মুখ্য Lehninger Principles of Biochemistry
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26 March 2020 (22:13)
Not the nice looking pdf.
06 October 2020 (03:02)
Pls upload latest version.
I am badly need this new version (lehninger principles of biochemistry 8e)
I am badly need this new version (lehninger principles of biochemistry 8e)
02 April 2021 (00:14)
This is again not the exact soft copy of the print version of this textbook
15 May 2021 (07:09)
Can someone tell me for which couse you actually use this book for please?
20 May 2021 (06:48)
Media Connections this edition, we introduce our new SaplingPlus with Lehninger W ith teaching and learning platform. Its online homework system provides robust, high-level questions that you can assign to students for practice and assessment, with hints and wrong-answer feedback. Below is a chapter-by-chapter list of the other media resources available on the SaplingPlus with Lehninger platform. • The Interactive Metabolic Map, including tutorials and concept check questions, allows students to zoom between overview and detailed views of the most commonly taught metabolic pathways. • Case Studies (6, with more to be added) ask students to solve a biochemical mystery by choosing from different investigation options. • Molecular Structure Tutorials (9) guide students through concepts using three-dimensional molecular models, now updated with multiple-choice assessment. • Simulations (11) allow students to interact with structures and processes in a gamelike format. • Animated Mechanism Figures (29) show key reactions in detail. • Living Graphs (18) allow students to alter the parameters in key equations and graph the results. • Nature Articles with Assessment (6) provide an article from Nature plus tailored assessment to engage students in reading primary literature and to encourage critical thinking. • Animated Biochemical Techniques (9) illustrate the principles behind some of the most commonly used biochemical techniques. Chapter 2 Water Living Graphs: Henderson-Hasselbalch Equation Titration Curve for a Weak Acid Chapter 3 Amino Acids, Peptides, and Proteins UPDATED Molecular Structure Tutorial: Protein Architecture, section on amino acids Animated Biochemical Technique: SDS Gel Electrophoresis Chapter 4 The Three-Dimensional Structure of Proteins UPDATED Molecular Structure Tutorial: Protein Architecture, including sections on: Sequence and Primary Structure The α Helix The β Sheet The β Turn Introduction to Tertiary Structure Tertiary Structure of Fibrous Proteins Tertiary Structure of Small Globula; r Proteins Tertiary Structure of Large Globular Proteins Quaternary Structure Chapter 5 Protein Function UPDATED Molecular Structure Tutorials: Oxygen-Binding Proteins, including sections on: Myoglobin: Oxygen Storage Hemoglobin: Oxygen Transport Hemoglobin Is Susceptible to Allosteric Regulation Defects in Hb Lead to Serious Disease MHC Molecules Living Graphs: Protein-Ligand Interactions Binding Curve for Myoglobin Cooperative Ligand Binding Hill Equation Animated Biochemical Technique: Immunoblotting Chapter 6 Enzymes NEW Case Studies: Toxic Alcohols—Enzyme Function A Likely Story—Enzyme Inhibition UPDATED Animated Mechanism Figure: Chymotrypsin Mechanism Living Graphs: Michaelis-Menten Equation Competitive Inhibitor Uncompetitive Inhibitor Mixed Inhibitor Lineweaver-Burk Equation Chapter 8 Nucleotides and Nucleic Acids UPDATED Molecular Structure Tutorial: Nucleotides NEW Simulations: Nucleotide Structure DNA/RNA Structure Sanger Sequencing Polymerase Chain Reaction NEW Nature Article with Assessment: LAMP: Adapting PCR for Use in the Field Animated Biochemical Techniques: Dideoxy Sequencing of DNA Polymerase Chain Reaction Chapter 9 DNA-Based Information Technologies UPDATED Molecular Structure Tutorial: Restriction Endonucleases NEW Simulation: CRISPR NEW Nature Articles with Assessment: Assessing Untargeted DNA Cleavage by CRISPR/Cas9 Genome Dynamics during Experimental Evolution Animated Biochemical Techniques: Plasmid Cloning Reporter Constructs Synthesizing an Oligonucleotide Array Screening an Oligonucleotide Array for Patterns of Gene Expression Yeast Two-Hybrid Systems Chapter 11 Biological Membranes and Transport Living Graphs: Free-Energy Change for Transport (graph) Free-Energy Change for Transport (equation) Free-Energy Change for Transport of an Ion Chapter 12 Biosignaling UPDATED Molecular Structure Tutorial: Trimeric G Proteins Chapter 13 Bioenergetics and Biochemical Reaction Types Living Graphs: Free-Energy Change Free-Energy of Hydrolysis of ATP (graph) Free-Energy of Hydrolysis of ATP (equation) Chapter 14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway NEW Interactive Metabolic Map: Glycolysis NEW Case Study: Sudden Onset—Introduction to Metabolism UPDATED Animated Mechanism Figures: Phosphohexose Isomerase Mechanism The Class I Aldolase Mechanism Glyceraldehyde 3-Phosphate Dehydrogenase Mechanism Phosphoglycerate Mutase Mechanism Alcohol Dehydrogenase Mechanism Pyruvate Decarboxylase Mechanism Chapter 16 The Citric Acid Cycle NEW Interactive Metabolic Map: The citric acid cycle NEW Case Study: An Unexplained Death—Carbohydrate Metabolism UPDATED Animated Mechanism Figures: Citrate Synthase Mechanism Isocitrate Dehydrogenase Mechanism Pyruvate Carboxylase Mechanism Chapter 17 Fatty Acid Catabolism NEW Interactive Metabolic Map: β-Oxidation NEW Case Study: A Day at the Beach—Lipid Metabolism UPDATED Animated Mechanism Figure: Fatty Acyl-CoA Synthetase Mechanism Chapter 18 Amino Acid Oxidation and the Production of Urea UPDATED Animated Mechanism Figures: Pyridoxal Phosphate Reaction Mechanisms (3) Carbamoyl Phosphate Synthetase Mechanism Argininosuccinate Synthetase Mechanism Serine Dehydratase Mechanism Serine Hydroxymethyltransferase Mechanism Glycine Cleavage Enzyme Mechanism Chapter 19 Oxidative Phosphorylation Living Graph: Free-Energy Change for Transport of an Ion Chapter 20 Photosynthesis and Carbohydrate Synthesis in Plants UPDATED Molecular Structure Tutorial: Bacteriorhodopsin UPDATED Animated Mechanism Figure: Rubisco Mechanism Chapter 22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules UPDATED Animated Mechanism Figures: Tryptophan Synthase Mechanism Thymidylate Synthase Mechanism Chapter 23 Hormonal Regulation and Integration of Mammalian Metabolism NEW Case Study: A Runner’s Experiment—Integration of Metabolism (Chs 14–18) Chapter 24 Genes and Chromosomes Animation: Three-Dimensional Packaging of Nuclear Chromosomes Chapter 25 DNA Metabolism UPDATED Molecular Structure Tutorial: Restriction Endonucleases NEW Simulations: DNA Replication DNA Polymerase Mutation and Repair NEW Nature Article with Assessment: Looking at DNA Polymerase III Up Close Animations: Nucleotide Polymerization by DNA Polymerase DNA Synthesis Chapter 26 RNA Metabolism UPDATED Molecular Structure Tutorial: Hammerhead Ribozyme NEW Simulations: Transcription mRNA Processing NEW Animated Mechanism Figure: RNA Polymerase NEW Nature Article with Assessment: Alternative RNA Cleavage and Polyadenylation Animations: mRNA Splicing Life Cycle of an mRNA Chapter 27 Protein Metabolism NEW Simulation: Translation NEW Nature Article with Assessment: Expanding the Genetic Code in the Laboratory Chapter 28 Regulation of Gene Expression UPDATED Molecular Structure Tutorial: Lac Repressor Lehninger Principles of Biochemistry Lehninger Principles of Biochemistry SEVENTH EDITION David L. Nelson Professor Emeritus of Biochemistry University of Wisconsin–Madison Michael M. Cox Professor of Biochemistry University of Wisconsin–Madison Vice President, STEM: Ben Roberts Senior Acquisitions Editor: Lauren Schultz Senior Developmental Editor: Susan Moran Assistant Editor: Shannon Moloney Marketing Manager: Maureen Rachford Marketing Assistant: Cate McCaffery Director of Media and Assessment: Amanda Nietzel Media Editor: Lori Stover Director of Content (Sapling Learning): Clairissa Simmons Lead Content Developer, Biochemistry (Sapling Learning): Richard Widstrom Content Development Manager for Chemistry (Sapling Learning): Stacy Benson Visual Development Editor (Media): Emiko Paul Director, Content Management Enhancement: Tracey Kuehn Managing Editor: Lisa Kinne Senior Project Editor: Liz Geller Copyeditor: Linda Strange Photo Editor: Christine Buese Photo Researcher: Roger Feldman Text and Cover Design: Blake Logan Illustration Coordinator: Janice Donnola Illustrations: H. Adam Steinberg Molecular Graphics: H. Adam Steinberg Production Manager: Susan Wein Composition: Aptara, Inc. Printing and Binding: RR Donnelley Front Cover Image: H. Adam Steinberg and Quade Paul Back Cover Photo: Yigong Shi Front cover: An active spliceosome from the yeast Schizosaccharomyces pombe. The structure, determined by cryo-electron microscopy, captures a molecular moment when the splicing reaction is nearing completion. It includes the snRNAs U2, U5, and U6, a spliced intron lariat, and many associated proteins. Structure determined by Yigong Shi and colleagues, Tsinghua University, Beijing, China (PDB ID 3JB9, C. Yan et al., Science 349:1182, 2015). Back cover: Randomly deposited individual spliceosome particles, viewed by electron microscopy. The structure on the front cover was obtained by computationally finding the orientations that are superposable, to reduce the noise and strengthen the signal—the structure of the spliceosome. Photo courtesy of Yigong Shi. Library of Congress Control Number: 2016943661 North American Edition ISBN-13: 978-1-4641-2611-6 ISBN-10: 1-4641-2611-9 ©2017, 2013, 2008, 2005 by W. H. Freeman and Company All rights reserved. Printed in the United States of America First printing W. H. Freeman and Company One New York Plaza Suite 4500 New York, NY 10004-1562 www.macmillanlearning.com International Edition Macmillan Higher Education Houndmills, Basingstoke RG21 6XS, England 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 Stanford 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 Director of the Center for Biology Education at the University of Wisconsin– Madison. He became Professor Emeritus in 2013. Nelson’s research focused on the signal transductions that regulate ciliary motion and exocytosis in the protozoan Paramecium. He has a distinguished record as a lecturer and research supervisor. For 43 years he taught (with Mike Cox) an intensive survey of biochemistry for advanced biochemistry undergraduates in the life sciences. He has also taught a survey of biochemistry for nursing students, as well as graduate courses on membrane structure and function and on molecular neurobiology. He has received awards for his outstanding teaching, including the Dreyfus Teacher– Scholar Award, the Atwood Distinguished Professorship, and the Underkofler Excellence in Teaching Award from the University of Wisconsin System. In 1991–1992 he was a visiting professor of chemistry and biology at Spelman College. Nelson’s second love is history, and in his dotage he teaches the history of biochemistry and collects antique scientific instruments for use in the Madison Science Museum, of which he is the founding president. Michael M. Cox was born in Wilmington, Delaware. In his first biochemistry course, the first edition of Lehninger’s Biochemistry was a major influence in refocusing his fascination with biology and inspiring him to pursue a career in biochemistry. After graduating from the University of Delaware in 1974, Cox went to Brandeis University to do his doctoral work with William P. Jencks, and then to Stanford in 1979 for postdoctoral study with I. Robert Lehman. He moved to the University of Wisconsin–Madison in 1983 and became a full professor of biochemistry in 1992. Cox’s doctoral research was on general acid and base catalysis as a model for enzyme-catalyzed reactions. At Stanford, he began work on the enzymes involved in genetic recombination. The work focused particularly on the RecA protein, designing purification and assay