Biochemistry

Cover
Dedication
About the Authors
Contents in Brief
Detailed Contents
Careers in Chemistry
PSAFE (Protein Structure and Function Exploration)
Laboratory Techniques in Biochemistry
Preface
Part I: Molecular Components of Cells
Chapter 1: The Facts of Life: Chemistry Is the Logic of Biological Phenomena
1.1 What Are the Distinctive Properties of Living Systems?
1.2 What Kinds of Molecules Are Biomolecules?
1.3 What Is the Structural Organization of Complex Biomolecules?
1.4 How Do the Properties of Biomolecules Reflect Their Fitness to the Living Condition?
1.5 What Are the Organization and Structure of Cells?
1.6 What Are Viruses?
Foundational Biochemistry
Problems
Further Reading
Chapter 2: Water: The Medium of Life
2.1 What Are the Properties of Water?
2.2 What Is pH?
2.3 What Are Buffers, and What Do They Do?
2.4 What Properties of Water Give It a Unique Role in the Environment?
Foundational Biochemistry
Problems
Further Reading
Chapter 3: Thermodynamics of Biological Systems
3.1 What Are the Basic Concepts of Thermodynamics?
3.2 What Is the Effect of Concentration on Net Free Energy Changes?
3.3 How May Standard State, Equilibrium, and Cellular Conditions Be Compared?
3.4 What Are the Characteristics of High-Energy Biomolecules?
3.5 How Do Group Transfer Potentials Quantify the Reactivity of Functional Groups?
3.6 What Are Reduction Potentials, and How Are They Used to Account for Free Energy Changes in Redox Reactions?
3.7 Why Are Coupled Processes Important to Living Things?
3.8 What Is the Daily Human Requirement for ATP?
Foundational Biochemistry
Problems
Further Reading
Chapter 4: Amino Acids and the Peptide Bond
4.1 What Are the Structures and Properties of Amino Acids?
4.2 What Are the Acid-Base Properties of Amino Acids?
4.3 What Reactions Do Amino Acids Undergo?
4.4 What Are the Optical and Stereochemical Properties of Amino Acids?
4.5 What Are the Spectroscopic Properties of Amino Acids?
4.6 How Are Amino Acid Mixtures Separated and Analyzed?
4.7 What Is the Fundamental Structural Pattern in Proteins?
Foundational Biochemistry
Problems
Further Reading
Chapter 5: Proteins: Their Primary Structure and Biological Functions
5.1 What Architectural Arrangements Characterize Protein Structure?
5.2 How Are Proteins Isolated and Purified from Cells?
5.3 How Is the Primary Structure of a Protein Determined?
5.4 What Is the Nature of Amino Acid Sequences?
5.5 How Are Polypeptides Synthesized in the Laboratory?
5.6 Do Proteins Have Chemical Groups Other Than Amino Acids?
5.7 What Are the Many Biological Functions of Proteins?
5.8 What Is the Proteome and What Does It Tell Us?
Foundational Biochemistry
Problems
Further Reading
Chapter 6: Proteins: Secondary, Tertiary, and Quaternary Structure
6.1 What Noncovalent Interactions Stabilize the Higher Levels of Protein Structure?
6.2 What Role Does the Amino Acid Sequence Play in Protein Structure?
6.3 What Are the Elements of Secondary Structure in Proteins, and How Are They Formed?
6.4 How Do Polypeptides Fold into Three-Dimensional Protein Structures?
6.5 How Do Protein Subunits Interact at the Quaternary Level of Protein Structure?
Foundational Biochemistry
Problems
Further Reading
Chapter 7: Carbohydrates and the Glycoconjugates of Cell Surfaces
7.1 How Are Carbohydrates Named?
7.2 What Are the Structure and Chemistry of Monosaccharides?
7.3 What Are the Structure and Chemistry of Oligosaccharides?
7.4 What Are the Structure and Chemistry of Polysaccharides?
7.5 What Are Glycoproteins, and How Do They Function in Cells?
7.6 How Do Proteoglycans Modulate Processes in Cells and Organisms?
7.7 How Do Carbohydrates Provide a Structural Code?
Foundational Biochemistry
Problems
Further Reading
Chapter 8: Lipids
8.1 What Are the Structures and Chemistry of Fatty Acids?
8.2 What Are the Structures and Chemistry of Triacylglycerols?
8.3 What Are the Structures and Chemistry of Glycerophospholipids?
8.4 What Are Sphingolipids, and How Are They Important for Higher Animals?
8.5 What Are Waxes, and How Are They Used?
8.6 What Are Terpenes, and What Is Their Relevance to Biological Systems?
8.7 What Are Steroids, and What Are Their Cellular Functions?
8.8 How Do Lipid Metabolites Act as Biological Signals?
8.9 What Can Lipidomics Tell Us about Cell, Tissue, and Organ Physiology?
Foundational Biochemistry
Problems
Further Reading
Chapter 9: Membranes and Membrane Transport
9.1 What Are the Chemical and Physical Properties of Membranes?
9.2 What Are the Structure and Chemistry of Membrane Proteins?
9.3 How Are Biological Membranes Organized?
9.4 What Are the Dynamic Processes That Modulate Membrane Function?
9.5 How Does Transport Occur across Biological Membranes?
9.6 What Is Passive Diffusion?
9.7 How Does Facilitated Diffusion Occur?
9.8 How Does Energy Input Drive Active Transport Processes?
9.9 How Are Certain Transport Processes Driven by Light Energy?
9.10 How Is Secondary Active Transport Driven by Ion Gradients?
Foundational Biochemistry
Problems
Further Reading
Chapter 10: Nucleotides and Nucleic Acids
10.1 What Are the Structure and Chemistry of Nitrogenous Bases?
10.2 What Are Nucleosides?
10.3 What Are the Structure and Chemistry of Nucleotides?
10.4 What Are Nucleic Acids?
10.5 What Are the Different Classes of Nucleic Acids?
10.6 Are Nucleic Acids Susceptible to Hydrolysis?
Foundational Biochemistry
Problems
Further Reading
Chapter 11: Structure of Nucleic Acids
11.1 How Do Scientists Determine the Primary Structure of Nucleic Acids?
11.2 What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt?
11.3 Can the Secondary Structure of DNA Be Denatured and Renatured?
11.4 How Does DNA Adopt Structures of Higher Complexity?
11.5 What Is the Structure of Eukaryotic Chromosomes?
11.6 How Can Nucleic Acids Be Synthesized Chemically?
11.7 What Are the Secondary and Tertiary Structures of RNA?
Foundational Biochemistry
Problems
Further Reading
Chapter 12: Recombinant DNA, Cloning, Gene Editing, and Synthetic Biology - An Introduction
