Biochemistry Books

Book SynopsisToxic plants and other natural toxicants have a variety of roles in the fields of human health, medical research and the production of safe food and also represent an economic problem in terms of animal health and crop production. Estimates of economic impact on livestock have ranged in the millions of dollars in countries such as Australia and the United States. This book brings together applied and fundamental research from botanists, chemists, biochemists, agricultural scientists, veterinarians and physicians and advice from regulatory bodies. It consists of more than 100 edited papers from the Fifth International Symposium on Poisonous Plants, held in Texas in May 1997. All aspects of poisonous plants, mycotoxicoses and herbal intoxications are covered. Their adverse effects are described, such as fatalities, reduced or failed reproduction, fetotoxicity, spontaneous abortions, deformities, reduced productivity and organ-specific toxicity. Methods of detection, isolation and identifTable of Contents1: Regional and Epidemiological Issues 2: Cardiopulmonary System 3: Diagnostic/Treatment Issues 4: Miscellaneous Topics 5: The Reproductive System and the Embryo 6: Public Health and Herbal Medicine Corners 7: The Musculoskeletal and the Neurological System 8: Mycotoxins and Mycotoxicoses 9: Detoxification, Digestion and Elimination 10: Index

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Book SynopsisThis book discusses the biology of seeds.Table of ContentsSECTION I: OPENING PRESENTATIONS 1: Travels With Seeds: a Cartography of Seed Science, M Black 2: Protein Synthesis in Seed Germination, E Sánchez de Jiménez SECTION II: DEVELOPMENT AND QUALITY 3: bZIP and DOF Transcription Factors in the Regulation of Gene Expression in Barley Endosperm, P Carbonero et al. 4: Impact of Amphiphile Partitioning on Desiccation Tolerance, F A Hoekstra et al. 5: Unravelling the Responses of Metabolism to Dehydration Points to a Role for Cytoplasmic Viscosity in Desiccation Tolerance, O Leprince, et al. 6: Soluble Sugars in Maturing Pea Seeds of Different Lines in Relation to Desiccation Tolerance, R J Górecki et al. 7: The Role of Stachyose Synthase in the Oligosaccharide Metabolism of Legume Seeds, A Richter, et al. 8: Compartmentation of Abscisic Acid in Developing Muskmelon (Cucumis melo L.) Seeds, G E Welbaum, et al. 9: Involvement of ABA and GAs in the Regulation of Dormancy in Developing Sorghum Seeds, R Benech-Arnold, et al. 10: Irrigation and Seed Quality Development in Rapid-Cycling Brassica, R H Ellis, et al. 11: Molecular Genetic Analysis of Arabidopsis Seed Quality, S P C Groot, et al. 12: Analysis of the Cell Cycle in Sugar Beet Seed During Development, Maturation and Germination, E Sliwinska 13: Phospheonolpyruvate Carboxylase and Pyruvate Kinase in Assimilate Partitioning in Maize Embryos, R Rodríguez-Sotres, et al. SECTION III: STORAGE AND VIGOUR 14: Effects of Seed Ageing on the Enzymic Antioxidant System of Maize Cultivars, I Bernal-Lugo, et al. 15: Towards the ex situ Conservation of Aquatic Angiosperms: A Review of Seed Storage Behaviour, F Hay, et al. 16: Treatment of Immature Embryos of Maize With Water Reduces Their Storability and Desiccation Tolerance, A Bochicchio, et al. 17: Maillard Reactions Cause Browning in Bean Seed coats During Ageing: Inhibition by Aminoguanidine, A G Taylor, et al. 18: Effects of Desiccation on the Subcellular Matrix of the Embryonic Axes of Quercus robur, D J Mycock, et al. 19: Loss of Viability in Rye Embryos at Different Levels of Hydration, I Boubriak, et al. 20: The Effect of Drying Rate on Recalcitrant Seeds, N W Pammenter, et al. 21: Conservation of Genetic Resources Naturally Occurring as Recalcitrant Seeds, P Berjak, et al. SECTION IV: GERMINATION 22: Gene Expression Prior to Radicle Emergence in Imbibed Tomato Seeds (Conference Lecture), K J Bradford, et al. 23: Characterization of Germination-Related Genes in Avena fatua Seeds, R Johnson 24: Cell Cycle Control During Maize Germination, J M Vázquez-Ramos 25: Recent Advances in ABA-Regulated Gene Expression in Cereal Seeds: Regulation by PKABA1 Protein Kinases, M K Walker-Simmons 26: Lettuce Endosperm Weakening: a Role for Endo-ß-Mannanase in Seed Germination at High Temperature, D J Cantiliffe, et al. 27: Effect of Free Mg2+ on the Kinetics of the Plasma Membrane H+-ATPase from Dry and Hydrated Maize Embryos, S Sánchez-Nieto, et al. 28: The Barley Scutellar Peptide Transporter: Relationship to Germination and Loss of Seed Viability, W M Waterworth, et al. 29: Molecular Cloning and Possible Role of an Asparaginyl Endopeptidase (REP-2) from Germinated Rice Seeds, H Kato et al. 30: Metabolism of Essential Oils During Inhibition of Wheat Seed Germination, N Dudai, et al. SECTION V: DORMANCY 30: Genetic Model for Dormancy in Wild Oat, M E Foley 31: Characterization and Expression of Two Protein Kinase and an EIN3-Like Genes in Dormant Fagus Seeds, O Lorenzo, et al. 32: Effects Of Fusicoccin and Gibberellic Acid on Germination and a-Amylase Expression in Barley Grains, R M van der Meulen, et al. 33: Smoke and Germination of Arable and Rangeland Weeds, S W Adkins, et al. SECTION VI: ECOLOGY 34: Intermittent Germination: Causes and Ecological Implications, P B Cavers, et al. 35: Seed Ecology at the Northern Limit of the Tropical Rain Forest in America, C Vázquez-Yanes, et al. 36: Genotypic and Phenotypic Germination Survival Strategies of Ecotypes and Species in the Negev Desert, Y Gutterman 37: Hydrothermal Time as a Tool in Comparative Germination Studies, P S Allen, et al. 38: Emergent Weedy Foxtail (Setaria spp) Seed Germinability Behaviour, J Dekker SECTION VII: APPLICATIONS OF SEED BIOLOGY 39: Biotechnological Applications of Seed Biology, D J Murphy 40: Manipulating Starch Quality in Seeds: a Genetic Approach, T L Wang, et al. 41: Identification of Germination-Specific Protein Markers and their Use in Seed Priming Technology, D Job, et al. 42: A Critical Assessment of the Role of Oligosaccharides on Intracellular Glass Stability, J Buitink et al. 43: Improvement of Tomato Seed Germination by Osmopriming as Related to Energy Metabolism, F Corbineau et al. 44: Bio-osmopriming Tomato (Lycopersicon esculentum Mill.) Seeds for Improved Seedling Establishment, J E Warren et al. 45: Use of Threshold Germination Models Under Variable Field Conditions, W E Finch-Savage, et al.

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Book SynopsisThis book is an essential reference source covering the chemical elements that are nutrients for plants or grazing animals. It deals with the concentrations and transformations of these elements in soils, grassland plants, and ruminant animals, particularly cattle and sheep. For each element, the following data are given: forms occurring in soil, factors that affect availability and concentration, uptake and distribution in grassland plants, role in animal nutrition, amounts and forms excreted by grazing animals, and concentrations needed by ruminant animals.Table of Contents1: Introduction 2: Amounts, Sources and Availability of Nutrient Elements in Soils 3: Uptake and Concentrations of Nutrient Elements in Grassland Herbage 4: Nutrient Elements in Ruminant Animals 5: Nitrogen 6: Phosphorus 7: Sulphur 8: Macronutrient Cations: Potassium, Sodium, Calcium and Magnesium 9: Micronutrient Cations: Iron, Manganese, Zinc, Copper and Cobalt 10: The Nutrient Halogens: Chlorine and Iodine 11: Boron, Molybdenum and Selenium

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Book SynopsisThe tools for detecting false positives, false negatives, and interference in interactions when testing and monitoring therapeutic drug use For physicians monitoring a patient''s progress, efficacy of treatment is often linked to a patient''s response to medication. Determining whether a patient is taking the prescribed amount, the drug or dosage is effective, or the prescribed medication is interacting with other drugs can be determined through drug testing. Written as a guide for toxicologists, chemists, and health professionals involved in patient care, Resolving Erroneous Reports in Toxicology and Therapeutic Drug Monitoring provides an up-to-date introduction to the tests and methodologies used in a toxicology lab as well as the sources of testing error that can lead to false positives, false negatives, and unreliable conclusions of drug abuse or under use. Covering a host of common therapeutic drugs as well as specific types of interference in immunTable of ContentsPreface vii Chapter 1 An Introduction to Tests Performed in Toxicology Laboratories 1 Chapter 2 Challenges in Drugs of Abuse Testing 31 Chapter 3 False-Positive Results Using Immunoassays for Drugs of Abuse Testing 53 Chapter 4 True-Positive Drugs of Abuse Test Results Due to Use of Prescriptions and Nonprescription Drugs 67 Chapter 5 When Toxicology Report Is Negative in a Suspected Overdosed Patient: The World of Designer Drugs 85 Chapter 6 Abuse of Magic Mushrooms, Peyote Cactus, Khat, and Solvents: No Readily Available Laboratory Tests 101 Chapter 7 Limitations of Blood Alcohol Measurements Using Automated Analyzers and Breath Analyzers 121 Chapter 8 Role of the Laboratory in Detecting Other Poisoning, Including Pesticides, Ethylene Glycol, and Methanol 139 Chapter 9 Poisoning with Warfarin and Superwarfarin: What Can Laboratory Testing Do? 161 Chapter 10 Plant Poisoning and the Clinical Laboratory 185 Chapter 11 Sources of Erroneous Results in Therapeutic Drug Monitoring Due to Preanalytical Errors, High Bilirubin, Hemolysis, and Lipids 213 Chapter 12 Challenges in Therapeutic Drug Monitoring of Digoxin Using Immunoassays 237 Chapter 13 Interference in Immunoassays Used for Monitoring Anticonvulsants and the Usefulness of Monitoring Free Anticonvulsants 265 Chapter 14 Interference in Immunoassays Used to Monitor Tricyclic Antidepressants 293 Chapter 15 Therapeutic Drug Monitoring of Immunosuppressants: Limitations of Immunoassays and the Need for Chromatographic Methods 323 Chapter 16 Effect of Drug–Herb Interactions on Therapeutic Drug Monitoring 355 Chapter 17 Pharmacogenomics and the Toxicology Laboratory 385 Chapter 18 Approaches for Eliminating Interference/Discordant Specimens in Therapeutic Drug Monitoring and Drugs of Abuse Testing 411 Index 429

