Fundamentals of Biochemistry: Life at the Molecular Level / Edition 3

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Fundamentals of Biochemistry, 2nd edition is a carefully organized, clearly written, and generously illustrated survey of the structures of biological molecules, the metabolic activities of cells, and the principles of molecular biology. The authors also include descriptions of major analytical techniques and wherever possible, correlate biochemical knowledge with human health and disease.
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Editorial Reviews

From The Critics
Donald Voet (U. of Pennsylvania) and Judith G. Voet (Swarthmore), two of this text's three authors (the third is Charlotte W. Pratt) already have under their belts a larger text, . The present text retains the philosophy of the earlier book, but it is less detailed and constitutes a re-vamped treatment of the subject both in organization and style. The material is organized to correspond with how the authors teach the course, but detailed division into sections and subsections allows instructors with other ideas to organize courses to their own tastes without apprehension that they've missed critical information. The included CD-ROM contains a variety of interactive three-dimensional molecular graphics displays and animations. Annotation c. Book News, Inc., Portland, OR (
Doody's Review Service
Reviewer: Sophie La Salle, PhD (Midwestern University Chicago College of Osteopathic Medicine)
Description: This book offers a broad, in-depth foundation of basic biochemical concepts by anchoring the biological content in its chemistry roots. This edition has been updated with the latest findings in biochemistry and their connection to human health, artwork to provide a clearer learning experience, and approaches to favor active learning. The previous edition was published in 2008.
Purpose: It serves many purposes, including delivering a solid foundation in modern biochemistry, developing problem-solving skills, and providing the historical background behind important biochemical discoveries. It is a complete guide to foundational biochemistry.
Audience: Although written for health sciences undergraduate and graduate students, the book may be used by premedical, medical, and other healthcare graduate students as a thorough reference. The authors are highly regarded educators, researchers, and teachers.
Features: Five major sections - an introduction, biomolecules, enzymes, metabolism and gene expression and replication — cover topics in modern biochemistry in the context of their chemical basis to help students understand the molecular foundation of biochemical reactions. In light of recent research findings, there is an emphasis on human health and diseases as well as novel pharmacological effectors. The book is well organized and beautifully illustrated, the artwork has been extensively revised, and process diagrams are clearly identified. It is enhanced with features that promote learning and self-assessment. For example, it includes "Key Concepts," reviews chemical principles when appropriate, provides sample calculations, contains "Checkpoint Questions" at the end of every section, and presents new end-of-chapter problems. It also contains a helpful glossary and a detailed index. The book is designed to provide a strong foundation in biochemistry by fostering student understanding rather than memorization.
Assessment: This is a magnificent textbook on biochemistry principles. (Readers looking for a quick review are advised to choose another book.) This edition includes up-to-date information and favors active learning by expanding its pedagogical tools and approaches. This book is of comparable caliber and coverage as Lehninger Principles of Biochemistry, 6th edition, Nelson and Cox, (W.H. Freeman, 2013). Students will certainly acquire a solid basis in biochemistry with this textbook.
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Product Details

  • ISBN-13: 9780470129302
  • Publisher: Wiley
  • Publication date: 1/9/2008
  • Edition description: Older Edition
  • Edition number: 3
  • Pages: 1240
  • Product dimensions: 8.60 (w) x 11.10 (h) x 1.80 (d)

Meet the Author

Donald Voet received a B.S. in Chemistry from the California Institute of Technology, a Ph.D. in Chemistry from Harvard University with William Lipscomb, and did postdoctoral research in the Biology Department at MIT with Alexander Rich. Upon completion of his postdoctoral research, Don took up a faculty position in the Chemistry Department at the University of Pennsylvania where, for the past 38 years, he has taught a variety of Biochemistry courses as well as general Chemistry. His major area of research is the X-ray crystallography of molecules of biological interest. He has been a visiting scholar at Oxford University, The University of California at San Diego, and the Weizmann Institute of Science in Israel. Together with Judith G. Voet, he is Co-Editor-in-Chief of the journal Biochemistry and Molecular Biology Education. He is a member of the Education Committee of the International Union of Biochemistry and Molecular Biology. His hobbies include backpacking, scuba diving, skiing, travel, photography, and writing Biochemistry textbooks.

