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Biochemistry The Molecular Basis of Life - Trudy McKee, James R McKee

Contents


CHAPTER ONE
What is Life?
1.1 The Living World
Bacteria
Archaea
Eukarya
1.3 Biomolecules
Functional Groups of Organic Biomolecules
Major Classes of Small Biomolecules
1.4 Is the Living Cell a Chemical Factory?
Biochemical Reactions
Energy
Overview of Metabolism
Biological Order
1.5 Systems Biology
Emergence
Robustness
Modularity
Biochemistry in the Lab: An Introduction
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions

CHAPTER TWO
Living Cells
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
Biochemistry in Perspective: Organelles in Human Disease
Plastids
Cytoskeleton
Ribosomes
Biochemistry in the Lab: Cell Technology
Available online:
Biochemistry in Perspective: Endosymbiosis
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER THREE
Water: The Matrix of Life
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: Water, Abiotic Stress, and Compatible Solutes
Biochemistry in the Lab: Dialysis
Available online:
Biochemistry in Perspective: Cell Volume Regulation and Metabolism
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER FOUR
Energy
4.1 Thermodynamics
The First Law of Thermodynamics
Second Law of Thermodynamics
4.2 Free Energy
Standard Free Energy Changes
Coupled Reactions
The Hydrophobic Effect Revisited
Biochemistry in Perspective: Non-Equilibrium Thermodynamics
4.4 The Role of ATP
Biochemistry in Perspective: The Extremophiles: Organisms that Make a Living in Hostile
Environments
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER FIVE
Amino Acids, Peptides, and Proteins
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
Biochemistry in Perspective: Molecular Machines
The Folding Problem
Biochemistry in Perspective: Protein Folding and Human Disease
Fibrous Proteins
Globular Proteins
Biochemistry in the Lab: Protein Technology
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER SIX
Enzymes
6.1 Properties of Enzymes
6.2 Classification of Enzymes
6.3 Enzyme Kinetics
Michaelis-Menten Kinetics
Lineweaver-Burk Plots
Enzyme Inhibition
Enzyme Kinetics, Metabolism and Macromolecular Crowding
6.4 Catalysis
Organic Reactions and the Transition State
Quantum Tunneling and Enzyme Catalysis
The Role of Amino Acids in Enzyme Catalysis
The Role of Cofactors in Enzyme Catalyses
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: Enzymes and Clinical Medicine
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER SEVEN
Carbohydrates
7.1 Monosaccharides
Monosaccharide Stereoisomers
Cyclic Structure of Monosaccharides
Reactions of Monosaccharides
Important Monosaccharides
Monosaccharide Derivatives
7.2 Disaccharides
7.3 Polysaccharides
Homopolysaccharides
Heteropolysaccharides
7.4 Glycoconjugates
Proteoglycans
Glycoproteins
7.5 The Sugar Code
Lectins: Translators of the Sugar Code
The Glycome
Biochemistry in Perspective: Sweet Medicine
Available online:
Biochemistry in Perspective: Scurvy and Ascorbic Acid
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER EIGHT
Carbohydrate Metabolism
8.1 Glycolysis
The Reactions of the Glycolytic Pathway
The Fates of Pyruvate
The Energetics of Glycolysis
Regulation of Glycolysis
Biochemistry in Perspective: Glycolysis and Jet Engines
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
Available online:
Biochemistry in Perspective: Fermentation: An Ancient Heritage
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER NINE
Aerobic Metabolism I: The Citric Acid Cycle
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 Glyoxylate Cycle
Biochemistry in Perspective: The Evolutionary History of the Citric Acid Cycle
Available online:
Biochemistry in Perspective: Hans Krebs and the Citric Acid Cycle
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER TEN
Aerobic Metabolism II: Electron Transport and Oxidative Phosphorylation
10.1 Electron Transport
Electron Transport and Its Components
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 Oxidative Stress
Reactive Oxygen Species
Antioxidant Enzyme Systems
Antioxidant Molecules
Biochemistry in Perspective: Ischemia and Reperfusion
Available online:
Biochemistry in Perspective: Glucose-6-Phosphate Dehydrogenase Deficiency
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER ELEVEN