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Book SynopsisFood proteins and bioactive peptides play a vital role in the growth and development of the body's structural integrity and regulation, as well as having a variety of other functional properties. Land animal-derived food proteins such as collagen and gelatine carry risks of contamination (such as BSE). Marine-derived proteins, which can provide equivalents to collagen and gelatin without the associated risks, are becoming more popular among consumers because of their numerous health beneficial effects. Most marine-derived bioactive peptides are currently underutilized. While fish and shellfish are perhaps the most obvious sources of such proteins and peptides, there is also the potential for further development of proteins and peptides from sources like algae, sea cucumber and molluscs. Marine-derived proteins and peptides also have potential uses in novel products, with the possibility of wide commercialization in the food, beverage, pharmaceutical and cosmetic industries, as wellTable of ContentsList of Contributors xxiii 1 Marine-derived Peptides: Development and Health Prospects 1 Se-Kwon Kim and Isuru Wijesekara 1.1 Introduction 1 1.2 Development of Marine Peptides 1 1.3 Health Benefits of Marine Peptides 2 1.4 Conclusion 3 References 3 2 Bioactive Proteins and Peptides from Macroalgae, Fish, Shellfish and Marine Processing Waste 5 Pádraigín A. Harnedy and Richard J. FitzGerald 2.1 Introduction 5 2.2 Macroalgal, Fish and Shellfish Proteins: Potential Sources of Bioactive Hydrolysates and Peptides 5 2.3 Enzymatic Hydrolysis of Macroalgal, Fish and Shellfish Processing Waste Proteins: Bioactive Protein Hydrolysates and Peptides 8 2.4 Endogenous Bioactive Peptides from Macroalgae, Fish and Shellfish 22 2.5 Bioactive Proteins from Macroalgae, Fish and Shellfish 22 2.6 Commercial Products Containing Marine-Derived Bioactive Protein Hydrolysates and Peptides 24 2.7 Conclusion 27 Acknowledgement 27 References 27 3 Lectins with Varying Specificity and Biological Activity from Marine Bivalves 41 Bishnu Pada Chatterjee and Mausumi Adhya 3.1 Introduction 41 3.2 Lectins 45 3.3 Isolation, Molecular Characterization and Carbohydrate Specificity of Bivalve Lectins 46 3.4 Biological Functions of Bivalve Lectins 60 Acknowledgement 63 References 63 4 Digestive Enzymes from Marine Sources 69 Juan Antonio, Noriega Rodr´ıguez, Ramiro Baeza Jim´enez and Hugo Sergio García 4.1 Introduction 69 4.2 Biodiversity and Availability 70 4.3 Marine Biocatalysts 70 4.4 Digestive Enzymes 73 4.5 Lipases 78 4.5.3 Transglutaminase 80 4.6 Industrial Applications 81 References 83 5 Kamaboko Proteins as a Potential Source of Bioactive Substances 91 Takeshi Nagai, Yasuhiro Tanoue, Norihisa Kai and Nobutaka Suzuki 5.1 Introduction 91 5.2 Creation of Healthier and Safer Foods 94 5.3 Enzymatic Modification of Food Proteins 95 5.4 Kamaboko 95 5.5 Chemical Properties of Kamaboko 98 5.6 Expression of Health the Function of Kamaboko Proteins 98 5.7 Antioxidative Activities of Kamaboko Proteins 100 5.8 Angiotensin I-Converting Enzyme-Inhibitory Activities of Kamaboko Proteins 104 5.9 Conclusion 108 References 108 6 Biological Activities of Fish-protein Hydrolysates 111 Irineu Batista 6.1 Introduction 111 6.2 Angiotensin I-Converting Enzyme Inhibitors 111 6.3 Antioxidative Properties 116 6.4 Anticancer Activity 124 6.5 Antimicrobial and Antiviral Activity 125 6.6 Calcium-Binding Peptides 125 6.7 Appetite Suppression 125 6.8 Anticoagulant Activity 126 6.9 Immunostimulant Activity 126 6.10 Hypocholesterolemic Activity 126 6.11 Hormone-Regulating Properties 127 6.12 Other Biological Activities 127 References 127 7 Biological Activities of Proteins and Marine-derived Peptides from Byproducts and Seaweeds 139 Maria Hayes 7.1 Introduction 139 7.2 Bioactive Peptides 140 7.3 Marine-derived Bioactive Peptides 141 7.4 Isolation and Characterisation of Marine-derived Bioactive Peptides 141 7.5 Lectins 144 7.5.1 Isolation of Lectins 145 7.6 Phycobiliproteins 145 7.7 Other Amino Acids and Peptides Present in and Derived from Macroalgae 146 7.8 Membrane Processing 147 7.9 Bioactivities of Marine-derived Peptides—inhibiting Proteases for Health 147 7.10 Heart-health Bioactive Peptides 148 7.11 Commercially Available Bioactive Peptides 156 7.12 Conclusion 156 References 159 8 Ability of Diverse Marine Invertebrate Lectins to Regulate Cell Functions 167 Yasuhiro Ozeki, Sarkar M. A. Kawsar, Yuki Fujii, Yukiko Ogawa, Shigeki Sugawara, Imtiaj Hasan, Yasuhiro Koide, Hidetaro Yasumitsu and Robert A. Kanaly 8.1 Introduction 167 8.2 Does a Feather Star Lectin have a Role in Regenerative Biology? 169 8.3 A Novel Lectin from the Mediterranean Mussel Induces Apoptosis and Glycosphingolipid Interaction 174 8.4 Downregulation of the Gene Expression of an ABC Transporter by a Novel Lectin-glycosphingolipid Pathway Involving a Suel-type Lectin Domain 176 8.5 Perspectives on Studies of Invertebrate Lectins and Their Diverse Properties 180 References 181 9 Routes in Innate Immunity Evolution: Galectins and Rhamnose-binding Lectins in Ascidians 185 Loriano Ballarin, Matteo Cammarata, Nicola Franchi and Nicoló Parrinello 9.1 Animal Lectins 185 9.2 Ascidians 185 9.3 Galectins 188 9.4 Rhamnose-binding Lectins 194 9.5 Conclusion 198 Acknowledgement 200 References 200 10 Production of Lactobacilli Proteinases for the Manufacture of Bioactive Peptides: Part I—Upstream Processes 207 Dominic Agyei, Ravichandra Potumarthi and Michael K. Danquah 10.1 Introduction: Bioactive Peptides—Production and Functionalities 207 10.2 Lactobacilli Metabolism 209 10.3 The Proteolytic System of The Lactobacilli 209 10.4 Sources of Proteases and Advantages of Microbial Proteases 211 10.5 Marine Lactobacilli 212 10.6 Proteinase Production Requirements 212 10.7 Effect of Fermentation Modes on Cell Growth and Proteinase Production 220 10.8 Cell Systems for Proteinase Production 222 10.9 Statistical Methods and Mathematical Models 222 10.10 Conclusion 223 Acknowledgement 223 References 223 11 Production of Lactobacilli Proteinases for the Manufacture of Bioactive Peptides: Part II—Downstream Processes 231 Dominic Agyei, Ravichandra Potumarthi and Michael K. Danquah 11.1 Introduction: Cell Recovery 231 11.2 Isolation: Proteinase-extraction Methodologies 231 11.3 Purification of Enzymes 237 11.4 Enzyme Concentration and Storage 244 11.5 Characterisation of Proteinase 244 11.6 Solvent and Enzyme Engineering for Enhanced Stability and Specificity 247 11.7 Conclusion 247 References 247 12 Recovery of Proteins and their Biofunctionalities from Marine Algae 253 You-Jin Jeon and Kalpa Samarakoon 12.1 Introduction 253 12.2 Importance of Proteolytic Enzyme-assisted Extractions 254 12.3 Marine-algal Functional Proteins and Peptides with Bioactivity 255 12.4 Marine-algal Proteins: Potential Sources for Future Applications 261 12.5 Conclusion 264 References 265 13 Fish Gelatin: A Versatile Ingredient for the Food and Pharmaceutical Industries 271 Venkateshwarlu Gudipati 13.1 Introduction 271 13.2 Structural Features of Fish Gelatin 272 13.3 Improvement of Functional Properties 273 13.4 Applications in the Food Industry 274 13.5 Applications in the Pharmaceutical Industry 284 13.6 Conclusion 287 References 288 14 Health Effects of Antioxidative and Antihypertensive Peptides from Marine Resources 297 Ida-Johanne Jensen, Karl-Erik Eilertsen, Hanne K. Mæhre, Edel O. Elvevoll and Rune Larsen 14.1 Introduction 297 14.2 Antioxidative Peptides 298 14.3 Antihypertensive Peptides 307 14.4 Conclusion 313 References 313 15 Potential Novel Therapeutics: Some Biological Aspects of Marine-derived Bioactive Peptides 323 Ruvini Liyanage, Barana C. Jayawardana and Suranga P. Kodithuwakku 15.1 Introduction 323 15.2 Marine-derived Proteins and Biopeptides with Antihypertensive Activity 325 15.3 Anticancer Effects of Marine-derived Bioactive Peptides 333 15.4 Antiviral Bioactivities of Marine-derived Bioactive Peptides 338 15.5 The Future of Marine Peptides as Therapeutics 340 References 341 16 Hormone-like Peptides Obtained by Marine-protein Hydrolysis and Their Bioactivities 351 Oscar Martínez-Alvarez 16.1 Introduction 351 16.2 Growth Hormone-Release Peptides 352 16.3 Opioid-Like Peptides 353 16.4 Immunomodulating Peptides 357 16.5 Glucose Uptake-Stimulating Peptides 358 16.6 Secretagogue and Calciotropic Activities 359 16.7 Limitations on the use of Hormone-like Peptides as Nutraceuticals 360 16.8 Further Development and Research Needs 361 References 362 17 Antimicrobial Activities of Marine Protein and Peptides 369 Mingyong Zeng, Zunying Liu, Yuanhui Zhao and Shiyuan Dong 17.1 Introduction 369 17.2 Preparation, Purification and Characterization 370 17.3 In Vitro Antimicrobial Studies 373 17.4 Antimicrobial Mechanisms 375 17.5 Applications and Prospects in Food Preservation 378 17.6 Conclusion 380 References 380 18 Production and Antioxidant Properties of Marine-derived Bioactive Peptides 385 Tao Wang, Qiancheng Zhao and Qiukuan Wang 18.1 Introduction 385 18.2 Production of Antioxidant Peptides 386 18.3 Antioxidant Mechanism and Structure–activity Relationship 392 18.4 Industrial Applications and Perspectives 400 References 401 19 Marine Peptides and Proteins with Cytotoxic and Antitumoral Properties 407 João Varela, Catarina Vizetto-Duarte, Luísa Custódio, Luísa Barreira and Fernando Albericio 19.1 Introduction 407 19.2 Current Pipeline of Oncological Drugs Based on Natural Products 407 19.3 Current Pipeline of Marine Peptides with Antitumoral Activity 408 19.4 Major Biological Sources of Marine Cytotoxic Peptides and Proteins 410 19.5 Structural Motifs in Cytotoxic Peptides 410 19.6 Cytotoxic Acyclic Peptides 416 19.7 Cytotoxic Cyclic Peptides 419 19.8 Cytotoxic (Poly)Peptides Obtained by Enzymatic Hydrolysis of Seafood 420 19.9 Cytotoxic Polypeptides 421 19.10 Conclusion 421 19.11 Acknowledgments 422 References 422 20 ACE-inhibitory Activities of Marine Proteins and Peptides 431 Mingyong Zeng, Yuanhui Zhao, Zunying Liu and Shiyuan Dong 20.1 Introduction 431 20.2 Determination of ACE-inhibitory Peptide Activity 432 20.3 ACE-inhibitory Peptides from Marine Sources 433 20.4 Types of ACE-Inhibitor Peptide 435 20.5 Structure–Activity Relationships of ACE-Inhibitory Peptides 435 20.6 Conclusion 437 References 437 21 Isolation and Biological Activities of Peptides from Marine Microalgae by Fermentation 441 BoMi Ryu and Se-Kwon Kim 21.1 Introduction 441 21.2 Utilization of Fermentation to Hydrolyze Protein 442 21.3 Microalgae As a Source of Protein 442 21.4 Metabolites of Proteolytic Hydrolysis by Fermentation 443 21.5 Hydrolyzed Microalgal Peptide Application 444 21.6 Conclusion 445 References 446 22 Antioxidant Activities of Marine Peptides from Fish and Shrimp 449 Mingyong Zeng, Shiyuan Dong, Yuanhui Zhao and Zunying Liu 22.1 Introduction 449 22.2 Production, Isolation, and Purification of Antioxidant Peptides 450 22.3 Methods Used to Measure Antioxidant Activity 453 22.4 Antioxidant Activity of Peptides 456 22.5 Antioxidant Mechanisms of Peptides 461 22.6 Applications and Prospects 462 References 464 23 Fish-elastin Hydrolysate: Development and Impact on the Skin and Blood Vessels 467 Eri Shiratsuchi, Misako Nakaba, Yasutaka Shigemura, Michio Yamada and Kenji Sato 23.1 Introduction 467 23.2 Starter Materials for Fish-elastin Hydrolysate 468 23.3 Preparation of Skipjack-elastin Hydrolysate 470 23.4 Impact of Ingestion of Skipjack-elastin Hydrolysate on Skin Conditions 471 23.5 Impact of Skipjack-elastin Hydrolysate on Blood Vessels 477 23.6 Safety of Skipjack-elastin Hydrolysate 479 23.7 Identification of Food-derived Elastin Peptide in Human Blood 480 23.8 Effect of Food-derived Elastin-peptide Pro-gly on Cells 482 23.9 Conclusion 483 References 484 24 Free Radical-scavenging Activity of Marine Proteins and Peptides 487 Dai-Nghiep Ngo 24.1 Introduction 487 24.2 Formation of Free Radicals and Methods of Assaying Antioxidant Activity 487 24.3 Free Radical-scavenging Activity of Marine Proteins and Peptides 491 24.4 Conclusion 494 References 494 25 Marine-derived Bioactive Peptides: Their Cardioprotective Activities and Potential Applications 499 M. Vijayakumar, A. Noorlidah, Abdul Bakrudeen Ali Ahmed, K. Priya and M. T. Rosna 25.1 Introduction 499 25.2 Cardiovascular Diseases and Nutraceuticals 500 25.3 Sources of Marine Peptides 500 25.4 Development of Marine Bioactive Peptides 502 25.5 Oxidative Stress 502 25.6 Antihypertensive Activity 503 25.7 Anticoagulant Activity 504 25.8 Conclusion 505 References 506 26 Biological Activities of Marine Bioactive Peptides 509 Dai-Hung Ngo, Thanh-Sang Vo and Se-Kwon Kim 26.1 Introduction 509 26.2 Physiological Properties of Marine Bioactive Peptides 510 26.3 Conclusion 517 Acknowledgement 517 References 518 27 Shark Fin Cartilage: Uses, Extraction and Composition Analysis 523 Chamila Jayasinghe 27.1 Introduction 523 27.2 History 523 27.3 Uses 524 27.4 Shark-fin Processing 525 27.5 Extraction of Elastoidin and Chondroitin Sulfate 526 27.6 Composition Analysis 526 References 530 28 Marine Bioactive Peptide Sources: Critical Points and the Potential for New Therapeutics 533 Ratih Pangestuti and Se-Kwon Kim 28.1 Introduction 533 28.2 Marine Bioactive Peptide Sources 534 28.3 Critical Points and the Potential for New Therapeutics 541 28.4 Conclusion 541 References 542 29 Applications of Marine-derived Peptides and Proteins in the Food Industry 545 D. M. Dilan Rasika, C. Senaka Ranadheera and Janak K. Vidanarachchi 29.1 Introduction 545 29.2 Marine-derived Proteins and Peptides Used in the Food Industry 546 29.3 Collagen and Gelatin 554 29.4 Extraction and Isolation of Marine-derived Proteins and Peptides 556 29.5 Food-related Applications of Marine-derived Proteins and Peptides 560 29.6 Conclusion 576 References 576 30 Processing and Industrial Aspects of Fish-scale Collagen: A Biomaterials Perspective 589 Santanu Dhara, Pallab Datta, Pallabi Pal and Soumi Dey Sarkar 30.1 Introduction 589 30.2 Structure and Composition of Collagen 589 30.3 Synthesis of Collagen 590 30.4 Type-I Collagen 591 30.5 Recombinant Collagen 593 30.6 Fish’s Potential as an Alternative Source of Collagen 594 30.7 Emerging Applications of Type-I Collagen 613 30.8 Conclusion 621 Acknowledgement 622 References 622 31 Properties, Biological Advantages and Industrial Significance of Marine Peptides 631 Abdul Bakrudeen Ali Ahmed, M. Vijayakumar, R. Pallela, N. Abdullah, and R. M. Taha 31.1 Introduction 631 31.2 Marine-peptide Properties 633 31.3 Industrial Development of Marine Bioactive Peptides 634 31.4 Biological Applications of Marine Peptides 636 31.5 Conclusion 638 References 638 32 Muscle Proteins of Fish and Their Functions 641 Byul-Nim Ahn and Se-Kwon Kim 32.1 Introduction 641 32.2 Fish Muscles 641 32.3 Myoglobin and Myofibrillar Proteins of Fish Muscle 642 32.4 Sarcoplasmic Protein 643 32.5 Antifreeze Proteins 643 References 644 33 Marine-derived Collagen: Biological Activity and Application 647 W. M. Niluni Methsala Wijesundara and Buddika O. Malaweera 33.1 Introduction 647 33.2 Sources of Marine Collagen 650 33.3 Applications of Marine Collagen 652 References 660 34 Marine Antifreeze Proteins: Types, Functions and Applications 667 Sung Gu Lee, Jun Hyuck Lee, Sung-Ho Kang and Hak Jun Kim 34.1 Introduction 667 34.2 Types of Marine AFP 670 34.3 Preparation of Fish AFPS 677 34.4 AFP Applications 679 34.5 Conclusion 684 References 685 35 Antimicrobial Peptides in Marine Mollusks and their Potential Applications 695 Mahanama De Zoysa 35.1 Introduction 695 35.2 Characteristics of AMPS 696 35.3 Diversity of AMPS in Marine Mollusks 696 35.4 Applications of Mollusk-derived AMPS 703 References 704 36 Protein Hydrolysates and Bioactive Peptides from Seafood and Crustacean Waste: Their Extraction, Bioactive Properties and Industrial Perspectives 709 Anil Kumar Anal, Athapol Noomhorm and Punchira Vongsawasdi 36.1 Introduction 709 36.2 Overall Chemical Composition of Seafood and Crustaceans 710 36.3 Extraction of Protein Hydrolysates and Bioactive Peptides from Seafood and Crustacean Waste 713 36.4 Characterization of Fish-protein Hydrolysates and Bioactive Peptides 722 36.5 Functional and Bioactive Properties of Proteins and Peptides from Seafood and Crustacean Waste 724 36.6 Conclusion 729 References 730 37 Production and Health Effects of Peptides from Fish Proteins 737 Mahinda Senevirathne and Se-Kwon Kim 37.1 Introduction 737 37.2 Sources of Fish Peptides 738 37.3 Production of Fish Peptides 739 37.4 Health-promoting ability of fish peptides 740 37.5 Future Trends of Peptides from Fish Proteins 746 37.6 Conclusion 746 References 747 Index 753

