1. Biochemistry: An Introduction
Opening Vignette: Life: It Is a Mystery!
1.1 What Is Life?
1.2 Biomolecules
Functional Groups of Organic Biomolecules
Major Classes of Small Biomolecules
1.3 Is the Living Cell a Chemical Factory?
Biochemical Reactions
Energy
Overview of Metabolism
Biological Order
1.4 Systems Biology
Emergence
Robustness
Modularity
Biochemistry in the Lab: An Introduction
2. Living Cells
Opening Vignette: Our Bodies, Our Selves
2.1 Basic Themes
Water
Biological Membranes
Self-Assembly
Molecular Machines
Macromolecular Crowding
Signal Transduction
2.2 Structure of Prokaryotic Cells
Cell Wall
Plasma Membrane
Cytoplasm
Pili and Flagella
2.3 Structure of Eukaryotic Cells
Plasma Membrane
Endoplasmic Reticulum
Golgi Apparatus
Nucleus
Vesicular Organelles
Mitochondria
Peroxisomes
Plastids
Cytoskeleton: An expanded section introduces the concept of intraflagellar transport.
Ribosomes
New! Biochemistry in Perspective: Primary Cilia and Human Disease: A new box describes how defects in the structural and functional properties of primary cilia contribute to human disease.
Biochemistry in the Lab: Cell Technology
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Biochemistry in Perspective: Organelles and Human Disease
3. Water: The Matrix of Life
Opening Vignette: Water, Water Everywhere
3.1 Molecular Structure of Water
3.2 Noncovalent Bonding
Ionic Interactions
Hydrogen Bonds
Van der Waals Forces
3.3 Thermal Properties of Water
3.4 Solvent Properties of Water
Hydrophillic Molecules, Cell Water Structuring, and Sol-Gel Transitions
Hydrophobic Molecules and the Hydrophobic Effect
Amphipathic Molecules
Osmotic Pressure
3.5 Ionization of Water
Acids, Bases, and pH
Buffers
Physiological Buffers
New! Biochemistry in Perspective: Cell Volume Regulation and Metabolism: A new box describes the relationship between metabolic pathways and cell volume changes triggered by osmotic imbalances.
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Biochemistry in Perspective: Water, Abiotic Stress, and Compatible Solutes
4. Energy
Opening Vignette: Energy and Life's Deep Dark Secrets
4.1 Thermodynamics
First Law of Thermodynamics
Second Law of Thermodynamics
4.2 Free Energy
Standard Free Energy Changes
Coupled Reactions
The Hydrophobic Effect Revisited
4.3 The Role of ATP
Biochemistry in Perspective: Nonequilibrium Thermodynamics and the Evolution of Life
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Biochemistry in Perspective: The Extremophiles: Organisms That Make a Living in Hostile Environments
5. Amino Acids, Peptides, and Proteins
Opening Vignette: Spider Silk: A Biosteel Protein
5.1 Amino Acids
Amino Acid Classes
Biologically Active Amino Acids
Modified Amino Acids in Proteins
Amino Acid Stereoisomers
Titration of Amino Acids
Amino Acid Reactions
5.2 Peptides
5.3 Proteins
Protein Structure
The Folding Problem: An updated section describes molecular chaperone-assisted protein folding.
Fibrous Proteins
Globular Proteins:
5.4 Molecular Machines
Motor Proteins
New! Biochemistry in Perspective: Spider Silk and Biomimetics: A new box describes the structural properties of spider silk fibers and the efforts of scientists to manufacture artificial spider silk.
Biochemistry in the Lab: Protein Technology
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Biochemistry in Perspective: Myosin: A Molecular Machine
Biochemistry in Perspective: Protein Folding and Human Disease
Biochemistry in Perspective: Protein Poisons
Biochemistry in the Lab: Protein Sequence Analysis: The Edman Degradation
6. Enzymes
Opening Vignette: Humans and Enzymes: A Brief History
6.1 Properties of Enzymes
6.2 Classification of Enzymes
6.3 Enzyme Kinetics
Michaelis-Menten Kinetics
Lineweaver-Burk Plots
Multisubstrate Reactions
Enzyme Inhibition
Enzyme Kinetics, Metabolism and Macromolecular Crowding
6.4 Catalysis
Organic Reactions and the Transition State
The Roles of Amino Acids in Enzyme Catalysis
The Role of Cofactors in Enzyme Catalysis
Effects of Temperature and pH on Enzyme-Catalyzed Reactions
Detailed Mechanisms of Enzyme Catalysis
6.5 Enzyme Regulation
Genetic Control
Covalent Modification
Allosteric Regulation
Compartmentation
New! Biochemistry in Perspective: Alcohol Dehydrogenase: A Tale of Two Organisms: A new box describes the remarkable ability of the yeast Saccaromyces cerevisiae to synthesize ethanol, and the properties of human alcohol dehydrogenases.
