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In the Fifth Edition, authors Dave Nelson and Mike Cox combine the best of the laboratory and best of the classroom, introducing exciting new developments while communicating basic principles through a variety of new learning tools--from new in-text worked examples and data analysis problems to the breakthrough eBook, which seamlessly integrates the complete text and its media components.

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• 1 The Foundations of Biochemistry
• 1.1 Cellular Foundations
• 1.2 Chemical Foundations
• 1.3 Physical Foundations
• 1.4 Genetic Foundations
• 1.5 Evolutionary Foundations
• 1-1 Molecular Weight, Molecular Mass, and Their Correct Units
• 1-2 Louis Pasteur and Optical Activity: In Vino, Veritas
• 1-3 Entropy: The Advantages of Being Disorganized
• Now introduces the concepts of proteomes and proteomics
• Updated section on how a new species evolves
• Increased emphasis on the interdependence of life forms in global cycles of energy
• I Structure and Catalysis
• 2 Water
• 2.1 Weak Interactions in Aqueous Systems
• 2.2 Ionization of Water, Weak Acids, and Weak Bases
• 2.3 Buffering against pH Changes in Biological Systems
• 2.4 Water as a Reactant
• 2.5 The Fitness of the Aqueous Environment for Living Organisms
• 2-1 Medicine: On Being One's Own Rabbit (Don't Try This at Home!)
• 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
• New section on ketoacidosis in diabetes
• 3 Amino Acids, Peptides, and Proteins
• 3.1 Amino Acids
• 3.2 Peptides and Proteins
• 3.3 Working with Proteins
• 3.4 The Structure of Proteins: Primary Structure
• 3-1 Methods: Absorption of Light by Molecules: The Lambert-Beer Law
• 3-2 Methods: Investigating Proteins with Mass Spectrometry
• 3-3 Medicine: Consensus Sequences and Sequence Logos
• Significant revision to bioinformatics
• More thorough explanation of consensus sequences, including an illustration of common ways to depict consensus sequences
• 4 The Three-Dimensional Structure of Proteins
• 4.1 Overview of Protein Structure
• 4.2 Protein Secondary Structure
• 4.3 Protein Tertiary and Quaternary Structures
• 4.4 Protein Denaturation and Folding
• 4-1 Methods: Knowing the Right Hand from the Left
• 4-2 Permanent Waving Is Biochemical Engineering
• 4-3 Medicine: Why Sailors, Explorers, and College Students Should Eat Their Fresh Fruits and Vegetables
• 4-4 The Protein Data Bank
• 4-5 Methods: Methods for Determining the Three-Dimensional Structure of a Protein
• 4-6 Medicine: Death by Misfolding: The Prion Diseases
• 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
• New section on circular dichroism
• 5 Protein Function
• 5.1 Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
• 5.2 Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins
• 5.3 Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors
• 5-1 Medicine: Carbon Monoxide: A Stealthy Killer
• 6 Enzymes
• 6.1 An Introduction to Enzymes
• 6.2 How Enzymes Work
• 6.3 Enzyme Kinetics as an Approach to Understanding Mechanism
• 6.4 Examples of Enzymatic Reactions
• 6.5 Regulatory Enzymes
• 6-1 Transformations of the Michaelis-Menten Equation: The Double-Reciprocal Plot
• 6-2 Kinetic Tests for Determining Inhibition Mechanisms
• 6-3 Evidence for Enzyme-Transition State Complementarity
• More explanatory text added to the mechanisms for the enolase and lysozyme reactions
• New section on pharmaceuticals developed from an understanding of enzyme mechanism, using penicillin and HIV protease inhibitors as examples
• 7 Carbohydrates and Glycobiology
• 7.1 Monosaccharides and Disaccharides
• 7.2 Polysaccharides
• 7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids
• 7.4 Carbohydrates as Informational Molecules: The Sugar Code
• 7.5 Working with Carbohydrates
• 7-1 Medicine: Blood Glucose Measurements in the Diagnosis and Treatment of Diabetes
• New medical box, introduces hemoglobin glycation and AGEs and their role in the pathology of advanced diabetes
