Biochemistry

Biochemistry provides a cohesive and well-balanced presentation of the subject, addressing the diverse needs of premed, biochemistry, and life science majors. Discussion of cutting-edge biomedical applications, as well as societal and ethical issues, helps students make connections to their future careers and see the “bigger picture” of how biochemistry applies to the world around them. Metabolism is introduced early in the text and then revisited and referenced throughout, minimizing rote memorization and allowing students to make immediate connections. By placing structure and function of biomolecules in the same chapter as their metabolism, the text covers biochemistry as a more integrated subject.

1 The Chemical Foundations of Biochemistry 1 Chemistry in Context 1 1.1 General Chemical Principles 2 1.2 Fundamental Concepts of Organic Chemistry 11 1.3 The Chemistry of Water 15 2 Nucleic Acids 26 Nucleic Acids in Context 26 2.1 Nucleic Acids Have Distinct Structures 27 2.2 Nucleic Acids Have Many Cellular Functions 37 2.3 The Manipulation of Nucleic Acids Has Transformed Biochemistry 45 3 Proteins I: An Introduction to Protein Structure and Function 67 Proteins in Context 67 3.1 Amino Acid Chemistry 69 3.2 Proteins Are Polymers of Amino Acids 74 3.3 Proteins Are Molecules of Defined Shape and Structure 79 3.4 Examples of Protein Structures and Functions 89 4 Proteins II: Enzymes 101 Enzymes in Context 101 4.1 Regarding Enzymes 103 4.2 Enzymes Increase Reaction Rate 108 4.3 The Mechanism of an Enzyme Can Be Deduced from Structural, Kinetic, and Spectral Data 117 4.4 Examples of Enzyme Regulation 127 5 Membranes and an Introduction to Signal Transduction 138 Biochemistry in Context 138 5.1 Membrane Structure and Function 139 5.2 Signal Transduction 149 6 Carbohydrates I: Mono- and Disaccharides, Glycolysis, Gluconeogenesis, and the Fates of Pyruvate 161 Carbohydrates in Context 161 6.1 Properties, Nomenclature, and Biological Functions of Monosaccharides 163 6.2 Properties, Nomenclature, and Biological Functions of Complex Carbohydrates 170 6.3 Glycolysis and an Introduction to Metabolic Pathways 177 6.4 Gluconeogenesis 193 6.5 The Fates of Pyruvate 196 7 The Common Catabolic Pathway: Citric Acid Cycle, the Electron Transport Chain, and ATP Biosynthesis 209 Electron Transport in Context 209 7.1 The Citric Acid Cycle 211 7.2 The Electron Transport Chain 223 7.3 ATP Biosynthesis 241 8 Carbohydrates II: Glycogen Metabolism, the Pentose Phosphate Pathway, Glycoconjugates, and Extracellular Matrices 253 Polysaccharides in Context 253 8.1 Glycogen Metabolism 255 8.2 The Pentose Phosphate Pathway 264 8.3 Carbohydrates in Glycoconjugates 273 8.4 Extracellular Matrices and Biofilms 284 9 Lipids I: Fatty Acids, Steroids, and Eicosanoids; Beta-Oxidation and Fatty Acid Biosynthesis 300 Lipids in Context 300 9.1 Properties, Nomenclature, and Biological Functions of Lipid Molecules 302 9.2 Fatty Acid Catabolism 311 9.3 Fatty Acid Biosynthesis 317 9.4 Ketone Body Metabolism 329 9.5 Steroid Metabolism 332 9.6 Eicosanoid and Endocannabinoid Metabolism 339 10 Lipids II: Metabolism and Transport of Complex Lipids 351 Complex Lipids in Context 351 10.1 Phospholipid Metabolism 353 10.2 Digestion of Triacylglycerols 361 10.3 Transport of Lipids in the Circulation 367 10.4 Entry of Lipids