Lehninger Principles of Biochemistry, 6th Edition PDF

Media Connections Chapter 5 Protein Function B elow is a chapter-by-chapter list of the media resources available on the Instructor’s CD-ROM and website Molecular Structure Tutorial...

Media Connections Chapter 5 Protein Function B elow is a chapter-by-chapter list of the media resources available on the Instructor’s CD-ROM and website Molecular Structure Tutorial: Oxygen-Binding Proteins—Myoglobin: Oxygen Storage www.courses.bfwpub.com/lehninger6e. Living Graphs: Protein-Ligand Interactions Mechanism Animations (12 total) show key Binding Curve for Myoglobin reactions in detail. Molecular Structure Tutorial: Oxygen-Binding Technique Animations (10 total) reveal the Proteins—Hemoglobin: Oxygen Transport experimental techniques available to researchers today. Living Graphs: Cooperative Ligand Binding Living Graphs (15 total) allow students to alter the parameters in key equations and Hill Equation graph the results. Molecular Structure Tutorials: Molecular Structure Tutorials (9 total) guide Oxygen-Binding Proteins—Hemoglobin Is students through concepts using three- Susceptible to Allosteric Regulation dimensional molecular models. Oxygen-Binding Proteins—Defects in Hb Lead to Serious Genetic Disease New animations will be added throughout the life MHC Molecules of the edition. Technique Animation: Immunoblotting Chapter 2 Water Living Graph: Henderson-Hasselbalch Equation Chapter 6 Enzymes Living Graphs: Chapter 3 Amino Acids, Peptides, and Proteins Michaelis-Menten Equation Molecular Structure Tutorials: Protein Competitive Inhibitor Architecture—Amino Acids Uncompetitive Inhibitor Technique Animation: SDS Gel Electrophoresis Mixed Inhibitor Chapter 4 The Three-Dimensional Structure of Proteins Mechanism Animation: Chymotrypsin Molecular Structure Tutorials: Mechanism Protein Architecture—Sequence and Primary Living Graph: Lineweaver-Burk Equation Structure Protein Architecture—The ␣ Helix Chapter 8 Nucleotides and Nucleic Acids Molecular Structure Tutorial: Nucleotides, Build- Protein Architecture—The ␤ Sheet ing Blocks of Amino Acids Protein Architecture—Turn Technique Animation: Dideoxy Sequencing Protein Architecture—Introduction to Tertiary of DNA Structure Protein Architecture—Tertiary Structure of Chapter 9 DNA-Based Information Technologies Fibrous Proteins Molecular Structure Tutorial: Restriction Protein Architecture—Tertiary Structure of Endonucleases Small Globular Proteins Technique Animations: Protein Architecture—Tertiary Structure of Plasmid Cloning Large Globular Proteins Reporter Constructs Protein Architecture—Quaternary Structure Polymerase Chain Reaction Synthesizing an Oligonucleotide Array Carbamoyl Phosphate Synthetase I Mechanism Screening an Oligonucleotide Array for Patterns Argininosuccinate Synthetase Mechanism of Gene Expression Yeast Two-Hybrid Systems Chapter 19 Oxidative Phosphorylation and Photophosphorylation Creating a Transgenic Mouse Living Graph: Free-Energy Change for Transport of an Ion Chapter 11 Biological Membranes and Transport Living Graphs: Molecular Structure Tutorial: Bacteriorhodopsin Free-Energy Change for Transport Chapter 20 Carbohydrate Biosynthesis in Free-Energy Change for Transport of an Ion Plants and Bacteria Mechanism Animation: Rubisco Mechanism Chapter 12 Biosignaling Molecular Structure Tutorial: Trimeric G Proteins— Chapter 22 Biosynthesis of Amino Acids, Nucleotides, Molecular On/Off Switches and Related Molecules Mechanism Animations: Chapter 13 Bioenergetics and Biochemical Reaction Types Tryptophan Synthase Mechanism Living Graphs: Free-Energy Change Thymidylate Synthase Mechanism Free-Energy of Hydrolysis of ATP Chapter 24 Genes and Chromosomes Animation: Three-Dimensional Packaging of Chapter 14 Glycolysis, Gluconeogenesis, and the Pentose Nuclear Chromosomes Phosphate Pathway Mechanism Animations: Chapter 25 DNA Metabolism Phosphohexose Isomerase Mechanism Molecular Structure Tutorial: Restriction Alcohol Dehydrogenase Mechanism Endonucleases Thiamine Pyrophosphate Mechanism Animation: Nucleotide Polymerization by DNA Polymerase Chapter 16 The Citric Acid Cycle DNA Synthesis Mechanism Animation: Citrate Synthase Mechanism Chapter 26 RNA Metabolism Animation: mRNA Splicing Chapter 17 Fatty Acid Catabolism Mechanism Animation: Fatty Acyl–CoA Molecular Structure Tutorial: Hammerhead Synthetase Mechanism Ribozyme Animation: Life Cycle of an mRNA Chapter 18 Amino Acid Oxidation and the Production of Urea Mechanism Animations: Chapter 28 Regulation of Gene Expression Pyridoxal Phosphate Reaction Mechanism Molecular Structure Tutorial: Lac Repressor Lehninger Principles of Biochemistry SIXTH EDITION David L. Nelson Michael