Biochemistry: An Integrative Approach, 1st Edition , International Adaptation

1 The Chemical Foundations of Biochemistry Chemistry in Context 1.1 General Chemical Principles 1.2 Fundamental Concepts of Organic Chemistry 1.3 The Chemistry of Water 2 Nucleic Acids Nucleic Acids in Context Nucleic acids are the Genetic Materials 2.1 Nucleic Acids Have Distinct Structures 2.2 Nucleic Acids Have Many Cellular Functions 2.3 The Manipulation of Nucleic Acids Has Transformed Biochemistry 3 Proteins I: An Introduction to Protein Structure, Function, and its Purification Proteins in Context 3.1 Amino Acid Chemistry 3.2 Proteins Are Polymers of Amino Acids 3.3 Proteins Are Molecules of Defined Shape and Structure 3.4 Examples of Protein Structures and Functions 3.5 Protein Purification Basics 3.6 Size-Exclusion Chromatography 3.7 Affinity Chromatography 4 Proteins II: Enzymes Enzymes in Context 4.1 Introduction to Enzymes 4.2 Enzymes Increase Reaction Rate 4.3 The Mechanism of an Enzyme Can Be Deduced from Structural, Kinetic, and Spectral Data 4.4 Examples of Enzyme Regulation 4.5 Allosterism and Cooperativity 4.6 Hemoglobin 4.7 Receptor-Ligand Interactions 5 Membranes and an Introduction to Signal Transduction Biochemistry in Context 5.1 Membrane Structure and Function 5.2 Signal Transduction 6 Carbohydrates I: Mono- and Disaccharides, Glycolysis, Gluconeogenesis, and the Fates of Pyruvate Carbohydrates in Context 6.1 Properties, Nomenclature, and Biological Functions of Monosaccharides 6.2 Properties, Nomenclature, and Biological Functions of Complex Carbohydrates 6.3 Glycolysis and an Introduction to Metabolic Pathways 6.4 Gluconeogenesis 6.5 The Fates of Pyruvate 7 The Common Catabolic Pathway: Citric Acid Cycle, the Electron Transport Chain, and ATP Biosynthesis Electron Transport in Context 7.1 The Citric Acid Cycle 7.2 The Electron Transport Chain 7.3 ATP Biosynthesis 8 Carbohydrates II: Glycogen Metabolism, the Pentose Phosphate Pathway, Glycoconjugates, and Extracellular Matrices Polysaccharides in Context 8.1 Glycogen Metabolism 8.2 The Pentose Phosphate Pathway 8.3 Carbohydrates in Glycoconjugates 8.4 Extracellular Matrices and Biofilms 9 Lipids I: Fatty Acids, Steroids, and Eicosanoids; Beta-Oxidation and Fatty Acid Biosynthesis Lipids in Context 9.1 Properties, Nomenclature, and Biological Functions of Lipid Molecules 9.2 Fatty Acid Biosynthesis 9.3 Fatty Acid Catabolism 9.4 Ketone Body Metabolism 9.5 Steroid Metabolism 9.6 Eicosanoid and Endocannabinoid Metabolism 10 Lipids II: Metabolism and Transport of Complex Lipids Complex Lipids in Context 10.1 Phospholipid Metabolism 10.2 Digestion of Triacylglycerols 10.3 Transport of Lipids in the Circulation 10.4 Entry of Lipids into the Cell 10.5 Neutral Lipid Biosynthesis 10.6 Lipid Storage Droplets, Fat Storage, and Mobilization 10.7 Lipid Rafts as a Biochemical Entity 11 Amino Acid and Amine Metabolism Amine Metabolism in Context 11.1 Digestion of Proteins 11.2 Amino Acid Deamination and Transamination 11.3 The Urea Cycle 11.4 Metabolism of Amino Acid Carbon Skeleton 11.5 The Detoxification of Other Amines and Xenobiotics 11.6 The Biochemistry of Renal Function 12 Regulation and Integration of Metabolism Metabolism in Context 12.1 A Review of the Pathways and Crossroads of Metabolism 12.2 Organ Specialization and Metabolic States 12.3 Communication between Organs 12.4 Metabolic Disease 13 Nucleotide and Deoxynucleotide Metabolism Nucleotides and Deoxynucleotides in Context 13.1 Purine Biosynthesis 13.2 Pyrimidine Biosynthesis 13.3 Deoxyribonucleotide Biosynthesis 13.4 Catabolism of Nucleotides 14 DNA Replication, Damage, and Repair DNA in Context 14.1 Challenges of DNA Replication 14.2 DNA Replication in Prokaryotes 14.3 DNA Replication in Eukaryotes 14.4 DNA Damage and Repair 14.5 Homologous Recombination 15 RNA Synthesis and Processing RNA Synthesis in Context 15.1 Transcription: RNA Synthesis 15.2 Processing of Nascent Eukaryotic RNA Messages 15.3 RNA Export from the Nucleus 16 Protein Biosynthesis Protein Synthesis in Context 16.1 The Genetic Code 16.2 Machinery Involved in in Protein Biosynthesis 16.3 Mechanism of Protein Biosynthesis 17 Control and Regulation of Gene Expression Gene Regulation in Context 17.1 DNA--Protein Interactions 17.2 Regulation of Gene Expression in Prokaryotes 17.3 Regulation of Gene Expression in Eukaryotes 18 Determination of Macromolecular Structure Macromolecular Structure in Context 18.1 An Introduction to Structure Determination 18.2 Electron Microscopy--Types and Advantages 18.3 X-Ray Diffraction and Neutron Scattering 18.4 Nuclear Magnetic Resonance 19 Protein Production, Engineering and Folding Protein Production, Engineering and Folding in Context 19.1 Protein Production 19.2 Protein Engineering 19.3 Protein Folding 20 Bioinformatics and Omics Bioinformatics in Context 20.1 Introduction to Bioinformatics 20.2 Generating Bioinformatic Data 20.3 Analyzing Bioinformatic Data 21 Signal Transduction Cell Signaling in Context 23.1 A Review of Signal Transduction 23.2 An Overview of Regulation of Signal Transduction 23.3 Six New Signal Transduction Pathways 22 Protein Trafficking Protein Trafficking in Context 24.1 Molecular Aspects of Protein Trafficking 24.2 Molecular Motor Proteins 24.3 Vesicular Fusion 23 Photosynthesis and Nitrogen Fixation Photosynthesis and Nitrogen Fixation in Context 25.1 Photosynthesis 25.2 Nitrogen Fixation Techniques Solutions Glossary Index