Biological Inorganic Chemistry Structure and Reactivity

ISBN-10: 1891389432
ISBN-13: 9781891389436
Edition: 2006
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Book details

List price: $125.00
Copyright year: 2006
Publisher: University Science Books
Publication date: 11/1/2006
Binding: Hardcover
Pages: 739
Size: 8.25" wide x 10.50" long x 1.50" tall
Weight: 3.850
Language: English

List of Contributors
Preface
Acknowledgments
Introduction and Text Overview
The Elements of Life
Functional Roles of Biological Inorganic Elements
A Guide to This Text
Overviews of Biological Inorganic Chemistry
Bioinorganic Chemistry and the Biogeochemical Cycles
Introduction
The Origin and Abundance of the Chemical Elements
The Carbon/Oxygen/Hydrogen Cycles
The Nitrogen Cycle
The Sulfur Cycle
The Interaction and Integration of the Cycles
Conclusions
Metal Ions and Proteins: Binding, Stability, and Folding
Introduction
The Metal Cofactor
Protein Residues as Ligands for Metal Ions
Genome Browsing
Folding and Stability of Metalloproteins
Kinetic Control of Metal Ion Delivery
Special Cofactors and Metal Clusters
Why Special Metal Cofactors?
Types of Cofactors, Structural Features, and Occurrence
Cofactor Biosynthesis
Transport and Storage of Metal Ions in Biology
Introduction
Metal Ion Bioavailability
General Properties of Transport Systems
Iron Illustrates the Problems of Metal Ion Transport
Transport of Metal Ions Other Than Iron
Mechanisms of Metal Ion Storage and Resistance
Intracellular Metal Ion Transport and Trafficking
Summary
Biominerals and Biomineralization
Introduction
Biominerals: Types and Functions
General Principles of Biomineralization
Conclusions
Metals in Medicine
Introduction
Metallotherapeutics
Imaging and Diagnosis
Molecular Targets
Metal Metabolism as a Therapeutic Target
Conclusions
Metal Ion Containing Biological Systems
Metal Ion Transport and Storage
Transferrin
Introduction: Iron Metabolism and the Aqueous Chemistry of Iron
Transferrin: The Iron Transporting Protein of Complex Organisms
Iron-Donating Function of Transferrin
Interaction of Transferrin with HFE
Ferritin
Introduction: The Need for Ferritins
Ferritin: Nature's Nanoreactor for Iron and Oxygen
Siderophores
Introduction: The Need for Siderophores
Siderophore Structures
Thermodynamics of Ferric Ion Coordination by Siderophores
Outer-Membrane Receptor Proteins for Ferric Siderophores
Marine Siderophores
Metallothioneins
Introduction
Classes of Metallothioneins
Induction and Isolation
Structural and Spectroscopic Properties
Reactivity and Function
Copper-Transporting ATPases
Introduction: Wilson and Menkes Diseases
Structure and Function
Metal Ion Binding and Conformational Changes
Metallochaperones
Introduction
The Need for Metallochaperones
COX17
ATX1
Copper Chaperone for SOD1
Metallochaperones for Other Metals?
