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| The Foundations of Biochemistry | |
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| Cellular Foundations | |
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| Chemical Foundations | |
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| Physical Foundations | |
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| Genetic Foundations | |
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| Evolutionary Foundations | |
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| Molecular Weight, Molecular Mass, and Their Correct Units | |
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| Louis Pasteur and Optical Activity: In Vino, Veritas | |
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| Entropy: The Advantages of Being Disorganized | |
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| Now introduces the concepts of proteomes and proteomics | |
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| Updated section on how a new species evolves | |
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| Increased emphasis on the interdependence of life forms in global cycles of energy | |
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| Structure and Catalysis | |
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| Water | |
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| Weak Interactions in Aqueous Systems | |
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| Ionization of Water, Weak Acids, and Weak Bases | |
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| Buffering against pH Changes in Biological Systems | |
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| Water as a Reactant | |
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| The Fitness of the Aqueous Environment for Living Organisms | |
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| Medicine: On Being One's Own Rabbit (Don't Try This at Home!) | |
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| Expanded discussion of blood pH buffering by the bicarbonate system,including a new box describing Haldane's use of himself as a guinea pig in experiments aimed at changing the acidity of blood | |
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| New section on ketoacidosis in diabetes | |
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| Amino Acids, Peptides, and Proteins | |
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| Amino Acids | |
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| Peptides and Proteins | |
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| Working with Proteins | |
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| The Structure of Proteins: Primary Structure | |
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| Methods: Absorption of Light by Molecules: The Lambert-Beer Law | |
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| Methods: Investigating Proteins with Mass Spectrometry | |
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| Medicine: Consensus Sequences and Sequence Logos | |
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| Significant revision to bioinformatics | |
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| More thorough explanation of consensus sequences, including an illustration of common ways to depict consensus sequences | |
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| The Three-Dimensional Structure of Proteins | |
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| Overview of Protein Structure | |
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| Protein Secondary Structure | |
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| Protein Tertiary and Quaternary Structures | |
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| Protein Denaturation and Folding | |
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| Methods: Knowing the Right Hand from the Left | |
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| Permanent Waving Is Biochemical Engineering | |
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| Medicine: Why Sailors, Explorers, and College Students Should Eat Their Fresh Fruits and Vegetables | |
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| The Protein Data Bank | |
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| Methods: Methods for Determining the Three-Dimensional Structure of a Protein | |
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| Medicine: Death by Misfolding: The Prion Diseases | |
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| New section, Defects in protein folding may be the molecular basis for a wide range of human genetic disorders, discusses a variety of amyloid diseases | |
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| New section on circular dichroism | |
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| Protein Function | |
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| Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins | |
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| Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins | |
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| Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors | |
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| Medicine: Carbon Monoxide: A Stealthy Killer | |
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| Enzymes | |
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| An Introduction to Enzymes | |
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| How Enzymes Work | |
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| Enzyme Kinetics as an Approach to Understanding Mechanism | |
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| Examples of Enzymatic Reactions | |
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| Regulatory Enzymes | |
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| Transformations of the Michaelis-Menten Equation: The Double-Reciprocal Plot | |
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| Kinetic Tests for Determining Inhibition Mechanisms | |
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| Evidence for Enzyme-Transition State Complementarity | |
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| More explanatory text added to the mechanisms for the enolase and lysozyme reactions | |
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| New section on pharmaceuticals developed from an understanding of enzyme mechanism, using penicillin and HIV protease inhibitors as examples | |
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| Carbohydrates and Glycobiology | |
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| Monosaccharides and Disaccharides | |
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| Polysaccharides | |
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| Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids | |
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| Carbohydrates as Informational Molecules: The Sugar Code | |
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| Working with Carbohydrates | |
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| Medicine: Blood Glucose Measurements in the Diagnosis and Treatment of Diabetes | |
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| New medical box, introduces hemoglobin glycation and AGEs and their role in the pathology of advanced diabetes | |
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| New section on sugar analogs as drugs that target viral neuraminidase | |
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| Introduction to the new field of glycomics, including methods for determining oligosaccharide structure using MALDI-MS | |
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| Nucleotides and Nucleic Acids | |
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| Some Basics | |
