Biochemistry, 6th Edition, Campbell & Farrell, 2009

Biochemistry, 6th Edition, Campbell & Farrell, 2009
By:Thomson Brooks/Cole-Thomson Coorporation
Published on 2009-07-09 by Bukupedia

Mary K. Campbell Mary K. Campbell is professor emeritus of chemistry at Mount Holyoke College, where she taught a one-semester biochemistry course and advised undergraduates working on biochemical research projects. She frequently taught general chemistry and physical chemistry as well. At some point in her 36 years at Mount Holyoke, she taught every subfield of chemistry, except the lecture portion of organic chemistry. Her avid interest in writing led to the publication of the first five highly successful editions of this textbook. Originally from Philadelphia, Mary received her Ph.D. from Indiana University and did postdoctoral work in biophysical chemistry at Johns Hopkins University. Her area of interest includes researching the physical chemistry of biomolecules, specifically, spectroscopic studies of protein–nucleic acid interactions. Mary enjoys traveling and has recently visited Australia and New Zealand. She can frequently be seen hiking the Appalachian Trail. Shawn O. Farrell Shawn O. Farrell grew up in northern California and received a B.S. degree in biochemistry from the University of California, Davis, where he studied carbohydrate metabolism. He completed his Ph.D. in biochemistry at Michigan State University, where he studied fatty acid metabolism. For the last 18 years, Shawn has worked at Colorado State University teaching undergraduate biochemistry lecture and laboratory courses. Because of his interest in biochemical education, Shawn has written a number of scientific journal articles about teaching biochemistry. He is the coauthor (with Lynn E. Taylor) of Experiments in Biochemistry: A Hands-On Approach. Shawn became interested in biochemistry while in college because it coincided with his passion for bicycle racing. An active outdoorsman, Shawn raced competitively for 17 years and now officiates at bicycle races around the world. He is currently the Technical Director of USA Cycling, the national governing body of bicycle racing in the United States. He is also a distance runner and an avid fly fisherman, and recently achieved his third-degree black belt in Tae Kwon Do and first-degree black belt in combat hapkido. Shawn has also written articles on fly fishing for Salmon Trout Steelheader magazine. His other passions are soccer, chess, and foreign languages. He is fluent in Spanish and French and is currently learning German and Italian. Preface This text is intended for students in any field of science or engineering who want a one-semester introduction to biochemistry but who do not intend to be biochemistry majors. Our main goal in writing this book is to make biochemistry as clear and applied as possible and to familiarize science students with the major aspects of biochemistry. For students of biology, chemistry, physics, geology, nutrition, sports physiology, and agriculture, biochemistry impacts greatly on the content of their fields, especially in the areas of medicine and biotechnology. For engineers, studying biochemistry is especially important for those who hope to enter a career in biomedical engineering or some form of biotechnology. Students who will use this text are at an intermediate level in their studies. A beginning biology course, general chemistry, and at least one semester of organic chemistry are assumed as preparation. New to This Edition All textbooks evolve to meet the interests and needs of students and instructors and to include the most current information. Several changes mark this edition. Integrated In-Text Questions We employ a new in-text question framework for this edition to emphasize key biochemistry concepts. This focused Q & A approach interjects questions about key concepts in biochemistry as they may naturally arise in a student’s mind. The questions are designed to help students master essential biochemistry concepts in each chapter. The in-text questions and their answers are also summarized at the end of each chapter, making it easier for student’s to study and learn this important material. New End-of-Chapter Summary Format Each end-of-chapter summary now summarizes the in-text questions posed throughout the chapter in an easy to study “Q & A” format that helps students master key concepts. New Section Summaries Each numbered section ends with a bulleted summary that highlights essential information in that section, further reinforcing students’ understanding of the critical material discussed in that section. New “Hot Topics in Biochemistry” Magazine A new supplement features up-todate articles on new breakthroughs and topics in the area of biochemistry such as blood doping, avian flu, SNPs, HPV, stem cells, and HIV. More Biochemical Connections Boxes In response to customers’ demand for more Biochemical Connection boxes, we have added several new boxes to the text, such as “Lactic Acid—Not Always the Bad Guy,” “Biofuels from Fermentation,” and “Catalysts for Green Chemistry.” Expanded and Updated Coverage of Selected Topics The concept of proteinfolding chaperones is introduced in Chapter 4 to lay the groundwork for development of protein folding in Chapter 12. Likewise, Chapter 5 introduces proteomics in preparation for treatment of gene-chip technology in Chapter 13. Coverage of