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Book SynopsisThis book serves as a manual of research techniques for electrochemically active biofilm research. Using examples from real biofilm research to illustrate the techniques used for electrochemically active biofilms, this book is of most use to researchers and educators studying microbial fuel cell and bioelectrochemical systems. The book emphasizes the theoretical principles of bioelectrochemistry, experimental procedures and tools useful in quantifying electron transfer processes in biofilms, and mathematical modeling of electron transfer in biofilms. It is divided into three sections: Biofilms: Microbiology and microbioelectrochemistry - Focuses on the microbiologic aspect of electrochemically active biofilms and details the key points of biofilm preparation and electrochemical measurement Electrochemical techniques to study electron transfer processes - Focuses on electrochemical characterization and data interpretation, highlighting key factors in the experimTable of Contents LIST OF CONTRIBUTORS vii PREFACE xi 1 Introduction to Electrochemically Active Biofilms 1Jerome T. Babauta and Haluk Beyenal 2 Theoretical and Practical Considerations for Culturing Geobacter Biofilms in Microbial Fuel Cells and Other Bioelectrochemical Systems 37Allison M. Speers and Gemma Reguera 3 Microbial Community Characterization on Polarized Electrode Surfaces 61John M. Regan and Hengjing Yan 4 Characterization of Electrode-Associated Biomass and Microbial Communities 83Orianna Bretschger, Shino Suzuki, Shun’ichi Ishii, Crystal Snowden, and Lisa McDonald 5 Biofilm Electrochemistry 121Jerome T. Babauta and Haluk Beyenal 6 Theory of Redox Conduction and The Measurement of Electron Transport Rates Through Electrochemically Active Biofilms 177Darryl A. Boyd, Jeffrey S. Erickson, Jared N. Roy, Rachel M. Snider, Sarah M. Strycharz-Glaven, and Leonard M. Tender 7 Electronic Conductivity in Living Biofilms: Physical Meaning, Mechanisms, and Measurement Methods 211Nikhil S. Malvankar and Derek R. Lovley 8 Electrochemical Impedance Spectroscopy as A Powerful Analytical Tool for The Study of Microbial Electrochemical Cells 249Rachel A. Yoho, Sudeep C. Popat, Francisco Fabregat-Santiago, Sixto Giménez, Annemiek Ter Heijne, and César I. Torres 9 Mathematical Modeling of Extracellular Electron Transfer in Biofilms 281Ryan Renslow, Jerome Babauta, Andrew Kuprat, Jim Schenk, Cornelius Ivory, Jim Fredrickson, and Haluk Beyenal 10 Applications of Bioelectrochemical Energy Harvesting in The Marine Environment 345Clare E. Reimers 11 Large-Scale Benthic Microbial Fuel Cell Construction, Deployment, and Operation 367Jeff Kagan, Lewis Hsu, and Bart Chadwick INDEX 00