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Biochemistry in Perspective: Quantum Tunneling and Catalysis
Biochemistry in Perspective: Enzymes and Clinical Medicine
7. Carbohydrates
Opening Vignette: Sweet and Bitter Tastes: The Role of Sugar Molecules
7.1 Monosaccharides
Monosaccharide Stereoisomers
Cyclic Structure of Monosaccharides
Reactions of Monosaccharides
Important Monosaccharides
Monosaccharide Derivatives
7.2 Disaccharides
7.3 Polysaccharides
Homoglycans
Heteroglycans
7.4 Glycoconjugates
Proteoglycans
Glycoproteins
7.5 The Sugar Code
Lectins: Translators of the Sugar Code
New! Biochemistry in the Lab: Glycomics: A new box describes the major technologies used to determine the structure of complex carbohydrate molecules.
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Biochemistry in Perspective: Sweet Medicine
Biochemistry in Perspective: Conversion of Fischer Monosaccharide Structure onto Haworth Structure
8. Carbohydrate Metabolism
Opening Vignette: Metabolism and Jet Engines
8.1 Glycolysis
The reactions of the Glycolytic Pathway
The Fates of Pyruvate
The Energetics of Glycolysis
Regulation of Glycolysis
8.2 Gluconeogenesis
Gluconeogenesis Reactions
Gluconeogenesis Substrates
Gluconeogenesis Regulation
8.3 The Pentose Phosphate Pathway
8.4 Metabolism of Other Important Sugars
Fructose Metabolism
8.5 Glycogen Metabolism
Glycogenesis
Glycogenolysis
Regulation of Glycogen Metabolism
New! Biochemistry in Perspective: Saccharomyces cerevisiae and the Crabtree Effect: A new box describes the metabolic mechanism whereby yeast cells convert glucose into ethanol molecules that kill competitor microbes.
New! Biochemistry in Perspective: Turbo Design Can Be Dangerous: A new box describes why turbo design pathways must be rigorously controlled.
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Biochemistry in Perspective: Fermentation: An Ancient Heritage
9. Aerobic Metabolism I: The Citric Acid Cycle
Opening Vignette: Oxygen and Evolution: Chance and Necessity
9.1 Oxidation-Reduction Reactions
Redox Coenzymes
Aerobic Metabolism
9.2 Citric Acid Cycle
Conversion of Pyruvate to Acetyl-CoA
Reactions of the Citric Acid Cycle
Fate of Carbon Atoms in the Citric Acid Cycle
The Amphibolic Citric Acid Cycle
Citric Acid Cycle Regulation
New! The Citric Acid Cycle and Human Disease: A new section describes why several rare human diseases have been attributed to deficits in the citric acid cycle.
The Glyoxylate Cycle
Biochemistry in Perspective: The Evolutionary History of the Citric Acid Cycle
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Hans Krebs and the Citric Acid Cycle
10. Aerobic Metabolism II: Electron Transport and Oxidative Phosphorylation
Opening Vignette: Oxygen: A Molecular Paradox
10.1 Electron Transport
Electron Transport and Its Components
New! Electron Transport: The Fluid State Model vs. the Solid-State Model: A new section describes the structural and functional properties of the respirasome.
Electron Transport Inhibitors
10.2 Oxidative Phosphorylation
The Chemiosmotic Theory
ATP Synthesis
Control of Oxidative Phosphorylation
The Complete Oxidation of Glucose
Uncoupled Electron Transport
10.3 Oxygen, Cell function and Oxidative Stress
Reactive Oxygen Species
Antioxidant Enzyme Systems
Antioxidant Molecules
Biochemistry in Perspective: Myocardial Infarct: Ischemia and Reperfusion: An expanded reading describes the damage caused by the reintroduction of oxygen after blood flow interruption in heart muscle.