RNA interference is expanded in Chapter 11. Also new to Chapter 11 is the definitive illustration of RNA polymerase in the act of transcribing messenger RNA; we thank Professor Roger Kornberg of Stanford University for his gracious permission to use it. Chapter 12 includes new material on so-called silent mutations. Extensive coverage of microarrays (gene-chip technology) is new to Chapter 13, bringing in an important aspect of biotechnology. Chapter 14 now focuses on viruses, cancer, and xiv Preface immunology; it provides essential background information for full understanding of the “Hot Topics” magazine. Explicit connections to nutrition and weight control have been added to the coverage of metabolism in Chapters 17–21. The treatment of fatty-acid biosynthesis in Chapter 21 now includes recent findings on the structure of fatty-acid synthase. Chapter 22, Photosynthesis, has new information about the role of chloroplast genes. Chapter 24 raises questions about calorie restriction and longevity. New Design and Enhanced Labeling in Art Updated labeling in the illustrations throughout the text enhances readability, which in turn enhances students’ ability to comprehend key concepts. As a corollary to the book’s updated art program, the design and color palette have also been modernized. Proven Features Technology Integration First, and foremost is the integration of BiochemistryNow™, the first assessment centered student learning tool for biochemistry! This powerful and interactive online resource helps students gauge their unique study needs, then gives them a Personalized Learning Plan that focuses their study time on the concepts and problems that will most enhance their computational skills and understanding. BiochemistryNow gives students the resources and responsibility to manage their concept mastery. The system includes diagnostic tests to determine where students need help, online tutorials to help turn student weaknesses into strengths, Active and Animated Figures to make concepts come alive, and more. Visual Impact One of the most distinctive features of this text is its visual impact. Its extensive four-color art program includes artwork by the late Irving Geis, John and Bette Woolsey, and Greg Gambino of 2064 Design. The illustrations convey meaning so powerfully, it is certain that many of them will become standard presentations in the field. Biochemical Connections The Biochemical Connections boxes highlight special topics of particular interest to students. Topics frequently have clinical implications, such as cancer, AIDS, and nutrition. These essays help students make the connection between biochemistry and the real world. Apply Your Knowledge The Apply Your Knowledge boxes are interspersed within chapters and are designed to provide students with problem-solving experience. The topics chosen are areas of study where students usually have the most difficulty. Solutions and problem-solving strategies are included, giving examples of the problemsolving approach for specific material. Early Inclusion of Thermodynamics Select material on thermodynamics appears much earlier in the text. Chapter 1 includes sections on Energy and Change, Spontaneity in Biochemical Reactions, and the connection between Life and Thermodynamics. Also, Chapter 4 contains an extended section on Protein Folding Dynamics. We feel it is critical that students understand the driving force of biological processes and that so much of biology (protein folding, protein–protein interactions, small molecule binding, etc.) is driven by the favorable disordering of water molecules. Summaries and Questions Each chapter closes with a concise summary, a broad selection of questions, and an annotated bibliography. As stated previously, the summaries have been completely revised to reflect the in-text “Q & A” framework. The number of questions has been expanded to provide additional self-testing of content mastery and more homework material. These exercises fall into four cat- egories: Recall, Reflect and Apply, Mathematical, and Biochemical Connections. The Recall questions are designed for students to quickly assess their mastery of the material, while the Reflect and Apply questions are for students to work through more thoughtprovoking questions. Biochemical Connections questions test students on the Biochemical Connections essays in that chapter. The Mathematical questions complete the selection of exercises. These questions are quantitative in nature and focus on calculations. Glossary and Answers The book ends with a glossary of important terms and concepts (including the section number where the term was first introduced), an answer section, and a detailed index. Organization Because biochemistry is a multidisciplinary science, the first task in presenting it to students of widely varying backgrounds is to put it in context. Chapters 1 and 2 provide the necessary background and connect biochemistry to the other sciences. Chapters 3 through 8 focus on the structure and dynamics of important cellular components. Molecular biology is covered in Chapters 9 through 14. The final part of the book is devoted to intermediary metabolism. Some topics are discussed several times, such as the control of carbohydrate metabolism. Subsequent discussions make use of and build on information students have already learned. It is particularly useful to return to a topic after