Biochemistry: The Molecular Basis of Life

Cover
Half Title Page
Title Page
Copyright
Dedication
Brief Contents
Contents
Chapter Opening Vignettes
Biochemistry in Perspective Essays
Biochemistry in the Lab Boxes
Preface
ABOUT THE AUTHORS
CHAPTER 1: Biochemistry: An Introduction
	Why Study Biochemistry?
	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
		Systems Biology Model Concepts
		Living Organisms and Robustness
	Biochemistry IN THE LAB: An Introduction
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 2: Living Cells
	Our Bodies, Our Selves
	2.1 BASIC THEMES
		Water
		Biological Membranes
		Self-Assembly
		Molecular Machines
		Macromolecular Crowding
		Proteostasis
		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
		Vesicular Organelles and Lysosomes: The Endocytic Pathway
		Nucleus
		Mitochondria
		Peroxisomes
		Chloroplasts
		Cytoskeleton
	Biochemistry IN PERSPECTIVE: Primary Cilia and Human Disease
	Biochemistry IN THE LAB: Cell Technology
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 3: Water: The Matrix of Life
	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
		Hydrophilic 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
	Biochemistry IN PERSPECTIVE: Cell Volume Regulation and Metabolism
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 4: Energy
	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
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 5: Amino Acids, Peptides, and Proteins
	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
		Other Protein Classifications
		Protein Structure
		The Folding Problem
		Fibrous Proteins
		Globular Proteins
	5.4 MOLECULAR MACHINES
		Motor Proteins
	Biochemistry IN PERSPECTIVE: Spider Silk and Biomimetics
	Biochemistry IN THE LAB: Protein Technology
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 6: Enzymes
	Humans and Enzymes: A Brief History
	6.1 PROPERTIES OF ENZYMES
		Enzyme Catalysts: The Basics
		Enzymes: Activation Energy and Reaction Equilibrium
		Enzymes and Macromolecular Crowding Effects
		Enzyme Specificity
	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
		Transition State Stabilization
		Catalytic Mechanisms
		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
	Biochemistry IN PERSPECTIVE: Alcohol Dehydrogenase: A Tale of Two Species
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER7: Carbohydrates
	Sweet and Bitter Taste: The Roles 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
		The Glycome
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 8: Carbohydrate Metabolism
	Metabolism and Jet Engines
	8.1 GLYCOLYSIS
		The Reactions of the Glycolytic Pathway
		The Fates of Pyruvate
		The Energetics of Glycolysis
		Regulation of Glycolysis
	Biochemistry IN PERSPECTIVE: Saccharomyces cerevisiae and the Crabtree Effect
	8.2 GLUCONEOGENESIS
		Gluconeogenesis Reactions
		Biochemistry IN PERSPECTIVE: Turbo Design Can Be Dangerous
		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
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 9: Aerobic Metabolism I: The Citric Acid Cycle
	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
		The Citric Acid Cycle and Human Disease
		The Glyoxylate Cycle
	Biochemistry IN PERSPECTIVE: Carcinogenesis: The Warburg Effect and Metabolic Reprogramming
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Untitled
	Thought Questions
CHAPTER 10: Aerobic Metabolism II: Electron Transport and Oxidative Phosphorylation
	Oxygen: A Molecular Paradox
	10.1 ELECTRON TRANSPORT
		Electron Transport and Its Components
		Electron Transport: The Fluid State and Solid State Models
		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
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 11: Lipids and Membranes
	The Low-Fat Diet
	11.1 LIPID CLASSES
		Fatty Acids
		The Eicosanoids
		Triacylglycerols
		Wax Esters
		Phospholipids
		Phospholipases
		Sphingolipids
		Sphingolipid Storage Diseases
		Isoprenoids
		Lipoproteins
	11.2 MEMBRANES
		Membrane Structure
		Membrane Function
	Biochemistry IN PERSPECTIVE: Botulism and Membrane Fusion
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 12: Lipid Metabolism
	Abetalipoproteinemia
	12.1 FATTY ACIDS, TRIACYLGLYCEROLS, AND THE LIPOPROTEIN PATHWAYS
		Dietary Fat: Digestion, Absorption, and Transport
		Triacylglycerol Metabolism in Adipocytes
		Fatty Acid Degradation
		The Complete Oxidation of a Fatty Acid
		Fatty Acid Oxidation: Double Bonds and Odd Chains
