Oxidation State 43
The Oxidation State of C in Organic Compounds and Recognition of Oxidation-Reduction Reactions 43
Other Kinds of Oxidation-Reduction Reactions 46
Free Radical Reactions 47
Transition State Theory of Reaction, and Enzyme Kinetics 47
Energy Profile and Transition State Theory of Reaction 48
Enzyme Kinetics 49
Enzyme Reaction Mechanism 50
CHAPTER 1 The Distribution of Elements 54
1.1. The Distribution of Elements in the Earth's Crust, Seawater, and Organisms 54
1.2. The Engines That Drive the Biochemical Cycling of the Elements 58
1.3. Flow of the Elements—Biogeochemical Cycling 59
1.4. Historical Change in the Biogeochemical Cycling of Elements 62
CHAPTER 2 Biological Needs for and the Behaviors of Inorganic Elements 70
2.1. Introduction 70
2.2. Inorganic Elements in the Biological Systems 71
2.2.1. Inorganic Elements Involved at the Molecular Level 71
2.2.2. Inorganic Elements Involved at the Cellular Level 72
2.2.3. Inorganic Elements Involved at the Physiological Level 72
2.2.4. Biological Systems Involved in the Metabolism of Inorganic Elements 73
2.3. Why Has a Specific Organism Chosen Specific Elements for Its Specific Needs? 75
2.4. Behaviors of Inorganic Elements-I: Fundamentals of Coordination Chemistry 75
2.4.1. Coordination Compounds or Metal Complexes 76
2.4.2. Ligand Field Theory—How the Predominant Structure Is Determined 77
2.4.3. Thermodynamic Tendency to Form Coordination Compounds 81
2.4.4. Chelate Effect 83
2.4.5. Ligand Substitution Reactions—Kinetic Factors 84
2.4.6. Oxidation–Reduction and Reduction Potential 85
2.5. Behaviors of Inorganic Elements-II: Basics of Organometallic Chemistry 90
2.5.1. Metal Carbonyls and the 18-Electron (18 e[sup(–)]) Rule 90
2.5.2. Other Organometallic Compounds 92
2.5.3. Some Special Types of Reactions Involving Organometallic Compounds 93
CHAPTER 3 How Do Enzymes Work? 98
3.1. Enzymatic Enhancement of Reaction Rate: General Considerations 98
3.1.1. Transition State Theory 99
3.1.2. The Dynamic Effects 102
3.1.3. A Composite Theory 104
3.2. Metalloenzymes/Proteins and Metal-Activated Enzymes 106
CHAPTER 4 Reactions of Acid-Base Type and the Functions of Metal Cations 110
4.1. General Considerations 110
4.1.1. Different Types (Definitions) of Acid-Base 110
4.1.2. Reactions of Acid-Base Type Catalyzed by Enzymes 111
4.1.3. Acidity Scale and Acid Character of Metal Cations: Prominence of Zn(II) and Mg(II) 112
4.1.4. Kinetic Factors 115
4.1.5. Enhancement of Reaction by Protein Residues 116
4.2. Mg(II)-Dependent Enzymes 117
4.2.1. Rubisco (Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase) 117
4.2.2. Pyruvate Kinase 118
4.3. Zn(II)-Dependent Enzymes 119
4.3.1. Carbonic Anhydrase 120
4.3.2. Thermolysin, Carboxypeptidase A, and Others 122
4.3.3. Leucine Aminopeptidase 123
4.3.4. Alkaline Phosphatase and Purple Acid Phosphatase 123
4.3.5. Alcohol Dehydrogenase 124
4.4. Other Metal Cation-Dependent Acid-Base Enzymes 125
4.4.1. Aconitase, an Iron-Sulfur Enzyme, and Others 125
4.4.2. Arginase: Mn Enzyme 126
4.4.3. Urease and Other Ni Enzymes 126
4.5. Structural Effects of Metal Ions 128
4.6. Metal Ions and Polynucleic Acids (DNA and RNA) 129
4.6.1. General Characteristics of Interactions of Metal Ions with Polynucleotides 130
4.6.1.1. Effects on Structures 130
4.6.1.2. Catalytic Metal Ions in DNA Polymerases and Nucleases 131
4.6.2. Gene Regulation and Metal Ions 133
4.6.3. Ribozymes 134
CHAPTER 5 Reactions of Oxidation–Reduction Type Including Electron Transfer Processes 140
5.1. General Consideration 140
5.1.1. Reduction Potential 141
5.1.1.1. Heme Proteins and Enzymes 141
5.1.1.2. Iron-Sulfur Proteins 144
5.1.1.3. Copper Proteins 147
5.1.1.4. Molybdenum and Tungsten Proteins 148
5.1.2. Kinetic Factors—Electron Transfer between and in Protein(s) 149