Judith ("Judy") Voet received her B.S. in Chemistry from Antioch College and her Ph.D. in Biochemistry from Brandeis University with Robert H. Abeles. She has done postdoctoral research at the University of Pennsylvania, Haverford College, and the Fox Chase Cancer Center. Her main area of research involves enzyme reaction mechanisms and inhibition. She taught Biochemistry at the University of Delaware before moving to Swarthmore College. She taught there for 26 years, reaching the position of James H. Hammons Professor of Chemistry and Biochemistry before going on "permanent sabbatical leave." She has been a visiting scholar at Oxford University, University of California, San Diego, University of Pennsylvania, and the Weizmann Institute of Science, Israel. She is Co-Editor-in-Chief of the journal Biochemistry and Molecular Biology Education. She has been a member of the Education and Professional Development Committee of the American Society for Biochemistry and Molecular Biology as well as the Education Committee of the International Union of Biochemistry and Molecular Biology. Her hobbies include hiking, backpacking, scuba diving, and tap dancing.

Charlotte Pratt received her B.S. in Biology from the University of Notre Dame and her Ph.D. in Biochemistry from Duke University under the direction of Salvatore Pizzo. Although she originally intended to be a marine biologist, she discovered that Biochemistry offered the most compelling answers to many questions about biological structure-function relationships and the molecular basis for human health and disease. She conducted postdoctoral researching the Center for Thrombosis and Hemostasis at the University of North Carolina at Chapel Hill. She has taught at the University of Washington and currently teaches at Seattle Pacific University. In addition to working as an editor of several Biochemistry textbooks, she has co-authored Essential Biochemistry and previous editions of Fundamentals of Biochemistry.

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Table of Contents


Chapter 1. Introduction to the Chemistry of Life.

1. The Origin of Life
      A. Biological Molecules Arose from Inorganic Materials
      B. Complex Self-replicating Systems Evolved from Simple Molecules
2. Cellular Architecture
      A. Cells Evolved to Carry Out Metabolic Reactions
      B. There Are Two Types of Cells: Prokaryotes and Eukaryotes
      C. Molecular Data Reveal Three Evolutionary Domains of Organisms
      D. Organisms Continue to Evolve
3. Thermodynamics
      A. The First Law of Thermodynamics States that Energy Is Conserved
      B. The Second Law of Thermodynamics States that Entropy Tends to Increase
      C. The Free Energy Change Determines the Spontaneity of a Process
      D. Free Energy Changes Can Be Calculated from Equilibrium Concentrations
      E. Life Obeys the Laws of Thermodynamics

Box 1-1 Pathways of Discovery
Lynn Margulis and the Theory of Endosymbiosis

Box 1-2 Perspectives in Biochemistry
Biochemical Conventions

Chapter 2. Water.

1. Physical Properties of Water
   A. Water Is a Polar Molecule
   B. Hydrophilic Substances Dissolve in Water
   C. The Hydrophobic Effect Causes Nonpolar Substances to Aggregate in Water
   D. Water Moves by Osmosis and Solutes Move by Diffusion
2. Chemical Properties of Water
   A. Water Ionizes to Form H+ and OH
   B. Acids and Bases Alter the pH
   C. Buffers Resist Changes in pH

Box 2-1 Biochemistry in Health and Disease
The Blood Buffering System


Chapter 3. Nucleotides, Nucleic Acids, and Genetic Information.

1. Nucleotides
2. Introduction to Nucleic Acid Structure
   A. Nucleic Acids Are Polymers of Nucleotides
   B. The DNA Forms a Double Helix
   C. RNA Is a Single-Stranded Nucleic Acid
3. Overview of Nucleic Acid Function
   A. DNA Carries Genetic Information
   B. Genes Direct Protein Synthesis
4. Nucleic Acid Sequencing
   A. Restriction Endonucleases Cleave DNA at Specific Sequences
   B. Electrophoresis Separates Nucleic Acids According to Size
   C. DNA Is Sequenced by the Chain-Terminator Method
   D. Entire Genomes Have Been Sequenced
   E. Evolution Results from Sequence Mutations
5. Manipulating DNA
   A. Cloned DNA Is an Amplified Copy
   B. DNA Libraries Are Collections of Cloned DNA
   C. DNA Is Amplified by the Polymerase Chain Reaction
   D. Recombinant DNA Technology Has Numerous Practical Applications

Box 3-1 Pathways of Discovery
Francis Collins and the Gene for Cystic Fibrosis

Box 3-2 Perspectives in Biochemistry
DNA Fingerprinting

Box 3-3 Perspectives in Biochemistry
Ethical Aspects of Recombinant DNA Technology

Chapter 4. Amino Acids.