methods that are still in use, and illuminating the process of DNA branch migration. Exploration of the enzymes of genetic recombination has remained a central theme of his research. David L. Nelson and Michael M. Cox. [Source: Robin Davies, UW–Madison Biochemistry MediaLab.] Mike Cox has coordinated a large and active research team at Wisconsin, investigating the enzymology, topology, and energetics of the recombinational DNA repair of double-strand breaks in DNA. The work has focused on the bacterial RecA protein, a wide range of proteins that play auxiliary roles in recombinational DNA repair, the molecular basis of extreme resistance to ionizing radiation, directed evolution of new phenotypes in bacteria, and the applications of all of this work to biotechnology. For more than three decades he has taught a survey of biochemistry to undergraduates and has lectured in graduate courses on DNA structure and topology, protein-DNA interactions, and the biochemistry of recombination. More recent projects are the organization of a new course on professional responsibility for first-year graduate students and establishment of a systematic program to draw talented biochemistry undergraduates into the laboratory at an early stage of their college career. He has received awards for both his teaching and his research, including the Dreyfus Teacher– Scholar Award, the 1989 Eli Lilly Award in Biological Chemistry, and the 2009 Regents Teaching Excellence Award from the University of Wisconsin. He is also highly active in national efforts to provide new guidelines for undergraduate biochemistry education. Cox’s hobbies include turning 18 acres of Wisconsin farmland into an arboretum, wine collecting, and assisting in the design of laboratory buildings. A Note on the Nature of Science I n this twenty-first century, a typical science education often leaves the philosophical underpinnings of science unstated, or relies on oversimplified definitions. As you contemplate a career in science, it may be useful to consider once again the terms science, scientist, and scientific method. Science is both a way of thinking about the natural world and the sum of the information and theory that result from such thinking. The power and success of science flow directly from its reliance on ideas that can be tested: information on natural phenomena that can be observed, measured, and reproduced and theories that have predictive value. The progress of science rests on a foundational assumption that is often unstated but crucial to the enterprise: that the laws governing forces and phenomena existing in the universe are not subject to change. The Nobel laureate Jacques Monod referred to this underlying assumption as the “postulate of objectivity.” The natural world can therefore be understood by applying a process of inquiry—the scientific method. Science could not succeed in a universe that played tricks on us. Other than the postulate of objectivity, science makes no inviolate assumptions about the natural world. A useful scientific idea is one that (1) has been or can be reproducibly substantiated, (2) can be used to accurately predict new phenomena, and (3) focuses on the natural world or universe. Scientific ideas take many forms. The terms that scientists use to describe these forms have meanings quite different from those applied by nonscientists. A hypothesis is an idea or assumption that provides a reasonable and testable explanation for one or more observations, but it may lack extensive experimental substantiation. A scientific theory is much more than a hunch. It is an idea that has been substantiated to some extent and provides an explanation for a body of experimental observations. A theory can be tested and built upon and is thus a basis for further advance and innovation. When a scientific theory has been repeatedly tested and validated on many fronts, it can be accepted as a fact. In one important sense, what constitutes science or a scientific idea is defined by whether or not it is published in the scientific literature after peer review by other working scientists. As of late 2014, about 34,500 peer-reviewed scientific journals worldwide were publishing some 2.5 million articles each year, a continuing rich harvest of information that is the birthright of every human being. Scientists are individuals who rigorously apply the scientific method to understand the natural world. Merely having an advanced degree in a scientific discipline does not make one a scientist, nor does the lack of such a degree prevent one from making important scientific contributions. A scientist must be willing to challenge any idea when new findings demand it. The ideas that a scientist accepts must be based on measurable, reproducible observations, and the scientist must report these observations with complete honesty. The scientific method is a collection of paths, all of which may lead to scientific discovery. In the hypothesis and experiment path, a scientist poses a hypothesis, then subjects it to experimental test. Many of the processes that biochemists work with every day were discovered in this manner. The DNA structure elucidated by James Watson and Francis Crick led to the hypothesis that base pairing is the basis for information transfer in polynucleotide synthesis. This hypothesis helped inspire the discovery of DNA and RNA polymerases. Watson and Crick produced their DNA structure through a process of model building and calculation. No actual experiments were involved, although the model building and calculations used data collected by other scientists. Many adventurous scientists have applied the process of exploration and observation as a path to discovery. Historical voyages of discovery (Charles Darwin’s 1831 voyage on H.M.S. Beagle among them) helped to map the planet, catalog its living occupants, and change the way we view the world. Modern scientists follow a similar path when they explore the ocean depths or launch probes to other planets. An analog of hypothesis and experiment is hypothesis and deduction. Crick reasoned that there must be an adaptor molecule that facilitated translation of the information in messenger RNA into protein. This adaptor hypothesis led to the discovery of transfer RNA by Mahlon Hoagland and Paul Zamecnik. Not all paths to discovery involve planning. Serendipity often plays a role. The discovery of penicillin by Alexander Fleming in 1928 and of RNA catalysts by Thomas Cech in the early 1980s were both chance discoveries, albeit by scientists well prepared to exploit them. Inspiration can also lead to important advances. The polymerase chain reaction (PCR), now a central part of biotechnology, was developed by Kary Mullis after a flash of inspiration during a road trip in northern California in 1983. These many paths to scientific discovery can seem quite different, but they have some important things in common. They are focused on the natural world. They rely on reproducible observation and/or experiment. All of the ideas, insights, and experimental facts that arise from these endeavors can be tested and reproduced by scientists anywhere in the world. All can be used by other scientists to build new hypotheses and make new discoveries. All lead to information that is properly included in the realm of science. Understanding our universe requires hard work. At the same time, no human endeavor is more exciting and potentially rewarding than trying, with occasional success, to understand some part of the natural world. Preface W ith the advent of increasingly robust technologies that provide cellular and organismal views of molecular processes, progress in biochemistry continues apace, providing both new wonders and new challenges. The image on our cover depicts an active spliceosome, one of the largest molecular machines in a eukaryotic cell, and one that is only now yielding to modern structural analysis. It is an example of our current understanding of life at the level of molecular structure. The image is a snapshot from a highly complex set of reactions, in better focus than ever before. But in the cell, this is only one of many steps linked spatially and temporally to many other complex processes that remain to be unraveled and eventually described in future editions. Our goal in this seventh edition of Lehninger Principles of Biochemistry, as always, is to strike a balance: to include new and exciting research findings without making the book overwhelming for students. The primary criterion for inclusion of an advance is that the new finding helps to illustrate an important principle of biochemistry. With every revision of this textbook, we have striven to maintain the qualities that made the original Lehninger text a classic: clear writing, careful explanations of difficult concepts, and insightful communication to students of the ways in which biochemistry is understood and practiced today. We have coauthored this text and taught introductory biochemistry together for three decades. Our thousands of students at the University of Wisconsin–Madison over those years have been an endless source of ideas on how to present biochemistry more clearly; they have enlightened and inspired us. We hope that this seventh edition of Lehninger will, in turn, enlighten current students of biochemistry everywhere, and inspire all of them to love biochemistry as we do. NEW Leading-Edge Science Among the new or substantially updated topics in this edition are: ■ Synthetic cells and disease genomics (Chapter 1) ■ Intrinsically disordered protein segments (Chapter 4) and their importance in signaling (Chapter 12) ■ Pre–steady state enzyme kinetics (Chapter 6) ■ Gene annotation (Chapter 9) ■ Gene editing with CRISPR (Chapter 9) ■ Membrane trafficking and dynamics (Chapter 11) Photos: (a) Pr. G. Giménez-Martín/Science Source. (b) Karen Meaburn and Tom Misteli/National Cancer Institute. Chromosomal organization in the eukaryotic nucleus ■ Additional roles for NADH (Chapter 13) ■ Cellulose synthase complex (Chapter 20) ■ Specialized pro-resolving mediators (Chapter 21) ■ Peptide hormones: incretins and blood glucose; irisin and exercise (Chapter 23) ■ Chromosome territories (Chapter 24) ■ New details of eukaryotic DNA replication (Chapter 25) ■ Cap-snatching; spliceosome structure (Chapter 26) ■ Ribosome rescue; RNA editing update (Chapter 27) ■ New roles for noncoding RNAs (Chapters 26, 28) ■ RNA recognition motif (Chapter 28) NEW Tools and Technology The emerging tools of systems biology continue to transform our understanding of biochemistry. These include both new laboratory methods and large, public databases that have become indispensable to researchers. New to this edition of Lehninger Principles of Biochemistry: ■ Next-generation DNA sequencing now includes ion semiconductor sequencing (Ion Torrent) and single-molecule real-time (SMRT) sequencing platforms, and the text discussion now follows the description of classical Sanger sequencing (Chapter 8). ■ Gene editing by CRISPR is one of many updates to the discussion of genomics (Chapter 9). ■ LIPID MAPS database and system of classifying lipids is included in the discussion of lipidomics (Chapter 10). ■ Cryo-electron microscopy is described in a new box (Chapter 19). ■ Ribosome profiling to determine which genes are being translated at any given moment, and many related technologies, are included to illustrate the versatility and power of deep DNA sequencing (Chapter 27). Photo: © Alberto Bartesaghi, PhD. Structure of the GroEL chaperone protein, as determined by cryo-EM ■ Online data resources such as NCBI, PDB, SCOP2, KEGG, and BLAST, mentioned in the text, are listed in the back endpapers for easy reference. NEW Consolidation of Plant Metabolism All of plant metabolism is now consolidated into a single chapter, Chapter 20, separate from the discussion of oxidative phosphorylation in Chapter 19. Chapter 20 includes light-driven