		Fatty Acid Biosynthesis
		Regulation of Fatty Acid Metabolism in Mammals
		Lipoprotein Metabolism: The Endogenous Pathway
	12.2 MEMBRANE LIPID METABOLISM
		Phospholipid Metabolism
	Biochemistry IN PERSPECTIVE: Atherosclerosis
	12.3 ISOPRENOID METABOLISM
		Cholesterol Metabolism
		The Cholesterol Biosynthetic Pathway and Drug Therapy
	Biochemistry IN PERSPECTIVE: Biotransformation
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 13: Photosynthesis
	Climate Change, Renewable Energy, and Photosynthesis
	13.1 CHLOROPHYLL AND CHLOROPLASTS
	13.2 LIGHT
	13.3 LIGHT REACTIONS
		Photosystem II and Water Oxidation
		Photosystem I and NADPH Synthesis
		Photophosphorylation
	13.4 THE LIGHT-INDEPENDENT REACTIONS
		The Calvin Cycle
		Photorespiration
		Alternatives to C3 Metabolism
	13.5 REGULATION OF PHOTOSYNTHESIS
		Light Control of Photosynthesis
		Control of Ribulose-1,5-Bisphosphate Carboxylase
	Biochemistry IN PERSPECTIVE: The Artificial Leaf: Biomimetic Photosynthesis
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 14: Nitrogen Metabolism I: Synthesis
	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
		Biosynthesis of the Amino Acids
	14.3 BIOSYNTHETIC REACTIONS INVOLVING AMINO ACIDS
		One-Carbon Metabolism
		Glutathione
		Neurotransmitters
		Biochemistry IN PERSPECTIVE: Gasotransmitters
		Nucleotides
		Heme
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 15: Nitrogen Metabolism II: Degradation
	Degradative Pathways and Human Disorders
	15.1 PROTEIN TURNOVER
		Ubiquitin Proteasomal System
		Autophagy-Lysosomal System
	15.2 AMINO ACID CATABOLISM
		Deamination
		Urea Synthesis
		Control of the Urea Cycle
		Catabolism of Amino Acid Carbon Skeletons
	Biochemistry IN PERSPECTIVE: Disorders of Amino Acid Catabolism
	15.3 NEUROTRANSMITTER DEGRADATION
	15.4 NUCLEOTIDE DEGRADATION
		Purine Catabolism
		Pyrimidine Catabolism
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 16: Integration of Metabolism
	Hypertension and Uric Acid: A Diet Connection?
	16.1 OVERVIEW OF METABOLISM
	16.2 HORMONES AND INTERCELLULAR COMMUNICATION
		Peptide Hormones
		Growth Factors
		Biochemistry IN PERSPECTIVE: Diabetes Mellitus
		Steroid and Thyroid Hormone Mechanisms
	16.3 METABOLISM IN THE MAMMALIAN BODY: THE FEEDING-FASTING CYCLE
		The Feeding Phase
		The Fasting Phase
		Feeding Behavior
	Biochemistry IN PERSPECTIVE: Obesity and the Metabolic Syndrome
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 17: Nucleic Acids
	What Makes Us Human?
	17.1 DNA
		DNA Structure: The Nature of Mutation
		DNA Structure: The Genetic Material
		DNA Structure: Variations on a Theme
		DNA Supercoiling
		Chromosomes and Chromatin
		Genome Structure
	17.2 RNA
		Biochemistry IN PERSPECTIVE: Epigenetics and the Epigenome: Genetic Inheritance beyond DNA Base Sequences
		Transfer RNA
		Biochemistry IN THE LAB: Nucleic Acid Methods
		Biochemistry IN PERSPECTIVE: Forensic Investigations
		Ribosomal RNA
		Messenger RNA
		Noncoding RNA
	17.3 VIRUSES
		Bacteriophage T4: A Viral Lifestyle
	Biochemistry IN PERSPECTIVE: HIV Infection
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 18: Genetic Information
	DNA and Chimeras: A Biological and Legal Mystery
	18.1 GENETIC INFORMATION: REPLICATION, REPAIR, AND RECOMBINATION
		DNA Replication
		DNA Repair
		Direct Repairs
		DNA Recombination
	Biochemistry IN THE LAB: Genomics
	18.2 TRANSCRIPTION
		Transcription in Prokaryotes
		RNAP and the Prokaryotic Transcription Process
		Transcription in Eukaryotes
	18.3 GENE EXPRESSION
		Gene Expression in Prokaryotes
		Gene Expression in Eukaryotes
	Biochemistry IN PERSPECTIVE: Carcinogenesis
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
CHAPTER 19: Protein Synthesis
	MRSA: The Superbug
	19.1 THE GENETIC CODE
		Codon Usage Bias
		Codon-Anticodon Interactions
		The Aminoacyl-tRNA Synthetase Reaction
	19.2 PROTEIN SYNTHESIS
		Prokaryotic Protein Synthesis
		Eukaryotic Protein Synthesis
		Biochemistry IN PERSPECTIVE: Trapped Ribosomes: RNA to the Rescue!
		Biochemistry IN PERSPECTIVE: Context-Dependent Coding Reassignment
	19.3 THE PROTEOSTASIS NETWORK
		The Heat Shock Response
		The Proteostasis Network and Human Disease
	Biochemistry IN THE LAB: Proteomics
	Chapter Summary
	Suggested Readings
	Key Words
	Review Questions
	Fill in the Blank
	Short Answer
	Thought Questions
Appendix: Solutions
Glossary
Credits
General and Organic Chemistry Review Primer