1. Amino Acid Structure
   A. Amino Acids Are Dipolar Ions
   B. Peptide Bonds Link Amino Acids
   C. Amino Acid Side Chains Are Nonpolar, Polar, or Charged
   D. The pK Values of Ionizable Groups Depend on Nearby Groups
   E. Amino Acid Names Are Abbreviated
2. Stereochemistry
3. Amino Acid Derivatives
   A. Protein Side Chains May be Modified
   B. Some Amino Acids Are Biologically Active

Box 4-1 Pathways of Discovery
William C. Rose and the Discovery of Threonine

Box 4-2 Perspectives in Biochemistry
The RS System

Box 4-3 Perspectives in Biochemistry
Green Fluorescent Protein

Chapter 5. Proteins: Primary Structure.

1. Polypeptide Diversity
2. Protein Purification and Analysis
   A. Purifying a Protein Requires a Strategy
   B. Salting Out Separates Proteins by Their Solubility
   C. Chromatography Involves Interaction with Mobile and Stationary Phases
   D. Electrophoresis Separates Molecules According to Charge and Size
3. Protein Sequencing
   A. The First Step Is to Separate Subunits
   B.  The Polypeptide Chains Are Cleaved
   C. Edman Degradation Removes a Peptide’s First Amino Acid Residue
   D. Mass Spectrometry Determines the Molecular Masses of Peptides
   E. Reconstructed Protein Sequences Are Stored in Databases
4. Protein Evolution
   A. Protein Sequences Reveal Evolutionary Relationships
   B. Proteins Evolve by the Duplication of Genes or Gene Segments

Box 5-1 Pathways of Discovery
Frederick Sanger and Protein Sequencing

Chapter 6. Proteins: Three-Dimensional Structure.

1. Secondary Structure
   A. The Planar Peptide Group Limits Polypeptide Conformations
   B. The Most Common Regular Secondary Structures Are the a Helix and the ß Sheet
   C. Fibrous Proteins Have Repeating Secondary Structures
   D. Most Proteins Include Nonrepetitive Structure
2. Tertiary Structure
   A. Most Protein Structures Have Been Determined by X-Ray Crystallography or Nuclear Magnetic Resonance
   B. Side Chain Location Varies with Polarity
   C. Tertiary Structures Contain Combinations of Secondary Structure
   D. Structure Is Conserved More than Sequence
   E. Structural Bioinformatics Provides Tools for Storing, Visualizing, and Comparing Protein Structural Information
3. Quaternary Structure and Symmetry
4. Protein Stability
   A. Proteins Are Stabilized by Several Forces
   B. Proteins Can Undergo Denaturation and Renaturation
5. Protein Folding
   A. Proteins Follow Folding Pathways
   B. Molecular Chaperones Assist Protein Folding
   C. Some Diseases Are Caused by Protein Misfolding

Box 6-1 Pathways of Discovery
Linus Pauling and Structural Biochemistry

Box 6-2 Biochemistry in Health and Disease
Collagen Diseases

Box 6-3 Perspectives in Biochemistry
Thermostable Proteins

Box 6-4 Perspectives in Biochemistry
Protein Structure Prediction and Protein Design

Chapter 7. Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies

1. Oxygen Binding to Myoglobin and Hemoglobin
   A. Myoglobin Is a Monomeric Oxygen-Binding Protein
   B.  Hemoglobin Is a Tetramer with Two Conformations
   C. Oxygen Binds Cooperatively to Hemoglobin
   D.  Hemoglobin’s Two Conformations Exhibit Different Affinities for Oxygen
   E. Mutations May Alter Hemoglobin’s Structure and Function
2. Muscle Contraction
   A.  Muscle Consists of Interdigitated Thick and Thin Filaments
   B.  Muscle Contraction Occurs When Myosin Heads Walk Up Thin Filaments
   C.  Actin Forms Microfilaments in Nonmuscle Cells
3. Antibodies
   A.  Antibodies Have Constant and Variable Regions
   B.  Antibodies Recognize a Huge Variety of Antigens

Box 7-1 Perspectives in Biochemistry
Other Oxygen-Transport Proteins

Box 7-2 Pathways of Discovery
Max Perutz and the Structure and Function of Hemoglobin

Box 7-3 Biochemistry in Health and Disease
High-Altitude Adaptation

Box 7-4 Pathways of Discovery
Hugh Huxley and the Sliding Filament Model

Box 7-5 Perspectives in Biochemistry
Monoclonal Antibodies

Chapter 8. Carbohydrates.