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Book SynopsisNew and expanded for its second edition, Environmental Microbiology: From Genomes to Biogeochemistry Second Edition, is a timely update to a classic text filled with ideas, connections, and concepts that advance an in-depth understanding of this growing segment of microbiology. Core principles are highlighted with an emphasis on the logic of the science and new methods-driven discoveries. Numerous up-to-date examples and applications boxes provide tangible reinforcement of material covered. Study questions at the end of each chapter require students to utilize analytical and quantitative approaches, to define and defend arguments, and to apply microbiological paradigms to their personal interests. Essay assignments and related readings stimulate student inquiry and serve as focal points for teachers to launch classroom discussions. A companion website with downloadable artwork and answers to study questions is also available. Environmental Microbiology: From GeTable of ContentsPreface viii About the Companion Website x 1 Significance, History, and Challenges of Environmental Microbiology 1 1.1 Core concepts can unify environmental microbiology 1 1.2 Synopsis of the significance of environmental microbiology 2 1.3 A brief history of environmental microbiology 6 1.4 Complexity of our world 10 1.5 Many disciplines and their integration 13 2 Formation of the Biosphere: Key Biogeochemical and Evolutionary Events 25 2.1 Issues and methods in Earth’s history and evolution 26 2.2 Formation of early planet Earth 26 2.3 Did life reach Earth from Mars? 30 2.4 Plausible stages in the development of early life 31 2.5 Mineral surfaces in marine hydrothermal vents: the early iron/sulphur world could have driven biosynthesis 35 2.6 Encapsulation (a key to cellular life) and an alternative (nonmarine) hypothesis for the habitat of precellular life 36 2.7 A plausible definition of the tree of life’s “Last universal common ancestor” (LUCA) 37 2.8 The rise of oxygen 39 2.9 Evidence for oxygen and cellular life in the sedimentary record 39 2.10 The evolution of oxygenic photosynthesis 42 2.11 Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon 45 2.12 Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria 48 3 Physiological Ecology: Resource Exploitation by Microorganisms 56 3.1 The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time 57 3.2 Biological and evolutionary insights from genomics 57 3.3 Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology 69 3.4 Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities 71 3.5 Cellular responses to starvation: resting stages, environmental sensing circuits, gene regulation, dormancy, and slow growth 76 3.6 A planet of complex mixtures in chemical disequilibrium 86 3.7 A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions 91 3.8 Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space 93 3.9 Overview of metabolism and the “logic of electron transport” 104 3.10 The flow of carbon and electrons in anaerobic food chains: syntrophy is the rule 105 3.11 The diversity of lithotrophic reactions 109 4 A Survey of the Earth’s Microbial Habitats 117 4.1 Terrestrial biomes 118 4.2 Soils: geographic features relevant to both vegetation and microorganisms 120 4.3 Aquatic habitats 124 4.4 Subsurface habitats: oceanic and terrestrial 131 4.5 Defining the prokaryotic biosphere: where do prokaryotes occur on Earth? 141 4.6 Life at the micron scale: an excursion into the microhabitat of soil microorganisms 145 4.7 Extreme habitats for life and microbiological adaptations 151 5 Microbial Diversity: Who is Here and How do we Know? 162 5.1 Defining cultured and uncultured microorganisms 163 5.2 Approaching a census: an introduction to the environmental microbiological “toolbox” 167 5.3 Criteria for census taking: recognition of distinctive microorganisms (species) 170 5.4 Proceeding toward census taking and measures of microbial diversity 175 5.5 The tree of life: our view of evolution’s blueprint for biological diversity 181 5.6 A Sampling of key traits of cultured microorganisms from the domains Eukarya, Bacteria, and Archaea 185 5.7 Placing the “uncultured majority” on the tree of life: what have nonculture-based investigations revealed? 205 5.8 Viruses: an overview of biology, ecology, and diversity 213 5.9 Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size 220 5.10 Biogeography of microorganisms 224 6 Generating and Interpreting Information in Environmental Microbiology: Methods and Their Limitations 238 6.1 How do we know? 239 6.2 Perspectives from a century of scholars and enrichment-cultivation procedures 239 6.3 Constraints on knowledge imposed by ecosystem complexity 243 6.4 Environmental microbiology’s “Heisenberg uncertainty principle”: model systems and their risks 245 6.5 Fieldwork: being sure sampling procedures are compatible with analyses and goals 247 6.6 Blending and balancing disciplines from field geochemistry to pure cultures 253 6.7 Overview of methods for determining the position and composition of microbial communities 257 6.8 Methods for determining in situ biogeochemical activities and when they occur 276 6.9 Cloning-based Metagenomics and related methods: procedures and insights 280 6.10 cloning-free, next-generation sequencing and omics methods: procedures and insights 290 6.11 Discovering the organisms responsible for particular ecological processes: linking identity with activity 325 7 Microbial Biogeochemistry: A Grand Synthesis 356 7.1 Mineral connections: the roles of inorganic elements in life processes 357 7.2 Greenhouse gases and lessons from biogeochemical modeling 361 7.3 The “stuff of life”: identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles 372 7.4 Elemental biogeochemical cycles: concepts and physiological processes 393 7.5 Cellular mechanisms of microbial biogeochemical pathways 409 7.6 Mass balance approaches to elemental cycles 418 8 Special and Applied Topics in Environmental Microbiology 432 8.1 Other organisms as microbial habitats: ecological relationships 432 8.2 Microbial residents of plants and humans 449 8.3 Biodegradation and bioremediation 461 8.4 Biofilms 489 8.5 Evolution of catabolic pathways for organic contaminants 493 8.6 Environmental biotechnology: overview and nine case studies 499 8.7 Antibiotic resistance 514 9 Future Frontiers in Environmental Microbiology 538 9.1 The influence of systems biology on environmental microbiology 538 9.2 Ecological niches and their genetic basis 546 9.3 Concepts help define future progress in environmental microbiology 551 Glossary 557 Index 564

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Book SynopsisLipidomics is an important aspect of personalized medicine in relation to nutrition and metabolism. This approach has become important due to the substantial presence of nutraceuticals in the market, since it gives personalized criteria on how to choose the right nutraceutical strategy for both prevention and for quality of life.Table of ContentsAbout the Authors xi Preface xiii Acknowledgments xvii Abbreviations xix Part I Molecular and Nutritional Basis of Cell Membranes and Lipidomics 1 1 Membranes for Life and Life for Membranes 3 1.1 Cell Membranes: The Role of Fatty Acids and the Exclusion of Trans Isomers 3 1.2 Organization and Homeostasis 11 1a In Depth: The Formation of a Cell Membrane 16 1b In Depth: Cholesterol and Membranes 17 1c In Depth: Lipid Rafts 19 2 Fatty Acid Families: Metabolism and Nutrition 21 2.1 Saturated Fatty Acids: Biosynthesis and Dietary Regulation 23 2.2 Monounsaturated Fatty Acids: The Importance to be cis 28 2a In Depth: The key Steps of Phospholipid Synthesis 31 2b In Depth: Biosynthesis of the Double Bond and Desaturase Features 34 2.3 Polyunsaturated Fatty Acids: The Essentiality for Human Cells 37 Concepts’ Summary 38 S1 Beware of the Nutritional Label! 38 S2 The Optimal Values of Fatty Acids in Tissues 38 S3 Structural Role of Fatty Acids 40 3 Essential Fatty Acids 41 3.1 The Omega-6 and Omega-3 Families: Cascades and Regulation 42 3a In Depth: The Definition of Omega-6 and Omega-3 48 3b The Polyunsaturated Fatty Acids in Cell Membrane Remodeling 50 3c In Depth: How do you Define an Inflammatory Pathway? 55 3.2 The Balance Between Omega-6 and Omega-3 Pathways: Nutritional and Metabolic Considerations 56 3.3 Food and Membranes: A Virtuous Cycle 60 4 Free Radicals and Lipids: Trans and Oxidized Fatty Acids 65 4.1 Trans Fatty Acids for Humans: The Nutritional Intake 66 4.2 Endogenous Sources of Trans Fatty Acids by Free Radical Stress 71 4.3 Free Radicals and Lipid Oxidation: The Threshold for Health 73 4.4 Lipoproteins and Development of Markers for Lipid Reactivity 79 4a In Depth: Oleic versus Linoleic Acid Reactivity with Free Radicals 83 Concepts’ Summary 84 S1 Fatty Acid Geometry: A “Radical” Change 84 S2 Antioxidants for Membranes 85 Part II Membrane Lipidomics for Personalized Health 87 5 What Is Lipidomics for Health 89 5.1 The Birth of the Postgenomics Era 89 5.2 Lipidomics in the Postgenomic Era 92 5.3 Fatty Acids Involved in Membrane and Mediator Lipidomics 93 5.4 Membrane Lipidomics: Cellular Stress, Turnover, and Opportunities 95 5.4.1 How Does the Stress Involve Membranes? 97 5.5 Phospholipids From Dietary Intakes to Biological Functions 100 6 Lipidomics of Erythrocyte Membranes 105 6.1 Erythrocyte as a Comprehensive Health Biomarker 107 6.2 The Optimal Value Intervals and The Membrane Unbalance Index 115 6.3 Lipid Biosynthesis and Related Indices 120 6.4 The Individuation of Molecular Indicators 122 7 Nutrilipidomics 127 7.1 When Fatty Acids Become Nutraceuticals: Membrane Therapy With Nutrilipidomics 128 7.2 Fatty Acid–Based Membrane Lipidomics and Nutrilipidomics: The Personalized Approach for Nutrition and Nutraceuticals in Health and Diseases 131 8 Lipidomic Profiles and Intervention Strategies in Prevention and Diseases 135 8.1 Lipidomics and Sport 137 8.2 Lipidomics and Pregnancy 140 8.3 Lipidomics and Aging 143 8.4 Lipidomics and Cardiovascular Health 145 8.5 Lipidomics and Overweight 148 8.6 Lipidomics and Dermatology 150 8.7 Lipidomics and Neurology 151 8.8 Lipidomics and Ophtalmology 153 8.9 Conclusive Remarks 154 9 Lipidomics and Tutorials 157 9.1 First Steps for the Lipidomic Analysis 159 9.1.1 Saturated Fatty Acid Excess 160 9.1.2 Monounsaturated Fatty Acid Excess 160 9.1.3 Omega-6 PUFA Excess 160 9.1.4 Omega-3 PUFA Deficit 161 9.2 Learning Verification 162 References and Notes 167 Index 181