Lipids and Membranes
11.1 Lipid Classes
Fatty Acids and Their Derivatives
The Elcasonoids
Triacylglycerols
Wax Esters
Phospholipids
Sphingolipids
Sphingolipids Storage Diseases
Isoprenoids
Lipoproteins
11.2 Membranes
Membrane Structure
Membrane Function
Biochemistry in Perspective: The Aquaporins
Available online:
Biochemistry in Perspective: Membrane Fusion and Botulism
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER TWELVE
Lipid Metabolism
12.1 Fatty Acids and Triacylglycerols
Fatty Acid Degradation
The Complete Oxidation of a Fatty Acid
Fatty Acid Oxidation: Double Bonds and Odd Chains
Fatty Acid Biosynthesis
Eicosanoid Metabolism
Regulation of Fatty Acid Metabolism in Mammals
Biochemistry in Perspective: Atherosclerosis
12.2 Membrane Lipid Metabolism
Phospholipid Metabolism
Sphingolipid Metabolism
12.3 Isoprenoid Metabolism
Cholesterol Metabolism
Steroid Hormone Synthesis
Biochemistry in Perspective: Biotransformation
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER THIRTEEN
Photosynthesis
13.1 Chlorophyll and Chloroplasts
13.2 Light
13.3 Light Reactions
Photosystem II and Oxygen Generation
Photosystem I and NADPH Synthesis
Photophosporylation
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: Photosynthesis in the Deep
Available online;
Biochemistry in Perspective: Starch and Sucrose metabolism
Available online:
Biochemistry in the Lab: Photosynthetic Studies
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER FOURTEEN
Nitrogen Metabolism I: Synthesis
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 of Amino Acids
One-Carbon Metabolism
Glutathione
Neurotransmitters
Biochemistry in Perspective: GASO-Transmitters
Alkaloids
Nucleotides
Heme
Available online:
Biochemistry in Perspective: Parkinson’s Disease and Dopamine
Biochemistry in Perspective: Lead Poisoning
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER FIFTEEN
Nitrogen Metabolism II: Degradation
15.1 Protein Turnover
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 Degradation of Selected Neurotransmitters
15.4 Nucleotide Degradation
Purine Catabolism
Pyrimidine Catabolism
15.5 Heme Biotransformation
Available online:
Biochemistry in Perspective: Hyperammonemia
Available online: Biochemistry in Perspective: Gout
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER SIXTEEN
Integration of Metabolism
16.1 Overview of Metabolism
16.2 Hormones and Intercellular Communication
Peptide Hormones
Biochemistry in Perspective: Diabetes Mellitus
Growth Factors
Steroid and Thyroid Hormone Mechanisms
16.3 Metabolism in the Mammalian Body: Division of Labor
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: Obesity and the Metabolic Syndrome
Available online:
Biochemistry in the Lab: Hormone Methods
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER SEVENTEEN
Nucleic Acids
17.1 DNA
DNA Structure: The Nature of Mutation
DNA Structure: From Mendel’s Garden to Watson and Crick
DNA Structure: Variations on a Theme
DNA Supercoiling
Chromosomes and Chromatin
Genome Structure
Biochemistry in the Lab: Nucleic Acid Methods
Biochemistry in Perspective: Forensic Investigations
17.2 RNA
Transfer RNA
Ribosomal RNA
Messenger RNA
Noncoding RNA
17.3 Viruses
The Structure of Viruses
Biochemistry in Perspective: Viral “Lifestyles”
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
CHAPTER EIGHTEEN
Genetic Information
18.1 Genetic Information: Replication, Repair, and Recombination
DNA Replication
DNA Repair
DNA Recombination
Biochemistry in the Lab: Genomics
18.2 Transcription
Transcription in Prokaryotes
Transcription in Eukaryotes
18.3 Gene Expression
Gene Expression in Prokaryotes
Gene Expression in Eukaryotes
Biochemistry in Perspective: Carcinogenesis
Summary
Suggested Readings
Key Words
Review Questions
Thought Question
CHAPTER NINETEEN
Protein Synthesis
19.1 The Genetic Code
Codon-Anticodon Interactions
The Aminoacyl-tRNA Synthetase Reaction: The Second Genetic Code
19.2 Protein Synthesis
Prokaryotic Protein Synthesis
Eukaryotic Protein Synthesis
Biochemistry in Perspective: EF-TU: A Motor Protein
Biochemistry in Perspective: Context-Dependent Coding Reassignment
Biochemistry in the Lab: Proteomics
Summary
Suggested Readings
Key Words
Review Questions
Thought Questions
Appendix A: Solutions

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