ATP synthesis, carbon fixation, photorespiration, the glyoxylate cycle, starch and cellulose synthesis, and regulatory mechanisms that ensure integration of all of these activities throughout the plant. Photo: © Courtesy Dr. Candace H. Haigler, North Carolina State University and Dr. Mark Grimson, Texas Tech University. Model for the synthesis of cellulose Medical Insights and Applications This icon is used throughout the book to denote material of special medical interest. As teachers, our goal is for students to learn biochemistry and to understand its relevance to a healthier life and a healthier planet. Many sections explore what we know about the molecular mechanisms of disease. The new and updated medical topics in this edition are: ■ UPDATED Lactase and lactose intolerance (Chapter 7) ■ NEW Guillain-Barré syndrome and gangliosides (Chapter 10) ■ NEW Golden Rice Project to prevent diseases of vitamin A deficiency (Chapter 10) ■ UPDATED Multidrug resistance transporters and their importance in clinical medicine (Chapter 11) ■ NEW Insight into cystic fibrosis and its treatment (Chapter 11) Effects of gut microbe metabolism on health ■ UPDATED Colorectal cancer: multistep progression (Chapter 12) ■ NEW Newborn screening for acyl-carnitine to diagnose mitochondrial disease (Chapter 17) ■ NEW Mitochondrial diseases, mitochondrial donation, and “three-parent babies” (Chapter 19) ■ UPDATED Cholesterol metabolism, plaque formation, and atherosclerosis (Chapter 21) ■ UPDATED Cytochrome P-450 enzymes and drug interactions (Chapter 21) ■ UPDATED Ammonia toxicity in the brain (Chapter 22) ■ NEW Xenobiotics as endocrine disruptors (Chapter 23) Special Theme: Metabolic Integration, Obesity, and Diabetes Obesity and its medical consequences, including cardiovascular disease and diabetes, are fast becoming epidemic in the industrialized world, and throughout this edition we include new material on the biochemical connections between obesity and health. Our focus on diabetes provides an integrating theme throughout the chapters on metabolism and its control. Some of the topics that highlight the interplay of metabolism, obesity, and diabetes are: ■ Acidosis in untreated diabetes (Chapter 2) ■ Defective protein folding, amyloid deposition in the pancreas, and diabetes (Chapter 4) ■ UPDATED Blood glucose and glycated hemoglobin in the diagnosis and treatment of diabetes (Box 7-1) ■ Advanced glycation end products (AGEs): their role in the pathology of advanced diabetes (Box 71) ■ Defective glucose and water transport in two forms of diabetes (Box 11-1) ■ NEW Na+-glucose transporter and the use of gliflozins in the treatment of type 2 diabetes (Chapter 11) ■ Glucose uptake deficiency in type 1 diabetes (Chapter 14) ■ MODY: a rare form of diabetes (Box 15-3) ■ Ketone body overproduction in diabetes and starvation (Chapter 17) ■ NEW Breakdown of amino acids: methylglyoxal as a contributor to type 2 diabetes (Chapter 18) ■ A rare form of diabetes resulting from defects in mitochondria of pancreatic ψ cells (Chapter 19) ■ Thiazolidinedione-stimulated glyceroneogenesis in type 2 diabetes (Chapter 21) ■ Role of insulin in countering high blood glucose (Chapter 23) ■ Secretion of insulin by pancreatic φ cells in response to changes in blood glucose (Chapter 23) ■ How insulin was discovered and purified (Box 23-1) ■ NEW AMP-activated protein kinase in the hypothalamus in integration of hormonal inputs from gut, muscle, and adipose tissues (Chapter 23) ■ UPDATED Role of mTORC1 in regulating cell growth (Chapter 23) ■ NEW Brown and beige adipose as thermogenic tissues (Chapter 23) ■ NEW Exercise and the stimulation of irisin release and weight loss (Chapter 23) ■ NEW Short-term eating behavior influenced by ghrelin, PYY3–36, and cannabinoids (Chapter 23) ■ NEW Role of microbial symbionts in the gut in influencing energy metabolism and adipogenesis (Chapter 23) ■ Tissue insensitivity to insulin in type 2 diabetes (Chapter 23) ■ UPDATED Management of type 2 diabetes with diet, exercise, medication, and surgery (Chapter 23) Special Theme: Evolution Every time a biochemist studies a developmental pathway in nematodes, identifies key parts of an enzyme active site by determining which parts are conserved among species, or searches for the gene underlying a human genetic disease, he or she is relying on evolutionary theory. Funding agencies support work on nematodes with the expectation that the insights gained will be relevant to humans. The conservation of functional residues in an enzyme active site telegraphs the shared history of all organisms on the planet. More often than not, the search for a disease gene is a sophisticated exercise in phylogenetics. Evolution is thus a foundational concept for our discipline. Some of the many areas that discuss biochemistry from an evolutionary viewpoint: ■ Changes in hereditary instructions that allow evolution (Chapter 1) ■ Origins of biomolecules in chemical evolution (Chapter 1) ■ RNA or RNA precursors as the first genes and catalysts (Chapters 1, 26) ■ Timetable of biological evolution (Chapter 1) ■ Use of inorganic fuels by early cells (Chapter 1) ■ Evolution of eukaryotes from simpler cells (endosymbiont theory) (Chapters 1, 19, 20) ■ Protein sequences and evolutionary trees (Chapter 3) ■ Role of evolutionary theory in protein structure comparisons (Chapter 4) ■ Evolution of antibiotic resistance in bacteria (Chapter 6) ■ Evolutionary explanation for adenine nucleotides being components of many coenzymes (Chapter 8) ■ Comparative genomics and human evolution (Chapter 9) ■ Using genomics to understand Neanderthal ancestry (Box 9-3) ■ Evolutionary relationships between V-type and F-type ATPases (Chapter 11) ■ Universal features of GPCR systems (Chapter 12) ■ Evolutionary divergence of β-oxidation enzymes (Chapter 17) ■ Evolution of oxygenic photosynthesis (Chapter 20) ■ NEW Presence of organelles, including nuclei, in planctomycete bacteria (Box 22-1) ■ Role of transposons in evolution of the immune system (Chapter 25) ■ Common evolutionary origin of transposons, retroviruses, and introns (Chapter 26) ■ Consolidated discussion of the RNA world hypothesis (Chapter 26) ■ Natural variations in the genetic code—exceptions that prove the rule (Box 27-1) ■ Natural and experimental expansion of the genetic code (Box 27-2) ■ Regulatory genes in development and speciation (Box 28-1) Regulation of feeding behavior Lehninger Teaching Hallmarks Students encountering biochemistry for the first time often have difficulty with two key aspects of the course: approaching quantitative problems and drawing on what they have learned in organic chemistry to help them understand biochemistry. These same students must also learn a complex language, with conventions that are often unstated. To help students cope with these challenges, we provide the following study aids: Focus on Chemical Logic ■ Section 13.2, Chemical Logic and Common Biochemical Reactions, discusses the common biochemical reaction types that underlie all metabolic reactions, helping students to connect organic chemistry with biochemistry. ■ Chemical logic figures highlight the conservation of mechanism and illustrate patterns that make learning pathways easier. Chemical logic figures are provided for each of the central metabolic pathways, including glycolysis (Fig. 14-3), the citric acid cycle (Fig. 16-7), and fatty acid oxidation (Fig. 17-9). ■ Mechanism figures feature step-by-step descriptions to help students understand the reaction process. These figures use a consistent set of conventions introduced and explained in detail with the first enzyme mechanism encountered (chymotrypsin, Fig. 6-23). ■ Further reading Students and instructors can find more about the topics in the text in the Further Reading list for each chapter, which can be accessed at www.macmillanlearning.com/LehningerBiochemistry7e as well as through the Sapling Plus for Lehninger platform. Each list cites accessible reviews, classic papers, and research articles that will help users dive deeper into both the history and current state of biochemistry. Alcohol dehydrogenase reaction mechanism Clear Art ■ Smarter renditions of classic figures are easier to interpret and learn from. ■ Molecular structures are created specifically for this book, using shapes and color schemes that are internally consistent. ■ Figures with numbered, annotated steps help explain complex processes. ■ Summary figures help students keep the big picture in mind while learning the specifics. CRISPR/Cas9 structure Problem-Solving Tools ■ In-text Worked Examples help students improve their quantitative problem-solving skills, taking them through some of the most difficult equations. ■ More than 600 end-of-chapter problems give students further opportunity to practice what they have learned. ■ Data Analysis Problems (one at the end of each chapter), contributed by Brian White of the University of Massachusetts Boston, encourage students to synthesize what they have learned and apply their knowledge to interpretation of data from the research literature. Key Conventions Many of the conventions that are so necessary for understanding each biochemical topic and the biochemical literature are broken out of the text and highlighted. These Key Conventions include clear statements of many assumptions and conventions that students are often expected to assimilate without being told (for example, peptide sequences are written from amino- to carboxyl-terminal end, left to right; nucleotide sequences are written from 5′ to 3′ end, left to right). Media and Supplements For this edition of Lehninger Principles of Biochemistry, we have thoroughly revised and refreshed the extensive set of online learning tools. In particular, we are moving to a wellestablished platform that, for the first time, allows us to provide a comprehensive online homework system. NEW for Lehninger This comprehensive and robust online teaching and learning platform incorporates the e-Book, all instructor and student resources, and instructor assignment and gradebook functionality. NEW Student Resources in for Lehninger Students are provided with media designed to enhance their understanding of biochemical principles and improve their problem-solving ability. NEW Online Homework Sapling Plus for Lehninger offers robust, high-level homework questions, with hints and wronganswer feedback targeted to students’ misconceptions, as well as detailed worked-out solutions to reinforce concepts. e-Book The e-Book contains the full contents of the text and embedded links to important media assets (listed on the next two pages). NEW Interactive Metabolic Map The Interactive Metabolic Map guides students through the most commonly taught metabolic pathways: glycolysis, the citric acid cycle, and β-oxidation. Students can navigate and zoom between overview and detailed views of the map, allowing them to integrate the big-picture connections and fine-grain details of the pathways. Tutorials guide students through the pathways to achieve key learning outcomes. Concept check questions along the way confirm understanding. NEW Case Studies By Justin Hines (Lafayette College) Each of several online case studies introduces students to a biochemical mystery and allows them to determine what investigations to complete as they search for a solution. Final assessments ensure that students have fully completed and understood each case study. ■ A Likely Story: Enzyme Inhibition ■ An Unexplained Death: Carbohydrate Metabolism ■ A Day at the Beach: Lipid Metabolism ■ The Runner’s Experiment: Integration of Metabolism ■ Sudden Onset: Introduction to Metabolism ■ Toxic Alcohols: Enzyme Function More case studies will be added over the course of this edition. UPDATED Molecular Structure Tutorials For the seventh edition, these tutorials are updated to JSmol, and now include assessment with targeted feedback to ensure that students grasp key concepts learned