Concluding Remarks
Hydrolytic Chemistry
Metal-Dependent Lyase and Hydrolase Enzymes. (I) General Metabolism
Introduction
Magnesium
Zinc
Manganese
Metal-Dependent Lyase and Hydrolase Enzymes. (II) Nucleic Acid Biochemistry
Introduction
Magnesium-Dependent Enzymes
Calcium
Zinc
Urease
Introduction
The Structure of Native Urease
The Structure of Urease Complexed with Transition State and Substrate Analogues
The Structure-Based Mechanism
The Structure of Urease Complexed with Competitive Inhibitors
The Molecular Basis for in vivo Urease Activation and Nickel Trafficking
Aconitase
Introduction
Stereochemistry of the Citrate-Isocitrate Isomerase Reaction
Characterization and Function of the Fe-S Cluster
Active Site Amino Acid Residues and the Reaction Mechanism
Cluster Reactivity and Cellular Function
Catalytic Nucleic Acids
Introduction and Discovery of Catalytic Nucleic Acids
Scope and Efficiency of Catalytic Nucleic Acids
Classification of Catalytic Nucleic Acids with Hydrolytic Activity
Metal Ions as Important Cofactors in Catalytic Nucleic Acids
Interactions between Metal Ions and Catalytic Nucleic Acids
The Role of Metal Ions in Catalytic Nucleic Acids
Expanding the Repertoire of Catalytic Nucleic Acids with Transition Metal Ions
Application of Catalytic Nucleic Acids
From Metalloproteins to Metallocatalytic Nucleic Acids
Electron Transfer, Respiration, and Photosynthesis
Electron-Transfer Proteins
Introduction
Determinants of Reduction Potentials
Iron-Sulfur Proteins
Cytochromes
Copper Proteins
A Further Comment on the Size of the Cofactor
Donor-Acceptor Interactions
Electron Transfer through Proteins
Introduction
Basic Concepts
Semiclassical Theory of Electron Transfer
Photosynthesis and Respiration
Introduction
Qualitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylation
An Interlude: Reduction Potentials
Maximizing Free Energy and ATP Production
Quantitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylation
Cellular Structures Involved in the Energy Transduction Process: Similarities among Bacteria, Mitochondria, and Chloroplasts
The Respiratory Chain
The Photosynthetic Electron-Transfer Chain
A Common Underlying Theme in Biological O[subscript 2]/H[subscript 2]O Metabolism: Metalloradical Active Sites
Dioxygen Production: Photosystem II
Introduction
Photosystem II Activity: Light-Catalyzed Two- and Four-Electron Redox Chemistry
Photosystem II Protein Structure and Redox Cofactors
Inorganic Ions of PSII
Modeling the Structure of the PSII Mn Cluster
Proposals for the Mechanism of Photosynthetic Water Oxidation
Oxygen Metabolism
Dioxygen Reactivity and Toxicity
Introduction
Chemistry of Dioxygen
Dioxygen Toxicity
Superoxide Dismutases and Reductases
Introduction
Superoxide Chemistry
Superoxide Dismutase and Superoxide Reductase Mechanistic Principles
Superoxide Dismutase and Superoxide Reductase Enzymes
Peroxidase and Catalases
Introduction
Overall Structure
Active-Site Structure
Mechanism
Reduction of Compounds I and II
Dioxygen Carriers
Introduction: Biological Dioxygen Transport Systems
Thermodynamic and Kinetic Aspects of Dioxygen Transport
Cooperativity and Dioxygen Transport
Biological Dioxygen Carriers
Protein Control of the Chemistry of Dioxygen, Iron, Copper, and Cobalt
Structural Basis of Ligand Affinities of Dioxygen Carriers
Final Remarks
Dioxygen Activating Enzymes
Introduction: Converting Carriers into Activators
Mononuclear Nonheme Metal Centers That Activate Dioxygen
Reducing Dioxygen to Water: Cytochrome c Oxidase
Introduction
Lessons from the X-Ray Structures of Bovine Heart Cytochrome c Oxidase
Reaction Mechanism
Reducing Dioxygen to Water: Multi-Copper Oxidases
Introduction
Occurrence and General Properties
Functions
X-Ray Structures
Structure-Function Relationships
Perspectives
Reducing Dioxygen to Water: Mechanistic Considerations
Hydrogen, Carbon, and Sulfur Metabolism
Hydrogen Metabolism and Hydrogenase
Introduction: Microbiology and Biochemistry of Hydrogen
Hydrogenase Structures
Biosynthesis
Hydrogenase Reaction Mechanism
Regulation by Hydrogen
Metalloenzymes in the Reduction of One-Carbon Compounds
Introduction: Metalloenzymes in the Reduction of One-Carbon Compounds to Methane and Acetic Acid
Electron Donors and Acceptors for One-Carbon Redox Reactions
Conversion to the "Formate" Oxidation Level by Two-Electron Reduction of Carbon Dioxide
Conversion from the "Formate" through the "Formaldehyde" to the "Methanol" Oxidation Level
Interconversions at the Methyl Level: Methyltransferases
Methyl Group Reduction or Carbonylation
Summary
Biological Nitrogen Fixation and Nitrification
Introduction
Biological Nitrogen Fixation: When and How Did Biological Nitrogen Fixation Evolve?
