Comprehensive Natural Products Chemistry

Name: Comprehensive Natural Products Chemistry
Brand: Elsevier
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O. Meth-Cohn(Editor)

Elsevier (Publisher)

1st Edition

Published on 18. February 1999

8500 pages

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Content

Cover Image
Table of Contents
Editors-in-Chief
Volume Editors
Introduction
Preface
Sir Derek Barton*
Abbreviations
A Brief History of Natural Products Chemistry*
1.01. Overview
1.01.1. Introduction
1.01.2. Fatty Acids and Polyketides
1.01.3. Polyketide Biosynthesis in Actinomycetes and Fungi
1.01.4. Biosynthesis of Natural Products Involving the Shikimate Pathway
1.01.5. Biosynthesis of Compounds Containing Sulfur, a CP Bond or a CN Group
1.02. Biosynthesis and Degradation of Fatty Acids
1.02.1. Introduction
1.02.2. Biosynthesis of Saturated Fatty Acids
1.02.3. Biosynthesis of Unsaturated Fatty Acids
1.02.4. Degradation of Fatty Acids
1.02.5. Conclusions
1.03. Biosynthesis of Cyclic Fatty Acids Containing Cyclopropyl-, Cyclopentyl-, Cyclohexyl-, and Cycloheptyl-rings
1.03.1. Introduction
1.03.2. Cyclopropyl and Cyclopropenyl Fatty Acids
1.03.3. ?-Cyclopentyl and ?-Cyclopentenyl Fatty Acids
1.03.4. ?-Cyclohexyl Fatty Acids
1.03.5. ?-Cycloheptyl Fatty Acids
1.04. Biosynthesis of So-called "Green Odor" Emitted by Green Leaves
1.04.1. Introduction
1.04.2. Synthesis of the Series of Positional and Geometric Isomers of Unsaturated C6 Alcohols and C6 Aldehydes
1.04.3. Chemical Structure-Odor Characteristics Relationships in n-Hexenols and n-Hexenals
1.04.4. Aromatization of Leaf Alcohol
1.04.5. Biosynthetic Pathway of Green Odor
1.04.6. Enzyme Systems in Green Odor Biosynthesis
1.04.7. Relationship Between Environmental Stimuli and Enzyme System Activities
1.04.8. Perspective
1.05. Biosynthesis of Jasmonoids and Their Functions
1.05.1. Introduction
1.05.2. Biosynthesis of Jasmonic Acid
1.05.3. Functions
1.05.4. Initiation of Jasmonate Biosynthesis
1.05.5. Structure-Activity Relationships
1.06. Biosynthesis of Butyrolactone and Cyclopentanoid Skeletons Formed by Aldol Condensation
1.06.1. Introduction
1.06.2. Biosynthesis of virginiae butanolide A-A Butyrolactone Autoregulator from streptomyces
1.06.3. Biosynthesis of the Chitinase Inhibitor Allosamidin
1.07. Eicosanoids in Mammals
1.07.1. Introduction
1.07.2. Biosynthesis, Structural Elucidation, and Chemistry of Eicosanoids
1.07.3. Biological Activities of Eicosanoids in Mammals
1.07.4. Synthesis of Eicosanoids
1.07.5. Synthesis of Agonists and Antagonists
1.07.6. Application to Medical Use
1.07.7. Eicosanoid Receptors
1.07.8. Conclusion
1.08. Eicosanoids in Nonmammals
1.08.1. Introduction
1.08.2. Eicosanoids from Bacteria and Microorganisms
1.08.3. Fungi, Algae, and Plants
1.08.4. Animals
1.08.5. Conclusion
1.09. Biosynthesis and Metabolism of Eicosanoids
1.09.1. Arachidonate Cascade
1.09.2. Phospholipase A2
1.09.3. Prostaglandin Endoperoxide Synthases
1.09.4. Prostaglandin Endoperoxide Metabolizing Enzymes
1.09.5. Prostaglandin Metabolism
1.09.6. Lipoxygenases
1.09.7. Hydroperoxy- and Epoxy-Eicosanoid Metabolizing Enzymes
1.09.8. Cytochrome P450 in Eicosanoid Metabolism
1.10. Molecular Evolution of Proteins Involved in the Arachidonic Acid Cascade
1.10.1. Introduction
1.10.2. Fatty Acid Cyclooxygenases-1 and -2
1.10.3. Prostaglandin D2 Synthase
1.10.4. Prostaglandin F2asynthase
1.10.5. Thromboxane Synthase and Prostaglandin I2 Synthase
1.10.6. Lipoxygenase
1.10.7. Leukotriene A4 Hydrolase
1.10.8. Leukotriene C4 Hydrolase and 5-lipoxygenase-activating Protein
1.10.9. Eicosanoid Receptors
1.10.10. Prostaglandin Transporter
1.10.11. Conclusion
1.11. Biosynthesis of Platelet-activating Factor and Structurally Related Bioactive Lipids
1.11.1. Introduction
1.11.2. Biosynthesis of Ether-Linked Phospholipids
1.11.3. Biosynthesis of Platelet-Activating Factor
1.11.4. Formation of PAF-Like Lipids
1.11.5. Concluding Remarks
1.12. Biosynthesis of Cyclic Bromoethers from Red Algae
1.12.1. Introduction
1.12.2. Biosynthesis with Lactoperoxidase
1.12.3. Purification of Bromoperoxidase
1.12.4. Biosynthesis with Bromoperoxidase
1.12.5. Discussion
1.13. Biosynthesis of Lipo-chitin Oligosaccharides: Bacterial Signal Molecules Which Induce Plant Organogenesis
1.13.1. Introduction
1.13.2. Biological Function of LCOs
1.13.3. Nodulation Genes
1.13.4. Biosynthesis of LCOs
1.13.5. Unusual Fatty Acids in the LCOs of R. Leguminosarum
1.13.6. a,ß-Unsaturated Fatty Acids in Plants
1.13.7. Properties of the Unusual Fatty Acids
1.13.8. Biosynthesis of Fatty Acids in Bacteria
1.13.9. Structure-Function Relationship of ACYL Carrier Proteins
1.13.10. Comparison of the Function of ACP and NodF
1.13.11. A Model for the Biosynthesis of Polyunsaturated Fatty Acids
1.13.12. Fatty Acid Transfer
1.14. Biosynthesis of 6-Methylsalicylic Acid
1.14.1. Introduction
1.14.2. Fatty Acid Synthases as Models for Polyketide Synthase
1.14.3. Isolation and Properties of 6-Methylsalicylic Acid Synthase
1.14.4. The Biosynthetic Pathway for 6-Methylsalicylic Acid and Its Relationship to Fatty Acid Biosynthesis
1.14.5. The Nucleotide Sequence of 6-Methylsalicylic Acid Synthase
1.14.6. Substrate Specificity of 6-Methylsalicylic Acid Synthase
1.14.7. Inactivation of 6-Methylsalicylic Acid by Cerulenin
1.14.8. Stereochemical Studies on The Enzyme Mechanism
1.14.9. Mechanistic Considerations for The Formation of 6-Methylsalicylic Acid
1.14.10. The Mechanism of Orsellinic Acid Synthase
1.14.11. Malonyl-Coa Decarboxylase Activity of 6-Methylsalicylic Acid Synthase
1.14.12. Pointers to The Three-Dimensional Structure of 6-Methylsalicylic Acid Synthase
