5th edition. — W.H. Freeman and Company, 2002. — 1515 p. — ISBN-10 0-7167-3051-0For more than 25 years, and through four editions, Stryer's Biochemistry has laid out this beautiful subject in an exceptionally appealing and lucid manner. The engaging writing style and attractive design have made the text a pleasure for our students to read and study throughout our years of teaching. Biochemistry is rapidly progressing from a science performed almost entirely at the laboratory bench to one that may be explored through computers. The recently developed ability to determine entire genomic sequences has provided the data needed to accomplish massive comparisons of derived protein sequences, the results of which may be used to formulate and test hypotheses about biochemical function. The power of these new methods is explained by the impact of evolution: many molecules and biochemical pathways have been generated by duplicating and modifying existing ones. Throughout the text, a stylized tree icon is positioned at the start of discussions focused primarily on protein homologies and evolutionary origins.Contents Dedication About the authors Рreface Tools and Techniques Clinical Applications Molecular Evolution Supplements Supporting Biochemistry, Fifth Edition Acknowledgments The Molecular Design of Life Prelude: Biochemistry and the Genomic Revolution DNA Illustrates the Relation between Form and Function Biochemical Unity Underlies Biological Diversity Chemical Bonds in Biochemistry Biochemistry and Human Biology Appendix: Depicting Molecular Structures Biochemical Evolution Key Organic Molecules Are Used by Living Systems Evolution Requires Reproduction, Variation, and Selective Pressure Energy Transformations Are Necessary to Sustain Living Systems Cells Can Respond to Changes in Their Environments Summary Problems Selected Readings Protein Structure and Function Proteins Are Built from a Repertoire of 20 Amino Acids Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar Cores Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure Summary Appendix: Acid-Base Concepts Problems Selected Readings Exploring Proteins The Purification of Proteins Is an Essential First Step in Understanding Their Function Amino Acid Sequences Can Be Determined by Automated Edman Degradation Immunology Provides Important Techniques with Which to Investigate Proteins Peptides Can Be Synthesized by Automated Solid-Phase Methods Three-Dimensional Protein Structure Can Be Determined by NMR Spectroscopy and XRay Crystallography Summary Problems Selected Readings DNA, RNA, and the Flow of Genetic Information A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double- Helical Structure DNA Is Replicated by Polymerases that Take Instructions from Templates Gene Expression Is the Transformation of DNA Information Into Functional Molecules Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point Most Eukaryotic Genes Are Mosaics of Introns and Exons Summary Problems Selected Readings Exploring Genes The Basic Tools of Gene Exploration Recombinant DNA Technology Has Revolutionized All Aspects of Biology Manipulating the Genes of Eukaryotes Novel Proteins Can Be Engineered by Site-Specific Mutagenesis Summary Problems Selected Reading Exploring Evolution Homologs Are Descended from a Common Ancestor Statistical Analysis of Sequence Alignments Can Detect Homology Examination of Three-Dimensional Structure Enhances Our Understanding of Evolutionary Relationships Evolutionary Trees Can Be Constructed on the Basis of Sequence Information Modern Techniques Make the Experimental Exploration of Evolution Possible Summary Problems Selected Readings Enzymes: Basic Concepts and Kinetics Enzymes Are Powerful and Highly Specific Catalysts Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes Enzymes Can Be Inhibited by Specific Molecules Vitamins Are Often Precursors to Coenzymes Summary Appendix: Vmax and KM Can Be Determined by Double-Reciprocal Plots Problems Selected Readings Catalytic Strategies Proteases: Facilitating a Difficult Reaction Making a Fast Reaction Faster: Carbonic Anhydrases Restriction Enzymes: Performing Highly Specific DNA-Cleavage Reactions Nucleoside Monophosphate Kinases: Catalyzing Phosphoryl Group Exchange between Nucleotides Without Promoting Hydrolysis Summary Problems Selected Readings Regulatory Strategies: Enzymes and Hemoglobin Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its Pathway Hemoglobin Transports Oxygen Efficiently by Binding Oxygen Cooperatively Isozymes Provide a Means of Regulation Specific to Distinct Tissues and Developmental Stages Covalent Modification Is a Means of Regulating Enzyme Activity Many Enzymes Are Activated by Specific Proteolytic Cleavage Summary Problems Selected Readings Carbohydrates Monosaccharides Are Aldehydes or Ketones with Multiple Hydroxyl Groups Complex Carbohydrates Are Formed by Linkage of