Lehninger Principles of Biochemistry, Fourth Edition - David L. Nelson, Michael M. Cox
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CONTENTS
Lehninger Principles of Biochemistry
Fourth Edition
David L. Nelson (U. of Wisconsin-Madison)
Michael M. Cox (U. of Wisconsin-Madison)
1. The Foundations of Biochemistry
1.1 Cellular Foundations
1.2 Chemical Foundations
1.3 Physical Foundations
1.4 Genetic Foundations
1.5 Evolutionary Foundations
Distilled and reorganized from Chapters 1-3 of the previous edition, this overview provides a refresher on the cellular, chemical, physical, genetic, and evolutionary background to biochemistry, while orienting students toward what is unique about biochemistry.
PART I. STRUCTURE AND CATALYSIS
2. Water
2.1 Weak Interactions in Aqueous Systems
2.2 Ionization of Water, Weak Acids, and Weak Bases
2.3 Buffering against pH Changes in Biological Systems
2.4 Water as a Reactant
2.5 The Fitness of the Aqueous Environment for Living Organisms Includes new coverage of the concept of protein-bound water, illustrated with
molecular graphics.
3. Amino Acids, Peptides, and Proteins
3.1 Amino Acids
3.2 Peptides and Proteins
3.3 Working with Proteins
3.4 The Covalent Structure of Proteins
3.5 Protein Sequences and Evolution
Adds important new material on genomics and proteomics and their implications for the study of protein structure, function, and evolution.
4. The Three-Dimensional Structure of Proteins
4.1 Overview of Protein Structure
4.2 Protein Secondary Structure
4.3 Protein Tertiary and Quaternary Structures
4.4 Protein Denaturation and Folding Adds a new box on scurvy.
5. Protein Function
5.1 Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins
5.2 Complementary Interactions between Proteins and Ligands: The Immune System and Immunoglobulins
5.3 Protein Interactions Modulated by Chemical Energy: Actin, Myosin, and Molecular Motors
Adds a new box on carbon monoxide poisoning
6. Enzymes
6.1 An Introduction to Enzymes
6.2 How Enzymes Work
6.3 Enzyme Kinetics as An Approach to Understanding Mechanism
6.4 Examples of Enzymatic Reactions
6.5 Regulatory Enzymes
Offers a revised presentation of the mechanism of chymotrypsin (the first reaction mechanism in the book), featuring a two-page figure that takes students through this particular mechanism, while serving as a step-by-step guide to interpreting any
reaction mechanism
Features new coverage of the mechanism for lysozyme including the controversial aspects of the mechanism and currently favored resolution based on work published in 2001.
7. Carbohydrates and Glycobiology
7.1 Monosaccharides and Disaccharides
7.2 Polysaccharides
7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids
7.4 Carbohydrates as Informational Molecules: The Sugar Code
7.5 Working with Carbohydrates
Includes new section on polysaccharide conformations.
A striking new discussion of the "sugar code" looks at polysaccharides as informational molecules, with detailed discussions of lectins, selectins, and oligosaccharide-bearing hormones.
Features new material on structural heteropolysaccharides and proteoglycans Covers recent techniques for carbohydrate analysis.
8. Nucleotides and Nucleic Acids
8.1 Some Basics
8.2 Nucleic Acid Structure
8.3 Nucleic Acid Chemistry
8.4 Other Functions of Nucleotides
9. DNA-Based Information Technologies
9.1 DNA Cloning: The Basics
9.2 From Genes to Genomes
9.3 From Genomes to Proteomes
9.4 Genome Alterations and New Products of Biotechnology
Introduces the human genome. Biochemical insights derived from the human genome are integrated throughout the text.
Tracking the emergence of genomics and proteomics, this chapter establishes DNA technology as a core topic and a path to understanding metabolism, signaling, and other topics covered in the middle chapters of this edition. Includes up-to-date coverage of microarrays, protein chips, comparative genomics, and techniques in cloning and analysis.
10. Lipids
10.1 Storage Lipids
10.2 Structural Lipids in Membranes
10.3 Lipids as Signals, Cofactors, and Pigments
10.4 Working with Lipids
Integrates new topics specific to chloroplasts and archaebacteria Adds material on lipids as signal molecules.