• New section on sugar analogs as drugs that target viral neuraminidase
• Introduction to the new field of glycomics, including methods for determining oligosaccharide structure using MALDI-MS
• 8 Nucleotides and Nucleic Acids
• 8.1 Some Basics
• 8.2 Nucleic Acid Structure
• 8.3 Nucleic Acid Chemistry
• 8.4 Other Functions of Nucleotides
• 9 DNA-Based Information Technologies
• 9.1 DNA Cloning: The Basics
• 9.2 From Genes to Genomes
• 9.3 From Genomes to Proteomes
• 9.4 Genome Alterations and New Products of Biotechnology
• 9-1 Medicine: A Potent Weapon in Forensic Medicine
• 9-2 Medicine: The Human Genome and Human Gene Therapy
• New material on the green fluorescent protein
• Thorough updating of genomics section
• 10 Lipids
• 10.1 Storage Lipids
• 10.2 Structural Lipids in Membranes
• 10.3 Lipids as Signals, Cofactors, and Pigments
• 10.4 Working with Lipids
• 10-1 Sperm Whales: Fatheads of the Deep
• 10-2 Medicine: Abnormal Accumulations of Membrane Lipids: Some Inherited Human Diseases
• New medical section on the role of polyunsaturated fatty acids and trans fatty acids in cardiovascular disease
• New section on lipidomics
• New descriptions of volatile lipids used as signals by plants, and pigments of bird feathers derived from colored lipids in plant foods
• 11 Biological Membranes and Transport
• 11.1 The Composition and Architecture of Membranes
• 11.2 Membrane Dynamics
• 11.3 Solute Transport across Membranes
• 11-1 Methods: Atomic Force Microscopy to Visualize Membrane Proteins
• 11-2 Medicine: Defective Glucose and Water Transport in Two Forms of Diabetes
• 11-3 Medicine: A Defective Ion Channel in Cystic Fibrosis
• Expanded section on bilayer dynamics covers flippases, floppases, scramblases, and bilayer asymmetry
• 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
• New information on the structural basis for voltage gating in a K+ channel
• 12 Biosignaling
• 12.1 General Features of Signal Transduction
• 12.2 G Protein-Coupled Receptors and Second Messengers
• 12.3 Receptor Tyrosine Kinases
• 12.4 Receptor Guanylyl Cyclases, cGMP, and Protein Kinase G
• 12.5 Multivalent Scaffold Proteins and Membrane Rafts
• 12.6 Gated Ion Channels
• 12.7 Integrins: Bidirectional Cell Adhesion Receptors
• 12.8 Regulation of Transcription by Steroid Hormones
• 12.9 Signaling in Microorganisms and Plants
• 12.10 Sensory Transduction in Vision, Olfaction, and Gustation
• 12.11 Regulation of the Cell Cycle by Protein Kinases
• 12.12 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death
• 12-1 Methods: Scatchard Analysis Quantifies the Receptor-Ligand Interaction
• 12-2 Medicine: G Proteins: Binary Switches in Health and Disease
• 12-3 Methods: FRET: Biochemistry Visualized in a Living Cell
• 12-4 Medicine: Color Blindness: John Dalton's Experiment from the Grave
• 12-5 Medicine: Development of Protein Kinase Inhibitors for Cancer Treatment
• New Medical section on G protein coupled receptors (GCPRs) discusses the range of diseases for which drugs target GPCRs
• New box on G proteins, proteins that regulate their GTPase activity, and the medical consequences of defective G protein function
• 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+
• New medical box on the use of protein kinase inhibitors in cancertherapy
• II Bioenergetics and Metabolism
• 13 Bioenergetics and Biochemical Reaction Types
• 13.1 Bioenergetics and Thermodynamics
• 13.2 Chemical Logic and Common Biochemical Reactions
• 13.3 Phosphoryl Group Transfers and ATP
• 13.4 Biological Oxidation-Reduction Reactions
• 13-1 Firefly Flashes: Glowing Reports of ATP
• New section, Chemical logic and common biochemical reactions, discusses common biochemical reaction types
• 14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
• 14.1 Glycolysis
• 14.2 Feeder Pathways for Glycolysis
• 14.3 Fates of Pyruvate under Anaerobic Conditions: Fermentation
• 14.4 Gluconeogenesis
• 14.5 Pentose Phosphate Pathway of Glucose Oxidation
• 14-1 Medicine: High Rate of Glycolysis in Tumors Suggests Targets for Chemotherapy and Facilitates Diagnosis