1.14.13. Summary
1.15. The Diels-Alder Reaction in Biosynthesis of Polyketide Phytotoxins
1.15.1. Introduction
1.15.2. Diels-Alder-Type Natural Products
1.15.3. Biological Diels-Alder Reaction in Biosynthesis of Polyketide Phytotoxins
1.15.4. Conclusion and Perspectives
1.16. Polyketide Biosynthesis in Filamentous Fungi
1.16.1. Introduction
1.16.2. Fungal Polyketide Compounds
1.16.3. Aromatic Polyketide Synthases
1.16.4. Nonaromatic Polyketide Synthases
1.16.5. Structure of Fungal Polyketide Synthases
1.16.6. Biosynthetic Reactions Acting on PKS Products
1.16.7. Concluding remarks
1.17. Biosynthesis of Aflatoxin
1.17.1. Introduction
1.17.2. Blocked Mutants
1.17.3. Common Polyketide Folding Pattern
1.17.4. Synthesis and Testing of Potential Intermediates
1.17.5. Molecular Biological Approaches to Afb1/st biosynthesis
1.18. Structure, Function, and Engineering of Bacterial Aromatic Polyketide Synthases
1.18.1. Introduction
1.18.2. Genes Encoding Bacterial Aromatic PKSs
1.18.3. Genetic Construction and Chemical Analysis of Recombinant PKSs
1.18.4. Biochemical Analysis of Bacterial Aromatic PKSs
1.18.5. Engineering of Bacterial Aromatic PKSs
1.18.6. Conclusions and Future Directions
1.19. Biosynthesis of Erythromycin and Related Macrolides
1.19.1. Introduction to Polyketide Structures
1.19.2. The Erythromycins
1.19.3. Rapamycin, FK506, and FK520
1.19.4. The Avermectins
1.19.5. Tylosin, Spiramycin, and Niddamycin
1.19.6. Rifamycin
1.19.7. Nargenicin A
1.19.8. Conclusions
1.20. Cyclosporin: The Biosynthetic Path to a Lipopeptide
1.20.1. Introduction
1.20.2. Discovery and Production Strains
1.20.3. Environmental Implications
1.20.4. Production Levels and Structural Analogues Obtained from Cultures
1.20.5. Biosynthesis
1.20.6. Future Prospects
1.21. Biosynthesis of Enediyne Antibiotics
1.21.1. New Class of Antibiotics
1.21.2. Biosynthesis of Dynemycin A
1.21.3. Biosynthesis of Esperamycin A1
1.21.4. Biosynthesis of Neocarzinosatin Chromophore
1.21.5. Comprehensive Analysis of Enediyne Core Biosynthesis
1.22. Enzymology and Molecular Biology of the Shikimate Pathway
1.22.1. Introduction
1.22.2. Dahp synthase
1.22.3. Dehydroquinate synthase
1.22.4. Dehydroquinase
1.22.5. The quinate pathway
1.22.6. Shikimate dehydrogenase
1.22.7. Shikimate kinase
1.22.8. 5-enolpyruvyl-shikimate 3-phosphate synthase
1.22.9. The arom pentafunctional protein
1.22.10. Chorismate synthase
1.22.11. Final comments
1.23. The Role of Isochorismic Acid in Bacterial and Plant Metabolism
1.23.1. Discovery of Isochorismic Acid
1.23.2. Biosynthesis of Isochorismic Acid
1.23.3. Metabolism of Isochorismic Acid in Bacteria
1.23.4. Metabolism of Isochorismic Acid in Higher Plants
1.23.5. Preparation by Metabolic Pathway Engineering of Metabolites Derived from Chorismic Acid
1.23.6. Conclusions
1.24. Biosynthesis of Coumarins
1.24.1. Introduction
1.24.2. Modulation of coumarin accumulation
1.24.3. Biosythesis
1.24.4. Conclusions
1.25. Lignans: Biosynthesis and Function
1.25.1. Introduction
1.25.2. Definition and Nomenclature
1.25.3. Evolution of the Lignan Pathway
1.25.4. Occurence
1.25.5. Optical Activity of Lignan Skeletal Types and Limitations to the Free Radical Random Coupling Hypothesis
1.25.6. 8-8´ Stereoselective Coupling: Dirigent Proteins and E-Coniferyl Alcohol Radicals
1.25.7. Pinoresinol Metabolism and Associated Metabolic Processes
1.25.8. Are Dirigent Protein Homologues Involved in Other 8-8´ Phenoxy Radical Coupling Processes?
1.25.9. Miscellaneous Coupling Modes: are Dirigent Proteins also Involved?
1.25.10. 8-5´ and 8-o-4´ Coupling of Monolignols and Allylphenols and Their Associated Metabolic Processes
1.25.11. Mixed Dimers Containing Monolignols and Relatedmonomers
1.25.12. Lignans and Sesquilignans: What is the Relationship to Lignin Formation?
1.25.13. Physiological Roles in Planta
1.25.14. Roles in Human Nutrition/Health Protection and Disease Treatment
1.25.15. Concluding Remarks
1.26. Biosynthesis of Flavonoids
1.26.1. Introduction
1.26.2. Flavonoid structure and major flavonoid classes
1.26.3. Elucidation and general overview of the flavonoid pathway
1.26.4. Formation of Flavonoid Precursors and Flavonoid Classes
1.26.5. Modification reactions
1.26.5.3. Glycosylation Reactions
1.26.5.4. Methylation Reactions
1.26.5.5. Acylation Reactions
1.26.5.6. Prenylation Reactions
1.26.5.7. Glutathione Transfer Reaction
1.26.6. Perspectives
1.27. The Chalcone/Stilbene Synthase-type Family of Condensing Enzymes
1.27.1. Introduction
1.27.2. CHS and STS
1.27.3. Function and Structure: Analysis of Mutant Protiens
1.27.4. A Superfamily of CHS/STS-Type Enzymes?
1.27.5. Evolution: How Old are Protiens of the CHS/STS-Type?
1.27.6. Modification of Reaction Intermediates
1.27.7. Pepspectives
1.27.8. Appendix: Sequencea Accession Numbers
1.28. Isoflavonoids: Biochemistry, Molecular Biology, and Biological Functions
1.28.1. Introduction: Chemical Classes and Biological Occurrence of Isoflavonoids
1.28.2. Biological Activities of Isoflavonoids
1.28.3. Biosynthesis of Isoflavonoids
1.28.4. Catabolism of Isoflavonoids
1.28.5. Integrated Control of Isoflavonoid Biosynthesis
1.28.6. Evolution of Isoflavonoid Phytoalexin Biosynthetic Pathways
1.29. Biosynthesis of Sulfur-containing Natural Products
1.29.1. Introduction
1.29.2. Enzyme Cofactors
1.29.3. Antibiotics
1.29.4. Miscellaneous
1.29.5. Conclusion
1.30. Biosynthesis of the Natural C-P Compounds, Bialaphos and Fosfomycin
1.30.1. Introduction
1.30.2. Biosynthesis of Bialaphos
1.30.3. Biosynthesis of Fosfomycin
1.30.4. Conclusion
1.31. Biosynthesis and Degradation of Cyanogenic Glycosides
1.31.1. Introduction