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Book SynopsisBioanalysis of Pharmaceuticals: Sample Preparation, Separation Techniques and Mass Spectrometry is the first student textbook on the separation science and mass spectrometry of pharmaceuticals present in biological fluids with an educational presentation of the principles, concepts and applications. It discusses the chemical structures and properties of low- and high-molecular drug substances; the different types of biological samples and fluids that are used; how to prepare the samples by extraction, and how to perform the appropriate analytical measurements by chromatographic and mass spectrometric methods. Bioanalysis of Pharmaceuticals: Sample Preparation, Separation Techniques and Mass Spectrometry: Is an introductory student textbook discussing the different principles and concepts clearly and comprehensively, with many relevant and educational examples Focuses on substances that are administered as human drugs, including low-moleculaTable of ContentsContributing Authors ix Preface xi 1. Introduction 1Stig Pedersen-Bjergaard 1.1 What Is Bioanalysis? 1 1.2 What Is the Purpose of Bioanalysis, and Where Is It Conducted? 2 1.3 Bioanalysis Is Challenging 6 1.4 The Different Sections of This Textbook 7 2. Physicochemical Properties of Drug Substances 9Steen Honoré Hansen and Leon Reubsaet 2.1 Bioanalysis in General 9 2.2 Protolytic Properties of Analytes 10 2.3 Partitioning of Substances 12 2.4 Stereochemistry 15 2.5 Peptides and Proteins 18 3. Biological Samples: Their Composition and Properties, and Their Collection and Storage 23Steen Honoré Hansen 3.1 Introduction 23 3.2 Blood, or Whole Blood 24 3.3 Plasma and Serum 26 3.4 Urine 26 3.5 Feces 27 3.6 Saliva 28 3.7 Cerebrospinal Fluid 28 3.8 Synovial Fluid 28 3.9 Hair and Nails 29 3.10 Tissue (Biopsies) 29 4. General Chromatographic Theory and Principles 31Steen Honoré Hansen 4.1 General Introduction 31 4.2 General Chromatographic Theory 32 4.3 Theory of Partition 33 4.4 Retention 34 4.5 Separation Efficiency 35 4.6 Resolution 36 4.7 Selectivity 37 4.8 The Separation Process 38 4.9 Chromatographic Principles 41 4.10 Reversed Phase Chromatography 45 4.11 Size Exclusion Chromatography (SEC) 54 4.12 Ion Exchange Chromatography 56 4.13 Chiral Separations 57 5. Quantitative and Qualitative Chromatographic Analysis 61Steen Honoré Hansen 5.1 Collection of Chromatographic Data 61 5.2 Quantitative Measurements 62 5.3 Calibration Methods 63 5.4 Validation 67 5.5 Qualitative Analysis 69 6. Sample Preparation 73Stig Pedersen-Bjergaard, Astrid Gjelstad, and Trine Grønhaug Halvorsen 6.1 Why Is Sample Preparation Required? 73 6.2 What Are the Main Strategies? 75 6.3 Protein Precipitation 75 6.4 Liquid–Liquid Extraction 80 6.5 Solid-Phase Extraction 94 6.6 Dilute and Shoot 110 6.7 What Are the Alternative Strategies? 113 7. High-Performance Liquid Chromatography (HPLC) and High-Performance Liquid Chromatography–Mass Spectrometry (LC-MS) 123Steen Honoré Hansen and Leon Reubsaet 7.1 Introduction 123 7.2 The Solvent Delivery System 125 7.3 Degassing and Filtering of Mobile Phases 127 7.4 Injection of Samples 128 7.5 Temperature Control 128 7.6 Mobile Phases 129 7.7 Stationary Phases and Columns 130 7.8 Detectors 135 7.9 Mass Spectrometric Detection 143 8. Gas Chromatography (GC) 173Stig Pedersen-Bjergaard 8.1 Basic Principles of GC 173 8.2 GC Instrumentation 174 8.3 Carrier Gas 177 8.4 Stationary Phases 178 8.5 Separation Selectivity in GC 180 8.6 Columns 182 8.7 Injection Systems 183 8.8 Detectors 185 8.9 Derivatization 187 8.10 Gas Chromatography–Mass Spectrometry (GC-MS) 188 9. Analysis of Small-Molecule Drugs in Biological Fluids 207Steen Honoré Hansen and Stig Pedersen-Bjergaard 9.1 Plasma and Serum Samples 207 9.2 Whole Blood Samples 234 9.3 Dried Blood Spots 241 9.4 Urine Samples 245 9.5 Saliva 253 References 259 10. Analysis of Peptide and Protein Drugs in Biological Fluids 261Leon Reubsaet and Trine Grønhaug Halvorsen References 282 11. Regulated Bioanalysis and Guidelines 283Martin Jørgensen and Morten A. Kall 11.1 Introduction 283 11.2 The Evolution of Regulated Bioanalysis 284 11.3 Bioanalytical Method Validation 286 11.4 Pre-study Validation 287 11.5 In-Study Validation 299 11.6 Documentation 300 11.7 Regulatory Requirements to Bioanalysis 300 11.8 Quality Systems in Regulated Bioanalysis 301 Index 305