• 14-2 Athletes, Alligators, and Coelacanths: Glycolysis at Limiting Concentrations of Oxygen
• 14-3 Ethanol Fermentations: Brewing Beer and Producing Biofuels
• 14-4 Medicine: Why Pythagoras Wouldn't Eat Falafel: Glucose 6-Phosphate Dehydrogenase Deficiency
• New medical box on glucose uptake deficiency in type 1 diabetes
• New medical box on how the high rate of glycolysis in cancerous tissue aids cancer diagnosis and treatment
• 15 Principles of Metabolic Regulation
• 15.1 Regulation of Metabolic Pathways
• 15.2 Analysis of Metabolic Control
• 15.3 Coordinated Regulation of Glycolysis and Gluconeogenesis
• 15.4 The Metabolism of Glycogen in Animals
• 15.5 Coordinated Regulation of Glycogen Synthesis and Breakdown
• 15-1 Methods: Metabolic Control Analysis: Quantitative Aspects
• 15-2 Isozymes: Different Proteins That Catalyze the Same Reaction
• 15-3 Medicine: Genetic Mutations That Lead to Rare Forms of Diabetes
• 15-4 Carl and Gerty Cori: Pioneers in Glycogen Metabolism and Disease
• New section on emerging role of ribulose 5-phosphate as central regulator of glycolysis and gluconeogenesis
• Expanded discussion of phosphoprotein phosphatases in metabolic regulation
• Expanded coverage of the role of transcriptional regulators in metabolic regulation
• New medical box on mutations that lead to rare forms of diabetes regulation (MODY)
• 16 The Citric Acid Cycle
• 16.1 Production of Acetyl-CoA (Activated Acetate)
• 16.2 Reactions of the Citric Acid Cycle
• 16.3 Regulation of the Citric Acid Cycle
• 16.4 The Glyoxylate Cycle
• 16-1 Moonlighting Enzymes: Proteins with More Than One Job
• 16-2 Synthases and Synthetases; Ligases and Lyases; Kinases,Phosphatases, and Phosphorylases: Yes, the Names Are Confusing!
• 16-3 Citrate: A Symmetric Molecule That Reacts Asymmetrically
• 16-4 Citrate Synthase, Soda Pop, and the World Food Supply
• New box on effect of diabetes on the citric acid cycle and ketone body formation
• Expanded discussion of substrate channeling
• New section on mutations in citric acid cycle that lead to cancer
• New box on moonlighting enzymes
• 17 Fatty Acid Catabolism
• 17.1 Digestion, Mobilization, and Transport of Fats
• 17.2 Oxidation of Fatty Acids
• 17.3 Ketone Bodies
• 17-1 Fat Bears Carry Out b Oxidation in Their Sleep
• 17-2 Coenzyme B12: A Radical Solution to a Perplexing Problem
• New section on the role of transcription factors (PPARs) in regulation of lipid catabolism
• 18 Amino Acid Oxidation and the Production of Urea
• 18.1 Metabolic Fates of Amino Groups
• 18.2 Nitrogen Excretion and the Urea Cycle
• 18.3 Pathways of Amino Acid Degradation
• 18-1 Medicine: Assays for Tissue Damage
• 18-2 Medicine: Scientific Sleuths Solve a Murder Mystery
• New section on pernicious anemia and associated problems in strict vegetarians.
• 19 Oxidative Phosphorylation and Photophosphorylation Oxidative Phosphorylation
• 19.1 Electron-Transfer Reactions in Mitochondria
• 19.2 ATP Synthesis
• 19.3 Regulation of Oxidative Phosphorylation
• 19.4 Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis
• 19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations Photosynthesis: Harvesting Light Energy
• 19.6 General Features of Photophosphorylation
• 19.7 Light Absorption
• 19.8 The Central Photochemical Event: Light-Driven Electron Flow
• 19.9 ATP Synthesis by Photophosphorylation
• 19.10 The Evolution of Oxygenic Photosynthesis
• 19-1 Hot, Stinking Plants and Alternative Respiratory Pathways
• Updated discussion of the structure of the electron transfer complexes of mitochondria and chloroplasts, and of the Fo complex
• Updated description of the water-splitting complex's structure in chloroplasts
• Expanded description of mitochondrial diseases and mitochondrial role in diabetes
• 20 Carbohydrate Biosynthesis in Plants and Bacteria
• 20.1 Photosynthetic Carbohydrate Synthesis
• 20.2 Photorespiration and the C4 and CAM Pathways
• 20.3 Biosynthesis of Starch and Sucrose
• 20.4 Synthesis of Cell Wall Polysaccharides: Plant Cellulose and Bacterial Peptidoglycan