1.31.2. Chemical Nature Of Cyanogenic Glycosides
1.31.3. Biosynthesis of Cyanogenic Glycosides
1.31.4. Degradation of Cyanogenic Glycosides
2.01. Isoprenoid Biosynthesis: Overview
2.01.1. Introduction
2.01.2. Biosynthesis of Isopentenyl Diphosphate
2.01.3. Isopentenyl Diphosphate Metabolism and the Biochemistry of Carbocations
2.01.4. Multidisciplinary Approaches to the Study of Isoprenoid Biosynthesis
2.02. Biosynthesis of Mevalonic Acid from Acetyl-CoA
2.02.1. Introduction
2.02.2. Acetoacetyl-CoA Synthase
2.02.3. HMG-CoA Synthase
2.02.4. HMG-CoA Reductase
2.03. A Mevalonate-independent Route to Isopentenyl Diphosphate
2.03.1. Introduction
2.03.2. Bacterial triterpenoids of the hopane series: the tools for the discovery of the mevalonate-independent pathway
2.03.3. Elucidation of the nonmevalonate pathway: the origin of the carbon atoms of isoprenic units in bacteria
2.03.4. The precursors of ipp in the mevalonate-independent pathway
2.03.5. Distribution of the mevalonate-independent pathway
2.03.6. Conclusions-further developments
2.04. Isopentenyl DiphosphateIsomerase and Prenyltransferases
2.04.1. Introduction
2.04.2. Isopentenyl diphosphate isomerase
2.04.3. Prenyltransferase
2.04.4. Summary
2.05. Monoterpene Biosynthesis
2.05.1. Introduction
2.05.2. Biological Considerations
2.05.3. Experimental Methods
2.05.4. Geranyl Diphosphate Biosynthesis
2.05.5. Cyclization Reactions
2.05.6. Secondary Transformations
2.05.7. Summary and Prospects
2.06. Sesquiterpene Biosynthesis: Cyclization Mechanisms
2.06.1. Introduction
2.06.2. Cyclization Mechanisms
2.06.3. Sesquiterpene Biosynthetic Pathways
2.06.4. Sesquiterpene Synthases
2.07. Cloning and Expression of Terpene Synthase Genes
2.07.1. Introduction
2.07.2. Cloning of Terpene Synthase Genes
2.07.3. Heterologous expression of terpene synthase genes
2.07.4. Implications for Future Research
2.08. Diterpene Biosynthesis
2.08.1. Introduction
2.08.2. Type A cyclization
2.08.3. Type A-Type B cyclization
2.08.4. Type B cyclization
2.08.5. Type B-Type A cyclizations
2.08.6. Tetracycles and Pentacycles
2.08.7. Summary and future prospects
2.09. Squalene Synthase
2.09.1. Introduction
2.09.2. Purification
2.09.3. Comparison Between Yeast, Plant and Mammalian Enzymes
2.09.4. Structure and Mechanism
2.09.5. Inhibitors
2.09.6. Regulation of the Mammalian Enzyme
2.09.7. Chromosomal Mapping of the Gene and Subcellular Localization of the Enzyme
2.09.8. Addendum
2.10. Squalene Epoxidase and Oxidosqualene : Lanosterol Cyclase-Key Enzymes in Cholesterol Biosynthesis
2.10.1. Introduction
2.10.2. Squalene Epoxidase
2.10.3. Oxidosqualene: Lanosterol Cyclase
2.10.4. Conclusions
2.11. Cycloartenol and Other Triterpene Cyclases
2.11.1. Introduction
2.11.2. Cycloartenol Cyclase
2.11.3. Amyrin cyclases and other trierpene cyclases
2.11.4. Hopine and Tetrahymanol Cyclases
2.11.5. Conclusion from Genetic Studies
2.11.6. Future Lines of Research
2.12. Carotenoid Genetics and Biochemistry
2.12.1. General introduction
2.12.2. Overview of carotenoid biosynthesis
2.12.3. Localization and functions of carotenoids
2.12.4. Carotenoid biosynthesis genes
2.12.5. Carotenoid biosynthesis enzymes
2.12.6. Regulation of carotenoid biosynthesis
2.12.7. Genetic engineering of carotenoid biosynthesis
2.12.8. Conclusions
2.13. Protein Prenylation
2.13.1. Introduction
2.13.2. Chemical Structures of Protein Prenyl Groups
2.13.3. Protein prenyltransferases
2.13.4. Prenyl Protein-Specific Endoproteinase
2.13.5. Prenyl protein-specific methyltransferase
2.13.6. Specific Examples of Prenylated Proteins
2.13.7. Methylation
2.13.8. Prenylation in Plants and Nonfungal Microorganisms
2.13.9. Future Prospects
2.14. Ginkgolide Biosynthesis
2.14.1. Introduction
2.14.2. Isopentenyl Diphosphate Biosynthesis
2.14.3. Ginkgolide Biosynthesis
2.14.4. Summary
3.01. The World of Carbohydrates and Associated Natural Products
3.01.1. Introduction
3.01.2. Overview
3.01.3. Part 1: Glycosidases, Glycosyltransferases, N- and O-Linked Glycoproteins, Glycosphingolipids, Glycosidase Inhibitors, and Proteoglycans
3.01.4. Part 2: Lipopolysaccharides, Peptidoglycan, Glycosyl-Phosphatidylinositols, Aminoglycoside and Aminocyclitol Antibiotics
3.01.5. Part 3: Deoxysugars, Aldolases
3.01.6. Part 4: Starch and Glycogen, Pectins and Galactomannans, Celluloses, Hemicelluloses, Lignin, Condensed and Hydrolyzable Tannins
3.01.7. Conclusions
3.02. Glycosidases of the Asparagine-linked Oligosaccharide Processing Pathway
3.02.1. Introduction
3.02.2. N-Glycans
3.02.3. a-Glucosidases
3.02.4. endo-a-Mannosidase
3.02.5. exo-a-Mannosidases
3.02.6. N-Acetylglucosaminidases
3.02.7. Processing Glycosidases and Quality Control
3.03. Glycosyltransferases Involved in N-Glycan Synthesis
3.03.1. Introduction
3.03.2. An Overview of the Structure and Biosynthesis of N-Glycans
3.03.3. UDP-Gal:GlcNAc-R ß1,4-Galactosyltransferase (E.C. 2.4.1.38/90
2.4.1.22)
3.03.4. Sialyltransferases
3.03.5. N-acetylglucosaminyltransferases
3.03.6. Fucosyltransferases
3.03.7. Concluding remarks
3.04. Glycosyltransferases Involved in the Synthesis of Ser/Thr-GalNAc O-Glycans
3.04.1. Introduction
3.04.2. O-Glycan Structures and Functions
3.04.3. Factors Controlling O-Glycan Biosynthesis
3.04.4. Initiation of O-Glycan Biosynthesis. UDP-GalNAc: Polypeptidea-N-Acetylgalactosaminyltransferase (Polypeptide GalNAc-T
EC 2.4.1.41)
3.04.5. Synthesis of O-Glycan Core Structures
3.04.6. Elongation and Branching of O-Glycans
3.04.7. Termination Reactions in the Synthesis of o-Glycans
3.05. Organization and Topology of Sphingolipid Metabolism
3.05.1. Introduction
3.05.2. Glycosphingolipid Biosynthesis in the Er-Golgi Complex
3.05.3. Pathways of Sphingolipid Transport