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Biochemistry in Perspective: Glucose-6-Phosphate Dehydrogenase Deficiency
11. Lipids and Membranes
Opening Vignette: The Low-Fat Diet
11.1 Lipid Classes
Fatty Acids
The Eicosanoids: An expanded discussion of the eicosanoids describes their biological functions and roles in human disease.
Triacylglycerols
Wax Esters
Phospholipids
New! Phospholipases: A new section describes the functions of phospholipases.
Sphingolipids
Sphingolipid Storage Diseases
Isoprenoids
Lipoproteins
11.2 Membranes
New! Membrane Structure: A new section describes the structural and functional properties of the red blood cell membrane protein AE1.
Membrane Function
New! Biochemistry in Perspective: Membrane Fusion and Botulism: A new box describes how botulinum toxin causes muscle paralysis by preventing membrane fusion in nerve cells.
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Biochemistry in Perspective: Glucose-6-Phosphate Dehydrogenase Deficiency
12. Lipid Metabolism
Opening Vignette: Abetalipoproteinemia
12.1 Fatty Acids, Triacylglycerols and the Lipoprotein Pathways: An expanded discussion focuses on the distribution of triacylglycerols to the body's tissues after digestion, the triacylglycerol cycle, and glycerogenesis.
Fatty Acid Degradation
The Complete Oxidation of a Fatty Acid
Fatty Acid Oxidation: Double Bonds and Odd Chains
Fatty Acid Biosynthesis: The structural and functional properties of fatty acid synthase are updated to reflect recent research.
New! A new table compares the details of fatty acid b-oxidation and synthesis.
Regulation of Fatty Acid Metabolism in Mammals: An expanded discussion places fatty acid metabolism regulation in the context of AMPK control of the body's biochemical pathways.
New! Lipoprotein Metabolism: The Endogenous Pathway: A new section focuses on the transport of synthesized lipid molecules from the liver to the body's tissues.
12.2 Membrane Lipid Metabolism
Phospholipid Metabolism
Sphingolipid Metabolism
12.3 Isoprenoid Metabolism
New! Cholesterol Metabolism: A new section describes the effects of selected drugs on the cholesterol biosynthetic pathway.
Biochemistry in Perspective: Atherosclerosis: The revised box describes how LDLs trapped in arterial walls become depleted of antioxidants and then contribute to atherosclerotic damage.
Biochemistry in Perspective: Biotransformation
13. Photosynthesis
Opening Vignette: Climate Change, Renewable Energy, and Photosynthesis
13.1 Chlorophyll and Chloroplasts: A revised introduction provides a more detailed overview of oxygenic photosynthesis in chloroplasts
13.2 Light
13.3 Light Reactions: The Z-scheme is updated to reflect recent research.
Photosystem II and Water Oxidation
Photosystem I and NADPH Synthesis
Photophosphorylation
13.4 The Light-Independent Reactions
The Calvin Cycle: The Calvin cycle reactions are expanded to include the ribulose-1,5- bisphosphate carboxylase mechanism.
Photorespiration
Alternatives to C3 Metabolism
13.5 Regulation of Photosynthesis
Light Control of Photosynthesis
Control of Ribulose-1,5-Bisphosphate Carboxylase
Biochemistry in Perspective: Photosynthesis in the Deep
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Biochemistry in Perspective: Starch and Sucrose Metabolism
Biochemistry in the Lab: Photosynthetic Studies
14. Nitrogen Metabolism I: Synthesis
Opening Vignette: Nitrogen and the Gulf of Mexico Dead Zone
14.1 Nitrogen Fixation
The Nitrogen Fixation Reaction
Nitrogen Assimilation
14.2 Amino Acid Biosynthesis
Amino Acid Metabolism Overview
Reactions of Amino Groups
Synthesis of the Amino Acids
14.3 Biosynthetic Reactions Involving Amino Acids
One-Carbon Metabolism
Glutathione: A newly revised section focuses on the roles of this vitally important intracellular reducing agent.