• 20.5 Integration of Carbohydrate Metabolism in the Plant Cell
• 21 Lipid Biosynthesis
• 21.1 Biosynthesis of Fatty Acids and Eicosanoids
• 21.2 Biosynthesis of Triacylglycerols
• 21.3 Biosynthesis of Membrane Phospholipids
• 21.4 Biosynthesis of Cholesterol, Steroids, and Isoprenoids
• 21-1 Mixed-Function Oxidases, Oxygenases, and Cytochrome P-450
• Revised and updated section on fatty acid synthase includes new structural information on FAS I
• Updated information on cyclooxygenase inhibitors (pain relievers Vioxx, Celebrex, Bextra)
• New information on HMG-CoA reductase and new medical box on statins
• 22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
• 22.1 Overview of Nitrogen Metabolism
• 22.2 Biosynthesis of Amino Acids
• 22.3 Molecules Derived from Amino Acids
• 22.4 Biosynthesis and Degradation of Nucleotides
• 22-1 Unusual lifestyles of the obscure but abundant
• 22-2 Medicine: On Kings and Vampires
• 22-3 Medicine: Curing African Sleeping Sickness with a Biochemical Trojan Horse
• Updated coverage of nitrogen cycle section includes a new box on anammox bacteria
• New information on therapy for acute lymphoblastic leukemia
• New information on folic acid deficiency
• 23 Hormonal Regulation and Integration of Mammalian Metabolism
• 23.1 Hormones: Diverse Structures for Diverse Functions
• 23.2 Tissue-Specific Metabolism: The Division of Labor
• 23.3 Hormonal Regulation of Fuel Metabolism
• 23.4 Obesity and the Regulation of Body Mass
• 23.5 Obesity, the Metabolic Syndrome, and Type 2 Diabetes
• 23-1 Medicine: How Is a Hormone Discovered? The Arduous Path to Purified Insulin
• Expanded coverage and updating of the biochemical connections between obesity, metabolic syndrome, and type 2 diabetes
• Updated discussion of the integration of fuel metabolism in fed and starved states in diabetes
• III Information Pathways
• 24 Genes and Chromosomes
• 24.1 Chromosomal Elements
• 24.2 DNA Supercoiling
• 24.3 The Structure of Chromosomes
• 24-1 Medicine: Curing Disease by Inhibiting Topoisomerases
• 24-2 Medicine: Epigenetics, Nucleosome Structure, and Histone Variants
• New material on histone modification, histone variants, and nucleosome deposition
• 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)
• New box on the role of histone modification and nucleosome deposition in the transmission of epigenetic information in heredity
• 25 DNA Metabolism
• 25.1 DNA Replication
• 25.2 DNA Repair
• 25.3 DNA Recombination
• 25-1 Medicine: DNA Repair and Cancer
• 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
• 26 RNA Metabolism
• 26.1 DNA-Dependent Synthesis of RNA
• 26.2 RNA Processing
• 26.3 RNA-Dependent Synthesis of RNA and DNA
• 26-1 Methods: RNA Polymerase Leaves Its Footprint on a Promoter
• 26-2 Fighting AIDS with Inhibitors of HIV Reverse Transcriptase
• 26-3 Methods: The SELEX Method for Generating RNA Polymers with New Functions
• 26-4 An Expanding RNA Universe Filled with TUF RNAs
• New section on the expanding roles of RNA in cells
• 27 Protein Metabolism
• 27.1 The Genetic Code
• 27.2 Protein Synthesis
• 27.3 Protein Targeting and Degradation
• 27-1 Exceptions That Prove the Rule: Natural Variations in the Genetic Code
• 27-2 From an RNA World to a Protein World
• 27-3 Natural and Unnatural Expansion of the Genetic Code
• 27-4 Induced Variation in the Genetic Code: Nonsense Suppression
• Expanded section on protein synthesis coupled to the advances in ribosome structure
• New information on the roles of RNA in protein biosynthesis
• 28 Regulation of Gene Expression
• 28.1 Principles of Gene Regulation
• 28.2 Regulation of Gene Expression in Bacteria
• 28.3 Regulation of Gene Expression in Eukaryotes
• 28-1 Of Fins, Wings, Beaks, and Things
• New information about roles of RNA in gene regulation
• New box on the connections between evolution and development
• Appendix A Common Abbreviations in the Biochemical Research Literature
• Appendix B Abbreviated Solutions to Problems
• Glossary
• Credits
• Index