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By Ei-Ichiro Ochiai
Audience
Lecturers and students studying bioinorganic chemistry in inorganic, natural-products chemistry, and biochemistry programs
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 organisms
0.1.2. Bodily structure of living organisms
0.2. Cells, the Basic Functional Units of Living Organisms
0.3.
Basic Biochemicals Essential to Life
0.3.1. Carbohydrates
0.3.1.1. Monosasccharides
0.3.1.2. Polysaccharides and derivatives
0.3.2.
Lipids
0.3.2.1. Fats and phospholipids
0.3.2.2. Steroids
0.3.3. Proteins and amino acids
0.3.3.1. Structures
0.3.3.2. Reactions – formation
and hydrolysis of protein
0.3.4. Nucleotides, vitamins (coenzymes) and others
0.3.4.1. Coenzymes
0.3.4.2. Nucleotides
0.3.4.3. Other
vitamins
0.3.4.4. Hormone, neurotransmitters and others
0.3.5. DNA/RNA (Polynucleotide)
0.3.5.1. Structures
0.3.5.2. Reactions
0.4.
Types of Biochemical Reactions
0.4.1. Reactions of acid-base type
0.4.2. Reactions of oxidation-reduction type
0.4.2.1. The idea of oxidation
state
0.4.2.2. The oxidation state of ?C? in organic compounds and recognition of oxidation-reduction reactions
0.4.2.3. Other kinds
of oxidation-reduction reactions
0.4.3. Free radical reactions
0.5. Transition State Theory of Reaction, and Enzyme Kinetics
0.5.1.
Energy profile and transition state theory of reaction
0.5.2. Enzyme Kinetics
0.5.3. Enzyme reaction mechanism
Chapt. 1. Distribution
of Elements
1.1. Distribution of Elements in Earth Crust/Sea Water/Organisms
1.2. The Engines to Drive the Biochemical Cycling of the
Elements
1.3. The Geochemical Cycling of Elements – Contribution by Biosphere
1.4. Historical Change in the Biogeochemical Cycling
of Elements
Chapt. 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 compounds
Chapt. 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/Proteins
Chapt. 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
4.6.1.1. Effects
on structures
4.6.1.2. Catalytic metal ions in DNA polymerases and nucleases
4.6.2. Gene regulation and metal
ions
4.6.2. Ribozymes
Chapt. 5. Reactions of Oxidation-Reduction Type including Electron Transfer Processes
5.1. General
Consideration
5.1.1. Reduction potential
5.1.1.1. Heme proteins and enzymes
5.1.1.2. Iron-sulfur
proteins
5.1.1.3. Copper proteins
5.1.1.4. 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 reductase
Chapt.
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 Synthase
Chapt. 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 Examples
Chapt. 8. Nitrogen Fixation
8.1. Nitrogen Metabolism
8.2. Chemistry
of N2 Reduction
8.3. Mo-dependent Nitrogenases
8.4. Other Nitrogenases
Chapt. 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
9.10.2.1. Formation of HOX by fungal chlorperoxidase
9.10.2.2. 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)
10.1.1.1 Ferric reductase
10.1.1.2. Divalent metal transporter
(DMT1)
10.1.1.3. Ferroxidase
10.1.1.4. Transferrin (Tf) and transerrin receptor (TfR)
10.1.1.5. Ferritin
10.1.1.6. Ferroportin (Fpn)/hepcidin
10.1.1.7. Regulation of ferritin and transferrin
10.1.1.8. Iron metabolism in bacteria, fungi and plants
10.1.2. Copper metabolism
10.2.1.1.
An outline of copper metabolism in mammals
10.2.1.2. Copper metabolism in bacteria and plants
10.1.3. Zinc
metabolism
10.1.3.1. In mammals
10.1.3.2. 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
10.2.1.1. Mechanism
10.2.1.2. Ion selectivity in metal ion transporters and channels – a general discussion
10.2.2. Ca(II) – second
messenger, and other functions
10.2.2.1. Control of cytoplasmic Ca(II) concentration
10.2.2.2. Basic mechanisms of Ca(II)-physiology
10.2.2.3. Synaptotagmin – as an example of physiology mediated by Ca(II)
10.2.2.4. Why calcium(II)?
10.2.3. ZEN
10.2.4.
Sensors for small molecules
10.2.4.1. Oxygen sensors
10.2.4.2. CO-sensors
10.2.4.3.
NO-sensors
10.2.4.4. H2 sensors
10.2.4.5. 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 phosphate
Chapt. 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
11.3.3.1. Cd(II) and Hg(II)
11.3.3.2. Pb(II)
11.3.3.3. Organometallic compounds
11.3.3.4. Orgnotin compounds
11.3.3.5. Be(II), Al(III)
11.3.3.6. Tl(I)
11.3.3.7. Cr
11.3.3.8.
Ni(II)
11.3.3.9. 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
11.4.2.1.
Metallothioneins
11.4.2.2. Copper-thionein
11.4.2.3. Phytochelatins
11.4.2.4.
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 bioremediation
Chapt. 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
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