1. Monosaccharides
   A. Monosaccharides Are Aldoses or Ketoses
   B. Monosaccharides Vary in Configuration and Conformation
   C. Sugars Can Be Modified and Covalently Linked
2. Polysaccharides
   A. Lactose and Sucrose Are Disaccharides
   B. Cellulose and Chitin Are Structural Polysaccharides
   C. Starch and Glycogen Are Storage Polysaccharides
   D. Glycosaminoglycans Form Highly Hydrated Gels
3. Glycoproteins
   A. Proteoglycans Contain Glycosaminoglycans
   B. Bacterial Cell Walls Are Made of Peptidoglycan
   C. Many Eukaryotic Proteins Are Glycosylated
   D. Oligosaccharides May Determine Glycoprotein Structure, Function, and Recognition

Box 8-1 Biochemistry in Health and Disease
Lactose Intolerance

Box 8-2 Perspectives in Biochemistry
Artificial Sweeteners

Box 8-3 Biochemistry in Health and Disease
Peptidoglycan-Specific Antibiotics

Chapter 9. Lipids and Biological Membranes.

1. Lipid Classification
   A. The Properties of Fatty Acids Depend on Their Hydrocarbon Chains
   B. Triacylglycerols Contain Three Esterified Fatty Acids
   C. Glycerophospholipids Are Amphiphilic
   D. Sphingolipids Are Amino Alcohol Derivatives
   E. Steroids Contain Four Fused Rings
   F. Other Lipids Perform a Variety of Metabolic Roles
2. Lipid Bilayers
   A. Bilayer Formation Is Driven by the Hydrophobic Effect
   B. Lipid Bilayers Have Fluidlike Properties
3. Membrane Proteins
   A. Integral Membrane Proteins Interact with Hydrophobic Lipids
   B. Lipid-Linked Proteins Are Anchored to the Bilayer
   C. Peripheral Proteins Associate Loosely with Membranes
4. Membrane Structure and Assembly
   A. The Fluid Mosaic Model Accounts for Lateral Diffusion
   B. The Membrane Skeleton Helps Define Cell Shape
   C. Membrane Lipids Are Distributed Asymmetrically
   D. The Secretory Pathway Generates Secreted and Transmembrane Proteins
   E. Intracellular Vesicles Transport Proteins
   F. Proteins Mediate Vesicle Fusion

Box 9-1 Biochemistry in Health and Disease
Lung Surfactant

Box 9-2 Pathways of Discovery
Richard Henderson and the Structure of Bacteriorhodopsin

Box 9-3 Biochemistry in Health and Disease
Tetanus and Botulinum Toxins Specifically Cleave SNAREs

Chapter 10. Membrane Transport.

1. Thermodynamics of Transport
2. Passive-Mediated Transport
   A. Ionophores Carry Ions across Membranes
   B. Porins Contain—Barrels
   C. Ion Channels Are Highly Selective
   D. Aquaporins Mediate the Transmembrane Movement of Water
   E. Transport Proteins Alternate between Two Conformations
3. Active Transport
   A. The (Na+–K+)–ATPase Transports Ions in Opposite Directions
   B. The Ca2+–ATPase Pumps Ca2+ out of the Cytosol
   C. ABC Transporters Are Responsible for Drug Resistance
   D. Active Transport May Be Driven by Ion Gradients

Box 10-1 Perspectives in Biochemistry
Gap Junctions

Box 10-2 Perspectives in Biochemistry
Differentiating Mediated and Nonmediated Transport

Box 10-3 Biochemistry in Health and Disease
The Action of Cardiac Glycosides


Chapter 11. Enzymatic Catalysis.

1. General Properties of Enzymes
   A. Enzymes Are Classified by the Type of Reaction They Catalyze
   B. Enzymes Act on Specific Substrates
   C. Some Enzymes Require Cofactors
2. Activation Energy and the Reaction Coordinate
3. Catalytic Mechanisms
   A. Acid–Base Catalysis Occurs by Proton Transfer
   B. Covalent Catalysis Usually Requires a Nucleophile
   C. Metal Ion Cofactors Act as Catalysts
   D. Catalysis Can Occur through Proximity and Orientation Effects
   E. Enzymes Catalyze Reactions by Preferentially Binding the Transition State
4. Lysozyme
   A. Lysozyme’s Catalytic Site Was Identified through Model Building
   B. The Lysozyme Reaction Proceeds via a Covalent Intermediate
5. Serine Proteases
   A. The Active Site Residues Were Identified by Chemical Labeling
   B. X-Ray Structures Provided Information about Catalysis, Substrate Specificity, and Evolution
   C. Serine Proteases Use Several Catalytic Mechanisms
   D. Zymogens Are Inactive Enzyme Precursors

Box 11-1 Perspectives in Biochemistry
Effects of pH on Enzyme Activity

Box 11-2 Perspectives in Biochemistry
Observing Enzyme Action by X-Ray Crystallography

Box 11-3 Biochemistry in Health and Disease
Nerve Poisons

Box 11-4 Biochemistry in Health and Disease
The Blood Coagulation Cascade

Chapter 12. Enzyme Kinetics, Inhibition, and Control.