M. Cox Professor of Biochemistry Professor of Biochemistry University of Wisconsin–Madison University of Wisconsin–Madison W. H. FREEMAN AND COMPANY New York  Publisher: SUSAN WINSLOW Senior Acquisitions Editor: LAUREN SCHULTZ Senior Developmental Editor: SUSAN MORAN Developmental Editor: MATTHEW TONTONOZ Associate Director of Marketing: DEBBIE CLARE Marketing Director: JOHN BRITCH Marketing Assistant LINDSAY NEFF Media Editor: ALLISON MICHAEL Managing Editor: PHILIP McCAFFREY Project Editor: JANE O’NEILL Photo Editor: TED SZCZEPANSKI Photo Researcher: ELYSE RIEDER Art Director: DIANA BLUME Illustration Coordinator: JANICE DONNOLA Illustrations: H. ADAM STEINBERG and DRAGONFLY MEDIA GROUP Molecular Graphics: H. ADAM STEINBERG Production Manager: SUSAN WEIN Composition: APTARA, INC. Printing and binding: QUAD/GRAPHICS VERSAILLES North American Edition Cover image: The network of interactions in an animal mitochondrion. Each dot represents a compound, and each line, an enzyme that interconverts the two com- pounds. The major nodes include ADP, ATP, NAD⫹, and NADH. The image was constructed with Cytoscape software by Anthony Smith in the laboratory of Alan Robinson, Medical Research Council Mitochondrial Biology Unit, Cambridge, UK, using data from MitoMiner (Smith, A.C., Blackshaw, J.A., & Robinson, A.J. (2012) MitoMiner: a data warehouse for mitochondrial proteomics data. Nucleic Acids Res. 40, D1160–D1167). Background: Transmission electron micrograph of inter- scapular brown adipose cell from a bat. (Don W. Fawcett/Science Source/Photo Researchers) International Edition Cover design: Dirk Kaufman Cover image: Nastco/iStockphoto.com Library of Congress Control Number: 2012948755 North American Edition International Edition ISBN-13: 978-1-4292-3414-6 ISBN-13: 978-1-4641-0962-1 ISBN-10: 1-4292-3414-8 ISBN-10: 1-4641-0962-1 ©2013, 2008, 2005, 2000 by W. H. Freeman and Company All rights reserved Printed in the United States of America First printing W. H. Freeman and Company Macmillan Higher Education 41 Madison Avenue Houndmills, Basingstoke New York, NY 10010 RG21 6XS, England www.whfreeman.com www.macmillanhighered.com/international To Our Teachers Paul R. Burton Albert Finholt William P. Jencks Eugene P. Kennedy Homer Knoss Arthur Kornberg I. Robert Lehman Earl K. Nelson Wesley A. Pearson David E. Sheppard Harold B. White About the Authors David L. Nelson, born in Fairmont, Minnesota, received his BS in Chemistry and Biology from St. Olaf College in 1964 and earned his PhD in Biochemistry at Stan- ford Medical School under Arthur Kornberg. He was a postdoctoral fellow at the Harvard Medical School with Eugene P. Kennedy, who was one of Albert Lehninger’s first graduate students. Nelson joined the faculty of the University of Wisconsin–Madison in 1971 and became a full professor of biochemistry in 1982. He was for eight years the Director of the Center for Biology Education at the University of Wisconsin–Madison. Nelson’s research has focused on the signal trans- ductions that regulate ciliary motion and exocytosis in the protozoan Paramecium. The enzymes of signal transductions, including a variety of protein kinases, are primary targets of study. His research group has David L. Nelson and Michael M. Cox used enzyme purification, immunological techniques, electron microscopy, genetics, molecular biology, and electrophysiology to study these processes. Dave Nelson has a distinguished record as a lec- particularly on the RecA protein, designing purification turer and research supervisor. For 40 years he has and assay methods that are still in use, and illuminating taught an intensive survey of biochemistry for advanced the process of DNA branch migration. Exploration of biochemistry undergraduates in the life sciences. He the enzymes of genetic recombination has remained the has also taught a survey of biochemistry for nursing central theme of his research. students, and graduate courses on membrane struc- Mike Cox has coordinated a large and active research ture and function and on molecular neurobiology. He team at Wisconsin, investigating the enzymology, topol- has sponsored numerous PhD, MS, and undergraduate ogy, and energetics of genetic recombination. A primary honors theses and has received awards for his outstand- focus has been the mechanism of RecA protein–mediated ing teaching, including the Dreyfus Teacher–Scholar DNA strand exchange, the role of ATP in the RecA sys- Award, the Atwood Distinguished Professorship, and tem, and the regulation of recombinational DNA repair. the Unterkofler Excellence in Teaching Award from the Part of the research program now focuses on organisms University of Wisconsin System. In 1991–1992 he was a