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Book SynopsisThis book provides an introduction to physical chemistry that is directed toward applications to the biological sciences. Advanced mathematics is not required. This book can be used for either a one semester or two semester course, and as a reference volume by students and faculty in the biological sciences.Table of ContentsPreface to First Edition xv Preface to Second Edition xvii THERMODYNAMICS 1 1. Heat, Work, and Energy 3 1.1 Introduction 3 1.2 Temperature 4 1.3 Heat 5 1.4 Work 6 1.5 Definition of Energy 9 1.6 Enthalpy 11 1.7 Standard States 12 1.8 Calorimetry 13 1.9 Reaction Enthalpies 16 1.10 Temperature Dependence of the Reaction Enthalpy 18 References 19 Problems 20 2. Entropy and Gibbs Energy 23 2.1 Introduction 23 2.2 Statement of the Second Law 24 2.3 Calculation of the Entropy 26 2.4 Third Law of Thermodynamics 28 2.5 Molecular Interpretation of Entropy 29 2.6 Gibbs Energy 30 2.7 Chemical Equilibria 32 2.8 Pressure and Temperature Dependence of the Gibbs Energy 35 2.9 Phase Changes 36 2.10 Additions to the Gibbs Energy 39 Problems 40 3. Applications of Thermodynamics to Biological Systems 43 3.1 Biochemical Reactions 43 3.2 Metabolic Cycles 45 3.3 Direct Synthesis of ATP 49 3.4 Establishment of Membrane Ion Gradients by Chemical Reactions 51 3.5 Protein Structure 52 3.6 Protein Folding 60 3.7 Nucleic Acid Structures 63 3.8 DNA Melting 67 3.9 RNA 71 References 72 Problems 73 4. Thermodynamics Revisited 77 4.1 Introduction 77 4.2 Mathematical Tools 77 4.3 Maxwell Relations 78 4.4 Chemical Potential 80 4.5 Partial Molar Quantities 83 4.6 Osmotic Pressure 85 4.7 Chemical Equilibria 87 4.8 Ionic Solutions 89 References 93 Problems 93 CHEMICAL KINETICS 95 5. Principles of Chemical Kinetics 97 5.1 Introduction 97 5.2 Reaction Rates 99 5.3 Determination of Rate Laws 101 5.4 Radioactive Decay 104 5.5 Reaction Mechanisms 105 5.6 Temperature Dependence of Rate Constants 108 5.7 Relationship Between Thermodynamics and Kinetics 112 5.8 Reaction Rates Near Equilibrium 114 5.9 Single Molecule Kinetics 116 References 118 Problems 118 6. Applications of Kinetics to Biological Systems 121 6.1 Introduction 121 6.2 Enzyme Catalysis: The Michaelis–Menten Mechanism 121 6.3 α-Chymotrypsin 126 6.4 Protein Tyrosine Phosphatase 133 6.5 Ribozymes 137 6.6 DNA Melting and Renaturation 142 References 148 Problems 149 QUANTUM MECHANICS 153 7. Fundamentals of Quantum Mechanics 155 7.1 Introduction 155 7.2 Schrödinger Equation 158 7.3 Particle in a Box 159 7.4 Vibrational Motions 162 7.5 Tunneling 165 7.6 Rotational Motions 167 7.7 Basics of Spectroscopy 169 References 173 Problems 174 8. Electronic Structure of Atoms and Molecules 177 8.1 Introduction 177 8.2 Hydrogenic Atoms 177 8.3 Many-Electron Atoms 181 8.4 Born–Oppenheimer Approximation 184 8.5 Molecular Orbital Theory 186 8.6 Hartree–Fock Theory and Beyond 190 8.7 Density Functional Theory 193 8.8 Quantum Chemistry of Biological Systems 194 References 200 Problems 201 SPECTROSCOPY 203 9. X-ray Crystallography 205 9.1 Introduction 205 9.2 Scattering of X-Rays by a Crystal 206 9.3 Structure Determination 208 9.4 Neutron Diffraction 212 9.5 Nucleic Acid Structure 213 9.6 Protein Structure 216 9.7 Enzyme Catalysis 219 References 222 Problems 223 10. Electronic Spectra 225 10.1 Introduction 225 10.2 Absorption Spectra 226 10.3 Ultraviolet Spectra of Proteins 228 10.4 Nucleic Acid Spectra 230 10.5 Prosthetic Groups 231 10.6 Difference Spectroscopy 233 10.7 X-Ray Absorption Spectroscopy 236 10.8 Fluorescence and Phosphorescence 236 10.9 RecBCD: Helicase Activity Monitored by Fluorescence 240 10.10 Fluorescence Energy Transfer: A Molecular Ruler 241 10.11 Application of Energy Transfer to Biological Systems 243 10.12 Dihydrofolate Reductase 245 References 247 Problems 248 11. Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization 253 11.1 Introduction 253 11.2 Optical Rotary Dispersion 254 11.3 Circular Dichroism 256 11.4 Optical Rotary Dispersion and Circular Dichroism of Proteins 257 11.5 Optical Rotation and Circular Dichroism of Nucleic Acids 259 11.6 Small Molecule Binding to DNA 260 11.7 Protein Folding 263 11.8 Interaction of DNA with Zinc Finger Proteins 266 11.9 Fluorescence Polarization 267 11.10 Integration of HIV Genome Into Host Genome 269 11.11 α-Ketoglutarate Dehydrogenase 270 References 272 Problems 273 12. Vibrations in Macromolecules 277 12.1 Introduction 277 12.2 Infrared Spectroscopy 278 12.3 Raman Spectroscopy 279 12.4 Structure Determination with Vibrational Spectroscopy 281 12.5 Resonance Raman Spectroscopy 283 12.6 Structure of Enzyme–Substrate Complexes 286 12.7 Conclusion 287 References 287 Problems 288 13. Principles of Nuclear Magnetic Resonance and Electron Spin Resonance 289 13.1 Introduction 289 13.2 NMR Spectrometers 292 13.3 Chemical Shifts 293 13.4 Spin–Spin Splitting 296 13.5 Relaxation Times 298 13.6 Multidimensional NMR 300 13.7 Magnetic Resonance Imaging 306 13.8 Electron Spin Resonance 306 References 310 Problems 310 14. Applications of Magnetic Resonance to Biology 315 14.1 Introduction 315 14.2 Regulation of DNA Transcription 315 14.3 Protein–DNA Interactions 318 14.4 Dynamics of Protein Folding 320 14.5 RNA Folding 322 14.6 Lactose Permease 325 14.7 Proteasome Structure and Function 328 14.8 Conclusion 329 References 329 STATISTICAL MECHANICS 331 15. Fundamentals of Statistical Mechanics 333 15.1 Introduction 333 15.2 Kinetic Model of Gases 333 15.3 Boltzmann Distribution 338 15.4 Molecular Partition Function 343 15.5 Ensembles 346 15.6 Statistical Entropy 349 15.7 Helix-Coil Transition 350 References 353 Problems 354 16. Molecular Simulations 357 16.1 Introduction 357 16.2 Potential Energy Surfaces 358 16.3 Molecular Mechanics and Docking 364 16.4 Large-Scale Simulations 365 16.5 Molecular Dynamics 367 16.6 Monte Carlo 373 16.7 Hybrid Quantum/Classical Methods 373 16.8 Helmholtz and Gibbs Energy Calculations 375 16.9 Simulations of Enzyme Reactions 376 References 379 Problems 379 SPECIAL TOPICS 383 17. Ligand Binding to Macromolecules 385 17.1 Introduction 385 17.2 Binding of Small Molecules to Multiple Identical Binding Sites 385 17.3 Macroscopic and Microscopic Equilibrium Constants 387 17.4 Statistical Effects in Ligand Binding to Macromolecules 389 17.5 Experimental Determination of Ligand Binding Isotherms 392 17.6 Binding of Cro Repressor Protein to DNA 395 17.7 Cooperativity in Ligand Binding 397 17.8 Models for Cooperativity 402 17.9 Kinetic Studies of Cooperative Binding 406 17.10 Allosterism 408 References 412 Problems 412 18. Hydrodynamics of Macromolecules 415 18.1 Introduction 415 18.2 Frictional Coefficient 415 18.3 Diffusion 418 18.4 Centrifugation 421 18.5 Velocity Sedimentation 422 18.6 Equilibrium Centrifugation 424 18.7 Preparative Centrifugation 425 18.8 Density Centrifugation 427 18.9 Viscosity 428 18.10 Electrophoresis 429 18.11 Peptide-Induced Conformational Change of a Major Histocompatibility Complex Protein 432 18.12 Ultracentrifuge Analysis of Protein–DNA Interactions 434 References 435 Problems 435 19. Mass Spectrometry 441 19.1 Introduction 441 19.2 Mass Analysis 441 19.3 Tandem Mass Spectrometry (MS/MS) 445 19.4 Ion Detectors 445 19.5 Ionization of the Sample 446 19.6 Sample Preparation/Analysis 449 19.7 Proteins and Peptides 450 19.8 Protein Folding 452 19.9 Other Biomolecules 455 References 455 Problems 456 APPENDICES 457 Appendix 1. Useful Constants and Conversion Factors 459 Appendix 2. Structures of the Common Amino Acids at Neutral pH 461 Appendix 3. Common Nucleic Acid Components 463 Appendix 4. Standard Gibbs Energies and Enthalpies of Formation at 298 K, 1 atm, pH 7, and 0.25 M Ionic Strength 465 Appendix 5. Standard Gibbs Energy and Enthalpy Changes for Biochemical Reactions at 298 K, 1 atm, pH 7.0, pMg 3.0, and 0.25M Ionic Strength 467 Appendix 6. Introduction to Electrochemistry 469 A6-1 Introduction 469 A6-2 Galvanic Cells 469 A6-3 Standard Electrochmical Potentials 471 A6-4 Concentration Dependence of the Electrochemical Potential 472 A6-5 Biochemical Redox Reactions 473 References 473 Index 475

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Book SynopsisUp to date, easy to use, and rich with vibrant illustrations, Lippincott® Illustrated Reviews: Cell and Molecular Biology, 3rd Edition, provides a highly visual presentation of essential cell and molecular biology with a focus on topics related to human health and disease. This engaging approach incorporates all of the most popular features of the bestselling Lippincott® Illustrated Reviews series, including abundant full-color illustrations, chapter summaries, and review questions that link basic science to real-life clinical situations. The updated, versatile 3rd Edition can be used for a standalone cell biology course in medical, health professions, or other graduate and upper-level undergraduate programs; as a review for course and board exams; or in conjunction with other Lippincott® Illustrated Reviews for a seamless integrated course. UPDATED! Revised content throughout—including updated unit overviews and chapter summaries—helps students master the latest cell and molecular biology knowledge. UPDATED! Clinical Application boxes reinforce key concepts and enrich students’ understanding and clinical application capability. More than 250 full-color, annotated illustrations clarify complex processes and simplify study. Online animations and interactive review questions strengthen comprehension and retention.