12.1 What Is DNA Cloning?
12.2 What Is a DNA Library?
12.3 Can the Genes in Libraries Be Transcribed and Translated?
12.4 How Is RNA Interference Used to Reveal the Function of Genes?
12.5 Gene Therapy: Is It Possible for Scientists to Alter or Rewrite the Genome of an Organism?
12.6 How Does High-Throughput Technology Allow Global Study of Millions of Genes or Molecules at Once?
12.7 What Is the Field of Synthetic Biology?
Foundational Biochemistry
Problems
Further Reading
Part II: Protein Dynamics
Chapter 13: Enzymes - Kinetics and Specificity
13.1 What Characteristic Features Define Enzymes?
13.2 How Can the Rate of an Enzyme-Catalyzed Reaction Be Defined in a Mathematical Way?
13.3 What Equations Define the Kinetics of Enzyme‑Catalyzed Reactions?
13.4 What Can Be Learned from the Inhibition of Enzyme Activity?
13.5 What Is the Kinetic Behavior of Enzymes Catalyzing Bimolecular Reactions?
13.6 How Can Enzymes Be So Specific?
13.7 Are All Enzymes Proteins?
13.8 Is It Possible to Design an Enzyme to Catalyze Any Desired Reaction?
Foundational Biochemistry
Problems
Further Reading
Chapter 14: Mechanisms of Enzyme Action
14.1 What Are the Magnitudes of Enzyme-Induced Rate Accelerations?
14.2 What Role Does Transition-State Stabilization Play in Enzyme Catalysis?
14.3 How Does Destabilization of the Enzyme-Substrate Complex Affect Enzyme Catalysis?
14.4 What Are Transition State Analogs and How Tightly Do They Bind to the Active Sites of Enzymes?
14.5 What Are the Mechanisms of Enzyme Catalysis?
14.6 What Can Be Learned from the Mechanisms of Some Typical Enzymes?
Foundational Biochemistry
Problems
Further Reading
Chapter 15: Enzyme Regulation
15.1 What Factors Influence Enzymatic Activity?
15.2 What Are the General Features of Allosteric Regulation?
15.3 Can Allosteric Regulation Be Explained by Conformational Changes in Proteins?
15.4 What Kinds of Covalent Modification Regulate the Activity of Enzymes?
15.5 Is the Activity of Some Enzymes Controlled by Both Allosteric Regulation and Covalent Modification?
15.6 What Is the Relationship between Quaternary Structure and Allosteric Regulation?
Foundational Biochemistry
Problems
Further Reading
Chapter 16: Molecular Motors
16.1 What Are the General Features of Molecular Motors?
16.2 What Is the Molecular Mechanism of Muscle Contraction?
16.3 What Are the Molecular Motors That Orchestrate the Mechanochemistry of Microtubules?
16.4 How Do Molecular Motors Unwind DNA?
16.5 How Do Bacterial Flagella Use a Proton Gradient to Drive Rotation?
Foundational Biochemistry
Problems
Further Reading
Part III: Metabolism and Its Regulation
Chapter 17: Metabolism: An Overview
17.1 Is Metabolism Similar in Different Organisms?
17.2 What Can Be Learned from Metabolic Maps?
17.3 How Do Anabolic and Catabolic Processes Form the Core of Metabolic Pathways?
17.4 What Experiments Can Be Used to Elucidate Metabolic Pathways?
17.5 What Can the Metabolome Tell Us about a Biological System?
17.6 What Food Substances Form the Basis of Human Nutrition?
Foundational Biochemistry
Problems
Further Reading
Chapter 18: Glycolysis
18.1 What Are the Essential Features of Glycolysis?
18.2 Why Are Coupled Reactions Important in Glycolysis?
18.3 What Are the Chemical Principles and Features of the First Phase of Glycolysis?
18.4 What Are the Chemical Principles and Features of the Second Phase of Glycolysis?
18.5 What Are the Metabolic Fates of NADH and Pyruvate Produced in Glycolysis?
18.6 How Do Cells Regulate Glycolysis?