into the Cell 377 10.5 Neutral Lipid Biosynthesis 380 10.6 Lipid Storage Droplets, Fat Storage, and Mobilization 384 10.7 Lipid Rafts as a Biochemical Entity 388 11 Amino Acid and Amine Metabolism 397 Amine Metabolism in Context 397 11.1 Digestion of Proteins 399 11.2 Transamination and Oxidative Deamination 404 11.3 The Urea Cycle 409 11.4 Pathways of Amino Acid Carbon Skeleton Scavenging 414 11.5 The Detoxification of Other Amines and Xenobiotics 423 11.6 The Biochemistry of Renal Function 429 12 Regulation and Integration of Metabolism 440 Metabolism in Context 440 12.1 A Review of the Pathways and Crossroads of Metabolism 442 12.2 Organ Specialization and Metabolic States 446 12.3 Communication between Organs 455 12.4 Metabolic Disease 463 13 Nucleotide and Deoxynucleotide Metabolism 477 Nucleotides and Deoxynucleotides in Context 477 13.1 Purine Biosynthesis 478 13.2 Pyrimidine Biosynthesis 484 13.3 Deoxyribonucleotide Biosynthesis 489 13.4 Catabolism of Nucleotides 495 14 DNA Replication, Damage, and Repair 506 DNA in Context 506 14.1 Challenges of DNA Replication 507 14.2 DNA Replication in Prokaryotes 512 14.3 DNA Replication in Eukaryotes 517 14.4 DNA Damage and Repair 523 14.5 Homologous Recombination 534 15 RNA Synthesis and Processing 546 RNA Synthesis in Context 546 15.1 Transcription: RNA Synthesis 548 15.2 Processing of Nascent Eukaryotic RNA Messages 557 15.3 RNA Export from the Nucleus 566 16 Protein Synthesis 576 Protein Synthesis in Context 576 16.1 The Genetic Code 577 16.2 RNA Structure Function in Protein Biosynthesis 580 16.3 Protein Biosynthesis 585 17 Control and Regulation of Gene Expression 606 Gene Regulation in Context 606 17.1 DNA–Protein Interactions 607 17.2 Regulation of Expression in Prokaryotes 613 17.3 Regulation of Expression in Eukaryotes 623 18 Determination of Macromolecular Structure 649 Macromolecular Structure in Context 649 18.1 An Introduction to Structure Determination 650 18.2 Electron Microscopy 654 18.3 X-Ray Diffraction and Neutron Scattering 658 18.4 Nuclear Magnetic Resonance 668 19 Allosterism and Receptor–Ligand Interactions 679 Allosterism in Context 679 19.1 Allosterism and Cooperativity 680 19.2 Hemoglobin 686 19.3 Receptor–Ligand Interactions 696 20 Designer Proteins and Protein Folding 706 Protein Engineering and Folding in Context 706 20.1 Protein Production 707 20.2 Protein Engineering 714 20.3 Protein Folding 724 21 Biomolecule Purification 736 Protein Purification in Context 736 21.1 Protein Purification Basics 737 21.2 Size-Exclusion Chromatography 745 21.3 Affinity Chromatography 751 22 Bioinformatics and Omics 764 Bioinformatics in Context 764 22.1 Introduction to Bioinformatics 765 22.2 Generating Bioinformatic Data 769 22.3 Analyzing Bioinformatic Data 778 23 Signal Transduction 790 Cell Signaling in Context 790 23.1 A Review of Signal Transduction 791 23.2 An Overview of Regulation of Signal Transduction 797 23.3 Six New Signal Transduction Pathways 800 24 Protein Trafficking 821 Protein Trafficking in Context 821 24.1 Molecular Aspects of Protein Trafficking 822 24.2 Molecular Motors 827 24.3 Vesicular Fusion 834 25 Photosynthesis and Nitrogen Fixation 841 Photosynthesis and Nitrogen Fixation in Context 841 25.1 Photosynthesis 842 25.2 Nitrogen Fixation 859 Techniques T-1 solutions A-1 Glossary G-1 Index I-1