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Book SynopsisIt has long been recognized that metal spin states play a central role in the reactivity of important biomolecules, in industrial catalysis and in spin crossover compounds. As the fields of inorganic chemistry and catalysis move towards the use of cheap, non-toxic first row transition metals, it is essential to understand the important role of spin states in influencing molecular structure, bonding and reactivity. Spin States in Biochemistry and Inorganic Chemistry provides a complete picture on the importance of spin states for reactivity in biochemistry and inorganic chemistry, presenting both theoretical and experimental perspectives. The successes and pitfalls of theoretical methods such as DFT, ligand-field theory and coupled cluster theory are discussed, and these methods are applied in studies throughout the book. Important spectroscopic techniques to determine spin states in transition metal complexes and proteins are explained, and the use of NMR for the analyTrade Review"Spin States in Biochemistry and Inorganic Chemistry: Influence on Structure and Reactivity, edited by Marcel Swart and Miquel Costas is impressive testimony to the advances in theory, computations, and experiment, especially regarding transition metals in recent years, and a revealing look at how much remains to be developed....The authors provide detailed comparison of various computational methods with each other and with experimental data in many cases. Each chapter is an extensively referenced focused review article. Chapters 1-3 emphasize computational methods....No single monograph can encompass a topic as broad as the title of this book, which is almost the entire chemistry of the periodic table. However, for the selected topics, the volume provides a very valuable concise snapshot of the field.Computational chemistry for compounds of CHNO have advanced to the point that many experimentalists can routinely apply standard methods in Gaussian and other such programs with confidence, guided only by the state of the art described in other publications. This book shows that in spite of enormous effort related to transition metal energy states and spin states, even the expert computational chemists need to proceed with caution and compare many functionals"- (Gareth Eaton- December 2016)Table of ContentsAbout the Editors xv List of Contributors xvii Foreword xxi Acknowledgments xxiii 1 General Introduction to Spin States 1Marcel Swart and Miquel Costas 1.1 Introduction 1 1.2 Experimental Chemistry: Reactivity, Synthesis and Spectroscopy 2 1.3 Computational Chemistry: Quantum Chemistry and Basis Sets 4 2 Application of Density Functional and Density Functional Based Ligand Field Theory to Spin States 7Claude Daul, Matija Zlatar, Maja Gruden-Pavlovic and Marcel Swart 2.1 Introduction 7 2.2 What Is the Problem with Theory? 9 2.2.1 Density Functional Theory 9 2.2.2 LF Theory: Bridging the Gap Between Experimental and Computational Coordination Chemistry 11 2.3 Validation and Application Studies 15 2.3.1 Use of OPBE, SSB-D and S12g Density Functionals for Spin-State Splittings 17 2.3.2 Application of LF-DFT 21 2.4 Concluding Remarks 25 3 Ab Initio Wavefunction Approaches to Spin States 35Carmen Sousa and Coen de Graaf 3.1 Introduction and Scope 35 3.2 Wavefunction-Based Methods for Spin States 35 3.2.1 Single Reference Methods 36 3.2.2 Multireference Methods 37 3.2.3 MR Perturbation Theory 39 3.2.4 Variational Approaches 40 3.2.5 Density Matrix Renormalization Group Theory 40 3.3 Spin Crossover 41 3.3.1 Choice of Active Space and Basis Set 41 3.3.2 The HS–LS Energy Difference 43 3.3.3 Light-Induced Excited Spin State Trapping (LIESST) 45 3.3.4 Spin Crossover in Other Metals 47 3.4 Magnetic Coupling 47 3.5 Spin States in Biochemical and Biomimetic Systems 50 3.6 Two-State Reactivity 52 3.7 Concluding Remarks 52 4 Experimental Techniques for Determining Spin States 59Carole Duboc and Marcello Gennari 4.1 Introduction 59 4.2 Magnetic Measurements 61 4.2.1 g-Anisotropy and Zero-Field Splitting (zfs) 64 4.2.2 Unquenched Orbital Moment in the Ground State 64 4.2.3 Exchange Interactions 64 4.2.4 Spin Transitions and Spin Crossover 66 4.3 EPR Spectroscopy 66 4.4 Mössbauer Spectroscopy 70 4.5 X-ray Spectroscopic Techniques 74 4.6 NMR Spectroscopy 77 4.7 Other Techniques 80 4.A Appendix 81 4.A.1 Theoretical Background 81 4.A.2 List of Symbols 82 5 Molecular Discovery in Spin Crossover 85Robert J. Deeth 5.1 Introduction 85 5.2 Theoretical Background 85 5.2.1 Spin Transition Curves 88 5.2.2 Light-Induced Excited Spin State Trapping 89 5.3 Thermal SCO Systems: Fe(II) 90 5.4 SCO in Non-d6 Systems 93 5.5 Computational Methods 95 5.6 Outlook 98 6 Multiple Spin-State Scenarios in Organometallic Reactivity 103Wojciech I. Dzik, Wesley Böhmer and Bas de Bruin 6.1 Introduction 103 6.2 "Spin-Forbidden" Reactions and Two-State Reactivity 104 6.3 Spin-State Changes in Transition Metal Complexes 107 6.3.1 Influence of the Spin State on the Kinetics of Ligand Exchange 108 6.3.2 Stoichiometric Bond Making and Breaking Reactions 109 6.3.3 Spin-State Situations Involving Redox-Active Ligands 115 6.4 Spin-State Changes in Catalysis 119 6.4.1 Catalytic (Cyclo)oligomerizations 119 6.4.2 Phillips Cr(II)/SiO2 Catalyst 121 6.4.3 SNS–CrCl3 Catalyst 123 6.5 Concluding Remarks 125 7 Principles and Prospects of Spin-States Reactivity in Chemistry and Bioinorganic Chemistry 131Dandamudi Usharani, Binju Wang, Dina A. Sharon and Sason Shaik 7.1 Introduction 131 7.2 Spin-States Reactivity 132 7.2.1 Two-State and Multi-State Reactivity 133 7.2.2 Origins of Spin-Selective Reactivity: Exchange-Enhanced Reactivity and Orbital Selection Rules 137 7.2.3 Considerations of Exchange-Enhanced Reactivity versus Orbital-Controlled Reactivity 140 7.2.4 Consideration of Spin-State Selectivity in H-Abstraction: The Power of EER 142 7.2.5 The Origins of Mechanistic Selection – Why Are C–H Hydroxylations Stepwise Processes? 146 7.3 Prospects of Two-State Reactivity and Multi-State Reactivity 148 7.3.1 Probing Spin-State Reactivity 148 7.3.2 Are Spin Inversion Probabilities Useful for Analyzing TSR? 150 7.4 Concluding Remarks 151 8 Multiple Spin-State Scenarios in Gas-Phase Reactions 157Jana Roithová 8.1 Introduction 157 8.2 Experimental Methods for the Investigation of Metal-Ion Reactions 158 8.3 Multiple State Reactivity: Reactions of Metal Cations with Methane 160 8.4 Effect of the Oxidation State: Reactions of Metal Hydride Cations with Methane 163 8.5 Two-State Reactivity: Reactions of Metal Oxide Cations 164 8.6 Effect of Ligands 171 8.7 Effect of Noninnocent Ligands 174 8.8 Concluding Remarks 177 9 Catalytic Function and Mechanism of Heme and Nonheme Iron(IV)–Oxo Complexes in Nature 185Matthew G. Quesne, Abayomi S. Faponle, David P. Goldberg and Sam P. de Visser 9.1 Introduction 185 9.2 Cytochrome P450 Enzymes 186 9.2.1 Importance of Cytochrome P450 Enzymes 187 9.2.2 P450 Activation of Long-Chain Fatty Acids 188 9.2.3 Heme Monooxygenases and Peroxygenases 188 9.2.4 Catalytic Cycle of Cytochrome P450 Enzymes 188 9.3 Nonheme Iron Dioxygenases 190 9.3.1 Cysteine Dioxygenase 191 9.3.2 AlkB Repair Enzymes 192 9.3.3 Nonheme Iron Halogenases 194 9.4 Conclusions 197 9.5 Acknowledgments 197 10 Terminal Metal–Oxo Species with Unusual Spin States 203Sarah A. Cook, David C. Lacy and Andy S. Borovik 10.1 Introduction 203 10.2 Bonding 204 10.2.1 Bonding Considerations: Tetragonal Symmetry 204 10.2.2 Bonding Considerations: Trigonal Symmetry 205 10.2.3 Methods of Characterization 206 10.3 Case Studies 206 10.3.1 Iron–Oxo Chemistry 206 10.3.2 Manganese–Oxo Chemistry 212 10.3.3 Cautionary Tales: Late Transition Metal Oxido Complexes 217 10.3.4 Effects of Redox Inactive Metal Ions 217 10.3.5 Metal–Oxyl Complexes 218 10.4 Reactivity 218 10.4.1 General Concepts: Proton versus Electron Transfer 218 10.4.2 Spin State and Reactivity 220 10.5 Summary 220 11 Multiple Spin Scenarios in Transition-Metal Complexes Involving Redox Non-Innocent Ligands 229Florian Heims and Kallol Ray 11.1 Introduction 229 11.2 Survey of Non-Innocent Ligands 231 11.3 Identification of Non-Innocent Ligands 232 11.3.1 X-ray Crystallography 232 11.3.2 EPR Spectroscopy 234 11.3.3 Mössbauer Spectroscopy 235 11.3.4 XAS Spectroscopy 236 11.4 Selected Examples of Biological and Chemical Systems Involving Non-Innocent Ligands 237 11.4.1 Copper–Radical Interaction 237 11.4.2 Iron–Radical Interaction 246 11.5 Concluding Remarks 252 12 Molecular Magnetism 263Guillem Aromí, Patrick Gamez and Olivier Roubeau 12.1 Introduction 263 12.2 Molecular Magnetism: Motivations, Early Achievements and Foundations 264 12.3 Molecular Nanomagnets (MNM) 265 12.3.1 Single-Molecule Magnets 266 12.3.2 Single-Chain Magnets (SCM) 268 12.3.3 Single-Ion Magnets (SIM) 271 12.4 Switchable Systems 273 12.4.1 Spin Crossover (SCO) 273 12.4.2 Valence Tautomerism (VT) 273 12.4.3 Charge Transfer (CT) 275 12.4.4 Light-Driven Ligand-Induced Spin Change (LD-LISC) 276 12.4.5 Photoswitching (PS) Through Intermetallic CT 277 12.5 Molecular-Based Magnetic Refrigerants 278 12.5.1 The Magneto-Caloric Effect, Its Experimental Determination and Key Parameters 278 12.5.2 Molecular to Extended Framework Coolers Towards Applications 280 12.6 Quantum Manipulation of the Electronic Spin for Quantum Computing 282 12.6.1 Organic Radicals 283 12.6.2 Transition Metal Clusters 284 12.6.3 Lanthanides as Realization of Qubits 285 12.6.4 Engineering of Molecular Quantum Gates with Lanthanide Qubits 285 12.7 Perspectives Toward Applications and Concluding Remarks 287 13 Electronic Structure, Bonding, Spin Coupling, and Energetics of Polynuclear Iron–Sulfur Clusters – A Broken Symmetry Density Functional Theory Perspective 297Kathrin H. Hopmann, Vladimir Pelmenschikov, Wen-Ge Han Du and Louis Noodleman 13.1 Introduction 297 13.2 Iron–Sulfur Coordination: Geometric and Electronic Structure 298 13.3 Spin Polarization Splitting and the Inverted Level Scheme 300 13.4 Spin Coupling and the Broken Symmetry Method 300 13.5 Electron Localization and Delocalization 301 13.6 Polynuclear Systems – Competing Heisenberg Interactions and Spin-Dependent Delocalization 303 13.7 Preamble to Three Major Topics: Iron–Sulfur–Nitrosyls, Adenosine-5'-Phosphosulfate Reductase, and the Proximal Cluster of Membrane-Bound [NiFe]-Hydrogenase 303 13.7.1 Nonheme Iron Nitrosyl Complexes 303 13.7.2 Adenosine-5'-Phosphosulfate Reductase 310 13.7.3 Proximal Cluster of O2-Tolerant Membrane-Bound [NiFe]-Hydrogenase in Three Redox States 315 13.8 Concluding Remarks 318 13.9 Acknowledgments 319 14 Environment Effects on Spin States, Properties, and Dynamics from Multi-level QM/MM Studies 327Alexander Petrenko and Matthias Stein 14.1 Introduction 327 14.1.1 Environmental Effects 328 14.1.2 Hybrid QM/MM Embedding Schemes 329 14.2 The Quantum Spin Hamiltonian – Linking Theory and Experiment 332 14.3 The Solvent as an Environment 335 14.3.1 Fourier Transform Infrared Spectroscopy 336 14.3.2 Nuclear Magnetic Resonance 336 14.3.3 Electron Paramagnetic Resonance 336 14.4 Effect of Different Levels of QM and MM Treatment 338 14.4.1 Convergence and Caveats at the QM Level 338 14.4.2 Accuracy of the MM Part 341 14.4.3 QM versus QM/MM Methods 341 14.5 Illustrative Bioinorganic Examples 343 14.5.1 Cytochrome P450 343 14.5.2 Hydrogenase Enzymes 349 14.5.3 Photosystem II and the Effect of QM Size 354 14.6 From Static Spin-State Properties to Dynamics and Kinetics of Electron Transfer 357 14.7 Final Remarks and Conclusions 359 14.8 Acknowledgments 362 15 High-Spin and Low-Spin States in {FeNO}7, FeIV=O, and FeIII–OOH Complexes and Their Correlations to Reactivity 369Edward I. Solomon, Kyle D. Sutherlin and Martin Srnec 15.1 Introduction 369 15.2 High- and Low-Spin {FeNO}7 Complexes: Correlations to O2 Activation 372 15.2.1 Spectroscopic Definition of the Electronic Structure of High-Spin {FeNO}7 372 15.2.2 Computational Studies of S = 3/2 {FeNO}7 Complexes and Related {FeO2}8 Complexes 375 15.2.3 Extension to IPNS and HPPD: Implications for Reactivity 377 15.2.4 Correlation to {FeNO}7 S = 1/2 385 15.3 Low-Spin (S = 1) and High-Spin (S = 2) FeIV=O Complexes 386 15.3.1 FeIV=O S = 1 Complexes: π* FMO 386 15.3.2 FeIV=O S = 2 Sites: π* and σ* FMOs 390 15.3.3 Contributions of FMOs to Reactivity 392 15.4 Low-Spin (S = 1/2) and High-Spin (S = 5/2) FeIII–OOH Complexes 396 15.4.1 Spin State Dependence of O–O Bond Homolysis 396 15.4.2 FeIII–OOH S = 1/2 Reactivity: ABLM 398 15.4.3 FeIII–OOH Spin State-Dependent Reactivity: FMOs 399 15.5 Concluding Remarks 401 15.6 Acknowledgments 402 16 NMR Analysis of Spin Densities 409Kara L. Bren 16.1 Introduction and Scope 409 16.2 Spin Density Distribution in Transition Metal Complexes 410 16.3 NMR of Paramagnetic Molecules 412 16.3.1 Chemical Shifts 413 16.3.2 Relaxation Rates 414 16.4 Analysis of Spin Densities by NMR 416 16.4.1 Factoring Contributions to Hyperfine Shifts 416 16.4.2 Relaxation Properties and Spin Density 418 16.4.3 DFT Approaches to Analyzing Hyperfine Shifts 419 16.4.4 Natural Bond Orbital Analysis 420 16.4.5 Application and Practicalities 421 16.5 Probing Spin Densities in Paramagnetic Metalloproteins 422 16.5.1 Heme Proteins 422 16.5.2 Iron-Sulfur Proteins 425 16.5.3 Copper Proteins 427 16.6 Conclusions and Outlook 429 17 Summary and Outlook 435Miquel Costas and Marcel Swart 17.1 Summary 435 17.2 Outlook 436 Index 439