from examining various molecular structures in depth. ■ Protein Architecture (Chapter 3) ■ Oxygen-Binding Proteins (Chapter 5) ■ Major Histocompatibility Complex (MHC) Molecules (Chapter 5) ■ Nucleotides: Building Blocks of Nucleic Acids (Chapter 8) ■ Trimeric G Proteins (Chapter 12) ■ Bacteriorhodopsin (Chapter 20) ■ Restriction Endonucleases (Chapter 25) ■ The Hammerhead Ribozyme: An RNA Enzyme (Chapter 26) ■ Lac Repressor: A Gene Regulator (Chapter 28) NEW Simulations Created using art from the text, these biochemical simulations reinforce students’ understanding by allowing them to interact with the structures and processes they have encountered. A gamelike format guides students through the simulations. Multiple-choice questions after each simulation ensure that instructors can assess whether students have thoroughly understood each topic. ■ Nucleotide Structure ■ DNA/RNA Structure ■ PCR ■ Sanger Sequencing ■ CRISPR ■ DNA Replication ■ DNA Polymerase ■ Mutation and Repair ■ Transcription ■ mRNA Processing ■ Translation UPDATED Animated Mechanism Figures Many mechanism figures from the text are available as animations, accompanied by assessment with targeted feedback. These animations help students learn about key mechanisms at their own pace. Living Graphs and Equations These offer students an intuitive way to explore the equations in the text, and they act as problem-solving tools for online homework. ■ Henderson-Hasselbalch Equation (Eqn 2-9) ■ Titration Curve for a Weak Acid (Fig. 2-17) ■ Binding Curve for Myoglobin (Eqn 5-11) ■ Cooperative Ligand Binding (Eqn 5-14) ■ Hill Equation (Eqn 5-16) ■ Protein-Ligand Interactions (Eqn 5-8) ■ Competitive Inhibitor (Eqn 6-28) ■ Lineweaver-Burk Equation (Box 6-1) ■ Michaelis-Menten Equation (Eqn 6-9) ■ Mixed Inhibitor (Eqn 6-30) ■ Uncompetitive Inhibitor (Eqn 6-29) ■ Free-Energy for Transport Equation (Eqn 11-3) ■ Free-Energy for Transport Graph (Eqn 11-3) ■ Free-Energy Change (Eqn 13-4) ■ Free-Energy of Hydrolysis of ATP Equation (Worked Example 13-2) ■ Free-Energy of Hydrolysis of ATP Graph (Worked Example 13-2) ■ Free-Energy for Transport of an Ion (Eqn 11-4, Eqn 19-8) NEW Nature Articles with Assessment Six articles from Nature are available accompanied by tailored, automatically gradable assessment to engage students in reading primary literature and to encourage critical thinking. Also included are open-ended questions that are suitable for use in flipped classrooms and active learning discussions either in class or online. Animated Biochemical Techniques Nine animations illustrate the principles behind some of the most commonly used laboratory methods. Problem-Solving Videos Created by Scott Ensign of Utah State University, these videos provide students with 24/7 online problem-solving help. Through a two-part approach, each 10-minute video covers a key textbook problem representing a topic that students traditionally struggle to master. Dr. Ensign first describes a proven problem-solving strategy and then applies the strategy to the problem at hand, in clear, concise steps. Students can easily pause, rewind, and review any steps until they firmly grasp, not just the solution, but also the reasoning behind it. Working through the problem in this way is designed to make students better and more confident at applying key strategies as they solve other textbook and exam problems. Student Print Resources: The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry, Seventh Edition, Study Guide and Solutions Manual, by Marcy Osgood (University of New Mexico School of Medicine) and Karen Ocorr (Sanford-Burnham Medical Research Institute); ISBN 1-46418797-5 This guide combines an innovative study guide with a reliable solutions manual (providing extended solutions to end-of-chapter problems) in one convenient volume. Thoroughly classtested, the study guide includes, for each chapter: ■ Major Concepts: a road map through the chapter ■ What to Review: questions that recap key points from previous chapters ■ Discussion Questions: provided for each section; designed for individual review, study groups, or classroom discussion ■ Self-Test: “Do you know the terms?”; crossword puzzles; multiple-choice, fact-driven questions; and questions that ask students to apply their new knowledge in new directions— plus answers! Instructor Resources Instructors are provided with a comprehensive set of teaching tools, each developed to support the text, lecture presentations, and individual teaching styles. All of these resources are available for download from Sapling Plus for Lehninger and from the catalog page at www.MacmillanLearning.com. Test Bank A comprehensive test bank, in editable Microsoft Word and Diploma formats, includes 30 to 50 new multiple-choice and short-answer problems per chapter, for a total of 100 questions or more per chapter, each rated by Bloom’s level and level of difficulty. Lecture Slides Editable lecture slides are tailored to the content of this new edition, with updated, optimized art and text. Clicker Questions These dynamic multiple-choice questions can be used with iClicker or other classroom response systems. The clicker questions are written specifically to foster active learning in the classroom and to better inform instructors on students’ misunderstandings. Fully Optimized Art Files Fully optimized files are available for every figure, photo, and table in the text, featuring enhanced color, high resolution, and enlarged fonts. These files are available as JPEGs or are preloaded into PowerPoint format for each chapter. Acknowledgments This book is a team effort, and producing it would be impossible without the outstanding people at W. H. Freeman and Company who have supported us at every step along the way. Susan Moran, Senior Developmental Editor, and Lauren Schultz, Executive Editor, helped develop the revision plan for this edition, made many helpful suggestions, encouraged us, and tried valiantly (if not always successfully) to keep us on schedule. Our outstanding Project Editor, Liz Geller, showed remarkable patience as we regularly failed to meet her deadlines. We thank Design Manager Blake Logan for her artistry in designing the text for the book. We thank Photo Researcher Roger Feldman and Photo Editor Christine Buese for their help in locating images and obtaining permission to use them, and Shannon Moloney for help in orchestrating reviews and providing administrative assistance at many turns. We also thank Lori Stover, Media Editor, Amanda Nietzel, Director of Media and Assessment, and Elaine Palucki, Senior Educational Technology Advisor, for envisioning and overseeing the increasingly important media components to supplement the text. Our gratitude also goes to Maureen Rachford, Marketing Manager, for coordinating the sales and marketing effort. We also wish to thank Kate Parker, whose work on previous editions is still visible in this one. In Madison, Brook Soltvedt is, and has been for all the editions we have worked on, our invaluable first-line editor and critic. She is the first to see manuscript chapters, aids in manuscript and art development, ensures internal consistency in content and nomenclature, and keeps us on task with more-or-less gentle prodding. The deft hand of Linda Strange, who has copyedited all but one edition of this textbook (including the first), is evident in the clarity of the text. She has encouraged and inspired us with her high scientific and literary standards. As she did for the three previous editions, Shelley Lusetti, of New Mexico State University, read every word of the text in proofs, caught numerous mistakes, and made many suggestions that improved the book. The new art and molecular graphics were created by Adam Steinberg of Art for Science, who often made valuable suggestions that led to better and clearer illustrations. We feel very fortunate to have such gifted partners as Brook, Linda, Shelley, and Adam on our team. We are also deeply indebted to Brian White of the University of Massachusetts Boston, who wrote the data analysis problems at the end of each chapter. Many others helped us shape this seventh edition with their comments, suggestions, and criticisms. To all of them, we are deeply grateful: Rebecca Alexander, Wake Forest University Richard Amasino, University of Wisconsin–Madison Mary Anderson, Texas Woman’s University Steve Asmus, Centre College Kenneth Balazovich, University of Michigan Rob Barber, University of Wisconsin–Parkside David Bartley, Adrian College Johannes Bauer, Southern Methodist University John Bellizzi, University of Toledo Chris Berndsen, James Madison University James Blankenship, Cornell University Kristopher Blee, California State University, Chico William Boadi, Tennessee State University Sandra Bonetti, Colorado State University–Pueblo Rebecca Bozym, La Roche College Mark Brandt, Rose-Hulman Institute of Technology Ronald Brosemer, Washington State University Donald Burden, Middle Tennessee State University Samuel Butcher, University of Wisconsin–Madison Jeffrey Butikofer, Upper Iowa University Colleen Byron, Ripon College Patricia Canaan, Oklahoma State University Kevin Cannon, Pennsylvania State Abington College Weiguo Cao, Clemson University David Casso, San Francisco State University Brad Chazotte, Campbell University College of Pharmacy & Health Sciences Brooke Christian, Appalachian State University Jeff Cohlberg, California State University, Long Beach Kathryn Cole, Christopher Newport University Jeannie Collins, University of Southern Indiana Megen Culpepper, Appalachian State University Tomas T. 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Brian Sato, University of California, Irvine Jamie Scaglione, Carroll University Ingeborg Schmidt-Krey, Georgia Institute of Technology Kimberly Schultz, University of Maryland, Baltimore County Jason Schwans, California State University, Long Beach Rhonda Scott, Southern Adventist University Allan Scruggs, Arizona State University Michael Sehorn, Clemson University Edward Senkbei, Salisbury University Amanda Sevcik, Baylor University Robert Shaw, Texas Tech University Nicholas Silvaggi, University of Wisconsin–Milwaukee Jennifer Sniegowski, Arizona State University Downtown Phoenix Campus Narasimha Sreerama, Colorado State University Andrea Stadler, St. Joseph’s College Scott Stagg, Florida State University Boris Steipe, University of Toronto Alejandra Stenger, University of Illinois at Urbana-Champaign Steven Theg, University of California, Davis Jeremy Thorner, University of California, Berkeley Kathryn Tifft, Johns Hopkins University Michael Trakselis, Baylor University Bruce 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David Tu, Pennsylvania State University Xuemin Wang, University of Missouri Yuqi Wang, Saint Louis University Paul Weber, Briar Cliff University Rodney Weilbaecher, Southern Illinois University School of Medicine Emily Westover, Brandeis University Susan White, Bryn Mawr College Enoka Wijekoon, University of Guelph Kandatege Wimalasena, Wichita State University Adrienne Wright, University of Alberta Chuan Xiao, University of Texas at El Paso Laura Zapanta, University of Pittsburgh Brent Znosko, Saint Louis University We lack the space here to acknowledge all the other individuals whose special efforts went into this book. We offer instead our sincere thanks—and the finished book that they helped guide to completion. We, of course, assume full responsibility for errors of fact or emphasis. We want especially to thank our students at the University of Wisconsin–Madison for their numerous comments and suggestions. If something in the book does not work, they are never shy about letting us know it. We are grateful to the students and staff of our past and present research groups, who helped us balance the competing demands on our time; to our colleagues in the Department of Biochemistry at the University of Wisconsin–Madison, who helped us with advice