that exhibit an especially robust capacity for DNA repair, visiting professor of chemistry and biology at Spelman such as Deinococcus radiodurans, and the applications College. His second love is history, and in his dotage he of those repair systems to biotechnology. has begun to teach the history of biochemistry to under- For almost 30 years he has taught (with Dave graduates and to collect antique scientific instruments Nelson) the survey of biochemistry to undergraduates for use in a laboratory course he teaches. and has lectured in graduate courses on DNA structure and topology, protein-DNA interactions, and the bio- Michael M. Cox was born in Wilmington, Delaware. In chemistry of recombination. More recent projects have his first biochemistry course, Lehninger’s Biochemistry been the organization of a new course on professional was a major influence in refocusing his fascination with responsibility for first-year graduate students and the biology and inspiring him to pursue a career in biochem- establishment of a systematic program to draw talented istry. After graduating from the University of Delaware biochemistry undergraduates into the laboratory at an in 1974, Cox went to Brandeis University to do his doc- early stage of their collegiate career. He has received toral work with William P. Jencks, and then to Stanford awards for both his teaching and his research, including in 1979 for postdoctoral study with I. Robert Lehman. the Dreyfus Teacher–Scholar Award, the 1989 Eli Lilly He moved to the University of Wisconsin–Madison in Award in Biological Chemistry, and the 2009 Regents 1983 and became a full professor of biochemistry in Teaching Excellence Award from the University of 1992. Wisconsin. He is also highly active in national efforts to Cox’s doctoral research was on general acid and provide new guidelines for undergraduate biochemistry base catalysis as a model for enzyme-catalyzed reac- education. His hobbies include turning 18 acres of Wis- tions. At Stanford, he began work on the enzymes consin farmland into an arboretum, wine collecting, and involved in genetic recombination. The work focused assisting in the design of laboratory buildings. iv  A Note on the Nature of Science I n this twenty-first century, a typical science education often leaves the philosophical underpinnings of sci- ence unstated, or relies on oversimplified definitions. As ideas that a scientist accepts must be based on measur- able, reproducible observations, and the scientist must report these observations with complete honesty. you contemplate a career in science, it may be useful to The scientific method is actually a collection of consider once again the terms science, scientist, and paths, all of which may lead to scientific discovery. In the scientific method. hypothesis and experiment path, a scientist poses a Science is both a way of thinking about the natural hypothesis, then subjects it to experimental test. Many of world and the sum of the information and theory that the processes that biochemists work with every day were result from such thinking. The power and success of discovered in this manner. The DNA structure elucidated science flow directly from its reliance on ideas that can by James Watson and Francis Crick led to the hypothesis be tested: information on natural phenomena that can that base pairing is the basis for information transfer in be observed, measured, and reproduced and theories polynucleotide synthesis. This hypothesis helped inspire that have predictive value. The progress of science rests the discovery of DNA and RNA polymerases. on a foundational assumption that is often unstated but Watson and Crick produced their DNA structure crucial to the enterprise: that the laws governing forces through a process of model building and calculation. and phenomena existing in the universe are not subject No actual experiments were involved, although the model to change. The Nobel laureate Jacques Monod referred building and calculations used data collected by other to this underlying assumption as the “postulate of objec- scientists. Many adventurous scientists have applied the tivity.” The natural world can therefore be understood process of exploration and observation as a path to dis- by applying a process of inquiry—the scientific method. covery. Historical voyages of discovery (Charles Darwin’s Science could not succeed in a universe that played 1831 voyage on H.M.S. Beagle among them) helped to tricks on us. Other than the postulate of objectivity, sci- map the planet, catalog its living occupants, and change ence makes no inviolate assumptions about the natural the way we view the world. Modern scientists follow world. A