1. Reaction Kinetics
   A. Chemical Kinetics Is Described by Rate Equations
   B. Enzyme Kinetics Often Follows the Michaelis–Menten Equation
   C. Kinetic Data Can Provide Values of Vmax and KM
   D. Bisubstrate Reactions Follow One of Several Rate Equations
2. Enzyme Inhibition
   A. Competitive Inhibition Involves Inhibitor Binding at an Enzyme’s Substrate Binding Site
   B. Uncompetitive Inhibition Involves Inhibitor Binding to the Enzyme–Substrate Complex
   C. Mixed Inhibition Involves Inhibitor Binding to Both the Free Enzyme and the Enzyme–Substrate Complex
3. Control of Enzyme Activity
   A.  Allosteric Control Involves Binding at a Site Other Than the Active Site
   B.  Control by Covalent Modification Often Involves Protein Phosphorylation
4. Drug Design
   A. Drug Discovery Employs a Variety of Techniques
   B. A Drug’s Bioavailability Depends on How It Is Absorbed and Transported in the Body
   C. Clinical Trials Test for Efficacy and Safety
   D. Cytochromes P450 Are Often Implicated in Adverse Drug Reactions

Box 12-1 Perspectives in Biochemistry
Isotopic Labeling

Box 12-2 Pathways of Discovery
J.B.S. Haldane and Enzyme Action

Box 12-3 Perspectives in Biochemistry
Kinetics and Transition State Theory

Box 12-4 Biochemistry in Health and Disease
HIV Enzyme Inhibitors

Chapter 13. Biochemical Signaling

1. Hormones
   A.  Pancreatic Islet Hormones Control Fuel Metabolism
   B.  Epinephrine and Norepinephrine Prepare the Body for Action
   C.  Steroid Hormones Regulate a Wide Variety of Metabolic and Sexual Processes
   D.  Growth Hormone Binds to Receptors in Muscle, Bone, and Cartilage
2. Receptor Tyrosine Kinases
   A.  Receptor Tyrosine Kinases Transmit Signals across the Cell Membrane
   B.  Kinase Cascades Relay Signals to the Nucleus
   C.  Some Receptors Are Associated with Nonreceptor Tyrosine Kinases
   D.  Protein Phosphatases Are Signaling Proteins in Their Own Right
3. Heterotrimeric G Proteins
   A.  G Protein–Coupled Receptors Contain Seven Transmembrane Helices
   B.  Heterotrimeric G Proteins Dissociate on Activation
   C.  Adenylate Cyclase Synthesizes cAMP to Activate Protein Kinase A
   D.  Phosphodiesterases Limit Second Messenger Activity
4. The Phosphoinositide Pathway
   A.  Ligand Binding Results in the Cytoplasmic Release of the Second Messengers IP3 and Ca2+
   B.  Calmodulin Is a Ca2+-Activated Switch
   C.  DAG Is a Lipid-Soluble Second Messenger that Activates Protein Kinase C
   D.  Epilog: Complex Systems Have Emergent Properties

Box 13-1 Pathways of Discovery
Rosalyn Yalow and the Radioimmunoassay (RIA)

Box 13-2 Perspectives in Biochemistry
Receptor-Ligand Binding Can Be Quantitated

Box 13-3 Biochemistry in Health and Disease
Oncogenes and Cancer

Box 13-4 Biochemistry in Health and Disease
Drugs and Toxins That Affect Cell Signaling

Box 13-5 Biochemistry in Health and Disease


Chapter 14. Introduction to Metabolism.