3.05.4. Functional Importance of Activator Proteins in Lysosomal Degradation of Sphingolipids
3.05.5. Concluding Remarks
3.06. Biosynthesis and Regulation of Glycosphingolipids
3.06.1. Introduction
3.06.2. Glycolipid Galactosyltransferases (GalTs)
3.06.3. Glycolipid: glucosyltransferase(GlcT)
3.06.4. Glycolipid: Fucosyltransferases (FucT OR FT)
3.06.5. Glycolipid: Sialyltransferases
3.06.6. Glycolipid: Glucuronyltransferase(GlcAT)
3.06.7. Glycolipid n-Acetylglucosaminyltransferases (GlcNAcTs)
3.06.8. Glycolipid n-Acetylgalactosaminyltransferases (GalNAcTs)
3.06.9. Regulation of Glycolipid Biosynthesis
3.07. Alkaloid Glycosidase Inhibitors
3.07.1. Introduction
3.07.2. Chemistry of Alkaloid Glycosidase Inhibitors
3.07.3. Glycosidase Inhibition
3.07.4. Biological Activity of Glycosidase Inhibitors
3.07.5. Processing of N-Linked Oligodsaccharides
3.07.6. Inhibitors of N-Linked Glycoprotein Processing
3.08. Biosynthesis of Proteoglycans
3.08.1. Introduction
3.08.2. Nomenclature and Classification
3.08.3. Core Protein Biosynthesis
3.08.4. Glycosaminoglycan Biosynthesis
3.08.5. Concluding Remarks
3.09. Lipopolysaccharides
3.09.1. Introduction
3.09.2. Biology of Endotoxin (Lipopolysaccharide)
3.09.3. Chemistry of Lipopolysaccharide
3.09.4. Physicochemistry of Lipopolysaccharide
3.09.5. Biosynthesis of Lipopolysaccharide
3.09.6. Final Remarks
3.10. Bacterial Peptidoglycan Biosynthesis and its Inhibition
3.10.1. Bacterial cell wall peptidoglycan structure
3.10.2. Biosynthesis of Peptidoglycan
3.10.3. Inhibition of Peptidoglycan Biosynthesis
3.11. Biosynthesis of Glycosylated Phosphatidylinositol in Parasitic Protozoa, Yeast, and Higher Eukaryotes
3.11.1. Introduction
3.11.2. Glycosylphosphatidylinositol Membrane Anchors
3.11.3. Lipophosphoglycans(LPGs) and Glycosylinositol Phospholipids(GIPLs)
3.12. Deoxysugars: Occurrence, Genetics, and Mechanisms of Biosynthesis
3.12.1. Introduction
3.12.2. Natural Occurrence of Deoxysugars
3.12.3. Biological Activity of Deoxysugars
3.12.4. Pathways and Mechanisms of Deoxysugar Biosynthesis
3.12.5. Genetics of Deoxysugar Biosynthesis
3.12.6. Concluding Remarks
3.13. Aldolases
3.13.1. Introduction
3.13.2. Schiff Base Forming Aldolases
3.13.3. Divalent Metal-Catalyzed Aldolases
3.13.4. Aldolases utilizing phosphoenolpyruvate
3.13.5. Thiamine-Dependent Aldolases
3.13.6. Pyridoxal-dependent aldolases
3.13.7. Aldolases of Undetermined Mechanism
3.13.8. Enzymes of glycolysis
3.14. Starch and Glycogen Biosynthesis
3.14.1. Introduction
3.14.2. The role of glycogen and starch
3.14.3. Synthesis of bacterial glycogen and starch
3.14.4. Properties of the bacterial and plant enzymes involved in the synthesis of glycogen and starch
3.14.5. The plastids, site of starch synthesis in plants
3.14.6. Synthesis of amylopectin in vivo: a hypothesis assigning specific roles to starch synthases, and to branching and debranching enzymes
3.14.7. Regulation of the synthesis of bacterial glycogen and starch
3.14.8. Properties of the glycogen biosynthetic enzymes of mammals
3.14.9. Regulation of mammalian glycogen synthesis
3.15. Biosynthesis of Pectins and Galactomannans
3.15.1. Introduction
3.15.2. Structure of Pectin
3.15.3. Subcellular Localization of Pectin Biosynthetic Enzymes
3.15.4. Nucleotide Sugar Substrates for Glycosyltransferases
3.15.5. Pectin Glycosyltransferases
3.15.6. Nonglycosyltransferase-Pectin Biosynthetic Enzymes
3.15.7. Direction of Pectin Polysaccharide Biosynthesis
3.15.8. Regulation of Pectin Biosynthesis
3.15.9. Galactomannans
3.15.10. Future Prospects
3.16. Celluloses
3.16.1. Introduction
3.16.2. Historical Perspective
3.16.3. Structures
3.16.4. Biological Aspects
3.16.5. Future Directions
3.17. Hemicelluloses
3.17.1. Introduction
3.17.2. The Hemicellulose Family
3.17.3. Localization and Association with Other Cell Wall Components
3.17.4. Sites of Biosynthesis
3.17.5. Enzymology
3.17.6. Regulation of Hemicellulose Biosynthesis
3.17.7. Identification of Genes Involved in Hemicellulose Biosynthesis
3.17.8. Hemicelluloses, a Target for Manipulation?
3.18. The Nature and Function of Lignins
3.18.1. Introduction
3.18.2. Evolution of the Phenylpropanoid Pathway and Lignin Biosynthetic Capacity
3.18.3. Monolignol Biosynthesis
3.18.4. Tissue and Subcellular Localization of Monolignol Pathway Enzymes and Associated Gene Expression
3.18.5. Monolignol Partitioning, Intracellular Transport, Glucosyltransferases, AND ß-Glucosidases
3.18.6. Lignins in Plant Tissues: Relationship with Other Cell Wall Components
3.18.7. Formation of Lignin Macromolecules in Vivo and in Vitro
3.18.8. Concluding Remarks
3.19. Condensed Tannins
3.19.1. Introduction
3.19.2. Nomenclature
3.19.3. Flavan-3-Ols, Flavan-3,4-Diols, Flavan-4-Ols, and Flavans as Building Blocks for Oligomeric Proanthocyanidins
3.19.4. Oligomeric Proanthocyanidins
3.19.5. Nonproanthocyanidins with Flavan or Flavan-3-Ol Constituent Units
3.19.6. Conformation of Proanthocyanidins
3.19.7. Astringency
3.19.8. Role of Polyphenols as Chemopreventers
3.20. Biosynthesis of Hydrolyzable Tannins
3.20.1. Introduction
3.20.2. Classification and Structural Principles
3.20.3. Origin of Gallic Acid
3.20.4. Biosynthesis of ß-Glucogallin
3.20.5. "Simple" Galloylglucose Esters-from ß-Glucogallin to Pentagalloylglucose
3.20.6. Biosynthesis of Gallotannins
3.20.7. Oxidation of Pentagalloylglucose to Ellagitannins
3.20.8. Enzymatic Degradation of Hydrolyzable Tannins
3.20.9. Preparation of Galloylglucoses
3.20.10. Conclusions and Perspectives
4.01. Overview of the Biosynthesis of Amino Acids, Peptides, Porphyrins, and Alkaloids with a Focus on the Biosynthesis of Aromatic Amino Acids