useful scientific idea is one that (1) has been or a similar path when they explore the ocean depths or can be reproducibly substantiated and (2) can be used launch probes to other planets. An analog of hypothesis to accurately predict new phenomena. and experiment is hypothesis and deduction. Crick rea- Scientific ideas take many forms. The terms that sci- soned that there must be an adaptor molecule that facili- entists use to describe these forms have meanings quite tated translation of the information in messenger RNA different from those applied by nonscientists. A hypoth- into protein. This adaptor hypothesis led to the discovery esis is an idea or assumption that provides a reasonable of transfer RNA by Mahlon Hoagland and Paul Zamecnik. and testable explanation for one or more observations, Not all paths to discovery involve planning. Serendip- but it may lack extensive experimental substantiation. ity often plays a role. The discovery of penicillin by Alex- A scientific theory is much more than a hunch. It is ander Fleming in 1928 and of RNA catalysts by Thomas an idea that has been substantiated to some extent Cech in the early 1980s were both chance discoveries, and provides an explanation for a body of experimental albeit by scientists well prepared to exploit them. Inspira- observations. A theory can be tested and built upon and tion can also lead to important advances. The polymerase is thus a basis for further advance and innovation. When chain reaction (PCR), now a central part of biotechnology, a scientific theory has been repeatedly tested and vali- was developed by Kary Mullis after a flash of inspiration dated on many fronts, it can be accepted as a fact. during a road trip in northern California in 1983. In one important sense, what constitutes science These many paths to scientific discovery can seem or a scientific idea is defined by whether or not it is quite different, but they have some important things in published in the scientific literature after peer review by common. They are focused on the natural world. They other working scientists. About 16,000 peer-reviewed rely on reproducible observation and/or experiment. scientific journals worldwide publish some 1.4 million All of the ideas, insights, and experimental facts that articles each year, a continuing rich harvest of informa- arise from these endeavors can be tested and repro- tion that is the birthright of every human being. duced by scientists anywhere in the world. All can be Scientists are individuals who rigorously apply used by other scientists to build new hypotheses and the scientific method to understand the natural world. make new discoveries. All lead to information that is Merely having an advanced degree in a scientific disci- properly included in the realm of science. Understand- pline does not make one a scientist, nor does the lack ing our universe requires hard work. At the same time, of such a degree prevent one from making important no human endeavor is more exciting and potentially scientific contributions. A scientist must be willing to rewarding than trying, and occasionally succeeding, to challenge any idea when new findings demand it. The understand some part of the natural world. v Preface A s we complete our work on this sixth edition of Lehninger Principles of Biochemistry, we are again struck by the remarkable changes in the field of biochem- to the molecular mechanisms of disease, highlighting the special role that biochemistry plays in advancing human health and welfare. A special theme is the metabolic basis istry that have occurred between editions. The sheer of diabetes and the factors that predispose to the disease. volume of new information from high-throughput DNA This theme is interwoven through many chapters and sequencing, x-ray crystallography, and the manipulation serves to integrate the discussion of metabolism. We also of genes and gene expression, to cite only three examples, underscore the importance of evolution to biochemistry. challenges both the seasoned researcher and the first-time Evolutionary theory is the bedrock upon which all biologi- biochemistry student. Our goal here is to strike a balance: cal sciences rest, and we have not wasted opportunities to to include new and exciting research findings without highlight its important role in our discipline. making the book overwhelming for students. The primary To a significant degree, research progress in bio- criterion for inclusion is that the new finding helps to illus- chemistry runs in parallel with the development of bet- trate an important principle of biochemistry. ter tools and techniques. We have therefore highlighted The image on our cover, a map