1. Overview of Metabolism
   A.  Nutrition Involves Food Intake and Use
   B.  Vitamins and Minerals Assist Metabolic Reactions
   C. Metabolic Pathways Consist of Series of Enzymatic Reactions
   D. Thermodynamics Dictates the Direction and Regulatory Capacity of Metabolic Pathways
   E. Metabolic Flux Must Be Controlled
2. “High-Energy” Compounds
   A. ATP Has a High Phosphoryl Group-Transfer Potential
   B. Coupled Reactions Drive Endergonic Processes
   C. Some Other Phosphorylated Compounds Have High Phosphoryl Group-Transfer Potentials
   D. Thioesters Are Energy-Rich Compounds
3. Oxidation–Reduction Reactions
   A. NAD+ and FAD Are Electron Carriers
   B. The Nernst Equation Describes Oxidation–Reduction Reactions
   C. Spontaneity Can Be Determined by Measuring Reduction Potential Differences
4. Experimental Approaches to the Study of Metabolism
   A. Labeled Metabolites Can Be Traced
   B. Studying Metabolic Pathways Often Involves Perturbing the System
   C.  Systems Biology Has Entered the Study of Metabolism

Box 14-1 Perspectives in Biochemistry
Oxidation States of Carbon

Box 14-2 Perspectives in Biochemistry
Mapping Metabolic Pathways

Box 14-3 Pathways of Discovery
Fritz Lipmann and “High-energy” Compounds

Box 14-4 Perspectives in Biochemistry
ATP and DG

Chapter 15. Glucose Catabolism.

1. Overview of Glycolysis
2. The Reactions of Glycolysis
   A. Hexokinase Uses the First ATP
   B. Phosphoglucose Isomerase Converts Glucose-6-Phosphate to Fructose-6-Phosphate
   C. Phosphofructokinase Uses the Second ATP
   D. Aldolase Converts a 6-Carbon Compound to Two 3-Carbon Compounds
   E. Triose Phosphate Isomerase Interconverts Dihydroxyacetone Phosphate and Glyceraldehyde-3-Phosphate
   F. Glyceraldehyde-3-Phosphate Dehydrogenase Forms the First “High-Energy” Intermediate
   G. Phosphoglycerate Kinase Generates the First ATP
   H. Phosphoglycerate Mutase Interconverts 3-Phosphoglycerate and 2-Phosphoglycerate
   I. Enolase Forms the Second “High-Energy” Intermediate
   J. Pyruvate Kinase Generates the Second ATP
3. Fermentation: The Anaerobic Fate of Pyruvate
   A. Homolactic Fermentation Converts Pyruvate to Lactate
   B. Alcoholic Fermentation Converts Pyruvate to Ethanol and CO2
   C. Fermentation is Energetically Favorable
4. Regulation of Glycolysis
   A.     Phosphofructokinase is The Major Flux-Controlling Enzyme of Glycolysis in Muscle
   B. Substrate Cycling Fine-Tunes Flux Control
5. Metabolism of Hexoses Other than Glucose
   A. Fructose Is Converted to Fructose-6-Phosphate or Glyceraldehyde-3-Phosphate
   B. Galactose Is Converted to Glucose-6-Phosphate
   C. Mannose Is Converted to Fructose-6-Phosphate
6. The Pentose Phosphate Pathway
   A. Oxidative Reactions Produce NADPH in Stage 1
   B. Isomerization and Epimerization of Ribulose-5-Phosphate Occur in Stage 2
   C. Stage 3 Involves Carbon–Carbon Bond Cleavage and Formation
   D. The Pentose Phosphate Pathway Must Be Regulated

Box 15-1 Pathways of Discovery
Otto Warburg and Studies of Metabolism

Box 15-2 Perspectives in Biochemistry
Synthesis of 2,3-Bisphosphoglycerate in Erythrocytes and Its Effect on the Oxygen Carrying Capacity of the Blood

Box 15-3 Perspectives in Biochemistry
Glycolytic ATP Production in Muscle

Box 15-4 Biochemistry in Health and Disease
Glucose-6-Phosphate Dehydrogenase Deficiency

Chapter 16. Glycogen Metabolism and Gluconeogenesis.

1. Glycogen Breakdown
   A. Glycogen Phosphorylase Degrades Glycogen to Glucose-1-Phosphate
   B. Glycogen Debranching Enzyme Acts as a Glucosyltransferase
   C. Phosphoglucomutase Interconverts Glucose-1-Phosphate and Glucose-6-Phosphate
2. Glycogen Synthesis
   A. UDP–Glucose Pyrophosphorylase Activates Glucosyl Units
   B. Glycogen Synthase Extends Glycogen Chains
   C. Glycogen Branching Enzyme Transfers Seven-Residue Glycogen Segments
3. Control of Glycogen Metabolism
   A. Glycogen Phosphorylase and Glycogen Synthase Are Under Allosteric Control
   B. Glycogen Phosphorylase and Glycogen Synthase Undergo Control by Covalent Modification
   C. Glycogen Metabolism Is Subject to Hormonal Control
4. Gluconeogenesis
   A. Pyruvate Is Converted to Phosphoenolpyruvate in Two Steps
   B. Hydrolysis Reactions Bypass Irreversible Glycolytic Reactions
   C. Gluconeogenesis and Glycolysis Are Independently Regulated
5. Other Carbohydrate Biosynthetic Pathways