Nitrogen-Fixing Organisms and Crop Plants
Relationships among Nitrogenases
Structures of the Mo-Nitrogenase Component Proteins and Their Complex
Mechanism of Nitrogenase Action
Future Perspectives for Nitrogen Fixation
Biological Nitrification: What Is Nitrification?
Enzymes Involved in Nitrification by Autotrophic Organisms
Nitrification by Heterotrophic Organisms
Anaerobic Ammonia Oxidation (Anammox)
Future Perspectives for Nitrification
Nitrogen Metabolism: Denitrification
Introduction
The Enzymes of Denitrification
Summary
Sulfur Metabolism
Introduction
Biological Role of Sulfur Compounds
Biological Sulfur Cycle
Molybdenum Enzymes
Introduction
The Active Sites of the Molybdenum Enzymes
Molybdenum Enzymes
Conclusions
Tungsten Enzymes
Introduction
Biochemical Properties of Tungstoenzymes
Structural Properties of Tungstoenzymes
Spectroscopic Properties of Tungstoenzymes
Mechanism of Action of Tungstoenzymes
Tungsten Model Complexes
Tungsten versus Molybdenum
Metalloenzymes with Radical Intermediates
Introduction to Free Radicals
Introduction
Free Radical Stability and Reactivity
Electron Paramagnetic Resonance Spectroscopy
Biological Radical Complexes
Cobalamins
Introduction
Nomenclature and Chemistry
Enzyme Systems Using AdoCbl
Unresolved Issues in AdoCbl Requiring Enzymes
MeCbl Using Methionine Synthase as a Case Study
Unresolved Issues in Methyl Transfer Reactions with MeCbl
Ribonucleotide Reductases
Introduction: Three Classes of Ribonucleotide Reductases
Mechanisms of Radical Formation
Conclusions
Fe-S Clusters in Radical Generation
Introduction
Glycyl Radical Generation
Isomerization Reactions
Cofactor Biosynthesis
DNA Repair
Radical-SAM Enzymes: Unifying Themes
Galactose Oxidase
Introduction
Active Site Structure
Oxidation-Reduction Chemistry
Catalytic Turnover Mechanism
Mechanism of Cofactor Biogenesis
Amine Oxidases
Introduction
Structural Characterization
Structure-Function Relationship
Mechanistic Considerations
Biogenesis of Amine Oxidases
Conclusion
Lipoxygenase
Introduction
Structure
Mechanism
Kinetics
Metal Ion Receptors and Signaling
Metalloregulatory Proteins
Introduction: Structural Metal Sites
Structural Zn Domains
Metal Ion Signaling
Metalloregulatory Proteins
Metalloregulation of Transcription
Metalloregulation of Post-Transcriptional Processes
Post-Translational Metalloregulation
Structural Zinc-Binding Domains
Introduction
Molecular and Macromolecular Interactions
Metal Coordination and Substitution
Zinc Fingers and Protein Design
Calcium in Mammalian Cells
Introduction
Concentration Levels of Ca[superscript 2+] in Higher Organisms
The Intracellular Ca[superscript 2+]-Signaling System
A Widespread Ca[superscript 2+]-Binding Motif: The EF-Hand
Ca[superscript 2+] Induced Structural Changes in Modulator Proteins (Calmodulin, Troponin C)
Ca[superscript 2+] Binding in Buffer or Transporter Proteins
Nitric Oxide
Introduction: Physiological Role and Chemistry of Nitric Oxide
Chemistry of Oxygen Activation
Overview of Nitric Oxide Synthase Architecture
Nitric Oxide Synthase Mechanism
Cell Biology, Biochemistry, and Evolution: Tutorial I
Life's Diversity
Evolutionary History
Genomes and Proteomes
Cellular Components
Metabolism
Fundamentals of Coordination Chemistry: Tutorial II
Introduction
Complexation Equilibria in Water
The Effect of Metal Ions on the pK[subscript a] of Ligands
Ligand Specificity: Hard versus Soft
Coordination Chemistry and Ligand-Field Theory
Consequences of Ligand-Field Theory
Kinetic Aspects of Metal Ion Binding
Redox Potentials and Electron-Transfer Reactions
Abbreviations
Glossary
The Literature of Biological Inorganic Chemistry
Introduction to the Protein Data Bank (PDB)
Index

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