5.2. Iron Enzymes and Proteins 150
5.2.1. Cytochromes and Iron-Sulfur Electron Transfer Proteins 151
5.2.2. Nitrite Reductase and Nitric Oxide Reductase 151
5.2.3. Horseradish Peroxidase (HRP), Catalase, and Cytochrome C Peroxidase 152
5.2.4. Hydrogenase 154
5.3. Copper Enzymes and Proteins 154
5.3.1. Blue Copper Proteins 155
5.3.2. Blue Copper Oxidases 156
5.3.3. Cytochrome C Oxidase 157
5.3.4. Nitrite Reductase and Nitrous Oxide Reductase 157
5.3.5. Amine Oxidases 159
5.3.6. Superoxide Dismutase (SOD) 161
5.4. Molybdenum Enzymes and Tungsten Enzymes 162
5.4.1. Xanthine Oxidase and Aldehyde Oxidase 162
5.4.2. Sulfite Oxidase and Nitrate Reductase (Assimilatory) 164
5.4.3. DMSO Reductase and Nitrate Reductase (Respiratory or Dissimilatory) 165
5.4.4. Tungsten Enzymes 167
5.5. Manganese Oxidoreductases 167
5.5.1. Manganese Catalase 168
5.5.2. Water Oxidase 168
5.6. Ni-Containing Redox Enzymes 170
5.6.1. Ni-Fe (Se) Hydrogenase 171
5.6.2. Carbon Monoxide Dehydrogenase (CODH) 172
5.6.3. Acetyl CoA Synthase (ACS) 173
5.6.4. Methyl-Coenzyme M Reductase 173
CHAPTER 6 Oxygen Carrying Processes and Oxygenation Reactions 178
6.1. The Chemistry of Oxygen, Dioxygen, and Related Entities 178
6.1.1. Electronic Structures 178
6.1.2. Basic Reactions of O and O[sub(2)] 179
6.1.3. Reactions of Ground State O and O[sub(2)] 180
6.1.4. Interactions of Ground State O[sub(2)] with Compounds of Transition Metals 181
6.1.5. Reactions of Oxygen Derivatives 184
6.2. Reversible O[sub(2)] Binding: Oxygen Carriers 185
6.3. Monooxygenases 186
6.3.1. Monooxygenases Dependent on Cytochrome P-450 187
6.3.2. Nonheme Mononuclear Iron Monooxygenases 190
6.3.3. Nonheme Dinuclear Iron Monooxygenases 193
6.3.4. Copper Monooxygenases 194
6.4. Dioxygenases 195
6.5. Prostaglandin Endoperoxide Synthase 198
CHAPTER 7 Metal-Involving Free Radical Reactions 202
7.1. A Survey of Biologically Relevant Free Radicals 202
7.2. Why Radicals? 204
7.3. Reactivities of Free Radicals 205
7.4. B[sub(12)]-Coenzyme (Adenosylcobalamin)-Dependent Enzymes 209
7.4.1. Mutases, Diol Dehydratase, and Ethanolamine Ammonia Lyase 209
7.4.1.1. Homolytic Cleavage of the Cobalt-to-Carbon Bond upon Binding a Substrate 210
7.4.1.2. Hydrogen Abstraction from Substrates 212
7.4.1.3. 1,2-Shift or Other Reactions of Substrate Free Radicals 212
7.4.2. Ribonucleotide Reductases (Cobalamin-Dependent) 215
7.5. S-Adenosyl Methionine (SAM)-Dependent Enzymes 216
7.6. Iron-Dependent Ribonucleotide Reductases 217
7.7. Galactose Oxidase 219
7.8. Other Examples 220
CHAPTER 8 Nitrogen Fixation 222
8.1. Nitrogen Metabolism 222
8.2. Chemistry of N[sub(2)] Reduction 223
8.3. Mo-Dependent Nitrogenase 225
8.4. Other Nitrogenases 231
CHAPTER 9 Other Essential Elements 234
9.1. Introduction 234
9.2. Biochemistry of Nitrogen Compounds 235
9.3. Biochemistry of Phosphorus 236
9.4. Biochemistry of Sulfur Compounds 236
9.4.1. Cellular Processes 236
9.4.2. Marine Biogeochemical Cycling 238
9.5. Selenium 239
9.5.1. Chemistry of Selenium as Compared to That of Sulfur 239
9.5.2. Glutathione and Selenium: Glutathione Peroxidase 239
9.5.3. Thioredoxin Reductase 241
9.5.4. Other Selenium-Containing Proteins and Enzymes 242
9.6. Boron 242
9.7. Silicon 244
9.7.1. Chemistry of Silicon 245
9.7.2. Frustules of Diatoms 246
9.7.3. Spicules in Sponge 247
9.7.4. Other Biological Functions of Silicon 248
9.8. Vanadium 249
9.8.1. Vanabins 249
9.8.2. Amavadin 250
9.8.3. Haloperoxidases 250
9.9. Chromium 252
9.10. Halogens and the Like 252
9.10.1. Formation of Volatile Halocarbons in Macroalgae 253
9.10.2. HOX Formation in Mammals and Others 253
9.10.2.1. Formation of HOX by a Fungal Chloroperoxidase 253
9.10.2.2. Formation of HOX by Mammalian Peroxidases 254
CHAPTER 10 Metal-Related Physiology 260
10.1. Metabolism of Metallic Elements 261
