,Dedication
About the authors
Preface
Tools and Techniques
Clinical Applications
Molecular Evolution
Supplements Supporting Biochemistry, Fifth Edition
Acknowledgments
I. The Molecular Design of Life
1. Prelude: Biochemistry and the Genomic Revolution
1.1. DNA Illustrates the Relation between Form and Function
1.2. Biochemical Unity Underlies Biological Diversity
1.3. Chemical Bonds in Biochemistry
1.4. Biochemistry and Human Biology
Appendix: Depicting Molecular Structures
2. Biochemical Evolution
2.1. Key Organic Molecules Are Used by Living Systems
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
2.3. Energy Transformations Are Necessary to Sustain Living Systems
2.4. Cells Can Respond to Changes in Their Environments
Summary
Problems
Selected Readings
3. Protein Structure and Function
3.1. Proteins Are Built from a Repertoire of 20 Amino Acids
3.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide
Chains
3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the
Alpha Helix, the Beta Sheet, and Turns and Loops
3.4. Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar
Cores
3.5. Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures
3.6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
Summary
Appendix: Acid-Base Concepts
Problems
Selected Readings
4. Exploring Proteins
4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function
, 4.2. Amino Acid Sequences Can Be Determined by Automated Edman Degradation
4.3. Immunology Provides Important Techniques with Which to Investigate Proteins
4.4. Peptides Can Be Synthesized by Automated Solid-Phase Methods
4.5. Three-Dimensional Protein Structure Can Be Determined by NMR Spectroscopy and X-
Ray Crystallography
Summary
Problems
Selected Readings
5. DNA, RNA, and the Flow of Genetic Information
5.1. A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone
5.2. A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double-
Helical Structure
5.3. DNA Is Replicated by Polymerases that Take Instructions from Templates
5.4. Gene Expression Is the Transformation of DNA Information Into Functional Molecules
5.5. Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
Summary
Problems
Selected Readings
6. Exploring Genes
6.1. The Basic Tools of Gene Exploration
6.2. Recombinant DNA Technology Has Revolutionized All Aspects of Biology
6.3. Manipulating the Genes of Eukaryotes
6.4. Novel Proteins Can Be Engineered by Site-Specific Mutagenesis
Summary
Problems
Selected Reading
7. Exploring Evolution
7.1. Homologs Are Descended from a Common Ancestor
7.2. Statistical Analysis of Sequence Alignments Can Detect Homology
7.3. Examination of Three-Dimensional Structure Enhances Our Understanding of
Evolutionary Relationships
7.4. Evolutionary Trees Can Be Constructed on the Basis of Sequence Information
7.5. Modern Techniques Make the Experimental Exploration of Evolution Possible
Summary
Problems
Selected Readings
8. Enzymes: Basic Concepts and Kinetics
8.1. Enzymes Are Powerful and Highly Specific Catalysts
8.2. Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes
8.3. Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State
8.4. The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes
8.5. Enzymes Can Be Inhibited by Specific Molecules
8.6. Vitamins Are Often Precursors to Coenzymes
Summary
Appendix: Vmax and KM Can Be Determined by Double-Reciprocal Plots
Problems
Selected Readings
9. Catalytic Strategies
9.1. Proteases: Facilitating a Difficult Reaction
9.2. Making a Fast Reaction Faster: Carbonic Anhydrases
, 9.3. Restriction Enzymes: Performing Highly Specific DNA-Cleavage Reactions
9.4. Nucleoside Monophosphate Kinases: Catalyzing Phosphoryl Group Exchange between
Nucleotides Without Promoting Hydrolysis
Summary
Problems
Selected Readings
10. Regulatory Strategies: Enzymes and Hemoglobin
10.1. Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its
Pathway
