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Berg J.M., Tymoczko J.L., Stryer L. Biochemistry

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Berg J.M., Tymoczko J.L., Stryer L. Biochemistry
5th edition. — W.H. Freeman and Company, 2002. — 1515 p. — ISBN-10 0-7167-3051-0
For 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.
About the authors

Tools and Techniques
Clinical Applications
Molecular Evolution
Supplements Supporting Biochemistry, Fifth Edition
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
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
Appendix: Acid-Base Concepts
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
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
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
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
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
Appendix: Vmax and KM Can Be Determined by Double-Reciprocal Plots
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
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
Selected Readings
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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