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Book SynopsisOrganic chemistry is required coursework for degrees in life, food, and medical sciences. To help the students discouraged by the belief that this topic cannot be mastered without significant memorization, Arrow Pushing in Organic Chemistry serves as a handy supplement for understanding the subject. Includes new chapters, an expanded index, and additional problem sets complete with detailed solutions Focuses on understanding the mechanics and logic of organic reaction mechanisms Introduces ionic and non-ionic reactive species and reaction mechanisms Teaches strategies to predict reactive species, sites of reactions, and reaction products Provides a solid foundation upon which organic chemistry students can advance with confidenceTable of ContentsPREFACE xi ACKNOWLEDGEMENTS xiii ABOUT THE AUTHOR xv 1. Introduction 1 1.1 Definition of Arrow-Pushing 1 1.2 Functional Groups 5 1.3 Nucleophiles and Leaving Groups 7 1.4 Summary 8 Problems 9 2. Free Radicals 19 2.1 What Are Free Radicals? 19 2.2 How Are Free Radicals Formed? 21 2.2.1 Free Radical Initiators 22 2.2.2 Electron Transfer 23 2.3 Free Radical Stability 23 2.4 What Types of Reactions Involve Free Radicals? 25 2.4.1 Halogenation Reactions 26 2.4.2 Polymerization Reactions 28 2.4.3 Oxidation Reactions 30 2.5 Summary 31 Problems 32 3. Acids 37 3.1 What Are Acids? 37 3.2 What Is Resonance? 38 3.3 How Is Acidity Measured? 41 3.4 Relative Acidities 42 3.5 Inductive Effects 47 3.6 Inductive Effects and Relative Acidities 49 3.7 Relative Acidities of Hydrocarbons 50 3.8 Summary 51 Problems 52 4. Bases and Nucleophiles 61 4.1 What Are Bases? 61 4.2 What Are Nucleophiles? 66 4.3 Leaving Groups 70 4.4 Summary 70 Problems 71 5. SN2 Substitution Reactions 81 5.1 What Is An SN2 Reaction? 81 5.2 What Are Leaving Groups? 83 5.3 Where Can SN2 Reactions Occur? 84 5.4 SN2′ Reactions 85 5.5 Summary 88 Problems 89 6. SN1 Substitution Reactions 97 6.1 What Is An SN1 Reaction? 97 6.2 How Are SN1 Reactions Initiated? 98 6.3 The Carbocation 99 6.3.1 Molecular Structure and Orbitals 100 6.3.2 Stability of Carbocations 103 6.4 Carbocation Rearrangements 105 6.4.1 1,2-Hydride Shifts 105 6.4.2 1,2-Alkyl Shifts 106 6.4.3 Preventing Side Reactions 109 6.5 Summary 109 Problems 110 7. Elimination Reactions 115 7.1 E1 Eliminations 115 7.2 E1cB Eliminations 118 7.3 E2 Eliminations 120 7.4 How Do Elimination Reactions Work? 121 7.5 E1cB Eliminations Versus E2 Eliminations 124 7.6 Summary 124 Problems 126 8. Addition Reactions 133 8.1 Addition of Halogens to Double Bonds 133 8.2 Markovnikov’s Rule 135 8.3 Additions to Carbonyls 137 8.3.1 1,2-Additions 137 8.3.2 1,4-Additions 138 8.3.3 Addition–Elimination Reactions 141 8.4 Summary 143 Problems 144 9. Carbenes 153 9.1 What Are Carbenes? 153 9.2 How Are Carbenes Formed? 154 9.3 Reactions with Carbenes 156 9.3.1 Carbene Dimerization 156 9.3.2 Cyclopropanation Reactions 157 9.3.3 O-H Insertion Reactions 161 9.4 Carbenes Versus Carbenoids 162 9.5 Summary 163 Problems 164 10. Pericyclic Reactions 171 10.1 What Are Pericyclic Reactions? 171 10.2 Electrocyclic Reactions 172 10.3 Cycloaddition Reactions 175 10.3.1 The Diels–Alder Reaction 175 10.3.2 The Ene Reaction 178 10.3.3 Dipolar Cycloaddition Reactions 180 10.4 Sigmatropic Reactions 182 10.4.1 The Cope Rearrangement 183 10.4.2 The Claisen Rearrangement 184 10.5 Summary 187 Problems 189 11. Moving Forward 195 11.1 Functional Group Manipulations 195 11.2 Name Reactions 196 11.3 Reagents 208 11.4 Final Comments 208 Problems 209 Appendix 1. pKa Values of Protons Associated with Common Functional Groups 219 Appendix 2. Answers and Explanations to Problems 223 Chapter 1 Solutions 224 Chapter 2 Solutions 234 Chapter 3 Solutions 241 Chapter 4 Solutions 258 Chapter 5 Solutions 270 Chapter 6 Solutions 285 Chapter 7 Solutions 293 Chapter 8 Solutions 303 Chapter 9 Solutions 318 Chapter 10 Solutions 334 Chapter 11 Solutions 347 Appendix 3. Student Reaction Glossary 369 Index 373 Periodic Table of Elements 401

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Book SynopsisPhotosynthesis and the complex network within plants is becoming more important than ever, because of the earth's changing climate. In addition, the concepts can be used in other areas, and the science itself is useful in practical applications in many branches of science, including medicine, biology, biophysics, and chemistry. This original, groundbreaking work by two highly experienced and well-known scientists introduces a new and different approach to thinking about living organisms, what we can learn from them, and how we can use the concepts within their scientific makeup in practice. This book describes the principles of complex signaling networks enabling spatiotemporally-directed macroscopic processes by the coupling of systems leading to a bottom-up information transfer in photosynthetic organisms. Top-down messengers triggered by macroscopic actuators like sunlight, gravity, environment or stress lead to an activation of the gene regulation on the molecular level.Table of ContentsAbstract ix Foreward 1 xi Foreward 2 xiii Preface xv 1 Multiscale Hierarchical Processes 1 1.1 Coupled Systems, Hierarchy and Emergence 2 1.2 Principles of Synergetics 12 1.3 Axiomatic Motivation of Rate Equations 15 1.4 Rate Equations in Photosynthesis 19 1.5 Top down and Bottom up Signaling 23 2 Photophysics, Photobiology and Photosynthesis 27 2.1 Light Induced State Dynamics 27 2.2 Rate Equations and Excited State Dynamics in Coupled Systems 41 2.3 Light-Harvesting, Energy and Charge Transfer and Primary Processes of Photosynthesis 64 2.4 Antenna Complexes in Photosynthetic Systems 70 2.5 Fluorescence Emission as a Tool for Monitoring PS II Function 91 2.6 Excitation Energy Transfer and Electron Transfer Steps in Cyanobacteria Modeled with Rate Equations 93 2.7 Excitation Energy and Electron Transfer in Higher Plants Modeled with Rate Equations 105 2.8 Nonphotochemical Quenching in Plants and Cyanobacteria 114 2.9 Hierarchical Architecture of Plants 118 3 Formation and Functional Role of Reactive Oxygen Species (ROS) 123 3.1 Generation, Decay and Deleterious Action of ROS 125 3.2 Monitoring of ROS 137 3.3 Signaling Role of ROS 151 4 ROS Signaling in Coupled Nonlinear Systems 157 4.1 Signaling by Superoxide and Hydrogen Peroxide in Cyanobacteria 158 4.2 Signaling by Singlet Oxygen and Hydrogen Peroxide in Eukaryotic Cells and Plants 163 4.3 ROS and Cell Redox Control and Interaction with the Nuclear Gene Expression 167 4.4 ROS as Top down and Bottom up Messengers 174 4.5 Second Messengers and Signaling Molecules in H2O2 Signaling Chains and (Nonlinear) Networking 191 4.6 ROS-Waves and Prey-Predator Models 192 4.7 Open Questions on ROS Coupling in Nonlinear Systems 196 5 Th e Role of ROS in Evolution 199 5.1 Th e Big Bang of the Ecosphere 200 5.2 Complicated Patterns Result from Simple Rules but Only the Useful Patterns are Stable 201 5.3 Genetic Diversity and Selection Pressure as Driving Forces for Evolution 205 6 Outlook: Control and Feedback in Hierarchical Systems in Society, Politics and Economics 209 Bibliography 213 Appendix 249 Index 259

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