4.01.1. Introduction
4.01.2. Biosynthesis of Aromatic Acids
4.01.3. Chorismic Acid-A Common Intermediate
4.01.4. Phenylalanine-Tyrosine Pathways
4.01.5. Tryptophan Branch
4.01.6. Regulation of Aromatic Amino Acid Biosynthesis
4.01.7. E. Coli Aromatic Amino Acid Biosynthesis
4.01.8. The Control of Aromatic Amino Acid Biosynthesis in S. cerevisiae
4.01.9. Herbicide Action and Aromatic Amino Acid Biosynthesis
4.01.10. Summary
4.01.11. The Future of Biosynthesis
4.02. Protein Palmitoylation
4.02.1. Introduction
4.02.2. Chemical Structures of Protein Palmitoyl Groups
4.02.3. Attachment of Palmitoyl Groups to Proteins
4.02.4. Functions of Protein Palmitoyl Groups
4.02.5. Future Prospects
4.03. Recent Advances in Biosynthesis of Alkaloids
4.03.1. Introduction
4.03.2. Alkaloids Derived from Ornithine
4.03.3. Alkaloids Derived from Lysine
4.03.4. Alkaloids Derived from Tyrosine and Phenylalanine
4.03.5. Alkaloids Derived from Tryptophan
4.03.6. Alkaloids Derived from Histidine
4.03.7. Conclusion and Future Prospects
4.04. Biosynthesis of Heme
4.04.1. Introduction
4.04.2. The Biosynthesis of 5-minolevulinic Acid
4.04.3. The Transformation of 5-aminolevulinic Acid into Uroporphyrinogen III
4.04.4. The Transformation of Uroporphyrinogen III into heme
4.04.5. Epilogue
4.05. Strictosidine-The Biosynthetic Key to Monoterpenoid Indole Alkaloids
4.05.1. Introduction
4.05.2. Occurrence of strictosidine
4.05.3. Cell-free formation of strictosidine
4.05.4. Significance of strictosidine
4.05.5. Purification of strictosidine synthase from C. Roseus
4.05.6. Preparative biosynthesis of strictosidine
4.05.7. Chemical synthesis of strictosidine
4.05.8. Strictosidine synthase from Rauwolfia serpentina cell suspension cultures
4.05.9. Genetic analyses of strictosidine synthase
4.05.10. Chemotaxonomic considerations based on the strictosidine synthase gene Str 1
4.05.11. Does strictosidine synthase have a regulatory function in alkaloid biosynthesis?
4.06. Enzymatically Controlled Steps in Vitamin B12 Biosynthesis
4.06.1. Introduction
4.06.2. The Oxygen-Requiring Pathway to Vitamin B12 as Exemplified by Pseudomonas Denitrificans
4.06.3. The Anoxic Pathway to Vitamin B12 as exemplified by S. typhimurium and P. shermanii
4.07. Biosynthesis of ß-Lactam Compounds in Microorganisms
4.07.1. Introduction
4.07.2. General aspects of ß-lactam compounds
4.07.3. Penicillins, Cephalosporins, and Cephamycins
4.07.4. Clavams
4.07.5. Carbapenms
4.07.6. Monoclactms
4.08. Multifunctional Peptide Synthetases Required for Nonribosomal Biosynthesis of Peptide Antibiotics
4.08.1. Introduction
4.08.2. Physiological Role of Metabolite Synthesis
4.08.3. Mechanisms for Prevention of Autointoxication
4.08.4. Bioactive Peptide Products
4.08.5. Towards Commercial Antibiotics
4.08.6. Characteristics of Peptide Products
4.08.7. Two Types of Peptide Synthesis
4.08.8. Overview of the Nonribosomal System
4.08.9. Proposed Mode of Nonribosomal Peptide Synthesis
4.08.10. Multi-Carrier Thiotemplate Model
4.08.11. Modular Arrangement of Peptide Synthetase
4.08.12. Multiple P-Pant Requiring Pathways
4.08.13. Models for Nonribosomal Peptide Biosynthesis
4.08.14. Strategies for Designing Novel Peptide Products
4.08.15. Conclusions
4.09. Catalysis of Amide and Ester Bond Formation by Peptide Synthetase Multienzymatic Complexes
4.09.1. Introduction
4.09.2. ACYL Transfer Reactions Catalyzed by PPS Enzymes
4.09.3. Acyltransferase Domains of PPS Enzymes
4.09.4. Mechanism of Epimerization by PPS Enzymes
4.09.5. Conclusions
4.10. Enzymatic Synthesis of Penicillins
4.10.1. General Introduction
4.10.2. Penicillins: structure and general properties
4.10.3. Classification of penicillins
4.10.4. Benzylpenicillin biosynthetic pathway
4.10.5. Location of penicillin biosynthetic enzymes
4.10.6. Penicillin biosynthetic genes
4.10.7. Benzylpenicillin biosynthetic enzymes
4.10.8. Enzymatic coupled systems
4.10.9. Biotechnological approach: expression of phaccoal from P. putida u in p. chrysogenum
4.10.10. Concluding remarks and future outlook
4.11. Genetics of Lantibiotic Biosynthesis
4.11.1. Introduction to a Group of Unique Peptides
4.11.2. Biosynthetic Pathway of Lantibiotics
4.11.3. Genetic Engineering of Lantibiotics
4.11.4. Outlook
4.12. Glycosylphosphatidylinositol (GPI)-anchor Biosynthesis
4.12.1. Introduction
4.12.2. Intracellular Site and Orientation of GPI-Anchor Biosynthesis
4.12.3. Structure of GPI and GPI-Anchored Protein
4.12.4. Genes Involved in GPI-Anchor Biosynthesis
4.12.5. GPI-Anchor Biosynthesis
4.12.6. Modification of GPI After the GPI : Protein Transamidase Reaction
4.13. Structure, Function, and Biosynthesis of Gramicidin S Synthetase
4.13.1. Introduction
4.13.2. Peptide Antibiotics from Bacillus Brevis Sp.
4.13.3. Biosynthesis of Gramicidin s and tyrocidine
4.13.4. Purification of Gramicidin S Synthetase
4.13.5. Gramicidin S and Tyrocidine Biosynthetic Genes
4.13.6. The Modular Structure of Gramicidin S Synthetase
4.13.7. The Mechanism of Nonribosomal Peptide Biosynthesis-The Multiple Carrier Thiotemplate Model
4.13.8. Approaching the Three-Dimensional Structure of Gramicidin S Synthetase
4.13.9. Prospects
4.14. Biosynthesis of Selenocysteine and its Incorporation into Proteins as the 21st Amino Acid
4.14.1. Introduction
4.14.2. Biosynthesis of Sec
4.14.3. The Codon for Sec is UGA
4.14.4. Universality of UGA as a Codon for Sec
4.14.5. Sec tRNA[Ser]Sec
4.14.6. Incorporation of Sec into Protein
4.14.7. Selenoproteins
4.14.8. Why is Sec used in Nature?
4.14.9. Conclusions
5.01. Biological Reactions-Mechanisms and Catalysts:An Overview
5.01.1. Introduction
5.01.2. Biological Reactions
5.01.3. Catalysts
5.02. Stabilization of Reactive Intermediates and Transition States in Enzyme Active Sites by Hydrogen Bonding
5.02.1. Introduction
5.02.2. Intermediates in Enzyme-Catalyzed Reactions
5.02.3. Quantitative Understanding of Reaction Profiles
5.02.4. Relationship of Intermediates and Transition States
5.02.5. Structures of Enzyme Active Sites
5.02.6. Importance of Hydrogen Bonds in Stabilizing Reactive Intermediates
5.02.7. Short, Strong Hyrogen Bonds
5.02.8. Physical Organic Models for Short Strong/Low Barrier Hydrogen Bonds
5.02.9. Experimental Evidence for Stabilization of Intermediates by Strong Hydrogen Bond
5.02.10. Stabilization of Intermediates by Electrostatic Interactions
5.02.11. Summary
5.03. Keto-Enol Tautomerism in Enzymatic Reactions
5.03.1. Introduction
5.03.2. Keto-Enol Tautomerization in Solution
5.03.3. Enone-Dienol Tautomerization in Solution
5.03.4. Unstable Enolate Intermediates: Triose Phosphate Isomerase
5.03.5. Metal-Stabilized Enolate Intermediates: Pyruvate Kinase
5.03.6. Moderately Stable Dienolate Intermediates: 3-OXO-?5-Steroid Isomerase
5.03.7. Stable Dienol(ate) Intermediates: 4-oxalocrotonate Tautomerase
5.03.8. Conclusions
5.04. Nucleophilic Epoxide Openings
5.04.1. Intoduction
5.04.2. Epoxide Hydrolases
5.04.3. Glutathione Transferases
5.05. Deamination of Nucleosides and Nucleotides and Related Reactions
5.05.1. Introduction to Deaminations of Purines and Pyrimidines
5.05.2. Deamination of Purines
5.05.3. Deamination of Pyrimidines
5.05.4. Conclusions
5.06. Ester Hydrolysis
5.06.1. Introduction
5.06.2. Phospholipase A2
5.06.3. Esterases of The a/ß Hydrolase Fold Family
5.06.4. Acid Lipases
5.06.5. Conclusions
5.07. Chemistry and Enzymology of Phosphatases
5.07.1. Introduction
5.07.2. Classification of Phosphatases
5.07.3. Mechanistic Concerns
5.07.4. Individual Phosphatases
5.07.5. Phosphatase Inhibitors
5.07.6. Conclusion
5.08. Mechanistic Investigations of Ribonucleotide Reductases
5.08.1. Introduction
5.08.2. Generation of Thiyl Radicals at an RNR Active Site by Adenosylcobalamin
5.08.3. Proposed Role of Protein-based Tyrosyl Radical in Catalysis and Model Studies in Support of This Role
5.08.4. Generation of the Thiyl Radical on R1 From the Tyrosyl Radical on R2
5.08.5. A Glycyl Radical May Generate an Active Site Thiyl Radical in the Anaerobic E. Coli RNR
5.08.6. The Mechanism of Nucleotide Reduction: Abstraction of the 3´ Hydrogen by a Thiyl Radical
5.08.7. Loss of the 2´ Hydroxy Group
5.08.8. Reduction of the 3´-keto-2´-deoxynucleotide Radical by Two Single Electron Transfers and Formation of Deoxynucleotide Product
5.08.9. Abstraction of Hydrogen from a Cysteine Thiol by the 3´-deoxynucleotide Radical: Completion of Nucleotide Reduction and Regeneration of the Thiyl Radical