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| Nucleic Acid Structure | |
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| Nucleic Acid Chemistry | |
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| Other Functions of Nucleotides | |
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| DNA-Based Information Technologies | |
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| DNA Cloning: The Basics | |
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| From Genes to Genomes | |
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| From Genomes to Proteomes | |
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| Genome Alterations and New Products of Biotechnology | |
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| Medicine: A Potent Weapon in Forensic Medicine | |
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| Medicine: The Human Genome and Human Gene Therapy | |
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| New material on the green fluorescent protein | |
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| Thorough updating of genomics section | |
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| Lipids | |
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| Storage Lipids | |
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| Structural Lipids in Membranes | |
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| Lipids as Signals, Cofactors, and Pigments | |
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| Working with Lipids | |
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| Sperm Whales: Fatheads of the Deep | |
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| Medicine: Abnormal Accumulations of Membrane Lipids: Some Inherited Human Diseases | |
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| New medical section on the role of polyunsaturated fatty acids and trans fatty acids in cardiovascular disease | |
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| New section on lipidomics | |
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| New descriptions of volatile lipids used as signals by plants, and pigments of bird feathers derived from colored lipids in plant foods | |
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| Biological Membranes and Transport | |
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| The Composition and Architecture of Membranes | |
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| Membrane Dynamics | |
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| Solute Transport across Membranes | |
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| Methods: Atomic Force Microscopy to Visualize Membrane Proteins | |
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| Medicine: Defective Glucose and Water Transport in Two Forms of Diabetes | |
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| Medicine: A Defective Ion Channel in Cystic Fibrosis | |
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| Expanded section on bilayer dynamics covers flippases, floppases, scramblases, and bilayer asymmetry | |
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| Expanded and updated section on lipid rafts and caveolae includes new material on membrane curvature and the proteins that influence it, and introduces amphitropic proteins and annular lipids | |
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| New information on the structural basis for voltage gating in a K+ channel | |
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| Biosignaling | |
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| General Features of Signal Transduction | |
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| G Protein-Coupled Receptors and Second Messengers | |
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| Receptor Tyrosine Kinases | |
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| Receptor Guanylyl Cyclases, cGMP, and Protein Kinase G | |
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| Multivalent Scaffold Proteins and Membrane Rafts | |
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| Gated Ion Channels | |
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| Integrins: Bidirectional Cell Adhesion Receptors | |
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| Regulation of Transcription by Steroid Hormones | |
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| Signaling in Microorganisms and Plants | |
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| Sensory Transduction in Vision, Olfaction, and Gustation | |
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| Regulation of the Cell Cycle by Protein Kinases | |
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| Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death | |
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| Methods: Scatchard Analysis Quantifies the Receptor-Ligand Interaction | |
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| Medicine: G Proteins: Binary Switches in Health and Disease | |
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| Methods: FRET: Biochemistry Visualized in a Living Cell | |
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| Medicine: Color Blindness: John Dalton's Experiment from the Grave | |
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| Medicine: Development of Protein Kinase Inhibitors for Cancer Treatment | |
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| New Medical section on G protein coupled receptors (GCPRs) discusses the range of diseases for which drugs target GPCRs | |
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| New box on G proteins, proteins that regulate their GTPase activity, and the medical consequences of defective G protein function | |
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| Expanded and integrated treatment of local signaling circuits, including AKAPs and signaling complexes that include protein kinase A, adenylyl cyclase, and phosphodiesterase, and localized puffs and waves of Ca2+ | |
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| New medical box on the use of protein kinase inhibitors in cancertherapy | |
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| Bioenergetics and Metabolism | |
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| Bioenergetics and Biochemical Reaction Types | |
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| Bioenergetics and Thermodynamics | |
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| Chemical Logic and Common Biochemical Reactions | |
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| Phosphoryl Group Transfers and ATP | |
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| Biological Oxidation-Reduction Reactions | |
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| Firefly Flashes: Glowing Reports of ATP | |
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| New section, Chemical logic and common biochemical reactions, discusses common biochemical reaction types | |
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| Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway | |
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| Glycolysis | |
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| Feeder Pathways for Glycolysis | |
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| Fates of Pyruvate under Anaerobic Conditions: Fermentation | |
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| Gluconeogenesis | |
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| Pentose Phosphate Pathway of Glucose Oxidation | |
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| Medicine: High Rate of Glycolysis in Tumors Suggests Targets for Chemotherapy and Facilitates Diagnosis | |
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| Athletes, Alligators, and Coelacanths: Glycolysis at Limiting Concentrations of Oxygen | |