Monosaccharides Carbohydrates Can Be Attached to Proteins to Form Glycoproteins Lectins Are Specific Carbohydrate-Binding Proteins Summary Problems Selected Readings Lipids and Cell Membranes Many Common Features Underlie the Diversity of Biological Membranes Fatty Acids Are Key Constituents of Lipids There Are Three Common Types of Membrane Lipids Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media Proteins Carry Out Most Membrane Processes Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane Eukaryotic Cells Contain Compartments Bounded by Internal Membranes Summary Problems Selected Readings Membrane Channels and Pumps The Transport of Molecules Across a Membrane May Be Active or Passive A Family of Membrane Proteins Uses ATP Hydrolysis to Pump Ions Across Membranes Multidrug Resistance and Cystic Fibrosis Highlight a Family of Membrane Proteins with ATP-Binding Cassette Domains Secondary Transporters Use One Concentration Gradient to Power the Formation of Another Specific Channels Can Rapidly Transport Ions Across Membranes Gap Junctions Allow Ions and Small Molecules to Flow between Communicating Cells Summary Problems Selected Readings Transducing and Storing Energy Metabolism: Basic Concepts and Design Metabolism Is Composed of Many Coupled, Interconnecting Reactions The Oxidation of Carbon Fuels Is an Important Source of Cellular Energy Metabolic Pathways Contain Many Recurring Motifs Summary Problems Selected Readings Signal-Transduction Pathways: An Introduction to Information Metabolism Seven-Transmembrane-Helix Receptors Change Conformation in Response to Ligand Binding and Activate G Proteins The Hydrolysis of Phosphatidyl Inositol Bisphosphate by Phospholipase C Generates Two Messengers Calcium Ion Is a Ubiquitous Cytosolic Messenger Some Receptors Dimerize in Response to Ligand Binding and Signal by Crossphosphorylation Defects in Signaling Pathways Can Lead to Cancer and Other Diseases Recurring Features of Signal-Transduction Pathways Reveal Evolutionary Relationships Summary Problems Selected Readings Glycolysis and Gluconeogenesis Glycolysis Is an Energy-Conversion Pathway in Many Organisms The Glycolytic Pathway Is Tightly Controlled Glucose Can Be Synthesized from Noncarbohydrate Precursors Gluconeogenesis and Glycolysis Are Reciprocally Regulated Summary Problems Selected Readings The Citric Acid Cycle The Citric Acid Cycle Oxidizes Two-Carbon Units Entry to the Citric Acid Cycle and Metabolism Through It Are Controlled The Citric Acid Cycle Is a Source of Biosynthetic Precursors The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate Summary Problems Selected Readings Oxidative Phosphorylation Oxidative Phosphorylation in Eukaryotes Takes Place in Mitochondria Oxidative Phosphorylation Depends on Electron Transfer The Respiratory Chain Consists of Four Complexes: Three Proton Pumps and a Physical Link to the Citric Acid Cycle A Proton Gradient Powers the Synthesis of ATP Many Shuttles Allow Movement Across the Mitochondrial Membranes The Regulation of Cellular Respiration Is Governed Primarily by the Need for ATP Summary Problems Selected Readings The Light Reactions of Photosynthesis Photosynthesis Takes Place in Chloroplasts Light Absorption by Chlorophyll Induces Electron Transfer Two Photosystems Generate a Proton Gradient and NADPH in Oxygenic Photosynthesis A Proton Gradient Across the Thylakoid Membrane Drives ATP Synthesis Accessory Pigments Funnel Energy Into Reaction Centers The Ability to Convert Light Into Chemical Energy Is Ancient Summary Problems Selected Readings The Calvin Cycle and the Pentose Phosphate Pathway The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water The Activity of the Calvin Cycle Depends on Environmental Conditions the Pentose Phosphate Pathway Generates NADPH and Synthesizes Five-Carbon Sugars The Metabolism of Glucose 6-Phosphate by the Pentose Phosphate Pathway Is Coordinated with Glycolysis Glucose 6-Phosphate Dehydrogenase Plays a Key Role in Protection Against Reactive Oxygen Species Summary Problems Selected Readings Glycogen Metabolism Glycogen Breakdown Requires the Interplay of Several Enzymes Phosphorylase Is Regulated by Allosteric Interactions and Reversible Phosphorylation Epinephrine and Glucagon Signal the Need for Glycogen Breakdown Glycogen Is Synthesized and Degraded by Different Pathways Glycogen Breakdown and Synthesis Are Reciprocally Regulated Summary Problems Selected Readings Fatty Acid Metabolism Triacylglycerols Are Highly Concentrated Energy Stores The Utilization of Fatty Acids as Fuel Requires Three Stages of Processing Certain Fatty Acids Require Additional Steps for Degradation Fatty Acids Are Synthesized and Degraded by Different Pathways Acetyl Coenzyme A Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism Elongation and Unsaturation of Fatty Acids Are Accomplished by Accessory Enzyme Systems Summary Problems Selected