5.08.10. Summary and Conclusions
5.09. Radical Reactions Featuring Lysine 2,3-Aminomutase
5.09.1. Introduction
5.09.2. Lysine2,3-Aminomutase
5.09.3. S-Adenosylmethionine and enzyme-radical formation
5.09.4. Oxygenation by Methane Monooxygenase
5.10. Structure, Function, and Inhibition of Prostaglandin Endoperoxide Synthases
5.10.1. Metabolic and Biological Roles
5.10.2. Gene/Protein Structure
5.10.3. Reactions Catalyzed
5.10.4. Peroxidase Activation of Cyclooxygenase
5.10.5. Kinetic Models of Cyclooxygenase/Peroxidase Integration and Arachidonic Acid Oxygenation
5.10.6. Arachidonic Acid Entry, Oxygenation, and Exit From PGH Synthase-2
5.10.7. Inhibition of Cyclooxygenase Activity by Nsaids
5.10.8. Steroid Inhibition of PGH Synthase-2 Expression
5.10.9. Conclusions
5.11. The Chemistry and Enzymology of Cobalamin-dependent Enzymes
5.11.1. Introduction
5.11.2. Cobalamin Chemistry and Reactivity
5.11.3. Role of the Protein-Interactions Between Enzyme, Coenzyme, and Substrate
5.11.4. Reaction Mechanism of Cobalamin-Dependent Enzymes
5.11.5. Conclusions
5.12. Glycosyl Transferase Mechanisms
5.12.1. Introduction
5.12.2. Transfers to Water
5.12.3. Other Glycosyl Transfers
5.12.4. Summary
5.13. Electrophilic Alkylations, Isomerizations, and Rearrangements
5.13.1. Introduction
5.13.2. FPP Synthase
5.13.3. Isoprene Cyclases
5.13.4. Dimethylallyltryptophan Synthase
5.13.5. Protein Farnesyltransferase
5.13.6. Isopentenyl Isomerase
5.13.7. Squalene Synthase and Phytoene Synthase
5.13.8. Conclusions
5.14. Catalysis by Chorismate Mutases
5.14.1. Introduction
5.14.2. Factors Affecting Rates of Claisen Rearrangements
5.14.3. Structural Requirements for Catalysis
5.14.4. Kinetic Properties of Mutases
5.14.5. Catalysts with Mutase-Like Activity
5.14.6. Structural Studies
5.14.7. Other Mechanistic Insights
5.14.8. Conclusions
5.15. Thymine Dimer Photochemistry: A Mechanistic Perspective
5.15.1. Introduction
5.15.2. The Cyclobutane Pyrimidine Photodimer
5.15.3. The (6-4) Photoproduct
5.15.4. The Dewar Pyrimidinone
5.15.5. The Spore Photoproduct
5.15.6. Nucleotide Excision Repair Pathway
5.15.7. The Base Excision Repair Pathway
5.15.8. Mutagenesis
5.15.9. Conclusions
5.16. Microbial Dehalogenases
5.16.1. Introduction
5.16.2. Aliphatic Dehalogenases
5.16.3. Aromatic Dehalogenases
5.16.4. Conclusions
5.17. Catalysis by Antibodies
5.17.1. Introduction
5.17.2. Pericyclic Reactions
5.17.3. Hydrolytic Reactions
5.17.4. Aldol Condensations
5.17.5. Catalytic Efficiency and Mechanism
5.17.6. Conclusion
6.01. Overview
6.02. A Spectroscopist's View of RNA Conformation: RNA Structural Motifs
6.02.1. Introduction
6.02.2. The Determination of RNA Structures by NMR
6.02.3. Solution Structures and Crystal Structures Compared
6.02.4. Lessons learned about motifs by NMR
6.03. Thermodynamics of RNA Secondary Structure Formation
6.03.1. Introduction
6.03.2. Thermodynamic Analysis of RNA Structural Transitions
6.03.3. Thermodynamics of RNA Secondary Structure Motifs
6.03.4. Applications
6.03.5. Future Perspectives
6.04. RNA Structures Determined by X-ray Crystallography
6.04.1. Introduction
6.04.2. Crystallization of RNA
6.04.3. Heavy Atom Derivatives of RNA Crystals
6.04.4. Duplex Structures
6.04.5. Transfer RNA
6.04.6. The Hammerhead Ribozyme
6.04.7. The P4-P6 Domain of the Tetrahymena Group I Self-Splicing Intron
6.04.8. 5S Ribosomal RNA Fragment
6.04.9. Future Directions
6.05. Chemical and Enzymatic Probing of RNA Structure
6.05.1. Introduction
6.05.2. Validation of RNA Structural Probing Approaches
6.05.3. Probes, Targets, and Methodology
6.05.4. Approaching Architectural Features of RNAs by Structural Probing
6.05.5. Probing RNAs in Complexes
6.05.6. Other applications of nucleotide modifications
6.05.7. Perspectives
6.06. Chemical RNA Synthesis (Including RNA with Unusual Constituents)
6.06.1. Introduction
6.06.2. Synthetic Methods for Oligonucleotides
6.06.3. Protecting Groups
6.06.4. Synthesis of Oligonucleotide Analogues
6.07. RNA Editing
6.07.1. Introduction to RNA Editing
6.07.2. Editing by Base Modification
6.07.3. Insertion/Deletion Editing
6.07.4. Summary and Perspectives
6.08. RNA Enzymes: Overview
6.08.1. Introduction
6.08.2. Classification
6.08.3. The Role of Proteins
6.08.4. Practical Applications
6.08.5. Miscellaneous
6.09. Ribozyme Selection
6.09.1. The History of Ribozymes and Ribozymes in History
6.09.2. In vitro Selection of Ribozymes
6.09.3. Identifying Functional Sequences and Structures
6.09.4. Improving and Changing Catalysis
6.09.5. Inventing Catalysis: the Road to the Ribosome
6.09.6. Assessing the Breadth and Depth of Selected Catalysts:the Ligases
6.09.7. Metalloribozymes
6.09.8. Modified Catalysts
6.09.9. Conclusions
6.10. Ribozyme Enzymology
6.10.1. Introduction
6.10.2. Types of RNA Catalysis and Reaction Mechanisms
6.10.3. Secondary and Tertiary Structures of RNA Enzymes
6.10.4. The Role of Metals in RNA Catalysis
6.10.5. Kinetics of the Tetrahymena and Hammerhead Ribozyme Reactions
6.10.6. Other catalytic RNAs
6.10.7. Conclusions
6.11. Viroids
6.11.1. Introduction
6.11.2. Classification of Viroids
6.11.3. Isolation, Purification, and Sequencing of Viroids
6.11.4. Domain Model for PSTV Group of Viroids
6.11.5. Sequence Patterns and Variation in Viroid Sequences
6.11.6. Replication of Viroids
6.11.7. Processing Reaction in vitro in Three Viroids Via the Hammerhead Self-Cleavage Reaction
6.11.8. What is the Processing Reaction During Rolling Circle Replication in the PSTV Group of Viroids?
6.11.9. How Do Viroids Exert their Pathogenic Effects?
6.12. Structural Elements of Ribosomal RNA
6.12.1. Introduction
6.12.2. Secondary Structure Elements of rRNAs
6.12.3. High-resolution Structures
6.12.4. Tertiary Structure of rRNAs
6.12.5. Conformational Switches in rRNA
6.13. Turnover of mRNA in Eukaryotic Cells
6.13.1. Introduction
6.13.2. Role of deadenylation in the decay of eukaryotic mRNAs
6.13.3. Deadenylation triggers decapping and 5´ to 3´ decay
6.13.4. Deadenylation-independent decapping of mRNAs
6.13.5. Control of mRNA Decapping
6.13.6. Deadenylation can also lead to 3´ to 5´ degradation
6.13.7. Role of Endonucleolytic Cleavages in the Decay of Eukaryotic mRNAS
6.13.8. Summary