Neurotransmitters
Nucleotides
Biochemistry in Perspective: Gasotransmitters
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Biochemistry in Perspective: Parkinson's Disease and Dopamine
Biochemistry in Perspective: Heme and Chlorophyll Biosynthesis
Biochemistry in Perspective: The Amine Neurotransmitters
Biochemistry in Perspective: Lead Poisoning
15. Nitrogen Metabolism II: Degradation
Opening Vignette: Degradative Pathways and Human Disorders
15.1 Protein Turnover: A newly revised section focuses on the ubiquitin proteasomal and autophagy lysosomal systems.
15.2 Amino Acid Catabolism
Deamination
Urea Synthesis
Control of the Urea Cycle
Catabolism of Amino Acid Carbon Skeletons
15.3 Degradation of Selected Neurotransmitters
15.4 Nucleotide Degradation
Purine Catabolism
Pyrimidine Catabolism
Biochemistry in Perspective: Disorders of Amino Acid Catabolism
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Biochemistry in Perspective: Hyperammonemia
Biochemistry in Perspective: Gout
Biochemistry in Perspective: Heme Biotransformation
16. Integration of Metabolism
Opening Vignette: Hypertension and Uric Acid: A Diet Connection?
16.1 Overview of Metabolism
16.2 Hormones and Intercellular Communication
Peptide Hormones: An expanded section provides a more detailed description of how insulin binding to its receptor alters intracellular processes
Growth Factors
Steroid and Thyroid Hormone Mechanisms
16.3 Metabolism in the Mammalian Body: Division of Labor: New emphasis is place on glucose transport mechanisms in the body's organs.
Gastrointestinal Tract
Liver
Muscle
Adipose Tissue
Brain
Kidney
16.4 The Feeding-Fasting Cycle
The Feeding Phase
The Fasting Phase
Feeding Behavior
Biochemistry in Perspective: Diabetes Mellitus: An extensively revised description of diabetes explains the causes and consequences of this metabolic disease.
Biochemistry in Perspective: Obesity and the Metabolic Syndrome: The box is revised to reflect recent research, including the contribution of dietary fructose to the current epidemics of obesity and metabolic syndrome.
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Biochemistry in Perspective: Mammalian Hormones and the Hormone Cascade System
Biochemistry in the Lab: Hormone Methods
17. Nucleic Acids
Opening Vignette: What Makes Us Human?
17.1 DNA
DNA Structure: The Nature of Mutation: A newly revised and expanded discussion describes mutation types and several classes of mutagens
DNA Structure: The Genetic Material
DNA Structure: Variations on a Theme
DNA Supercoiling: A newly enhanced description of supercoiling makes this difficult topic easier to understand
Chromosomes and Chromatin
Genome Structure
17.2 RNA
Transfer RNA
Ribosomal RNA
Messenger RNA
Noncoding RNA
17.3 Viruses
Bacteriophage T4: A Viral Lifestyle
Biochemistry in the Lab: Nucleic Acid Methods
New! Biochemistry in Perspective: Epigenetics and the Epigenome: Genetic Inheritance Beyond DNA Base Sequences: A new box provides an accessible introduction to a mechanism that alters gene expression during development.
Biochemistry in Perspective: HIV: An updated box reading describes the infective mechanism of HIV
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Biochemistry in Perspective: A Short History of DNA Research: The Early Days
18. Genetic Information
Opening Vignette: DNA and Chimeras: A Biological and Medical Mystery
18.1 Genetic Information: Replication, Repair, and Recombination
DNA Replication: Expanded sections describe the functions of the prokaryotic and eukaryotic DNA polymerases.
DNA Repair: An updated and expanded section describes transcription-associated, mismatch, and double-strand repair.
DNA Recombination
18.2 Transcription
Transcription in Prokaryotes
Transcription in Eukaryotes: The structural and functional properties of RNA pol II are updated.
18.3 Gene Expression
Gene Expression in Prokaryotes
New! Gene Expression in Eukaryotes: A new section describes posttranscriptional gene silencing.
Biochemistry in Perspective: Genomics
New! Biochemistry in Perspective: Carcinogenesis: A new section outlines the roles of tumor suppressors.
19. Protein Synthesis
Opening Vignette: MRSA, the Superbug
19.1 The Genetic Code
Codon-Anticodon Interactions
The Aminoacyl-tRNA Synthease Reaction
19.2 Protein Synthesis
Prokaryotic Protein Synthesis
Eukaryotic Protein Synthesis: Eukaryotic translation initiation is updated. New sections describe mitochondrial posttranslational protein import and mTOR-mediated translation control.
New! Biochemistry in Perspective: Trapped Ribosomes: RNA to the Rescue: A new box describes the tactics used by living organisms to release ribosomes attempting to translate truncated mRNAs without stop codons.
Biochemistry in Perspective: Context-Dependent Coding Rearrangement
Biochemistry in the Lab: Proteomics
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Biochemistry in Perspective: EF-Tu: A Motor Protein