and criticism; and to the many students and teachers who have written to suggest ways of improving the book. We hope our readers will continue to provide input for future editions. Finally, we express our deepest appreciation to our wives, Brook and Beth, and our families, who showed extraordinary patience with, and support for, our book writing. David L. Nelson Michael M. Cox Madison, Wisconsin June 2016 Contents Cover Media Connections Half Title Front Matter Title Page Copyright Dedication About the Authors A Note on the Nature of Science Preface Media and Supplements Acknowledgments 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 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 3 Amino Acids, Peptides, and Proteins 3.1 Amino Acids 3.2 Peptides and Proteins 3.3 Working with Proteins 3.4 The Structure of Proteins: Primary Structure 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 5 Protein Function 5.1 Reversible Binding of a Protein to a Ligand: OxygenBinding 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 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 7 Carbohydrates and Glycobiology 7.1 Monosaccharides and Disaccharides 7.2 Polysaccharides 7.3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycosphingolipids 7.4 Carbohydrates as Informational Molecules: The Sugar Code 7.5 Working with Carbohydrates 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 Studying Genes and Their Products 9.2 Using DNA-Based Methods to Understand Protein Function 9.3 Genomics and the Human Story 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 11 Biological Membranes and Transport 11.1 The Composition and Architecture of Membranes 11.2 Membrane Dynamics 11.3 Solute Transport across Membranes 12 Biosignaling 12.1 General Features of Signal Transduction 12.2 G Protein–Coupled Receptors and Second Messengers 12.3 GPCRs in Vision, Olfaction, and Gustation 12.4 Receptor Tyrosine Kinases 12.5 Receptor Guanylyl Cyclases, cGMP, and Protein Kinase G 12.6 Multivalent Adaptor Proteins and Membrane Rafts 12.7 Gated Ion Channels 12.8 Regulation of Transcription by Nuclear Hormone Receptors 12.9 Signaling in Microorganisms and Plants 12.10 Regulation of the Cell Cycle by Protein Kinases 12.11 Oncogenes, Tumor Suppressor Genes, and Programmed Cell Death PART II BIOENERGETICS AND METABOLISM 13 Bioenergetics and Biochemical Reaction Types 13.1 Bioenergetics and Thermodynamics 13.2 Chemical Logic and Common Biochemical Reactions 13.3 Phosphoryl Group Transfers and ATP 13.4 Biological Oxidation-Reduction Reactions 14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway 14.1 Glycolysis 14.2 Feeder Pathways for Glycolysis 14.3 Fates of Fermentation Pyruvate under Anaerobic Conditions: 14.4 Gluconeogenesis 14.5 Pentose Phosphate Pathway of Glucose Oxidation 15 Principles of Metabolic Regulation 15.1 Regulation of Metabolic Pathways 15.2 Analysis of Metabolic Control 15.3 Coordinated Regulation of Glycolysis and Gluconeogenesis 15.4 The Metabolism of Glycogen in Animals 15.5 Coordinated Regulation of Glycogen Breakdown and Synthesis 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 17 Fatty Acid Catabolism 17.1 Digestion, Mobilization, and Transport of Fats 17.2 Oxidation of Fatty Acids 17.3 Ketone Bodies 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 19. Oxidative Phosphorylation 19.1 The Mitochondrial Respiratory Chain 19.2 ATP Synthesis 19.3 Regulation of Oxidative Phosphorylation 19.4 Mitochondria in Thermogenesis, Steroid Synthesis, and Apoptosis 19.5 Mitochondrial Genes: Their Origin and the Effects of Mutations 20 Photosynthesis and Carbohydrate Synthesis in Plants 20.1 Light Absorption 20.2 Photochemical Reaction Centers 20.3 ATP Synthesis by Photophosphorylation 20.4 Evolution of Oxygenic Photosynthesis 20.5 Carbon-Assimilation Reactions 20.6 Photorespiration and the C4 and CAM Pathways 20.7 Biosynthesis of Starch, Sucrose, and Cellulose 20.8 Integration of Carbohydrate Metabolism in Plants 21 Lipid Biosynthesis 21.1 Biosynthesis of Fatty Acids and Eicosanoids 21.2 Biosynthesis of Triacylglycerols 21.3 Biosynthesis of Membrane Phospholipids 21.4 Cholesterol, Steroids, and Isoprenoids: Biosynthesis, Regulation, and Transport 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 23 Hormonal Regulation and Integration of Mammalian Metabolism 23.1 Hormones: Diverse Structures for Diverse Functions 23.2 Tissue-Specific Metabolism: The Division of Labor 23.3 Hormonal Regulation of Fuel Metabolism 23.4 Obesity and the Regulation of Body Mass 23.5 Obesity, Metabolic Syndrome, and Type 2 Diabetes PART III INFORMATION PATHWAYS 24 Genes and Chromosomes 24.1 Chromosomal Elements 24.2 DNA Supercoiling 24.3 The Structure of Chromosomes 25 DNA Metabolism 25.1 DNA Replication 25.2 DNA Repair 25.3 DNA Recombination 26 RNA Metabolism 26.1 DNA-Dependent Synthesis of RNA 26.2 RNA Processing 26.3 RNA-Dependent Synthesis of RNA and DNA 27 Protein Metabolism 27.1 The Genetic Code 27.2 Protein Synthesis 27.3 Protein Targeting and Degradation 28 Regulation of Gene Expression 28.1 Principles of Gene Regulation 28.2 Regulation of Gene Expression in Bacteria 28.3 Regulation of Gene Expression in Eukaryotes Abbreviated Solutions to Problems Glossary Index CHAPTER 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 Self-study tools that will help you practice what you’ve learned and reinforce this chapter’s concepts are available online. Go to www.macmillanlearning.com/LehningerBiochemistry7e. A bout fourteen billion years ago, the universe arose as a cataclysmic explosion of hot, energyrich subatomic particles. Within seconds, the simplest elements (hydrogen and helium) were formed. As the universe expanded and cooled, material condensed under the influence of gravity to form stars. Some stars became enormous and then exploded as supernovae, releasing the energy needed to fuse simpler atomic nuclei into the more complex elements. Atoms and molecules formed swirling masses of dust particles, and their accumulation led eventually to the formation of rocks, planetoids, and planets. Thus were produced, over billions of years, Earth itself and the chemical elements found on Earth today. About four billion years ago, life arose—simple microorganisms with the ability to extract energy from chemical compounds and, later, from sunlight, which they used to make a vast array of more complex biomolecules from the simple elements and compounds on the Earth’s surface. We and all other living organisms are made of stardust. Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different biomolecules. When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter—as do all the processes occurring in living organisms. The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life governed solely by the physical and chemical laws that govern the nonliving universe. Yet organisms possess extraordinary attributes, properties that distinguish them from other collections of matter. What are these distinguishing features of living organisms? A high degree of chemical complexity and microscopic organization. Thousands of different molecules make up a cell’s intricate internal structures (Fig. 1-1a). These include very long polymers, each with its characteristic sequence of subunits, its unique threedimensional structure, and its highly specific selection of binding partners in the cell. Systems for extracting, transforming, and using energy from the environment (Fig. 1-1b), enabling organisms to build and maintain their intricate structures and to do mechanical, chemical, osmotic, and electrical work. This counteracts the tendency of all matter to decay toward a more disordered state, to come to equilibrium with its surroundings. Defined functions for each of an organism’s components and regulated interactions among them. This is true not only of macroscopic structures, such as leaves and stems or hearts and lungs, but also of microscopic intracellular structures and individual chemical compounds. The interplay among the chemical components of a living organism is dynamic; changes in one component cause coordinating or compensating changes in another, with the whole ensemble displaying a character beyond that of its individual parts. The collection of molecules carries out a program, the end result of which is reproduction of the program and self-perpetuation of that collection of molecules—in short, life. FIGURE 1-1 Some characteristics of living matter. (a) Microscopic complexity and organization are apparent in this colorized image of a thin section of several secretory cells from the pancreas, viewed with the electron microscope. (b) A prairie falcon acquires nutrients and energy by consuming a smaller bird. (c) Biological reproduction occurs with nearperfect fidelity. [Sources: (a) SPL/Science Source. (b) W. Perry Conway/Corbis. (c) F1online digitale Bildagentur GmbH/Alamy.] Mechanisms for sensing and responding to alterations in their surroundings. Organisms constantly adjust to these changes by adapting their internal chemistry or their location in the environment. A capacity for precise self-replication and self-assembly (Fig. 1-1c). A single bacterial cell placed in a sterile nutrient medium can give rise to a billion identical “daughter” cells in 24 hours. Each cell contains thousands of different molecules, some extremely complex; yet each bacterium is a faithful copy of the original, its construction directed entirely by information contained in the genetic material of the original cell. On a larger scale, the progeny of a vertebrate animal share a striking resemblance to their parents, also the result of their inheritance of parental genes. A capacity to change over time by gradual evolution. Organisms change their inherited life strategies, in very small steps, to survive in new circumstances. The result of eons of evolution is an enormous diversity of life forms, superficially very different (Fig. 1-2) but fundamentally related through their shared ancestry. This fundamental unity of living organisms is reflected at the molecular level in the similarity of gene sequences and protein structures. FIGURE 1-2 Diverse living organisms share common chemical features. Birds, beasts, plants, and soil microorganisms share with humans the same basic structural units (cells) and the same kinds of macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits (nucleotides, amino acids). They utilize the same pathways for synthesis of cellular components, share the same genetic code, and derive from the same evolutionary ancestors. [Source: The Garden of Eden, 1659 (oil on canvas) by Jan van Kessel the Elder (1626–79)/Johnny van Haeften Gallery, London, UK/Bridgeman Images.] Despite these common properties and the fundamental unity of life they reveal, it is difficult to make generalizations about living organisms. Earth has an enormous diversity of organisms. The range of habitats, from hot springs to Arctic tundra, from animal intestines to college dormitories, is matched by a correspondingly wide range of specific biochemical adaptations, achieved within a common chemical framework. For the sake of clarity, in this book we sometimes risk certain generalizations, which, though not perfect, remain useful; we also frequently point out the exceptions to these generalizations, which can prove illuminating. Biochemistry describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms. Although biochemistry provides important insights and practical applications in medicine, agriculture, nutrition, and industry, its ultimate concern is with the wonder of life itself. In this introductory chapter we give an overview of the cellular, chemical, physical, and genetic backgrounds to biochemistry and the overarching principle of evolution—how life emerged and evolved into the diversity of organisms we see today. As you read through the book, you may find it helpful to refer back to this chapter at intervals to refresh your memory of this background material. 