Box 16-1 Pathways of Discovery
Carl and Gerty Cori and Glucose Metabolism

Box 16-2 Biochemistry in Health and Disease
Glycogen Storage Diseases

Box 16-3 Perspectives in Biochemistry
Optimizing Glycogen Structure

Box 16-4 Perspectives in Biochemistry
Lactose Synthesis

Chapter 17. Citric Acid Cycle.

1. Overview of the Citric Acid Cycle
2. Synthesis of Acetyl-Coenzyme A
   A. Pyruvate Dehydrogenase Is a Multienzyme Complex
   B. The Pyruvate Dehydrogenase Complex Catalyzes Five Reactions
3. Enzymes of the Citric Acid Cycle
   A. Citrate Synthase Joins an Acetyl Group to Oxaloacetate
   B. Aconitase Interconverts Citrate and Isocitrate
   C. NAD+-Dependent Isocitrate Dehydrogenase Releases CO2
   D. a-Ketoglutarate Dehydrogenase Resembles Pyruvate Dehydrogenase
   E. Succinyl-CoA Synthetase Produces GTP
   F. Succinate Dehydrogenase Generates FADH2
   G. Fumarase Produces Malate
   H. Malate Dehydrogenase Regenerates Oxaloacetate
4. Regulation of the Citric Acid Cycle
   A. Pyruvate Dehydrogenase Is Regulated by Product Inhibition and Covalent Modification
   B. Three Enzymes Control the Rate of the Citric Acid Cycle
5. Reactions Related to the Citric Acid Cycle
   A. Other Pathways Use Citric Acid Cycle Intermediates
   B. Some Reactions Replenish Citric Acid Cycle Intermediates
   C. The Glyoxylate Cycle Shares Some Steps with the Citric Acid Cycle

Box 17-1 Pathways of Discovery
Hans Krebs and the Citric Acid Cycle

Box 17-2 Biochemistry in Health and Disease
Arsenic Poisoning

Box 17-3 Perspectives in Biochemistry
Evolution of the Citric Acid Cycle

Chapter 18. Electron Transport and Oxidative Phosphorylation.

1. The Mitochondrion
   A. Mitochondria Contain a Highly Folded Inner Membrane
   B. Ions and Metabolites Enter Mitochondria via Transporters
2. Electron Transport
   A. Electron Transport Is an Exergonic Process
   B. Electron Carriers Operate in Sequence
   C. Complex I Accepts Electrons from NADH
   D. Complex II Contributes Electrons to Coenzyme Q
   E. Complex III Translocates Protons via the Q Cycle
   F. Complex IV Reduces Oxygen to Water
3. Oxidative Phosphorylation
   A. The Chemiosmotic Theory Links Electron Transport to ATP Synthesis
   B. ATP Synthase Is Driven by the Flow of Protons
   C. The P/O Ratio Relates the Amount of ATP Synthesized to the Amount of Oxygen Reduced
   D. Oxidative Phosphorylation Can be Uncoupled from Electron Transport
4. Control of Oxidative Metabolism
   A. The Rate of Oxidative Phosphorylation Depends on the ATP and NADH Concentrations
   B. Aerobic Metabolism Has Some Disadvantages

Box 18-1 Perspectives in Biochemistry
Cytochromes Are Electron-Transport Heme Proteins

Box 18-2 Pathways of Discovery
Peter Mitchell and the Chemiosmotic Theory

Box 18-3 Perspectives in Biochemistry
Bacterial Electron Transport and Oxidative Phosphorylation

Box 18-4 Perspectives in Biochemistry
Uncoupling in Brown Adipose Tissue Generates Heat

Box 18-5 Biochemistry in Health and Disease
Oxygen Deprivation in Heart Attack and Stroke

Chapter 19. Photosynthesis.