18.7 Are Substrates Other Than Glucose Used in Glycolysis?
18.8 How Do Cells Respond to Hypoxic Stress?
Foundational Biochemistry
Problems
Further Reading
Chapter 19: The Tricarboxylic Acid Cycle
19.1 What Is the Chemical Logic of the TCA Cycle?
19.2 How Is Pyruvate Oxidatively Decarboxylated to Acetyl-CoA?
19.3 How Are Two CO2 Molecules Produced from Acetyl-CoA?
19.4 How Is Oxaloacetate Regenerated to Complete the TCA Cycle?
19.5 What Are the Energetic Consequences of the TCA Cycle?
19.6 Can the TCA Cycle Provide Intermediates for Biosynthesis?
19.7 What Are the Anaplerotic, or Filling Up, Reactions?
19.8 How Is the TCA Cycle Regulated?
19.9 Can Any Organisms Use Acetate as Their Sole Carbon Source?
Foundational Biochemistry
Problems
Further Reading
Chapter 20: Electron Transport and Oxidative Phosphorylation
20.1 Where in the Cell Do Electron Transport and Oxidative Phosphorylation Occur?
20.2 How Is the Electron-Transport Chain Organized?
20.3 What Are the Thermodynamic Implications of Chemiosmotic Coupling?
20.4 How Does a Proton Gradient Drive the Synthesis of ATP?
20.5 What Is the P/O Ratio for Mitochondrial Oxidative Phosphorylation?
20.6 How Are the Electrons of Cytosolic NADH Fed into Electron Transport?
20.7 How Do Mitochondria Mediate Apoptosis?
Foundational Biochemistry
Problems
Further Reading
Chapter 21: Photosynthesis
21.1 What Are the General Properties of Photosynthesis?
21.2 How Is Solar Energy Captured by Chlorophyll?
21.3 What Kinds of Photosystems Are Used to Capture Light Energy?
21.4 What Is the Molecular Architecture of Photosynthetic Reaction Centers?
21.5 What Is the Quantum Yield of Photosynthesis?
21.6 How Does Light Drive the Synthesis of ATP?
21.7 How Is Carbon Dioxide Used to Make Organic Molecules?
21.8 How Does Photorespiration Limit CO2 Fixation?
Foundational Biochemistry
Problems
Further Reading
Chapter 22: Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway
22.1 What Is Gluconeogenesis, and How Does It Operate?
22.2 How Is Gluconeogenesis Regulated?
22.3 How Are Glycogen and Starch Catabolized in Animals?
22.4 How Is Glycogen Synthesized?
22.5 How Is Glycogen Metabolism Controlled?
22.6 How Does Glucose Provide Electrons for Biosynthesis?
Foundational Biochemistry
Problems
Further Reading
Chapter 23: Fatty Acid Catabolism
23.1 How Are Fats Mobilized from Dietary Intake and Adipose Tissue?
23.2 How Are Fatty Acids Broken Down?
23.3 How Are Odd-Carbon Fatty Acids Oxidized?
23.4 How Are Unsaturated Fatty Acids Oxidized?
23.5 Are There Other Ways to Oxidize Fatty Acids?
23.6 What Are Ketone Bodies, and What Role Do They Play in Metabolism?
Foundational Biochemistry
Problems
Further Reading
Chapter 24: Lipid Biosynthesis
24.1 How Are Fatty Acids Synthesized?
24.2 How Are Complex Lipids Synthesized?
24.3 How Are Eicosanoids Synthesized, and What Are Their Functions?
24.4 How Is Cholesterol Synthesized?
24.5 How Are Lipids Transported Throughout the Body?
24.6 How Are Bile Acids Biosynthesized?
24.7 How Are Steroid Hormones Synthesized and Utilized?
Foundational Biochemistry
Problems
Further Reading
Chapter 25: Nitrogen Acquisition and Amino Acid Metabolism
25.1 Which Metabolic Pathways Allow Organisms to Live on Inorganic Forms of Nitrogen?
25.2 What Is the Metabolic Fate of Ammonium?
25.3 What Regulatory Mechanisms Act on Escherichia coli Glutamine Synthetase?
25.4 How Do Organisms Synthesize Amino Acids?
25.5 How Does Amino Acid Catabolism Lead into Pathways of Energy Production?
Foundational Biochemistry
Problems
Further Reading