1.1 Cellular Foundations The unity and diversity of organisms become apparent even at the cellular level. The smallest organisms consist of single cells and are microscopic. Larger, multicellular organisms contain many different types of cells, which vary in size, shape, and specialized function. Despite these obvious differences, all cells of the simplest and most complex organisms share certain fundamental properties, which can be seen at the biochemical level. Cells Are the Structural and Functional Units of All Living Organisms Cells of all kinds share certain structural features (Fig. 1-3). The plasma membrane defines the periphery of the cell, separating its contents from the surroundings. It is composed of lipid and protein molecules that form a thin, tough, pliable, hydrophobic barrier around the cell. The membrane is a barrier to the free passage of inorganic ions and most other charged or polar compounds. Transport proteins in the plasma membrane allow the passage of certain ions and molecules; receptor proteins transmit signals into the cell; and membrane enzymes participate in some reaction pathways. Because the individual lipids and proteins of the plasma membrane are not covalently linked, the entire structure is remarkably flexible, allowing changes in the shape and size of the cell. As a cell grows, newly made lipid and protein molecules are inserted into its plasma membrane; cell division produces two cells, each with its own membrane. This growth and cell division (fission) occurs without loss of membrane integrity. The internal volume enclosed by the plasma membrane, the cytoplasm (Fig. 1-3), is composed of an aqueous solution, the cytosol, and a variety of suspended particles with specific functions. These particulate components (membranous organelles such as mitochondria and chloroplasts; supramolecular structures such as ribosomes and proteasomes, the sites of protein synthesis and degradation) sediment when cytoplasm is centrifuged at 150,000 g (g is the gravitational force of Earth). What remains as the supernatant fluid is the cytosol, a highly concentrated solution containing enzymes and the RNA molecules that encode them; the components (amino acids and nucleotides) from which these macromolecules are assembled; hundreds of small organic molecules called metabolites, intermediates in biosynthetic and degradative pathways; coenzymes, compounds essential to many enzyme-catalyzed reactions; and inorganic ions (K+, Na+, Mg2+, and Ca2+, for example). FIGURE 1-3 The universal features of living cells. All cells have a nucleus or nucleoid containing their DNA, a plasma membrane, and cytoplasm. The cytosol is defined as that portion of the cytoplasm that remains in the supernatant after gentle breakage of the plasma membrane and centrifugation of the resulting extract at 150,000 g for 1 hour. Eukaryotic cells contain a variety of membrane-bounded organelles (including mitochondria, chloroplasts) and large particles (ribosomes, for example), which are sedimented by this centrifugation and can be recovered from the pellet. All cells have, for at least some part of their life, either a nucleoid or a nucleus, in which the genome—the complete set of genes, composed of DNA—is replicated and stored, with its associated proteins. The nucleoid, in bacteria and archaea, is not separated from the cytoplasm by a membrane; the nucleus, in eukaryotes, is enclosed within a double membrane, the nuclear envelope. Cells with nuclear envelopes make up the large domain Eukarya (Greek eu, “true,” and karyon, “nucleus”). Microorganisms without nuclear membranes, formerly grouped together as prokaryotes (Greek pro, “before”), are now recognized as comprising two very distinct groups: the domains Bacteria and Archaea, described below. Cellular Dimensions Are Limited by Diffusion Most cells are microscopic, invisible to the unaided eye. Animal and plant cells are typically 5 to 100 μm in diameter, and many unicellular microorganisms are only 1 to 2 μm long (see the inside of the back cover for information on units and their abbreviations). What limits the dimensions of a cell? The lower limit is probably set by the minimum number of each type of biomolecule required by the cell. The smallest cells, certain bacteria known as mycoplasmas, are 300 nm in diameter and have a volume of about 10−14 mL. A single bacterial ribosome is about 20 nm in its longest dimension, so a few ribosomes take up a substantial fraction of the volume in a mycoplasmal cell. The upper limit of cell size is probably set by the rate of diffusion of solute molecules in aqueous systems. For example, a bacterial cell that depends on oxygen- consuming reactions for energy extraction must obtain molecular oxygen by diffusion from the surrounding medium through its plasma membrane. The cell is so small, and the ratio of its surface area to its volume is so large, that every part of its cytoplasm is easily reached by O2 diffusing into the cell. With increasing cell size, however, surface-to-volume ratio decreases, until metabolism consumes O2 faster than diffusion can supply it. Metabolism that requires O2 thus becomes impossible as cell size increases beyond a certain point, placing a theoretical upper limit on the size of cells. Oxygen is only one of many low molecular weight species that must diffuse from outside the cell to various regions of its interior, and the same surface-to-volume argument applies to each of them as well. Many types of animal cells have a highly folded or convoluted surface that increases their surface-to-volume ratio and allows higher rates of uptake of materials from their surroundings (Fig. 1-4). FIGURE 1-4 Most animal cells have intricately folded surfaces. Colorized scanning electron micrographs show (a) the highly convoluted surface of two HeLa cells, a line of human cancer cells cultured in the laboratory, and (b) a neuron with its many extensions, each capable of making connections with other neurons. [Sources: (a) NIH National Institute of General Medical Sciences. (b) 2012 National Center for Microscopy & Imaging Research.] Organisms Belong to Three Distinct Domains of Life The development of techniques for determining DNA sequences quickly and inexpensively has greatly improved our ability to deduce evolutionary relationships among organisms. Similarities between gene sequences in various organisms provide deep insight into the course of evolution. In one interpretation of sequence similarities, all living organisms fall into one of three large groups (domains) that define three branches of the evolutionary tree of life originating from a common progenitor (Fig. 1-5). Two large groups of single-celled microorganisms can be distinguished on genetic and biochemical grounds: Bacteria and Archaea. Bacteria inhabit soils, surface waters, and the tissues of other living or decaying organisms. Many of the Archaea, recognized as a distinct domain by Carl Woese in the 1980s, inhabit extreme environments—salt lakes, hot springs, highly acidic bogs, and the ocean depths. The available evidence suggests that the Archaea and Bacteria diverged early in evolution. All eukaryotic organisms, which make up the third domain, Eukarya, evolved from the same branch that gave rise to the Archaea; eukaryotes are therefore more closely related to archaea than to bacteria. FIGURE 1-5 Phylogeny of the three domains of life. Phylogenetic relationships are often illustrated by a “family tree” of this type. The basis for this tree is the similarity in nucleotide sequences of the ribosomal RNAs of each group; the more similar the sequences, the closer the location of the branches, with the distance between branches representing the degree of difference between two sequences. Phylogenetic trees can also be constructed from similarities across species of the amino acid sequences of a single protein. For example, sequences of the protein GroEL (a bacterial protein that assists in protein folding) were compared to generate the tree in Figure 3-35. The tree in Figure 3-36 is a “consensus” tree, which uses several comparisons such as these to derive the best estimates of evolutionary relatedness among a group of organisms. Genomic sequences from a wide range of bacteria, archaea, and eukaryotes also are consistent with a twodomain model in which eukaryotes are subsumed under the Archaea domain. As more genomes are sequenced, one model may emerge as the clear best fit for the data. [Source: Information from C. R. Woese, Microbiol. Rev. 51:221, 1987, Fig. 4.] Within the domains of Archaea and Bacteria are subgroups distinguished by their habitats. In aerobic habitats with a plentiful supply of oxygen, some resident organisms derive energy from the transfer of electrons from fuel molecules to oxygen within the cell. Other environments are anaerobic, devoid of oxygen, and microorganisms adapted to these environments obtain energy by transferring electrons to nitrate (forming N2), sulfate (forming H2S), or CO2 (forming CH4). Many organisms that have evolved in anaerobic environments are obligate anaerobes: they die when exposed to oxygen. Others are facultative anaerobes, able to live with or without oxygen. Organisms Differ Widely in Their Sources of Energy and Biosynthetic Precursors We can classify organisms according to how they obtain the energy and carbon they need for synthesizing cellular material (as summarized in Fig. 1-6). There are two broad categories based on energy sources: phototrophs (Greek trophē, “nourishment”) trap and use sunlight, and chemotrophs derive their energy from oxidation of a chemical fuel. Some chemotrophs oxidize inorganic fuels— HS− to S0 (elemental sulfur), S0 to , , to or Fe2+ to Fe3+, for example. Phototrophs and chemotrophs may be further divided into those that can synthesize all of their biomolecules directly from CO2 (autotrophs) and those that require some preformed organic nutrients made by other organisms (heterotrophs). We can describe an organism’s mode of nutrition by combining these terms. For example, cyanobacteria are photoautotrophs; humans are chemoheterotrophs. Even finer distinctions can be made, and many organisms can obtain energy and carbon from more than one source under different environmental or developmental conditions. FIGURE 1-6 All organisms can be classified according to their source of energy (sunlight or oxidizable chemical compounds) and their source of carbon for the synthesis of cellular material. Bacterial and Archaeal Cells Share Common Features but Differ in Important Ways The best-studied bacterium, Escherichia coli, is a usually harmless inhabitant of the human intestinal tract. The E. coli cell (Fig. 1-7a) is an ovoid about 2 μm long and a little less than 1 μm in diameter, but other bacteria may be spherical or rod-shaped, and some are substantially larger. E. coli has a protective outer membrane and an inner plasma membrane that encloses the cytoplasm and the nucleoid. Between the inner and outer membranes is a thin but strong layer of a high molecular weight polymer (peptidoglycan) that gives the cell its shape and rigidity. The plasma membrane and the layers outside it constitute the cell envelope. The plasma membranes of bacteria consist of a thin bilayer of lipid molecules penetrated by proteins. Archaeal plasma membranes have a similar architecture, but the lipids can be strikingly different from those of bacteria (see Fig. 10-11). Bacteria and archaea have group-specific specializations of their cell envelopes (Fig. 1-7b–d). Some bacteria, called gram-positive because they are colored by Gram’s stain (introduced by Hans Peter Gram in 1882), have a thick layer of peptidoglycan outside their plasma membrane but lack an outer membrane. Gram-negative bacteria have an outer membrane composed of a lipid bilayer into which are inserted complex lipopolysaccharides and proteins called porins that provide transmembrane channels for the diffusion of low molecular weight compounds and ions across this outer membrane. The structures outside the plasma membrane of archaea differ from organism to organism, but they, too, have a layer of peptidoglycan or protein that confers rigidity on their cell envelopes. FIGURE 1-7 Some common structural features of bacterial and archaeal cells. (a) This correct-scale drawing of E. coli serves to illustrate some common features. (b) The cell envelope of gram-positive bacteria is a single membrane with a thick, rigid layer of peptidoglycan on its outside surface. A variety of polysaccharides and other complex polymers are interwoven with the peptidoglycan, and surrounding the whole is a porous “solid layer” composed of glycoproteins. (c) E. coli is gram-negative and has a double membrane. Its outer membrane has a lipopolysaccharide (LPS) on the outer surface and phospholipids on the inner surface. This outer membrane is studded with protein channels (porins) that allow small molecules, but not proteins, to diffuse through. The inner (plasma) membrane, made of phospholipids and proteins, is impermeable to both large and small molecules. Between the inner and outer membranes, in the periplasm, is a thin layer of peptidoglycan, which gives the cell shape and rigidity, but does not retain Gram’s stain. (d) Archaeal membranes vary in structure and composition, but all have a single membrane surrounded by an outer layer that includes either a peptidoglycanlike structure, a porous protein shell (solid layer), or both. [Sources: (a) David S. Goodsell. (b, c, d) Information from S.