1. Chloroplasts
   A. The Light Reactions Take Place in the Thylakoid Membrane
   B. Pigment Molecules Absorb Light
2. The Light Reactions
   A. Light Energy Is Transformed to Chemical Energy
   B. Electron Transport in Photosynthetic Bacteria Follows a Circular Path
   C. Two-Center Electron Transport Is a Linear Pathway That Produces O2 and NADPH
   D. The Proton Gradient Drives ATP Synthesis by Photophosphorylation
3. The Dark Reactions
   A. The Calvin Cycle Fixes CO2
   B. Calvin Cycle Products Are Converted to Starch, Sucrose, and Cellulose
   C. The Calvin Cycle Is Controlled Indirectly by Light
   D. Photorespiration Competes with Photosynthesis

Box 19-1 Perspectives in Biochemistry
Segregation of PSI and PSII

Chapter 20. Lipid Metabolism.

1. Lipid Digestion, Absorption, and Transport
   A. Triacylglycerols Are Digested before They Are Absorbed
   B. Lipids Are Transported as Lipoproteins
2. Fatty Acid Oxidation
   A. Fatty Acids Are Activated by Their Attachment to Coenzyme A
   B. Carnitine Carries Acyl Groups across the Mitochondrial Membrane
   C. ? Oxidation Degrades Fatty Acids to Acetyl-CoA
   D. Oxidation of Unsaturated Fatty Acids Requires Additional Enzymes
   E. Oxidation of Odd-Chain Fatty Acids Yields Propionyl-CoA
F. Peroxisomal—Oxidation Differs from Mitochondrial—Oxidation
3. Ketone Bodies
4. Fatty Acid Biosynthesis
   A. Mitochondrial Acetyl-CoA Must Be Transported into the Cytosol
   B. Acetyl-CoA Carboxylase Produces Malonyl-CoA
   C. Fatty Acid Synthase Catalyzes Seven Reactions
   D. Fatty Acids May Be Elongated and Desaturated
   E. Fatty Acids Are Esterified to Form Triacylglycerols
5. Regulation of Fatty Acid Metabolism
6. Synthesis of Other Lipids
   A. Glycerophospholipids Are Built from Intermediates of Triacylglycerol Synthesis
   B. Sphingolipids Are Built from Palmitoyl-CoA and Serine
   C. C20 Fatty Acids Are the Precursors of Prostaglandins
7. Cholesterol Metabolism
   A. Cholesterol Is Synthesized from Acetyl-CoA
   B. HMG-CoA Reductase Controls the Rate of Cholesterol Synthesis
   C. Abnormal Cholesterol Transport Leads to Atherosclerosis

Box 20-1 Biochemistry in Health and Disease
Vitamin B12 Deficiency

Box 20-2 Pathways of Discovery
Dorothy Crowfoot Hodgkin and the Structure of Vitamin B12

Box 20-3 Perspectives in Biochemistry
Triclosan: An Inhibitor of Fatty Acid Synthesis

Box 20-4 Biochemistry in Health and Disease
Sphingolipid Degradation and Lipid Storage Diseases

Chapter 21. Amino Acid Metabolism.

Chapter 22. Mammalian Fuel Metabolism: Integration and Regulation.


Chapter 23. Nucleotide Metabolism.

Chapter 24. Nucleic Acid Structure.

Chapter 25. DNA Replication, Repair, and Recombination.

Chapter 26. Transcription and RNA Processing.

Chapter 27. Protein Synthesis.

Chapter 28. Regulation of Gene Expression.

1. Genome Organization
   A. Gene Number Varies among Organisms
   B. Some Genes Occur in Clusters
   C. Eukaryotic Genomes Contain Repetitive DNA Sequences
2. Regulation of Prokaryotic Gene Expression
   A. The lac Operon Is Controlled by a Repressor
   B. Catabolite-Repressed Operons Can Be Activated
   C. Attenuation Regulates Transcription Termination
   D. Riboswitches Are Metabolite-Sensing RNAs
3. Regulation of Eukaryotic Gene Expression
   A. Chromatin Structure Influences Gene Expression
   B. Eukaryotes Contain Multiple Transcriptional Activators
   C. Posttranscriptional Control Mechanisms Include RNA Degradation
   D. Antibody Diversity Results from Somatic Recombination and Hypermutation
4.  The Cell Cycle, Cancer, and Apoptosis
   A. Progress Through the Cell Cycle Is Tightly Regulated
   B.  Tumor Suppressors Prevent Cancer
   C.  Apoptosis Is an Orderly Process
   D.  Development Has a Molecular Basis

Box 28-1 Biochemistry in Health and Disease
Trinucleotide Repeat Diseases

Box 28-2 Perspectives in Biochemistry
X Chromosome Inactivation

Box 28-3 Perspectives in Biochemistry
Nonsense-Mediated Decay


Solutions to Problems.



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