10.1.1. Iron Metabolism (in Mammals) 261
10.1.1.1. Ferric Reductase 262
10.1.1.2. Divalent Metal Transporter (DMT1) 263
10.1.1.3. Ferroxidase 263
10.1.1.4. Transferrin (Tf) and Transferrin Receptor (TfR) 263
10.1.1.5. Ferritin 265
10.1.1.6. Ferroportin (Fpn)/Hepcidin 266
10.1.1.7. Regulation of Ferritin and Transferrin 266
10.1.1.8. Iron Metabolism in Bacteria, Fungi, and Plants 267
10.1.2. Copper Metabolism 269
10.1.2.1. Outline of Copper Metabolism in Mammals 269
10.1.2.2. Copper Metabolism in Bacteria and Plants 270
10.1.3. Zinc Metabolism 271
10.1.3.1. In Mammals 271
10.1.3.2. In E. coli 272
10.1.4. A Mg(II) Transporter 273
10.2. Physiological Roles Played by Metallic Elements 273
10.2.1. Na/K-ATPase and Ca-ATPase 273
10.2.1.1. Mechanism 273
10.2.1.2. Ion Selectivity in Metal Ion Transporters and Channels—A General Discussion 274
10.2.2. Ca(II)—Second Messenger and Other Functions 276
10.2.2.1. Control of Cytoplasmic Ca(II) Concentration 277
10.2.2.2. Basic Mechanisms of Ca(II)—Physiology 278
10.2.2.3. Synaptotagmin, an Example of Physiology Mediated by Ca(II) 279
10.2.2.4. Why Calcium(II)? 280
10.2.3. Zinc-Enriched Neuron (ZEN) 283
10.2.4. Sensors for Small Molecules 283
10.2.4.1. Oxygen Sensors 284
10.2.4.2. CO-Sensors 285
10.2.4.3. NO-Sensors 286
10.2.4.4. H[sub(2)]-Sensors 287
10.2.4.5. Redox Sensors 287
10.2.5. Plant Hormone Ethylene and Copper 288
10.2.6. Magnetic Navigation 288
10.2.7. Radiation Shields 289
10.3. Biological Skeletons (Biominerals) 289
10.3.1. Calcium Carbonate 290
10.3.2. Calcium Oxalate 292
10.3.3. Calcium Phosphate 292
CHAPTER 11 Environmental Bioinorganic Chemistry 296
11.1. General Considerations 296
11.2. Toxicity of Inorganic Compounds 298
11.2.1. Abundance and Toxicity 298
11.2.2. Toxicity of Reactive Oxygen Species, and Defense Mechanisms Against Them 299
11.3. Molecular Mechanisms of Toxicity of Inorganic Compounds 301
11.3.1. Discrimination of Elements by Organisms—General Considerations 301
11.3.2. Oxidative Stress and Metals and As—General Effects 305
11.3.3. Individual Element's (Acute) Toxicity 307
11.3.3.1. Cd(II) and Hg(II) 307
11.3.3.2. Pb(II) 307
11.3.3.3. Organometallic Compounds 308
11.3.3.4. Organotin Compounds 309
11.3.3.5. Be(II), Al(III) 309
11.3.3.6. Tl(I) 310
11.3.3.7. Cr 310
11.3.3.8. Ni(II) 310
11.3.3.9. Anions 311
11.3.4. Alzheimer's Disease and Metals 311
11.4. Biological Defenses against Toxicity 312
11.4.1. Biological Defense against Mercury 313
11.4.2. Metallothioneins and Phytochelatins 315
11.4.2.1. Metallothioneins 315
11.4.2.2. Copper-Thionein (Cu-MT) 316
11.4.2.3. Phytochelatins 317
11.4.2.4. Use of Sulfide 318
11.4.3. Defense against Lead 318
11.4.4. Biotransformation of Arsenic 319
11.5. Bioremediaion of Metals 320
11.5.1. Biosorption by Brown Algae and by Microbial Surfactants 320
11.5.2. Phytoremediation (Phytoextraction of Metals from Soil) 322
11.5.3. Phytoextraction by Microalgae (Remediation of Polluted Water) 325
11.5.4. Other Types of Bioremediation 325
CHAPTER 12 Medical Applications of Inorganic Compounds: Medicinal Inorganic Chemistry 328
12.1. Introduction 328
12.2. Cancer Therapy 329
12.2.1. Platinum Compounds 330
12.2.2. Bleomycin 333
12.2.3. Radioactive Pharmaceuticals 336
12.3. Gold Compounds for Rheumatoid Arthritis 336
12.4. Vanadium Compounds for Diabetes 337
12.5. Lithium Compounds for Psychiatric Disorders 339
12.6. Other Potential Drugs Containing Inorganic Compounds 340
12.7. Diagnostic (Imaging) Agents 340
12.7.1. Gd(III)-Contrasting Agents for MRI 340
12.7.2. [sub(99m)]Tc-Radioactive Diagnostic Pharmaceuticals 341
Appendix 344
References 346
Index 368
A 368
B 368
C 368
D 369
E 369
F 369
G 370
H 370
I 370
K 370
L 370
M 370
N 371
O 371
P 371
Q 372
R 372
S 372
T 372
U 372
V 373
W 373
X 373
Y 373
Z 373