10.2. Hemoglobin Transports Oxygen Efficiently by Binding Oxygen Cooperatively
10.3. Isozymes Provide a Means of Regulation Specific to Distinct Tissues and
Developmental Stages
10.4. Covalent Modification Is a Means of Regulating Enzyme Activity
10.5. Many Enzymes Are Activated by Specific Proteolytic Cleavage
Summary
Problems
Selected Readings
11. Carbohydrates
11.1. Monosaccharides Are Aldehydes or Ketones with Multiple Hydroxyl Groups
11.2. Complex Carbohydrates Are Formed by Linkage of Monosaccharides
11.3. Carbohydrates Can Be Attached to Proteins to Form Glycoproteins
11.4. Lectins Are Specific Carbohydrate-Binding Proteins
Summary
Problems
Selected Readings
12. Lipids and Cell Membranes
12.1. Many Common Features Underlie the Diversity of Biological Membranes
12.2. Fatty Acids Are Key Constituents of Lipids
12.3. There Are Three Common Types of Membrane Lipids
12.4. Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media
12.5. Proteins Carry Out Most Membrane Processes
12.6. Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane
12.7. Eukaryotic Cells Contain Compartments Bounded by Internal Membranes
Summary
Problems
Selected Readings
13. Membrane Channels and Pumps
13.1. The Transport of Molecules Across a Membrane May Be Active or Passive
13.2. A Family of Membrane Proteins Uses ATP Hydrolysis to Pump Ions Across
Membranes
13.3. Multidrug Resistance and Cystic Fibrosis Highlight a Family of Membrane Proteins
with ATP-Binding Cassette Domains
13.4. Secondary Transporters Use One Concentration Gradient to Power the Formation of
Another
13.5. Specific Channels Can Rapidly Transport Ions Across Membranes
13.6. Gap Junctions Allow Ions and Small Molecules to Flow between Communicating Cells
Summary
Problems
Selected Readings
II. Transducing and Storing Energy
About the authors
Preface
Tools and Techniques
Clinical Applications
Molecular Evolution
Supplements Supporting Biochemistry, Fifth Edition
Acknowledgments
I. The Molecular Design of Life
1. Prelude: Biochemistry and the Genomic Revolution
1.1. DNA Illustrates the Relation between Form and Function
1.2. Biochemical Unity Underlies Biological Diversity
1.3. Chemical Bonds in Biochemistry
1.4. Biochemistry and Human Biology
Appendix: Depicting Molecular Structures
2. Biochemical Evolution
2.1. Key Organic Molecules Are Used by Living Systems
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
2.3. Energy Transformations Are Necessary to Sustain Living Systems
2.4. Cells Can Respond to Changes in Their Environments
Summary
Problems
Selected Readings
3. Protein Structure and Function
3.1. Proteins Are Built from a Repertoire of 20 Amino Acids
3.2. Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide
Chains
3.3. Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the
Alpha Helix, the Beta Sheet, and Turns and Loops
3.4. Tertiary Structure: Water-Soluble Proteins Fold Into Compact Structures with Nonpolar
Cores
3.5. Quaternary Structure: Polypeptide Chains Can Assemble Into Multisubunit Structures
3.6. The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure
Summary
Appendix: Acid-Base Concepts
Problems
Selected Readings
4. Exploring Proteins
4.1. The Purification of Proteins Is an Essential First Step in Understanding Their Function
, 4.2. Amino Acid Sequences Can Be Determined by Automated Edman Degradation
4.3. Immunology Provides Important Techniques with Which to Investigate Proteins
4.4. Peptides Can Be Synthesized by Automated Solid-Phase Methods
4.5. Three-Dimensional Protein Structure Can Be Determined by NMR Spectroscopy and X-
Ray Crystallography
Summary
Problems
Selected Readings
5. DNA, RNA, and the Flow of Genetic Information
5.1. A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar-Phosphate Backbone
5.2. A Pair of Nucleic Acid Chains with Complementary Sequences Can Form a Double-
Helical Structure
5.3. DNA Is Replicated by Polymerases that Take Instructions from Templates