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| Ethanol Fermentations: Brewing Beer and Producing Biofuels | |
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| Medicine: Why Pythagoras Wouldn't Eat Falafel: Glucose 6-Phosphate Dehydrogenase Deficiency | |
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| New medical box on glucose uptake deficiency in type 1 diabetes | |
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| New medical box on how the high rate of glycolysis in cancerous tissue aids cancer diagnosis and treatment | |
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| Principles of Metabolic Regulation | |
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| Regulation of Metabolic Pathways | |
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| Analysis of Metabolic Control | |
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| Coordinated Regulation of Glycolysis and Gluconeogenesis | |
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| The Metabolism of Glycogen in Animals | |
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| Coordinated Regulation of Glycogen Synthesis and Breakdown | |
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| Methods: Metabolic Control Analysis: Quantitative Aspects | |
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| Isozymes: Different Proteins That Catalyze the Same Reaction | |
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| Medicine: Genetic Mutations That Lead to Rare Forms of Diabetes | |
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| Carl and Gerty Cori: Pioneers in Glycogen Metabolism and Disease | |
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| New section on emerging role of ribulose 5-phosphate as central regulator of glycolysis and gluconeogenesis | |
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| Expanded discussion of phosphoprotein phosphatases in metabolic regulation | |
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| Expanded coverage of the role of transcriptional regulators in metabolic regulation | |
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| New medical box on mutations that lead to rare forms of diabetes regulation (MODY) | |
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| The Citric Acid Cycle | |
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| Production of Acetyl-CoA (Activated Acetate) | |
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| Reactions of the Citric Acid Cycle | |
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| Regulation of the Citric Acid Cycle | |
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| The Glyoxylate Cycle | |
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| Moonlighting Enzymes: Proteins with More Than One Job | |
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| Synthases and Synthetases; Ligases and Lyases; Kinases,Phosphatases, and Phosphorylases: Yes, the Names Are Confusing! | |
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| Citrate: A Symmetric Molecule That Reacts Asymmetrically | |
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| Citrate Synthase, Soda Pop, and the World Food Supply | |
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| New box on effect of diabetes on the citric acid cycle and ketone body formation | |
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| Expanded discussion of substrate channeling | |
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| New section on mutations in citric acid cycle that lead to cancer | |
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| New box on moonlighting enzymes | |
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| Fatty Acid Catabolism | |
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| Digestion, Mobilization, and Transport of Fats | |
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| Oxidation of Fatty Acids | |
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| Ketone Bodies | |
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| Fat Bears Carry Out b Oxidation in Their Sleep | |
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| Coenzyme B12: A Radical Solution to a Perplexing Problem | |
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| New section on the role of transcription factors (PPARs) in regulation of lipid catabolism | |
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| Amino Acid Oxidation and the Production of Urea | |
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| Metabolic Fates of Amino Groups | |
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| Nitrogen Excretion and the Urea Cycle | |
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| Pathways of Amino Acid Degradation | |
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| Medicine: Assays for Tissue Damage | |
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| Medicine: Scientific Sleuths Solve a Murder Mystery | |
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| New section on pernicious anemia and associated problems in strict vegetarians. | |
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| Oxidative Phosphorylation and Photophosphorylation Oxidative Phosphorylation | |
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| Electron-Transfer Reactions in Mitochondria | |
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| ATP Synthesis | |
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| Regulation of Oxidative Phosphorylation | |
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| Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis | |
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| Mitochondrial Genes: Their Origin and the Effects of Mutations Photosynthesis: Harvesting Light Energy | |
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| General Features of Photophosphorylation | |
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| Light Absorption | |
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| The Central Photochemical Event: Light-Driven Electron Flow | |
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| ATP Synthesis by Photophosphorylation | |
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| The Evolution of Oxygenic Photosynthesis | |
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| Hot, Stinking Plants and Alternative Respiratory Pathways | |
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| Updated discussion of the structure of the electron transfer complexes of mitochondria and chloroplasts, and of the Fo complex | |
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| Updated description of the water-splitting complex's structure in chloroplasts | |
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| Expanded description of mitochondrial diseases and mitochondrial role in diabetes | |
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| Carbohydrate Biosynthesis in Plants and Bacteria | |
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| Photosynthetic Carbohydrate Synthesis | |
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| Photorespiration and the C4 and CAM Pathways | |
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| Biosynthesis of Starch and Sucrose | |
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| Synthesis of Cell Wall Polysaccharides: Plant Cellulose and Bacterial Peptidoglycan | |
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| Integration of Carbohydrate Metabolism in the Plant Cell | |
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| Lipid Biosynthesis | |
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| Biosynthesis of Fatty Acids and Eicosanoids | |
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| Biosynthesis of Triacylglycerols | |
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| Biosynthesis of Membrane Phospholipids | |