6.14. Ribonucleotide Analogues and Their Applications
6.14.1. Introduction
6.14.2. Incorporation of Analogues into Oligoribonucleotides
6.14.3. Phosphorothioate Internucleotidic Linkages
6.14.4. S-Bridging Phosphorothiolates
6.14.5. Modification of the Nucleobases
6.14.6. Ribose Modification at the 2´-Position
6.14.7. Fluorescent Labels for Oligoribonucleotides
6.14.8. Nucleic Acid Cross-Linking
6.14.9. Conclusions
6.15. Ribozyme Structure and Function
6.15.1. Introduction
6.15.2. Hammerhead Ribozymes
6.15.3. Hairpin Ribozymes
6.15.4. Hepatitis Delta Virus (HDV) Ribozyme
6.15.5. Group I Ribozymes
6.15.6. Group II Ribozymes
6.15.7. Ribonuclease P
6.15.8. DNA enzymes
6.15.9. Conclusions
7.01. Overview
7.01.1. DNA as an Organic Natural Product
7.01.2. Important Products Interact with DNA
7.01.3. The Relevance of Molecular Biology to Chemistry
7.01.4. What is Covered in This Volume
7.01.5. The Future of DNA Chemistry Research
7.02. Thermodynamics and Kinetics of Nucleic Acid Association/Dissociation and Folding Processes
7.02.1. Nucleic Acid Thermodynamics
7.02.2. Nucleic Acid Kinetics
7.03. Probing DNA Structure by NMR Spectroscopy
7.03.1. Introduction
7.03.2. Elements of DNA Structure
7.03.3. 1H-NMR Spectra of Nucleic Acids
7.03.4. 31P-NMR of Nucleic Acids
7.03.5. 15N- and 13C-NMR of Nucleic Acids
7.03.6. Hydrogen Exchange and BPair Dynamics
7.03.7. DNA Conformations
7.04. Molecular Probes of DNA Structure
7.04.1. Introduction
7.04.2. DNA Intercalators
7.04.3. Transition Metals and Metal Complexes
7.04.4. Base-Specific Reagents
7.04.5. Cross-Linkers
7.04.6. Antibiotics
7.04.7. Conclusions
7.05. Oligonucleotide Synthesis
7.05.1. Introduction
7.05.2. Solid Supports for Oligonucleotide Synthesis
7.05.3. Protecting Groups in Oligonucleotide Synthesis
7.05.4. Mechanism of Internucleotidic Coupling Reaction
7.05.5. Solid-Phase Oligonucleotide Synthesis
7.05.6. Synthesis of RNA
7.05.7. Conclusion
7.06. Attachment of Reporter and Conjugate Groups to DNA
7.06.1. Introduction
7.06.2. Attachment of Reporter and Conjugate Groups at Either the 5´- or 3´-Terminus of DNA Oligonucleotides
7.06.3. Attachment of Reporter and Conjugate Groups to the Nucleobases of DNA Oligonucleotides
7.06.4. Modification of the Carbohydrate Portion of Nucleosides for the Attachment of Reporter and Conjugate Groups to DNA Oligonucleotides
7.06.5. Attachment of Reporter and Conjugate Groups to the Internucleotidic Phosphodiester Functions of DNA Oligonucleotides
7.06.6. Summary
7.07. Use of Nucleoside Analogues to Probe Biochemical Processes
7.07.1. Introduction
7.07.2. Design of Nucleoside Analogues
7.07.3. Synthetic Procedures
7.07.4. Interpretation of Biochemical Results
7.07.5. Protein-Nucleic Acid Interactions
7.07.6. DNA Triple Helices
7.07.7. RNA Catalysis
7.07.8. Summary
7.08. DNA with Altered Backbones in Antisense Applications
7.08.1. Introduction
7.08.2. Why alter the dna backbone?
7.08.3. Classification
7.08.4. Design considerations
7.08.5. Conclusions
7.09. DNA with Altered Bases
7.09.1. Introduction
7.09.2. Pyrimidine Modifications
7.09.3. Purine modifications
7.09.4. Purine Analogues
7.09.5. C-linked nucleosides
7.09.6. Miscellaneous
7.09.7. Concluding Remarks
7.10. Topological Modification of DNA: Circles, Loops, Knots,and Branches
7.10.1. Introduction
7.10.2. Natural Topological Variants of Nucleic Acids
7.10.3. Topology and Nucleic Acid Replication
7.10.4. Natural Molecules Which Recognize DNA Using Altered Topology
7.10.5. Man-Made DNA Structures Having Nonlinear Topology
7.10.6. Circular Permutation and DNA Bending
7.10.7. Molecular Recognition by Topologically Modified Oligonucleotides
7.10.8. Interactions of Proteins with Topologically Modified Synthetic DNA
7.10.9. Synthesis of Topologically Modified DNA
7.10.10. Conclusions and Future Prospects
7.11. Chemistry of DNA Damage
7.11.1. Introduction
7.11.2. Generation and Reactivity of Deoxyribose-Centered Reactive Intermediates
7.11.3. Generation and reactivity of nucleobase-reactive intermediates
7.11.4. DNA Damage Sensitization and Protection Agents
7.11.5. The Formation of Bistranded Lesions and Double strand Breaks in DNA
7.12. DNA Intercalators
7.12.1. Introduction
7.12.2. Variety of Intercalators and Intercalation Sites
7.12.3. More Complex Intercalators
7.12.4. Extension of the Types of Aromatic Ring System that Bind by Intercalation
7.12.5. Partial Intercalation of Small Aromatic Systems
7.12.6. Intercalation into Multistranded Helixes and Distorted Duplexes
7.12.7. Intercalators that React with DNA
7.12.8. Overview
7.13. DNA-binding Peptides
7.13.1. Introduction
7.13.2. DNA-Binding Peptides Based on Protein Motifs
7.13.3. Peptide Minor Groove Binders
7.13.4. Peptide Intercalators
7.13.5. Conclusions
7.14. Covalent Modification of DNA by Natural Products
7.14.1. Introduction
7.14.2. DNA-Damaging Natural Products
7.15. DNA-damaging Enediyne Compounds
7.15.1. Introduction
7.15.2. Biosynthesis of Naturally Occurring Enediyne Antibiotics
7.15.3. Structure and Mechanism of Enediyne Antibiotics
7.15.4. Role of Apoprotein
7.15.5. DNA/RNA Damage Mechanisms
7.16. DNA Topoisomerase Inhibitors
7.16.1. Introduction
7.16.2. DNA Topoisomerase And Its Inhibitors
7.16.3. DNA Topoisomerase II and its Inhibitors
7.16.4. Conclusion
7.17. DNA Selection and Amplification
7.17.1. Introduction
7.17.2. Goals of DNA Selex
7.17.3. Techniques Associated with Selex
7.17.4. Strategies for Selex
7.17.5. The Utility of DNA Selex
7.17.6. Discussion
7.18. Cloning as a Tool for Organic Chemists
7.18.1. Introduction
7.18.2. Selection of a Target DNA Sequence
7.18.3. Selection of an Expression System
7.18.4. Obtaining Oligonucleotides in Quantity using the Polymerase Chain Reaction
7.18.5. Restriction Digests
7.18.6. Dephosphorylation
7.18.7. Ligation
7.18.8. Transformation of DNA into E. Coli
7.18.9. Screening for Insert
7.18.10. Verification of Insert Identity
7.18.11. Large Scale Production of Protein in E. Coli Culture
7.18.12. Case Studies in Cloning
7.18.13. Conclusions
8.01. Overview
8.01.1. Scope of Volume 8
8.01.2. General Remarks on the Investigation of Bioactive Natural Products
8.01.3. Significance of Chirality
8.01.4. Future Perspectives in the Investigation of Bioactive Natural Products