11. Biological Membranes and Transport
11.1 The Composition and Architecture of Membranes
11.2 Membrane Dynamics
11.3 Solute Transport across Membranes
Includes a description of membrane rafts and microdomains within membranes, and a new box on the use of atomic force microscopy to visualize them.
Looks at the role of caveolins in the formation of membrane caveolae Covers the investigation of hop diffusion of membrane lipids using FRAP (fluorescence recovery after photobleaching)
Adds new details to the discussion of the mechanism of Ca2- ATPase (SERCA
pump), revealed by the recently available high-resolution view of its structure
Explores new facets of the mechanisms of the K+ selectivity filter, brought to light by recent high-resolution structures of the K+ channel
Illuminates the structure, role, and mechanism of aquaporins with important new details
Describes ABC transporters, with particular attention to the multidrug transporter (MDR1)
Includes the newly solved structure of the lactose transporter of E. coli.
12. Biosignaling
12.1 Molecular Mechanisms of Signal Transduction
12.2 Gated Ion Channels
12.3 Receptor Enzymes
12.4 G Protein-Coupled Receptors and Second Messengers
12.5 Multivalent Scaffold Proteins and Membrane Rafts
12.6 Signaling in Microorganisms and Plants
12.7 Sensory Transduction in Vision, Olfaction, and Gustation
12.8 Regulation of Transcription by Steroid Hormones
12.9 Regulation of the Cell Cycle by Protein Kinases
12.10 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death
Updates the previous edition's groundbreaking chapter to chart the continuing rapid
development of signaling research
Includes discussion on general mechanisms for activation of protein kinases in cascades
Now covers the roles of membrane rafts and caveolae in signaling pathways, including the activities of AKAPs (A Kinase Anchoring Proteins) and other scaffold proteins
Examines the nature and conservation of families of multivalent protein binding modules, which combine to create many discrete signaling pathways
Adds a new discussion of signaling in plants and bacteria, with comparison to mammalian signaling pathways
Features a new box on visualizing biochemistry with fluorescence resonance energy transfer (FRET) with green fluorescent protein (GFP)
PART II: BIOENERGETICS AND METABOLISM
13. Principles of Bioenergetics
13.1 Bioenergetics and Thermodynamics
13.2 Phosphoryl Group Transfers and ATP
13.3 Biological Oxidation-Reduction Reactions
Examines the increasing awareness of the multiple roles of polyphosphate
Adds a new discussion of niacin deficiency and pellagra.
14. Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
14.1 Glycolysis
14.2 Feeder Pathways for Glycolysis
14.3 Fates of Pyruvate under Anaerobic Conditions: Fermentation
14.4 Gluconeogenesis
14.5 Pentose Phosphate Pathway of Glucose Oxidation
Now covers gluconeogenesis immediately after glycolysis, discussing their relatedness, differences, and coordination and setting up the completely new chapter on metabolic regulation that follows
Adds coverage of the mechanisms of phosphohexose isomerase and aldolase
Revises the presentation of the mechanism of glyceraldehyde 3-phosphate dehydrogenase.
New Chapter 15. Principles of Metabolic Regulation, Illustrated with Glucose and Glycogen Metabolism
15.1 The Metabolism of Glycogen in Animals
15.2 Regulation of Metabolic Pathways
15.3 Coordinated Regulation of Glycolysis and Gluconeogenesis
15.4 Coordinated Regulation of Glycogen Synthesis and Breakdown
15.5 Analysis of Metabolic Control
Brings together the concepts and principles of metabolic regulation in one chapter Concludes with the latest conceptual approaches to the regulation of metabolism, including metabolic control analysis and contemporary methods for studying and predicting the flux through metabolic pathways
16. The Citric Acid Cycle
16.1 Production of Acetyl-CoA (Activated Acetate)
16.2 Reactions of the Citric Acid Cycle
16.3 Regulation of the Citric Acid Cycle
16.4 The Glyoxylate Cycle
Expands and updates the presentation of the mechanism for pyruvate carboxylase. Adds coverage of the mechanisms of isocitrate dehydrogenase and citrate synthase.