Chapter 26: Synthesis and Degradation of Nucleotides
26.1 How Do Cells Synthesize Nucleotides?
26.2 How Do Cells Synthesize Purines?
26.3 Can Cells Salvage Purines?
26.4 How Are Purines Degraded?
26.5 How Do Cells Synthesize Pyrimidines?
26.6 How Are Pyrimidines Degraded?
26.7 How Do Cells Form the Deoxyribonucleotides That Are Necessary for DNA Synthesis?
26.8 How Are Thymine Nucleotides Synthesized?
Foundational Biochemistry
Problems
Further Reading
Chapter 27: Metabolic Integration and Organ Specialization
27.1 Can Systems Analysis Simplify the Complexity of Metabolism?
27.2 What Underlying Principle Relates ATP Coupling to the Thermodynamics of Metabolism?
27.3 Is There a Good Index of Cellular Energy Status?
27.4 How Is Overall Energy Balance Regulated in Cells?
27.5 How Is Metabolism Integrated in a Multicellular Organism?
27.6 What Regulates Our Eating Behavior?
27.7 Can You Really Live Longer by Eating Less?
Foundational Biochemistry
Problems
Further Reading
Part IV: Information Transfer
Chapter 28: DNA Metabolism: Replication, Recombination, and Repair
28.1 How Is DNA Replicated?
28.2 What Are the Functions of DNA Polymerases?
28.3 Why Are There So Many DNA Polymerases?
28.4 How Is DNA Replicated in Eukaryotic Cells?
28.5 How Are the Ends of Chromosomes Replicated?
28.6 How Are RNA Genomes Replicated?
28.7 How Is the Genetic Information Rearranged by Genetic Recombination?
28.8 Can DNA Be Repaired?
28.9 What Is the Molecular Basis of Mutation?
28.10 Can Genetic Recombination Create Protein Diversity?
Foundational Biochemistry
Problems
Further Reading
Chapter 29: Transcription and the Regulation of Gene Expression
29.1 How Are Genes Transcribed in Bacteria?
29.2 How Is Transcription Regulated in Bacteria?
29.3 How Are Genes Transcribed in Eukaryotes?
29.4 How Do Gene Regulatory Proteins Recognize Specific DNA Sequences?
29.5 How Are Eukaryotic Transcripts Processed and Delivered to the Ribosomes for Translation?
29.6 Can Gene Expression Be Regulated Once the Transcript Has Been Synthesized?
29.7 Can We Propose a Unified Theory of Gene Expression?
Foundational Biochemistry
Problems
Further Reading
Chapter 30: Protein Synthesis
30.1 What Is the Genetic Code?
30.2 How Is an Amino Acid Matched with Its Proper tRNA?
30.3 What Are the Rules in Codon-Anticodon Pairing?
30.4 What Is the Structure of Ribosomes, and How Are They Assembled?
30.5 What Are the Mechanics of mRNA Translation?
30.6 How Are Proteins Synthesized in Eukaryotic Cells?
30.7 Do Protein Synthesis Inhibitors Have Clinical Applications?
Foundational Biochemistry
Problems
Further Reading
Chapter 31: Completing the Protein Life Cycle: Folding, Processing, and Degradation
31.1 How Do Newly Synthesized Proteins Fold?
31.2 How Are Proteins Processed Following Translation?
31.3 How Do Protein Translocation Pathways Target Proteins to Subcellular Compartments?
31.4 How Does Protein Degradation Regulate Cellular Levels of Specific Proteins?
Foundational Biochemistry
Problems
Further Reading
Chapter 32: The Reception and Transmission of Extracellular Information
32.1 What Are Hormones?
32.2 What Is Signal Transduction?
32.3 How Do Signal-Transducing Receptors Respond to the Hormonal Message?
32.4 How Are Receptor Signals Transduced?
32.5 How Do Effectors Convert the Signals to Actions in the Cell?
32.6 How Are Signaling Pathways Organized and Integrated?
32.7 How Do Neurotransmission Pathways Control the Function of Sensory Systems?
Foundational Biochemistry
Problems
Further Reading
Abbreviated Answers to Problems
Index