of the known meta- some of these crucial developments. Chapter 9, DNA- bolic transformations in a mitochondrion, illustrates the Based Information Technologies, in particular, has been richness of factual material now available about bio- significantly revised to include the latest advances in chemical transformations. We can no longer treat meta- genomics and next-generation sequencing. bolic “pathways” as though they occurred in isolation; a Finally, we have devoted considerable attention to single metabolite may be simultaneously part of many making the text and the art even more useful to stu- pathways in a three-dimensional network of metabolic dents learning biochemistry for the first time. To those transformations. Biochemical research focuses more and familiar with the book, some of these changes will be more upon the interactions among these pathways, the obvious as soon as you crack the cover. regulation of their interactions at the level of gene and With every revision of this textbook, we have striven protein, and the effects of regulation upon the activities to maintain the qualities that made the original Lehninger of a whole cell or organism. text a classic—clear writing, careful explanations of diffi- This edition of LPOB reflects these realities. Much of cult concepts, and insightful communication to students the new material that we have added reflects our increas- of the ways in which biochemistry is understood and ingly sophisticated understanding of regulatory mecha- practiced today. The authors have written together for nisms, including those involved in altering the synthesis almost 25 years and taught introductory biochemistry of enzymes and their degradation, those responsible for together for nearly 30. Our thousands of students at the the control and timing of DNA synthesis and the cell University of Wisconsin–Madison over those years have cycle, and those that integrate the metabolism of car- been an endless source of ideas about how to present bohydrates, fats, and proteins over time in response to biochemistry more clearly; they have enlightened and changes in the environment and in different cell types. inspired us. We hope that this sixth edition of Lehninger Even as we strive to incorporate the latest major will in turn enlighten and inspire current students of bio- advances, certain hallmarks of the book remain unchanged. chemistry everywhere, and perhaps lead some of them to We continue to emphasize the relevance of biochemistry love biochemistry as we do. New Art (a) Folding intermediate delivered by Hsp70-ADP (b) GroES The most obvious change to the book is the completely revamped art program. Our goal 7 ATP ATP ADP ADP hydrolysis throughout has been to improve pedagogy, GroEL ATP ATP ATP ATP ADP ADP ATP ATP ATP ATP ADP ADP drawing on modern graphic resources to make ADP ADP 7 ADP 7Pi our subject as clear as humanly possible. Many figures illustrate new topics, and much of the or art has been reconceived and modernized in Slow-folding Native intermediate protein style. Defining features of the new art program include: 7Pi 7 ADP ADP ADP ADP ADP u Smarter renditions of classic figures ADP ADP ATP ATP ADP ATP ADP ADP ATP ADP ADP ADP are easier to interpret and learn from; ATP ADP ADP ATP ATP ATP hydrolysis 7 Folding intermediate GroES delivered by Hsp70-ADP Chaperonins in protein folding vi  Preface vii 1 Protein degradation 9 Excess u Figures that pair molecular models with yields schematic cartoons, generated specifically for ketone glucogenic bodies amino acids. end up in urine. this book, use shapes and color schemes that are 2 Urea 4 Glucose 8 Ketone bodies are 5 Fatty acids internally consistent; is exported is exported exported via the (imported from to the kidney and excreted to the brain via the bloodstream to the brain, which uses adipose tissue) are oxidized as fuel, u Figures with numbered, annotated steps help in urine. bloodstream. them as fuel. producing acetyl-CoA. explain complex processes; in many cases, we Urea Glucose have moved descriptive text out of the legends Ketone bodies and into the figure itself; Pi Acetoacetyl-CoA Fatty acids NH3 Glucose 6-phosphate u Summary figures help the student to keep the 7 Acetyl-CoA accumulation favors ketone body synthesis. big picture in mind while learning the specifics. Amino Phosphoenol- Acetyl-CoA acids pyruvate 6 Lack of oxaloacetate 3 Citric acid cycle prevents acetyl-CoA entry intermediates into the citric acid cycle; are diverted to acetyl-CoA accumulates. gluconeogenesis. Oxaloacetate Citrate Fuel metabolism in the liver during prolonged fasting or in uncontrolled diabetes mellitus Updated Genomics (a) Add blocked, fluorescently Remove labels and