5.4. Gene Expression Is the Transformation of DNA Information Into Functional Molecules
5.5. Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point
5.6. Most Eukaryotic Genes Are Mosaics of Introns and Exons
Summary
Problems
Selected Readings
6. Exploring Genes
6.1. The Basic Tools of Gene Exploration
6.2. Recombinant DNA Technology Has Revolutionized All Aspects of Biology
6.3. Manipulating the Genes of Eukaryotes
6.4. Novel Proteins Can Be Engineered by Site-Specific Mutagenesis
Summary
Problems
Selected Reading
7. Exploring Evolution
7.1. Homologs Are Descended from a Common Ancestor
7.2. Statistical Analysis of Sequence Alignments Can Detect Homology
7.3. Examination of Three-Dimensional Structure Enhances Our Understanding of
Evolutionary Relationships
7.4. Evolutionary Trees Can Be Constructed on the Basis of Sequence Information
7.5. Modern Techniques Make the Experimental Exploration of Evolution Possible
Summary
Problems
Selected Readings
8. Enzymes: Basic Concepts and Kinetics
8.1. Enzymes Are Powerful and Highly Specific Catalysts
8.2. Free Energy Is a Useful Thermodynamic Function for Understanding Enzymes
8.3. Enzymes Accelerate Reactions by Facilitating the Formation of the Transition State
8.4. The Michaelis-Menten Model Accounts for the Kinetic Properties of Many Enzymes
8.5. Enzymes Can Be Inhibited by Specific Molecules
8.6. Vitamins Are Often Precursors to Coenzymes
Summary
Appendix: Vmax and KM Can Be Determined by Double-Reciprocal Plots
Problems
Selected Readings
9. Catalytic Strategies
9.1. Proteases: Facilitating a Difficult Reaction
9.2. Making a Fast Reaction Faster: Carbonic Anhydrases
, 9.3. Restriction Enzymes: Performing Highly Specific DNA-Cleavage Reactions
9.4. Nucleoside Monophosphate Kinases: Catalyzing Phosphoryl Group Exchange between
Nucleotides Without Promoting Hydrolysis
Summary
Problems
Selected Readings
10. Regulatory Strategies: Enzymes and Hemoglobin
10.1. Aspartate Transcarbamoylase Is Allosterically Inhibited by the End Product of Its
Pathway
10.2. Hemoglobin Transports Oxygen Efficiently by Binding Oxygen Cooperatively
10.3. Isozymes Provide a Means of Regulation Specific to Distinct Tissues and
Developmental Stages
10.4. Covalent Modification Is a Means of Regulating Enzyme Activity
10.5. Many Enzymes Are Activated by Specific Proteolytic Cleavage
Summary
Problems
Selected Readings
11. Carbohydrates
11.1. Monosaccharides Are Aldehydes or Ketones with Multiple Hydroxyl Groups
11.2. Complex Carbohydrates Are Formed by Linkage of Monosaccharides
11.3. Carbohydrates Can Be Attached to Proteins to Form Glycoproteins
11.4. Lectins Are Specific Carbohydrate-Binding Proteins
Summary
Problems
Selected Readings
12. Lipids and Cell Membranes
12.1. Many Common Features Underlie the Diversity of Biological Membranes
12.2. Fatty Acids Are Key Constituents of Lipids
12.3. There Are Three Common Types of Membrane Lipids
12.4. Phospholipids and Glycolipids Readily Form Bimolecular Sheets in Aqueous Media
12.5. Proteins Carry Out Most Membrane Processes
12.6. Lipids and Many Membrane Proteins Diffuse Rapidly in the Plane of the Membrane
12.7. Eukaryotic Cells Contain Compartments Bounded by Internal Membranes
Summary
Problems
Selected Readings
13. Membrane Channels and Pumps
13.1. The Transport of Molecules Across a Membrane May Be Active or Passive
13.2. A Family of Membrane Proteins Uses ATP Hydrolysis to Pump Ions Across
Membranes
13.3. Multidrug Resistance and Cystic Fibrosis Highlight a Family of Membrane Proteins
with ATP-Binding Cassette Domains
13.4. Secondary Transporters Use One Concentration Gradient to Power the Formation of
Another
13.5. Specific Channels Can Rapidly Transport Ions Across Membranes
13.6. Gap Junctions Allow Ions and Small Molecules to Flow between Communicating Cells
Summary
Problems
Selected Readings
II. Transducing and Storing Energy