17. Fatty Acid Catabolism
17.1 Digestion, Mobilization, and Transport of Fats
17.2 Oxidation of Fatty Acids
17.3 Ketone Bodies
Updates coverage of trifunctional protein
New section on the role of perilipin phosphorylation in the control of fat mobilization New discussion of the role of acetyl-CoA in the integration of fatty acid oxidation and synthesis
Updates coverage of the medical consequences of genetic defects in fatty acyl-CoA dehydrogenases
Takes a fresh look at medical issues related to peroxisomes
18. Amino Acid Oxidation and the Production of Urea
18.1 Metabolic Fates of Amino Groups
18.2 Nitrogen Excretion and the Urea Cycle
18.3 Pathways of Amino Acid Degradation
Integrates the latest on regulation of reactions throughout the chapter, with new material on genetic defects in urea cycle enzymes, and updated information on the regulatory function of N-acetylglutamate synthase.
Reorganizes coverage of amino acid degradation to focus on the big picture Adds new material on the relative importance of several degradative pathways Includes a new description of the interplay of the pyridoxal phosphate and tetrahydrofolate cofactors in serine and glycine metabolism
19. Oxidative Phosphorylation and Photophosphorylation
Oxidative Phosporylation
19.1 Electron-Transfer Reactions in Mitochondria
19.2 ATP Synthesis
19.3 Regulation of Oxidative Phosphorylation
19.4 Mitochondrial Genes: Their Origin and the Effects of Mutations
19.5 The Role of Mitochondria in Apoptosis and Oxidative Stress Photosynthesis: Harvesting Light Energy
19.6 General Features of Photophosphorylation
19.7 Light Absorption
19.8 The Central Photochemical Event: Light-Driven Electron Flow
19.9 ATP Synthesis by Photophosphorylation
Adds a prominent new section on the roles of mitochondria in apoptosis and oxidative stress
Now covers the role of IF1 in the inhibition of ATP synthase during ischemia
Includes revelatory details on the light-dependent pathways of electron transfer in photosynthesis, based on newly available molecular structures
20. Carbohydrate Biosynthesis in Plants and Bacteria
20.1 Photosynthetic Carbohydrate Synthesis
20.2 Photorespiration and the C4 and CAM Pathways
20.3 Biosynthesis of Starch and Sucrose
20.4 Synthesis of Cell Wall Polysaccharides: Plant Cellulose and Bacterial Peptidoglycan
20.5 Integration of Carbohydrate Metabolism in the Plant Cell
Reorganizes the coverage of photosynthesis and the C4 and CAM pathways
Adds a major new section on the synthesis of cellulose and bacterial peptidoglycan
21. Lipid Biosynthesis
21.1 Biosynthesis of Fatty Acids and Eicosanoids
21.2 Biosynthesis of Triacylglycerols
21.3 Biosynthesis of Membrane Phospholipids
21.4 Biosynthesis of Cholesterol, Steroids, and Isoprenoids
Features an important new section on glyceroneogenesis and the triacylglycerol cycle between adipose tissue and liver, including their roles in fatty acid metabolism (especially during starvation) and the emergence of thiazolidinediones as regulators of glyceroneogenesis in the treatment of type II diabetes
Includes a timely new discussion on the regulation of cholesterol metabolism at the genetic level, with consideration of sterol regulatory element-binding proteins (SREBPs).
22. Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
22.1 Overview of Nitrogen Metabolism
22.2 Biosynthesis of Amino Acids
22.3 Molecules Derived from Amino Acids
22.4 Biosynthesis and Degradation of Nucleotides
Adds material on the regulation of nitrogen metabolism at the level of transcription
Significantly expands coverage of synthesis and degradation of heme
23. Integration and Hormonal Regulation of Mammalian Metabolism
23.1 Tissue-Specific Metabolism: The Division of Labor
23.2 Hormonal Regulation of Fuel Metabolism
23.3 Long Term Regulation of Body Mass
23.4 Hormones: Diverse Structures for Diverse Functions
Reorganized presentation leads students through the complex interactions of integrated metabolism step by step
Features extensively revised coverage of insulin and glucagon metabolism that includes the integration of carbohydrate and fat metabolism
New discussion of the role of AMP-dependent protein kinase in metabolic integration
Updates coverage of the fast-moving field of obesity, regulation of body mass, and the leptin and adiponectin regulatory systems
Adds a discussion of Ghrelin and PYY3-36 as regulators of short-term eating behavior
Covers the effects of diet on the regulation of gene expression, considering the role of peroxisome proliferator-activated receptors (PPARs)
PART III. INFORMATION PATHWAYS
24. Genes and Chromosomes
24.1 Chromosomal Elements
24.2 DNA Supercoiling
24.3 The Structure of Chromosomes