students have had time to assimilate and reflect on it. The first two chapters of the book relate biochemistry to other fields of science. Chapter 1 deals with some of the less obvious relationships, such as the connections of biochemistry with physics, astronomy, and geology, mostly in the context of the origins of life. Functional groups on organic molecules are discussed from the point of view of their role in biochemistry. This chapter goes on to the more readily apparent linkage of biochemistry with biology, especially with respect to the distinction between prokaryotes and eukaryotes, as well as the role of organelles in eukaryotic cells. Chapter 2 builds on material familiar from general chemistry, such as buffers and the solvent properties of water, but emphasizes the biochemical point of view toward such material. Chapters 3 through 8, covering the structure of cellular components, focus on the structure and dynamics of proteins and membranes in addition to giving an introduction to some aspects of molecular biology. Chapters 3, 4, 6, and 7 deal with amino acids, peptides, and the structure and action of proteins including enzyme catalysis. Chapter 4 includes more material on thermodynamics, such as hydrophobic interactions. The discussion of enzymes is split into two chapters (Chapters 6 and 7) to give students more time to fully understand enzyme kinetics and enzyme mechanisms. Chapter 5 focuses on techniques for isolating and studying proteins. Chapter 8 treats the structure of membranes and their lipid components. Chapters 9 through 14 explore the topics of molecular biology. Chapter 9 introduces the structure of nucleic acids. In Chapter 10, the replication of DNA is discussed. Chapter 11 focuses on transcription and gene regulation. This material on the biosynthesis of nucleic acids is split into two chapters to give students ample time to appreciate the workings of these processes. Chapter 12 finishes the topic with translation of the genetic message and protein synthesis. Chapter 13 focuses on biotechnology techniques, and Chapter 14 deals with viruses, cancer, and immunology. Chapters 15 through 24 explore intermediary metabolism. Chapter 15 opens the topic with chemical principles that provide some unifying themes. Thermodynamic concepts learned earlier in general chemistry and in Chapter 1 are applied specifically to biochemical topics such as coupled reactions. In addition, this chapter explicitly makes the connection between metabolism and electron transfer (oxidation– reduction) reactions. Preface xv xvi Preface Coenzymes are introduced in this chapter and are discussed in later chapters in the context of the reactions in which they play a role. Chapter 16 discusses carbohydrates. Chapter 17 begins the overview of the metabolic pathways by discussing glycolysis. Glycogen metabolism, gluconeogenesis, and the pentose phosphate pathway (Chapter 18) provide bases for treating control mechanisms in carbohydrate metabolism. Discussion of the citric acid cycle is followed by the electron transport chain and oxidative phosphorylation in Chapters 19 and 20. The catabolic and anabolic aspects of lipid metabolism are dealt with in Chapter 21. In Chapter 22, photosynthesis rounds out the discussion of carbohydrate metabolism. Chapter 23 completes the survey of the pathways by discussing the metabolism of nitrogencontaining compounds such as amino acids, porphyrins, and nucleobases. Chapter 24 is a summary chapter. It gives an integrated look at metabolism, including a treatment of hormones and second messengers. The overall look at metabolism includes a brief discussion of nutrition and a somewhat longer one of the immune system. This text gives an overview of important topics of interest to biochemists and shows how the remarkable recent progress of biochemistry impinges on other sciences. The length is intended to provide instructors with a choice of favorite topics without being overwhelming for the limited amount of time available in one semester. Alternative Teaching Options The order in which individual chapters are covered can be changed to suit the needs of specific groups of students. Although we prefer an early discussion of thermodynamics, the portions of Chapters 1 and 4 that deal with thermodynamics can be covered at the beginning of Chapter 15, “The Importance of Energy Changes and Electron Transfer in Metabolism.” All of the molecular biology chapters (Chapters 9 through 14) can precede metabolism or can follow it, depending on the instructor’s choice. The order in which the material on molecular biology is treated can be varied according to the preference of the instructor. Supplements This sixth edition of Campbell and Farrell’s Biochemistry is accompanied by the following rich array of Web-based, electronic, and print supplements. Instructor Resources PowerLecture Instructor’s Resource CD-ROM This dual-platform CD-ROM is a digital library and presentation tool that includes Brooks/Cole’s text-specific PowerPoint® Lectures, which instructors can customize if desired by importing their own lecture slides or other materials. The CD also contains art, photos, and tables from the text in a variety of electronic formats, multimedia animations to supplement lectures, as well as the Instructor’s Manual, Test Bank, and ExamView® testing software. With ExamView’s friendly interface, instructors can create, deliver, and