-V. Albers and B. H. Meyer, Nature Rev. Microbiol. 9:414, 2011, Fig. 2.] The cytoplasm of E. coli contains about 15,000 ribosomes, various numbers (10 to thousands) of copies of each of 1,000 or so different enzymes, perhaps 1,000 organic compounds of molecular weight less than 1,000 (metabolites and cofactors), and a variety of inorganic ions. The nucleoid contains a single, circular molecule of DNA, and the cytoplasm (like that of most bacteria) contains one or more smaller, circular segments of DNA called plasmids. In nature, some plasmids confer resistance to toxins and antibiotics in the environment. In the laboratory, these DNA segments are especially amenable to experimental manipulation and are powerful tools for genetic engineering (see Chapter 9). Other species of bacteria, as well as archaea, contain a similar collection of biomolecules, but each species has physical and metabolic specializations related to its environmental niche and nutritional sources. Cyanobacteria, for example, have internal membranes specialized to trap energy from light (see Fig. 20-27). Many archaea live in extreme environments and have biochemical adaptations to survive in extremes of temperature, pressure, or salt concentration. Differences in ribosomal structure gave the first hints that Bacteria and Archaea constituted separate domains. Most bacteria (including E. coli) exist as individual cells, but often associate in biofilms or mats, in which large numbers of cells adhere to each other and to some solid substrate beneath or at an aqueous surface. Cells of some bacterial species (the myxobacteria, for example) show simple social behavior, forming many-celled aggregates in response to signals between neighboring cells. Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study Typical eukaryotic cells (Fig. 1-8) are much larger than bacteria—commonly 5 to 100 μm in diameter, with cell volumes a thousand to a million times larger than those of bacteria. The distinguishing characteristics of eukaryotes are the nucleus and a variety of membrane-enclosed organelles with specific functions. These organelles include mitochondria, the site of most of the energy-extracting reactions of the cell; the endoplasmic reticulum and Golgi complexes, which play central roles in the synthesis and processing of lipids and membrane proteins; peroxisomes, in which very long-chain fatty acids are oxidized; and lysosomes, filled with digestive enzymes to degrade unneeded cellular debris. In addition to these, plant cells also contain vacuoles (which store large quantities of organic acids) and chloroplasts (in which sunlight drives the synthesis of ATP in the process of photosynthesis) (Fig. 1-8). Also present in the cytoplasm of many cells are granules or droplets containing stored nutrients such as starch and fat. In a major advance in biochemistry, Albert Claude, Christian de Duve, and George Palade developed methods for separating organelles from the cytosol and from each other—an essential step in investigating their structures and functions. In a typical cell fractionation (Fig. 1-9), cells or tissues in solution are gently disrupted by physical shear. This treatment ruptures the plasma membrane but leaves most of the organelles intact. The homogenate is then centrifuged; organelles such as nuclei, mitochondria, and lysosomes differ in size and therefore sediment at different rates. These methods were used to establish, for example, that lysosomes contain degradative enzymes, mitochondria contain oxidative enzymes, and chloroplasts contain photosynthetic pigments. The isolation of an organelle enriched in a certain enzyme is often the first step in the purification of that enzyme. The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic Fluorescence microscopy reveals several types of protein filaments crisscrossing the eukaryotic cell, forming an interlocking three-dimensional meshwork, the cytoskeleton. Eukaryotes have three general types of cytoplasmic filaments—actin filaments, microtubules, and intermediate filaments (Fig. 1-10)—differing in width (from about 6 to 22 nm), composition, and specific function. All types provide structure and organization to the cytoplasm and shape to the cell. Actin filaments and microtubules also help to produce the motion of organelles or of the whole cell. Each type of cytoskeletal component consists of simple protein subunits that associate noncovalently to form filaments of uniform thickness. These filaments are not permanent structures; they undergo constant disassembly into their protein subunits and reassembly into filaments. Their locations in cells are not rigidly fixed but may change dramatically with mitosis, cytokinesis, amoeboid motion, or changes in cell shape. The assembly, disassembly, and location of all types of filaments are regulated by other proteins, which serve to link or bundle the filaments or to move cytoplasmic organelles along the filaments. (Bacteria contain actinlike proteins that serve similar roles in those cells.) The picture that emerges from this brief survey of eukaryotic cell structure is of a cell with a meshwork of structural fibers and a complex system of membrane-enclosed compartments (Fig. 1-8). The filaments disassemble and then reassemble elsewhere. Membranous vesicles bud from one organelle and fuse with another. Organelles move through the cytoplasm along protein filaments, their motion powered by energy-dependent motor proteins. The endomembrane system segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur. Exocytosis and endocytosis, mechanisms of transport (out of and into cells, respectively) that involve membrane fusion and fission, provide paths between the cytoplasm and surrounding medium, allowing the secretion of substances produced in the cell and uptake of extracellular materials. FIGURE 1-8 Eukaryotic cell structure. Schematic illustrations of two major types of eukaryotic cell: (a) a representative animal cell and (b) a representative plant cell. Plant cells are usually 10 to 100 μm in diameter—larger than animal cells, which typically range from 5 to 30 μm. Structures labeled in red are unique to animal cells; those labeled in green are unique to plant cells. Eukaryotic microorganisms (such as protists and fungi) have structures similar to those in plant and animal cells, but many also contain specialized organelles not illustrated here. This structural organization of the cytoplasm is far from random. The motion and positioning of organelles and cytoskeletal elements are under tight regulation, and at certain stages in its life, a eukaryotic cell undergoes dramatic, finely orchestrated reorganizations, such as the events of mitosis. The interactions between the cytoskeleton and organelles are noncovalent, reversible, and subject to regulation in response to various intracellular and extracellular signals. FIGURE 1-9 Subcellular fractionation of tissue. A tissue such as liver is first mechanically homogenized to break cells and disperse their contents in an aqueous buffer. The sucrose medium has an osmotic pressure similar to that in organelles, thus balancing diffusion of water into and out of the organelles, which would swell and burst in a solution of lower osmolarity (see Fig. 2-13). The large and small particles in the suspension can be separated by centrifugation at different speeds. Larger particles sediment more rapidly than small particles, and soluble material does not sediment. By careful choice of the conditions of centrifugation, subcellular fractions can be separated for biochemical characterization. [Source: Information from B. Alberts et al., Molecular Biology of the Cell, 2nd edn, Garland Publishing, Inc., 1989, p. 165.] FIGURE 1-10 The three types of cytoskeletal filaments: actin filaments, microtubules, and intermediate filaments. Cellular structures can be labeled with an antibody (that recognizes a characteristic protein) covalently attached to a fluorescent compound. The stained structures are visible when the cell is viewed with a fluorescence microscope. (a) In this cultured fibroblast cell, bundles of actin filaments are stained red; microtubules, radiating from the cell center, are stained green; and chromosomes (in the nucleus) are stained blue. (b) A newt lung cell undergoing mitosis. Microtubules (green), attached to structures called kinetochores (yellow) on the condensed chromosomes (blue), pull the chromosomes to opposite poles, or centrosomes (magenta), of the cell. Intermediate filaments, made of keratin (red), maintain the structure of the cell. [Sources: (a) James J. Faust and David G. Capco, Arizona State University/NIH National Institute of General Medical Sciences. (b) Dr. Alexey Khodjakov, Wadsworth Center, New York State Department of Health.] Cells Build Supramolecular Structures Macromolecules and their monomeric subunits differ greatly in size (Fig. 1-11). An alanine molecule is less than 0.5 nm long. A molecule of hemoglobin, the oxygen-carrying protein of erythrocytes (red blood cells), consists of nearly 600 amino acid subunits in four long chains, folded into globular shapes and associated in a structure 5.5 nm in diameter. In turn, proteins are much smaller than ribosomes (about 20 nm in diameter), which are much smaller than organelles such as mitochondria, typically 1,000 nm in diameter. It is a long jump from simple biomolecules to cellular structures that can be seen with the light microscope. Figure 1-12 illustrates the structural hierarchy in cellular organization. FIGURE 1-11 The organic compounds from which most cellular materials are constructed: the ABCs of biochemistry. Shown here are (a) six of the 20 amino acids from which all proteins are built (the side chains are shaded light red); (b) the five nitrogenous bases, two five-carbon sugars, and phosphate ion from which all nucleic acids are built; (c) five components of membrane lipids (including phosphate); and (d) D-glucose, the simple sugar from which most carbohydrates are derived. The monomeric subunits of proteins, nucleic acids, and polysaccharides are joined by covalent bonds. In supramolecular complexes, however, macromolecules are held together by noncovalent interactions—much weaker, individually, than covalent bonds. Among these noncovalent interactions are hydrogen bonds (between polar groups), ionic interactions (between charged groups), aggregations of nonpolar groups in aqueous solution brought about by the hydrophobic effect (sometimes called hydrophobic interactions), and van der Waals interactions (also called London forces)—all of which have energies much smaller than those of covalent bonds. These noncovalent interactions are described in Chapter 2. The large numbers of weak interactions between macromolecules in supramolecular complexes stabilize these assemblies, producing their unique structures. FIGURE 1-12 Structural hierarchy in the molecular organization of cells. The organelles and other relatively large components of cells are composed of supramolecular complexes, which in turn are composed of smaller macromolecules and even smaller molecular subunits. For example, the nucleus of this plant cell contains chromatin, a supramolecular complex that consists of DNA and basic proteins (histones). DNA is made up of simple monomeric subunits (nucleotides), as are proteins (amino acids). [Source: Information from W. M. Becker and D. W. Deamer, The World of the Cell, 2nd edn, Benjamin/Cummings Publishing Company, 1991, Fig. 2-15.] In Vitro Studies May Overlook Important Interactions among Molecules One approach to understanding a biological process is to study purified molecules in vitro (“in glass”—in the test tube), without interference from other molecules present in the intact cell—that is, in vivo (“in the living”). Although this approach has been remarkably revealing, we must keep in mind that the inside of a cell is quite different from the inside of a test tube. The “interfering” components eliminated by purification may be critical to the biological function or regulation of the molecule purified. For example, in vitro studies of pure enzymes are commonly done at very low enzyme concentrations in thoroughly stirred aqueous solutions. In the cell, an enzyme is dissolved or suspended in the gel-like cytosol with thousands of other proteins, some of which bind to that enzyme and influence its activity. Some enzymes are components of multienzyme complexes in which reactants are channeled from one enzyme to another, never entering the bulk solvent. When all of the known macromolecules in a cell are represented in their known dimensions and concentrations (Fig. 1-13), it is clear that the cytosol is very crowded and that diffusion of macromolecules within the cytosol must be slowed by collisions with other large structures. In short, a given molecule may behave quite differently in the cell and in vitro. A central challenge of biochemistry is to understand the influences of cellular organization and macromolecular associations on the function of individual enzymes and other biomolecules—to understand function in vivo as well as in vitro. FIGURE 1-13 The crowded cell. This drawing by David Goodsell is an accurate representation of the relative sizes and numbers of macromolecules in one small region of an E. coli cell. This concentrated cytosol, crowded with proteins and nucleic acids, is very different from the typical extract of cells used in biochemical studies, in which the cytosol has been diluted manyfold and the interactions between diffusing macromolecules have been strongly altered. [Source: © David S. Goodsell 1999.] SUMMARY 1.1 Cellular Foundations ■ All cells are bounded by a plasma membrane; have a cytosol containing metabolites, coenzymes, inorganic ions, and enzymes; and have a set of genes contained within a nucleoid (bacteria and archaea) or nucleus (eukaryotes). ■ All organisms require a source of energy to perform cellular work. Phototrophs obtain energy from sunlight; chemotrophs obtain energy from chemical fuels, oxidizing the fuel and passing electrons to good electron acceptors: inorganic compounds, organic compounds, or molecular oxygen. ■ Bacterial and archaeal cells contain cytosol, a nucleoid, and plasmids, all within a cell envelope. Eukaryotic cells have a nucleus and are multicompartmented, with certain processes segregated in specific organelles; organelles can be separated and studied in isolation. ■ Cytoskeletal proteins assemble into long filaments that give cells shape and rigidity and serve as rails along which cellular organelles move throughout the cell. ■ Supramolecular complexes held together by noncovalent interactions are part of a hierarchy of structures, some visible with the light microscope. When individual molecules are removed from these complexes to be studied in vitro, interactions important in the living cell may be lost. 1.2 Chemical Foundations Biochemistry aims to explain biological form and function in chemical terms. By the late eighteenth century, chemists had concluded that the composition of living matter is strikingly different from that of the inanimate world. Antoine-Laurent Lavoisier (1743–1794) noted the relative chemical simplicity of the “mineral world” and contrasted it with the complexity of the “plant and animal worlds”; the latter, he knew, were composed of compounds rich in the elements carbon, oxygen, nitrogen, and phosphorus. During the first half of the twentieth century, parallel biochemical investigations of glucose breakdown in yeast and in animal muscle cells revealed remarkable chemical similarities between these two apparently very different cell types; the breakdown of glucose in yeast and in muscle cells involved the same 10 chemical intermediates and the same 10 enzymes. Subsequent studies of many other biochemical processes in many different organisms have confirmed the generality of this observation, neatly summarized in 1954 by Jacques Monod: “What is true of E. coli is true of the elephant.” The current understanding that all organisms share a common evolutionary origin is based in part on this observed universality of chemical intermediates and transformations, often termed “biochemical unity.” Fewer than 30 of the more than 90 naturally occurring chemical elements are essential to organisms. Most of the elements in living matter have a relatively low atomic number; only three have an atomic number above that of selenium, 34 (Fig. 1-14). The four most abundant elements in living organisms, in terms of percentage of total number of atoms, are hydrogen, oxygen, nitrogen, and carbon, which together make up more than 99% of the mass of most cells. They are the lightest elements capable of efficiently forming one, two, three, and four bonds, respectively; in general, the lightest elements form the strongest bonds. The trace elements represent a miniscule fraction of the weight of the human body, but all are essential to life, usually because they are essential to the function of specific proteins, including many enzymes. The oxygen-transporting capacity of the hemoglobin molecule, for example, is absolutely dependent on four iron ions that make up only 0.3% of its mass. Biomolecules Are Compounds of Carbon with a Variety of Functional Groups The chemistry of living organisms is organized around carbon, which accounts for more than half of the dry weight of cells. Carbon can form single bonds with hydrogen atoms, and both single and double bonds with oxygen and nitrogen atoms (Fig. 1-15). Of greatest significance in biology is the ability of carbon atoms to form very stable single bonds with up to four other carbon atoms. Two carbon atoms also can share two (or three) electron pairs, thus forming double (or triple) bonds. The four single bonds that can be formed by a carbon atom project from the nucleus to the four apices of a tetrahedron (Fig. 1-16), with an angle of about 109.5° between any two bonds and an average bond length of 0.154 nm. There is free rotation around each single bond, unless very large or highly charged groups are attached to both carbon atoms, in which case rotation may be restricted. A double bond is shorter (about 0.134 nm) and rigid, and allows only limited rotation about its axis. FIGURE 1-14 Elements essential to animal life and health. Bulk elements (shaded light red) are structural components of cells and tissues and are required in the diet in gram quantities daily. For trace elements (shaded yellow), the requirements are much smaller: for humans, a few milligrams per day of Fe, Cu, and Zn, even less of the others. The elemental requirements for plants and microorganisms are similar to those shown here; the ways in which they acquire these elements vary. FIGURE 1-15 Versatility of carbon bonding. Carbon can form covalent single, double, and triple bonds (all bonds in red), particularly with other carbon atoms. Triple bonds are rare in biomolecules. FIGURE 1-16 Geometry of carbon bonding. (a) Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds. (b) Carbon–carbon single bonds have freedom of rotation, as shown for the compound ethane (CH3— CH3). (c) Double bonds are shorter and do not allow free rotation. The two doubly bonded carbons and the atoms designated A, B, X, and Y all lie in the same rigid plane. Covalently linked carbon atoms in biomolecules can form linear chains, branched chains, and cyclic structures. It seems likely that the bonding versatility of carbon, with itself and with other elements, was a major factor in the selection of carbon compounds for the molecular machinery of cells during the origin and evolution of living organisms. No other chemical element can form molecules of such widely different sizes, shapes, and composition. Most biomolecules can be regarded as derivatives of hydrocarbons, with hydrogen atoms replaced by a variety of functional groups that confer specific chemical properties on the molecule, forming various families of organic compounds. Typical of these are alcohols, which have one or more hydroxyl groups; amines, with amino groups; aldehydes and ketones, with carbonyl groups; and carboxylic acids, with carboxyl groups (Fig. 1-17). Many biomolecules are polyfunctional, containing two or more types of functional groups (Fig. 1-18), each with its own chemical characteristics and reactions. The chemical “personality” of a compound is determined by the chemistry of its functional groups and their disposition in three-dimensional space. Cells Contain a Universal Set of Small Molecules Dissolved in the aqueous phase (cytosol) of all cells is a collection of perhaps a thousand different small organic molecules (Mr ∼100 to ∼500), with intracellular concentrations ranging from nanomolar to millimolar (see Fig. 15-4). (See Box 1-1 for an explanation of the various ways of referring to molecular weight.) These are the central metabolites in the major pathways occurring in nearly every cell—the metabolites and pathways that have been conserved throughout the course of evolution. This collection of molecules includes the common amino acids, nucleotides, sugars and their phosphorylated derivatives, and mono-, di-, and tricarboxylic acids. The molecules may be polar or charged and are water-soluble. They are trapped in the cell because the plasma membrane is impermeable to them, although specific membrane transporters can catalyze the movement of some molecules into and out of the cell or between compartments in eukaryotic cells. The universal occurrence of the same set of compounds in living cells reflects the evolutionary conservation of metabolic pathways that developed in the earliest cells. BOX 1-1 Molecular Weight, Molecular Mass, and Their Correct Units There are two common (and equivalent) ways to describe molecular mass; both are used in this text. The first is molecular weight, or relative molecular mass, denoted Mr. The molecular weight of a substance is defined as the ratio of the mass of a molecule of that substance to one-twelfth the mass of an atom of carbon-12 (12C). Since Mr is a ratio, it is dimensionless—it has no associated units. The second is molecular mass, denoted m. This is simply the mass of one molecule, or the molar mass divided by Avogadro’s number. The molecular mass, m, is expressed in daltons (abbreviated Da).