8.02. Plant Hormones
8.02.1. Introduction
8.02.2. Auxins
8.02.3. Gibberellins
8.02.4. Cytokinins
8.02.5. Abscisic Acid
8.02.6. Ethylene
8.02.7. Brassinosteroids
8.02.8. Jasmonic Acid and Related Compounds
8.03. Plant Chemical Ecology
8.03.1. Constitutive Chemical Defence
8.03.2. Induced Chemical Defense
8.03.3. Sequestration of Plant Toxins by Insects
8.03.4. Plant Compounds Involved in Insect Oviposition
8.03.5. Plant Chemistry and Pollination
8.03.6. Plant Chemistry and Seed Dispersal
8.03.7. Allelopathy
8.03.8. Biochemistry of Symbiotic Associations
8.03.9. Mycotoxins
8.03.10. Phytotoxins
8.03.11. Constitutive Antimicrobial Defense
8.03.12. Phytoalexins
8.04. Pheromones
8.04.1. Introduction
8.04.2. Isolation and identification techniques
8.04.3. General remarks
8.04.4. Acetogenins: pheromones with unbranched carbon skeletons
8.04.5. Isoprenoids in systems of chemical communication
8.04.6. Propanogenins and related compounds
8.05. Insect Hormones and Insect Chemical Ecology
8.05.1. Introduction
8.05.2. Insect Juvenile Hormone
8.05.3. Ecdysteroids
8.05.4. Insect Neuropeptides
8.05.5. Plant Substances Toxic and Deterrent to Insects
8.05.6. Insect Toxins
8.06. Microbial Hormones and Microbial Chemical Ecology
8.06.1. Introduction
8.06.2. Autoregulators of Streptomycetes
8.06.3. Autoinducers with N-Acyl Homoserine Lactone Skeleton in Gram-Negative Bacteria
8.06.4. Compounds Regulating Morphological Differentiation in Prokaryotes
8.06.5. Other Microbial Hormone-Like Signal Substances
8.07. Marine Natural Products and Marine Chemical Ecology
8.07.1. Introduction
8.07.2. Feeding Attractants and Stimulants
8.07.3. Pheromones
8.07.4. Symbiosis
8.07.5. Biofouling
8.07.6. Bioluminescence
8.07.7. Chemical Defense Including Antifeedant Activity
8.07.8. Marine Toxins
8.07.9. Bioactive Marine Natural Products
Formula Index

Abbreviations The most commonly used abbreviations in Comprehensive Natural Products Chemistry are listed below. Please note that in some instances these may differ from those used in other branches of chemistry
A adenine
ABA abscisic acid
Ac acetyl
ACAC acetylacetonate
ACTH adrenocorticotropic hormone
ADP adenosine 5´-diphosphate
AIBN 2,2´-azobisisobutyronitrile
Ala alanine
AMP adenosine 5´-monophosphate
APS adenosine 5´-phosphosulfate
Ar aryl
Arg arginine
ATP adenosine 5´-triphosphate
B nucleoside base (adenine, cylosine, guanine, thymine or uracil)
9-BBN 9-borabicyclo[3.3.1]nonane
BOC t-butoxycarbonyl (or carbo-t-butoxy)
BSA N,O-bis(trimethylsilyl)acetamide
BSTFA N,O-bis(trimethylsilyl)trifluoroacetamide
Bu butyl
Bun n-butyl
Bui isobutyl
Bus s-butyl
But t-butyl
Bz benzoyl
CAN ceric ammonium nitrate
CD cyclodextrin
CDP cytidine 5´-diphosphate
CMP cytidine 5´-monophosphate
CoA coenzyme A
COD cyclooctadiene
COT cyclooctatetraene
Cp h5-cyclopentadiene
Cp* pentamethylcyclopentadiene
12-Crown-4 1,4,7,10-tetraoxacyclododecane
15-Crown-5 1,4,7,10,13-pentaoxacyclopentadecane
18-Crown-6 1,4,7,10,13,16-hexaoxacyclooctadecane
CSA camphorsulfonic acid
CSI chlorosulfonyl isocyanate
CTP cytidine 5´-triphosphate
cyclic AMP adenosine 3´,5´-cyclic monophosphoric acid
CySH cysteine
DABCO 1,4-diazabicyclo[2.2.2]octane
DBA dibenz[a,h]anthracene
DBN 1,5-diazabicyclo[4.3.0]non-5-ene
DBU 1,8-diazabicyclo[5.4.0]undec-7-ene
DCC dicyclohexylcarbodiimide
DEAC diethylaluminum chloride
DEAD diethyl azodicarboxylate
DET diethyl tartrate (+ or -)
DHET dihydroergotoxine
DIBAH diisobutylaluminum hydride
Diglyme diethylene glycol dimethyl ether (or bis(2-methoxyethyl)ether)
DiHPhe 2,5-dihydroxyphenylalanine
Dimsyl Na sodium methylsufinylmethide
DIOP 2,3-O-isopropylidene-2,3-dihydroxy-1,4-bis(diphenylphosphino)butane
dipt diisopropyl tartrate (+ or -)
DMA dimethylacetamide
DMAD dimethyl acetylenedicarboxylate
DMAP 4-dimethylaminopyridine
DME 1,2-dimethoxyethane (glyme)
DMF dimethylformamide
DMF-DMA dimethylformamide dimethyl acetal
DMI 1,3-dimethyl-2-imidazalidinone
DMSO dimethyl sulfoxide
DMTSF dimethyl(methylthio)sulfonium fluoroborate
DNA deoxyribonucleic acid
DOCA deoxycorticosterone acetate
EADC ethylaluminum dichloride
EDTA ethylenediaminetetraacetic acid
EEDQ N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline
Et ethyl
EVK ethyl vinyl ketone
FAD flavin adenine dinucleotide
FI flavin
FMN flavin mononucleotide
G guanine
GABA 4-aminobutyric acid
GDP guanosine 5´-diphosphate
GLDH glutamate dehydrogenase
gln glutamine
Glu glutamic acid
Gly glycine
GMP guanosine 5´-monophosphate
GOD glucose oxidase
G-6-P glucose-6-phosphate
GTP guanosine 5´-triphosphate
Hb hemoglobin
His histidine
HMPA hexamethylphosphoramide (or hexamethylphosphorous triamide)
Ile isoleucine
INAH isonicotinic acid hydrazide
IpcBH isopinocampheylborane
Ipc2BH diisopinocampheylborane
KAPA potassium 3-aminopropylamide
K-Slectride potassium tri-s-butylborohydride
LAH lithium aluminum hydride
LAP leucine aminopeptidase
LDA lithium diisopropylamide
LDH lactic dehydrogenase
Leu leucine
LICA lithium isopropylcyclohexylamide
L-Selectride lithium tri-s-butylborohydride
LTA lead tetraacetate
Lys lysine
MCPBA m-chloroperoxybenzoic acid
Me methyl
MEM methoxyethoxymethyl
MEM-Cl ß-methoxyethoxymethyl chloride
Met methionine
MMA methyl methacrylate
MMC methyl magnesium carbonate
MOM methoxymethyl
Ms mesyl (or methanesulfonyl)
MSA methanesulfonic acid
MsCl methanesulfonyl chloride
MVK methyl vinyl ketone
NAAD nicotinic acid adenine dinucleotide
NAD nicotinamide adenine dinucleotide
NADH nicotinamide adenine dinucleotide phosphate, reduced
NBS N-bromosuccinimider
NMO N-methylmorpholine N-oxide monohydrate
NMP N-methylpyrrolidone
PCBA p-chlorobenzoic acid
PCBC p-chlorobenzyl chloride
PCBN p-chlorobenzonitrile
PCBTF p-chlorobenzotrifluoride
PCC pyridinium chlorochromate
PDC pyridinium dichromate
PG prostaglandin
Ph phenyl
Phe phenylalanine
Phth phthaloyl
PPA polyphosphoric acid
PPE polyphosphate ester (or ethyl m-phosphate)
Pr propyl
Pri isopropyl
Pro proline
Py pyridine
RNA ribonucleic acid
Rnase ribonuclease
Ser serine
Sia2BH disiamylborane
TAS tris(diethylamino)sulfonium
TBAF tetra-n-butylammonium fluoroborate
TBDMS t-butyldimethylsilyl
TBDMS-Cl t-butyldimethylsilyl chloride
TBDPS...

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