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| Biosynthesis of Cholesterol, Steroids, and Isoprenoids | |
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| Mixed-Function Oxidases, Oxygenases, and Cytochrome P-450 | |
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| Revised and updated section on fatty acid synthase includes new structural information on FAS I | |
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| Updated information on cyclooxygenase inhibitors (pain relievers Vioxx, Celebrex, Bextra) | |
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| New information on HMG-CoA reductase and new medical box on statins | |
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| Biosynthesis of Amino Acids, Nucleotides, and Related Molecules | |
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| Overview of Nitrogen Metabolism | |
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| Biosynthesis of Amino Acids | |
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| Molecules Derived from Amino Acids | |
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| Biosynthesis and Degradation of Nucleotides | |
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| Unusual lifestyles of the obscure but abundant | |
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| Medicine: On Kings and Vampires | |
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| Medicine: Curing African Sleeping Sickness with a Biochemical Trojan Horse | |
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| Updated coverage of nitrogen cycle section includes a new box on anammox bacteria | |
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| New information on therapy for acute lymphoblastic leukemia | |
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| New information on folic acid deficiency | |
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| Hormonal Regulation and Integration of Mammalian Metabolism | |
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| Hormones: Diverse Structures for Diverse Functions | |
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| Tissue-Specific Metabolism: The Division of Labor | |
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| Hormonal Regulation of Fuel Metabolism | |
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| Obesity and the Regulation of Body Mass | |
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| Obesity, the Metabolic Syndrome, and Type 2 Diabetes | |
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| Medicine: How Is a Hormone Discovered? The Arduous Path to Purified Insulin | |
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| Expanded coverage and updating of the biochemical connections between obesity, metabolic syndrome, and type 2 diabetes | |
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| Updated discussion of the integration of fuel metabolism in fed and starved states in diabetes | |
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| Information Pathways | |
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| Genes and Chromosomes | |
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| Chromosomal Elements | |
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| DNA Supercoiling | |
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| The Structure of Chromosomes | |
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| Medicine: Curing Disease by Inhibiting Topoisomerases | |
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| Medicine: Epigenetics, Nucleosome Structure, and Histone Variants | |
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| New material on histone modification, histone variants, and nucleosome deposition | |
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| New medical box on the use of topoisomerase inhibitors in the treatment of bacterial infections and cancer, includes material on ciprofloxacin (the antibiotic effective for anthrax) | |
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| New box on the role of histone modification and nucleosome deposition in the transmission of epigenetic information in heredity | |
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| DNA Metabolism | |
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| DNA Replication | |
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| DNA Repair | |
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| DNA Recombination | |
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| Medicine: DNA Repair and Cancer | |
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| New information on the initiation of replication and the dynamics at the replication fork, introducing AAA+ ATPases and their functions in replication and other aspects of DNA metabolism | |
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| RNA Metabolism | |
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| DNA-Dependent Synthesis of RNA | |
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| RNA Processing | |
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| RNA-Dependent Synthesis of RNA and DNA | |
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| Methods: RNA Polymerase Leaves Its Footprint on a Promoter | |
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| Fighting AIDS with Inhibitors of HIV Reverse Transcriptase | |
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| Methods: The SELEX Method for Generating RNA Polymers with New Functions | |
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| An Expanding RNA Universe Filled with TUF RNAs | |
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| New section on the expanding roles of RNA in cells | |
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| Protein Metabolism | |
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| The Genetic Code | |
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| Protein Synthesis | |
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| Protein Targeting and Degradation | |
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| Exceptions That Prove the Rule: Natural Variations in the Genetic Code | |
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| From an RNA World to a Protein World | |
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| Natural and Unnatural Expansion of the Genetic Code | |
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| Induced Variation in the Genetic Code: Nonsense Suppression | |
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| Expanded section on protein synthesis coupled to the advances in ribosome structure | |
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| New information on the roles of RNA in protein biosynthesis | |
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| Regulation of Gene Expression | |
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| Principles of Gene Regulation | |
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| Regulation of Gene Expression in Bacteria | |
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| Regulation of Gene Expression in Eukaryotes | |
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| Of Fins, Wings, Beaks, and Things | |
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| New information about roles of RNA in gene regulation | |
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| New box on the connections between evolution and development | |
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| Common Abbreviations in the Biochemical Research Literature | |
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| Abbreviated Solutions to Problems | |
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| Glossary | |
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| Credits | |
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| Index | |