labeled nucleotides. blocking groups; Modern genomic techniques have transformed our wash; add blocked, labeled nucleotides. Remove labels and blocking groups; Remove labels and C understanding of biochemistry. In this edition, we have wash; add blocked, blocking groups; A C labeled nucleotides. wash; add blocked, A T A T A T A T labeled nucleotides. dramatically updated our coverage of genomic methods T A C C G C G C G C G G T A C G C G C G C G C and their applications. Chapter 9, DNA-Based Informa- T A G T A G T T A A T T A T A T A T A T tion Technologies, has been completely revised to 3 Thymine nucleotide G 3 G C G G C G added; fluorescent incorporate the latest genomic methods. Many other C Adenine nucleotide C 3 C G C color observed added; fluorescent and recorded. Cytosine nucleotide A color observed A A 3 A added; fluorescent chapters have been updated to reflect advances gained G T and recorded. G T color observed and recorded. G T Guanine nucleotide T added; fluorescent G from these methods. Among the new genomic methods C C C color observed and recorded. C discussed in this edition are: A 5 A 5 A 5 A 5 u Next-generation DNA sequencing, including the (b) dNTP incorporated Illumina and 454 sequencing methods and TACGGTCTC: CCCCCCAGT: platforms (Chapter 9) u Applications of genomics, including the use of (c) haplotypes to trace human migrations and phylogenetics to locate human genes associated with inherited diseases (Chapter 9) u Forensic genotyping and the use of personalized genomics in medicine (Chapter 9) Next-generation reversible terminator sequencing New Science ( a) (c) Every chapter has been thoroughly revised and updated Cyclin A to include both the most important advances in bio- N terminus chemistry and information needed in a modern bio- C terminus chemistry text. Among the new and updated topics in Sirtuin this edition are: u Prebiotic evolution, black smokers, and the RNA (b) world (Chapter 1) 1.0 CBP bromo domain PONDR score u Intrinsically disordered proteins (Chapter 4) 0.5 s100B(bb) u Transition-state analogs and irreversible inhibition 0.0 0 100 200 300 400 (Chapter 6) Amino acid residues u Blood coagulation pathways in the context of Binding of the intrinsically disordered carboxyl terminus of p53 enzymatic regulation (Chapter 6) to its binding partners viii Preface u Asymmetric lipid distribution in bilayers u Microbial symbionts in the gut and their influence on (Chapter 11) energy metabolism and adipogenesis (Chapter 23) u Role of BAR superfamily proteins in membrane u Nucleosomes: their modification and positioning curvature (Chapter 11) and higher-order chromatin structure (Chapter 24) u Scaffold proteins (AKAPS and others) and their u DNA polymerases and homologous recombination regulatory roles (Chapter 12) (Chapter 25) u Reactive oxygen species as byproducts and as u Loading of eukaryotic RNA polymerase II signals (Chapter 19) (Chapter 26) u Structure and function of the oxygen-evolving u Mutation-resistant nature of the genetic code metal cluster in PSII (Chapter 19) (Chapter 27) u Formation and transport of lipoproteins in u Regulation of eukaryotic gene expression by mammals, including the roles of SREBP SCAP, and miRNAs (Chapters 26 and 28). Insig in cholesterol regulation (Chapter 21) u DNA looping, combinatorial control, chromatin u Integration of carbohydrate and lipid metabolism remodeling, and positive regulation in eukaryotes by PPARs, SREBPs, mTORC1, and LXR (Chapters (Chapter 28) 21, 23) u Regulation of the initiation of transcription in u Creatine phosphate and the role of creatine kinase eukaryotes (Chapter 28) in moving ATP to the cytosol (Chapter 23) u Steroid-binding nuclear receptors (Chapter 28) New Biochemical Methods An appreciation of biochemistry often requires an under- u Modern genomic methods (Chapter 9) standing of how biochemical information is obtained. u Genetic engineering of photosynthetic organisms Some of the new methods or updates described in this (Chapter 20) edition are: u Use of positron emission tomography (PET) to u Modern Sanger protein sequencing and mass visualize tumors and brown adipose tissue spectrometry (Chapter 3) (Chapter 23) u Mass spectrometry applied to proteomics, glycomics, u Development of bacterial strains with altered lipidomics, and metabolomics (Chapters 3, 7, 10) genetic codes for site-specific insertion of novel u Oligosaccharide microarrays to explore protein- amino acids into proteins (Chapter 27) oligosaccharide interactions and the “carbohydrate code” (Chapter 7) New Medical Applications This icon is used throughout the book to denote u Multidrug resistance transporters and their material of special medical interest. As teach- importance