customize tests based on questions authored specifically for this text. Online Instructor’s Manual The Online Instructor’s Manual was written by Michael A. Stypes at Pennsylvania State University. Each chapter includes a chapter summary, lecture outline, and answers to all the exercises in the text. Electronic files are available for download on the instructor’s website. Testbank on eBank Multiple-choice exam questions authored by Michael A. Stypes at Pennsylvania State University are available as Word and PDF files and in ExamView on the PowerLecture CD-ROM. You can also download them on request from eBank. Transparency Acetates A set of 150 full-color overhead transparency acetates of text images is available for use in lectures. Student Resources BiochemistryNOW™ This interactive online resource, developed in concert with the text, empowers students by helping them determine their unique study needs. Each chapter is annotated with captions that alert students to tutorials, animations, and coached problems that enhance their problem-solving skills and conceptual understanding. In addition, students are provided with a Personalized Learning Plan—based on a diagnostic Pre-Test—that targets their study needs. A PIN code is required to access BiochemistryNOW and may be packaged with a new copy of the text or purchased separately. Experiments in Biochemistry: A Hands-On Approach This interactive manual, by Shawn O. Farrell and Lynn E. Taylor, is for the introductory biochemistry laboratory course. It offers a great selection of classroom-tested experiments, each designed to be completed in a normal laboratory period. Lecture Notebook This notebook contains all the instructor overhead transparency images printed in booklet format and includes pages for student notes. It can be packaged for free with each new copy of the text. Acknowledgments The help of many made this book possible. A grant from the Dreyfus Foundation made possible the experimental introductory course that was the genesis of many of the ideas for this text. Edwin Weaver and Francis DeToma from Mount Holyoke College gave much of their time and energy in initiating that course. Many others at Mount Holyoke were generous with their support, encouragement, and good ideas, especially Anna Harrison, Lilian Hsu, Dianne Baranowski, Sheila Browne, Janice Smith, Jeffrey Knight, Sue Ellen Frederick Gruber, Peter Gruber, Marilyn Pryor, Craig Woodard, Diana Stein, and Sue Rusiecki. Particular thanks go to Sandy Ward, science librarian, and to Rosalia Tungaraza, a biochemistry major in the class of 2004. Special thanks to Laurie Stargell, Marve Paule, and Steven McBryant at Colorado State University for their help and editorial assistance. We thank the many biochemistry students who have used and commented on early versions of this text. We would like to acknowledge colleagues who contributed their ideas and critiques of the manuscript. Some reviewers responded to specific queries regarding the text itself. We thank them for their efforts and their helpful suggestions. Reviewers Acknowledgments Clanton C. Black, University of Georgia Daniel D. Clark, California State University, Chico Helen Henry, University of California, Riverside Roger E. Koeppe II, University of Arkansas Lisa Lindert, California Polytechnic State University, San Luis Obispo Smita Mohanty, Auburn State University Kerry Smith, Clemson University Sandra Turchi, Millersville University Bryan A. White, University of Illinois We would also like to thank the people at Brooks/Cole, a part of Cengage Learning, who were essential to the development of this book: Alyssa White, development editor, whose creative ideas added so much to this new edition; Teresa Trego, senior production manager, who directed production, making what could have been Preface xvii xviii Preface a dreary chore so much easier; David Harris, publisher; and Lisa Lockwood, executive editor, who was a source of so much encouragement. Sheila McGill of Lachina Publishing Services served diligently as our production editor. Dena Digilio-Betz, photo researcher, did wonders with challenging searches. We extend our most sincere gratitude to those listed here and to all others to whom we owe the opportunity to do this book. Instrumental in the direction given to this project was the late John Vondeling. John was a legend in the publishing field. His guidance and friendship shall be missed. A Final Note from Mary Campbell I thank my family and friends, whose moral support has meant so much to me in the course of my work. When I started this project years ago, I did not realize that it would become a large part of my life. It has been a thoroughly satisfying one. A Final Note from Shawn Farrell I cannot adequately convey how impossible this project would have been without my wonderful family, who put up with a husband and father who became a hermit in the back office. My wife, Courtney, knows the challenge of living with me when I am working on four hours of sleep per night. It isn’t pretty, and few would have been so understanding. I would also like to thank David Hall, book representative, for starting me down this path, and John Vondeling for giving me an opportunity to expand into other types of books and projects. Lastly, of course, I thank all of my students who have helped proofread the sixth edition.

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