Readings Protein Turnover and Amino Acid Catabolism Proteins Are Degraded to Amino Acids Protein Turnover Is Tightly Regulated The First Step in Amino Acid Degradation Is the Removal of Nitrogen Ammonium Ion Is Converted Into Urea in Most Terrestrial Vertebrates Carbon Atoms of Degraded Amino Acids Emerge as Major Metabolic Intermediates Inborn Errors of Metabolism Can Disrupt Amino Acid Degradation Summary Problems Selected Readings Synthesizing the Molecules of Life The Biosynthesis of Amino Acids Nitrogen Fixation: Microorganisms Use ATP and a Powerful Reductant to Reduce Atmospheric Nitrogen to Ammonia Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways Amino Acid Biosynthesis Is Regulated by Feedback Inhibition Amino Acids Are Precursors of Many Biomolecules Summary Problems Selected Readings Nucleotide Biosynthesis In de Novo Synthesis, the Pyrimidine Ring Is Assembled from Bicarbonate, Aspartate, and Glutamine Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways Deoxyribonucleotides Synthesized by the Reduction of Ribonucleotides Through a Radical Mechanism Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition NAD+, FAD, and Coenzyme A Are Formed from ATP Disruptions in Nucleotide Metabolism Can Cause Pathological Conditions Summary Problems Selected Readings The Biosynthesis of Membrane Lipids and Steroids Phosphatidate Is a Common Intermediate in the Synthesis of Phospholipids and Triacylglycerols Cholesterol Is Synthesized from Acetyl Coenzyme A in Three Stages The Complex Regulation of Cholesterol Biosynthesis Takes Place at Several Levels Important Derivatives of Cholesterol Include Bile Salts and Steroid Hormones Summary Problems Selected Readings DNA Replication, Recombination, and Repair DNA Can Assume a Variety of Structural Forms DNA Polymerases Require a Template and a Primer Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites Double-Stranded DNA Molecules with Similar Sequences Sometimes Recombine Mutations Involve Changes in the Base Sequence of DNA Summary Problems Selected Readings RNA Synthesis and Splicing Transcription Is Catalyzed by RNA Polymerase Eukaryotic Transcription and Translation Are Separated in Space and Time The Transcription Products of All Three Eukaryotic Polymerases Are Processed The Discovery of Catalytic RNA Was Revealing in Regard to Both Mechanism and Evolution Summary Problems Selected Readings Protein Synthesis Protein Synthesis Requires the Translation of Nucleotide Sequences Into Amino Acid Sequences Aminoacyl-Transfer RNA Synthetases Read the Genetic Code A Ribosome Is a Ribonucleoprotein Particle (70S) Made of a Small (30S) and a Large (50S) Subunit Protein Factors Play Key Roles in Protein Synthesis Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation Summary Problems Selected Readings The Integration of Metabolism Metabolism Consist of Highly Interconnected Pathways Each Organ Has a Unique Metabolic Profile Food Intake and Starvation Induce Metabolic Changes Fuel Choice During Exercise Is Determined by Intensity and Duration of Activity Ethanol Alters Energy Metabolism in the Liver Summary Problems Selected Readings The Control of Gene Expression Prokaryotic DNA-Binding Proteins Bind Specifically to Regulatory Sites in Operons The Greater Complexity of Eukaryotic Genomes Requires Elaborate Mechanisms for Gene Regulation Transcriptional Activation and Repression Are Mediated by Protein-Protein Interactions Gene Expression Can Be Controlled at Posttranscriptional Levels Summary Problems Selected Readings Responding to Environmental Changes Systems A Wide Variety of Organic Compounds Are Detected by Olfaction Taste Is a Combination of Senses that Function by Different Mechanisms Photoreceptor Molecules in the Eye Detect Visible Light Hearing Depends on the Speedy Detection of Mechanical Stimuli Touch Includes the Sensing of Pressure, Temperature, and Other Factors Summary Problems Selected Readings The Immune System Antibodies Possess Distinct Antigen-Binding and Effector Units The Immunoglobulin Fold Consists of a Beta-Sandwich Framework with Hypervariable Loops Antibodies Bind Specific Molecules Through Their Hypervariable Loops Diversity Is Generated by Gene Rearrangements Major-Histocompatibility-Complex Proteins Present Peptide Antigens on Cell Surfaces for Recognition by T-Cell Receptors Immune Responses Against Self-Antigens Are Suppressed Summary Problems Selected Readings Molecular Motors Most Molecular-Motor Proteins Are Members of the P-Loop NTPase Superfamily Myosins Move Along Actin Filaments Kinesin and Dynein Move Along Microtubules A Rotary Motor Drives Bacterial Motion Summary Problems Selected Readings Appendix: Physical Constants and Conversion of Units Appendix: Acidity Constants Appendix: Standard Bond Lengths Glossary of Compounds Answers to Problems Common Abbreviations in Biochemistry
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