in clinical medicine (Chapter 11) ers, our goal is for students to learn biochemistry and u Multistep progression to colorectal cancer to understand its relevance to a healthier life and a (Chapter 12) healthier planet. Many sections explore what we know about the molecular mechanisms of disease. A few u Cholesterol metabolism, cardiovascular disease, of the new or revised medical applications in this edi- and mechanism of plaque formation in tion are: atherosclerosis (Chapter 21) u Box 4-6, Death by Misfolding: The Prion Diseases u P-450 and drug interactions (Chapter 21) u Paganini and Ehlers-Danlos syndrome (Chapter 4) u HMG-CoA reductase (Chapter 21) and Box 21–3, The Lipid Hypothesis and the Development of u HIV protease inhibitors and how basic enzymatic Statins principles influenced their design (Chapter 6) u Box 24–1, Curing Disease by Inhibiting u Blood coagulation cascade and hemophilia Topoisomerases, describing the use of (Chapter 6) topoisomerase inhibitors in the treatment of u Curing African sleeping sickness with an enzymatic bacterial infections and cancer, including material suicide inhibitor (Chapter 6) on ciprofloxacin (the antibiotic effective for u How researchers locate human genes involved in anthrax) inherited diseases (Chapter 9) u Stem cells (Chapter 28)  Preface ix Special Theme: Understanding Metabolism through Obesity and Diabetes Obesity and its medical consequences—cardiovascular u Adipose Tissue Generates Glycerol 3-phosphate by disease and diabetes—are fast becoming epidemic in Glyceroneogenesis (Chapter 21) the industrialized world, and we include new material u Diabetes Mellitus Arises from Defects in Insulin on the biochemical connections between obesity and Production or Action (Chapter 23) health throughout this edition. Our focus on diabetes provides an integrating theme throughout the chapters u Section 23.4, Obesity and the Regulation of Body on metabolism and its control, and this will, we hope, Mass, includes a new discussion of the roles of inspire some students to find solutions for this disease. TORC1 in regulating cell growth Some of the sections and boxes that highlight the inter- u Section 23.5, Obesity, the Metabolic Syndrome, play of metabolism, obesity, and diabetes are: and Type 2 Diabetes, discusses the role of ectopic u Untreated Diabetes Produces Life-Threatening lipids and inflammation in the development of Acidosis (Chapter 2) insulin resistance and the management of type 2 diabetes with exercise, diet, and medication u Box 7–1, Blood Glucose Measurements in the Diagnosis and Treatment of Diabetes, Lean Overweight Pro-inflammatory state Chronic inflammation introduces hemoglobin glycation and AGEs 1 TAGdiet  TAGcatabolized 2 TAGdiet  TAGcatabolized 3 Enlarged adipocytes produce macrophage 4 Macrophages infiltrate adipose and their role in the pathology of advanced chemotaxis protein (MCP-1). tissue in response to MCP-1. diabetes Small adipocytes Larger adipocytes Larger adipocytes Larger adipocytes 5 Macrophages in adipose tissue produce TNFa, which u Glucose Uptake Is Deficient in Type 1 TAG MCP-1 TNFa favors export of fatty acids. Diabetes Mellitus (Chapter 14) 6 Adipocytes export fatty acids to muscle, where Fatty Fatty Fatty Fatty ectopic lipid deposits form. Ketone Bodies Are Overproduced in acids acids acids acids u Diabetes and during Starvation (Chapter 17) 7 Ectopic lipid interferes with GLUT4 movement to the myocyte surface, producing Glucose Glucose Glucose Glucose ATP ATP ATP insulin resistance. u Some Mutations in Mitochondrial Genomes Cause Disease (Chapter 19) Insulin-sensitive Insulin-resistant muscle with normal muscle with reduced u Diabetes Can Result from Defects in the glucose transport glucose transport Mitochondria of Pancreatic  Cells Overloading adipocytes with triacylglycerols triggers inflammation in fat tissue, (Chapter 19) ectopic lipid deposition, and insulin resistance. Special Theme: Evolution Every time a biochemist studies a developmental pathway u Box 9–3, Getting to Know the Neanderthals in nematodes, identifies key parts of an enzyme active site u ABC Transporters Use ATP to Drive the Active by determining what parts are conserved between spe- Transport of a Wide Variety of Substrates cies, or searches for the gene underlying a human genetic (Chapter 11) disease, he or she is relying on evolutionary theory. Fund- ing agencies support the work in nematodes knowing that u Signaling Systems of Plants Have Some of the the insights will be relevant to humans. The conservation Same Components Used by Microbes and of functional residues in an enzyme active site telegraphs Mammals (Chapter 12) the shared history of every organism on the planet. More u The -Oxidation Enzymes of Different Organelles often than not, the search for a disease gene is a sophis- Have Diverged during Evolution (Chapter 17) ticated exercise in phylogenetics. Evolution is thus a u Section 19.10, The Evolution of Oxygenic foundational concept to our discipline. Some of the many Photosynthesis sections and boxes that deal with evolution include: u Mitochondria and Chloroplasts Evolved from u Section 1.5, Evolutionary Foundations, discusses Endosymbiotic Bacteria (Chapter 19) how life may have evolved and recounts some of the early milestones in the evolution of eukaryotic u Photosystems I and II Evolved from Bacterial cells Photosystems (Chapter 19) u Genome Sequencing Informs Us about Our u RNA Synthesis Offers Important Clues to Humanity (Chapter 9) Biochemical Evolution (Chapter 26) u Genome Comparisons Help Locate Genes Involved u Box 27–1, Exceptions That Prove the Rule: Natural in Disease (Chapter 9) Variations in the Genetic Code u Genome Sequences Inform Us about Our Past and u Box 27–2, From an RNA World to a Protein World Provide Opportunities for the Future (Chapter 9) u Box 28-1, Of Fins, Wings, Beaks, and Things x Preface Lehninger Teaching Hallmarks 1 Claisen condensation: Acetyl-CoA methyl group of Students encountering biochemistry for the first O acetyl-CoA converted to methylene in citrate. 8 time often have difficulty with two key aspects Dehydrogenation: CH3 C S-CoA H2O CoA-SH of the course: approaching quantitative problems oxidation of —OH completes oxidation Oxaloacetate citrate synthase Citrate CH2 COO and drawing on what they learned in organic sequence; generates carbonyl positioned to O C COO HO C COO Dehydration/rehydration: —OH group of citrate facilitate Claisen chemistry to help them understand biochem- condensation in next step. CH2 COO  CH2 COO  repositioned in isocitrate to set up decarboxylation istry. Those same students must also learn a in next step. malate Citric acid cycle aconitase H2O complex language, with conventions that are 7 Malate dehydrogenase COO often unstated. To help students cope with these Hydration: addition of HO CH CH2 COO water across challenges, we provide the following study aids: double bond introduces CH2 C COO cis-Aconitate COO C COO —OH group H Focus on Chemical Logic for next oxidation step. fumarase (3) NADH H2O aconitase u Section 13.2, Chemical Logic and H2O (Rehydration) Common Biochemical Reactions, COO CH2 COO Fumarate CH COO discusses the common biochemical H C HC Isocitrate HO C H reaction types that underlie all metabolic COO FADH2 isocitrate COO 3 6 Oxidative reactions, helping students to connect Dehydrogenation: succinate dehydrogenase dehydrogenase decarboxylation: —OH group oxidized organic chemistry with biochemistry. introduction of double bond initiates CH2 COO CO2 to carbonyl, which in turn facilitates methylene oxidation CH2 COO a-ketoglutarate decarboxylation by u NEW chemical logic figures highlight sequence. CH2 succinyl-CoA synthetase dehydrogenase complex CH2 stabilizing carbanion formed on adjacent C O the conservation of mechanism and Succinate COO CH2 COO COO carbon. CH2 illustrate patterns that make learning CoA-SH a-Ketoglutarate CoA-SH GTP C S-CoA CO2 4 pathways easier. Chemical logic figures are 5 (ATP) GDP O (ADP) Succinyl-CoA Oxidative decarboxylation: pyruvate-dehydrogenase-like provided for each of the central metabolic Substrate-level phosphorylation: energy of thioester conserved in  Pi mechanism; dependent on carbonyl on adjacent carbon. pathways, including glycolysis (Fig. 14–3), phosphoanhydride bond of GTP or ATP. citric acid cycle (Fig. 16–7), and fatty acid oxidation (Fig. 17–9). Reactions of the citric acid cycle (a) OH OH CH CH CH2 O P Indole-3-glycerol phosphate N H An aldol cleavage OH tryptophan O produces indole synthase and glyceraldehyde a subunits C CH CH2 O P 3-phosphate; PLP is not required. 1 H Glyceraldehyde 3-phosphate Indole traverses tunnel between a and b subunits. N Indole H  NH3 u Mechanism figures feature step-by-step Dehydration of tryptophan  CH2 CH COO  (b) descriptions to help students understand the reaction process. These figures use a serine forms a synthase OH Serine PLP-aminoacrylate b subunits PLP intermediate. Glyceraldehyde 2 H2O 3-phosphate Indole consistent set of conventions introduced ␣ B and explained in detail with the first enzyme mechanism encountered H  ␤ N H H2C C COO Tunnel (chymotrypsin, pp. 216–217).  Indole NH ␤␤ HC P O CH2 OH Indole From serine ␤  N CH3 H Quinonoid PLP-aminoacrylate Indole condenses adduct with the aminoac- rylate intermediate 3 (2 steps). B HB H H  CH2 COO NH3 CH2 CH COO Enzyme PLP C H2O  N  CH2 CH COO H  N NH NH H ␤␤ HC ␤ HC P O CH2 OH 4 P O CH2 OH 5