Biochemistry: Concepts and Connections 2nd Edition

Book Preface

Biochemistry: Concepts and Connections
As genomics and informatics revolutionize biomedical science and health care, we must prepare students for the challenges of the twentyfirst century and ensure their ability to apply quantitative reasoningskills to the science most fundamental to medicine: biochemistry.
We have written Biochemistry: Concepts and Connections to provide students with a clear understanding of the chemical logic underlying the mechanisms, pathways, and processes in living cells. The title reinforces our vision for this book—twin emphases upon fundamental concepts at the expense of lengthy descriptive information, and upon connections, showing how biochemistry relates to all other life sciences and to practical applications in medicine, agricultural sciences, environmental sciences, and forensics.

Inspired by our experience as authors of the biochemistry majors’ text, Biochemistry, Fourth Edition and the first edition of this book,
and as teachers of biochemistry majors’ and mixed-science-majors’ courses, we believe there are several requirements that a textbook for the mixed-majors’ course must address:
• The need for students to understand the structure and function of biological molecules before moving into metabolism and dynamic aspects of biochemistry.
• The need for students to understand that biochemical concepts derive from experimental evidence, meaning that the principles of biochemical techniques must be presented to the greatest extent possible.
• The need for students to encounter many and diverse real-world applications of biochemical concepts.
• The need for students to understand the quantitative basis for biochemical concepts. The Henderson–Hasselbalch equation, the quantitative expressions of thermodynamic laws, and the Michaelis–Menten equation, for example, are not equations to be memorized and forgotten when the course moves on. The basis for these and other quantitative statements must be understood and constantly repeated as biochemical concepts, such as mechanisms of enzyme action, are developed. They are essential to help students grasp the concepts.

In designing Biochemistry: Concepts and Connections, we have stayed with the organization that serves us well in our own classroom experience. The first 10 chapters cover structure and function of biological molecules, the next 10 deal with intermediary metabolism, and the final 6 with genetic biochemistry. Our emphasis on biochemistry as a quantitative science can be seen in Chapters 2 and 3, where we focus on water, the matrix of life, and bioenergetics. Chapter 4 introduces nucleic acid structure, with a brief introduction to nucleic acid and protein synthesis—topics covered in much more detail at the end of the book.

Chapters 11 through 20 deal primarily with intermediary metabolism.
We cover the major topics in carbohydrate metabolism, lipid metabolism, and amino acid metabolism in one chapter each (12, 16, and 18, respectively). Our treatment of cell signaling is a bit unconventional, since it appears in Chapter 20, well after we present hormonal control of carbohydrate and lipid metabolism. However, this treatment allows more extended presentation of receptors, G proteins, oncogenes, and neurotransmission.

In addition, because cancer often results from aberrant signaling processes, our placement of the signaling chapter leads fairly naturally into genetic biochemistry, which follows, beginning in Chapter 21. With assistance from talented artists, we have built a compelling visual narrative from the ground up, composed of a wide range of graphic representations, from macromolecules to cellular structures as well as reaction mechanisms and metabolic pathways that highlight and reinforce overarching themes (chemical logic, regulation, interface between chemistry and biology). In addition, we have added two new Foundation Figures to the Second Edition, bringing the total number to 10. These novel Foundation Figures integrate core chemical and biological connections visually, providing a way to organize the complex and detailed material intellectually, thus making relationships among key concepts clear and easier to study. The “CONCEPT” and “CONNECTION” statements within the narrative, which highlight fundamental concepts and real-world applications of biochemistry, have been reviewed and revised for the Second Edition.

In Biochemistry: Concepts and Connections, we emphasize our field as an experimental science by including 17 separate sections, called Tools of Biochemistry, that highlight the most important research techniques. We also provide students with references (about 12 per chapter), choosing those that would be most appropriate for our target audience, such as links to Nobel Prize lectures.

We consider end-of-chapter problems to be an indispensable learning tool and provide 15 to 25 problems for each chapter. (In the Second Edition we have added 3 to 4 new end-of-chapter problems to each chapter.) About half of the problems have brief answers at the end of the book, with complete answers provided in a separate solutions manual. Additional tutorials in Mastering Chemistry will help students with some of the most basic concepts and operations. See the table of Instructor and Student Resources on the following page.

Producing a book of this magnitude involves the efforts of dedicated editorial and production teams. We have not had the pleasure of meeting all of these talented individuals, but we consider them close colleagues nonetheless. First, of course, is Jeanne Zalesky, our sponsoring editor, now Editor-in-Chief, Physical Sciences, who always found a way to keep us focused on our goal. Susan Malloy, Program Manager, kept us organized and on schedule, juggling disparate elements in this complex project—later replaced by Anastasia Slesareva. Jay McElroy, Art Development Editor, was our intermediary with the talented artists at Imagineering, Inc., and displayed considerable artistic and editorial gifts in his own right. We also worked with an experienced development editor, Matt Walker. His suggested edits, insights, and attention to detail were invaluable. Beth Sweeten, Senior Project Manager, coordinated the production of the main text and preparation of the Solutions Manual for the end-of-chapter problems. Gary Carlton provided great assistance with many of the illustrations. Chris Hess provided the inspiration for our cover illustration, and Mo Spuhler helped us locate much excellent illustrative material. Once the book was in production, Mary Tindle skillfully kept us all on a complex schedule.

The three of us give special thanks to friends and colleagues who provided unpublished material for us to use as illustrations. These contributors include John S. Olson (Rice University), Jack Benner (New England BioLabs), Andrew Karplus (Oregon State University), Scott Delbecq and Rachel Klevit (University of Washington), William Horton (Oregon Health and Science University), Cory Hamada (Western Washington University), Nadrian C. Seaman (New York University), P. Shing Ho (Colorado State University), Catherine Drennan and Edward Brignole (MIT), John G. Tesmer (University of Michigan), Katsuhiko Murakami (Penn State University), Alan Cheung (University College London), Joyce Hamlin (University of Virginia), Stefano Tiziani, Edward Marcotte, David Hoffman, and Robin Gutell (University of Texas at Austin), Dean Sherry and Craig Malloy (University ofTexas-Southwestern Medical Center), and Stephen C. Kowalczykowski (University of California, Davis). The cover image, representing in part the structure of the human splicesome, was kindly provided by Karl Bertram (University of Göttingen, Germany).

We are also grateful to the numerous talented biochemists retained by our editors to review our outline, prospectus, chapter drafts, and solutions to our end-of-chapter problems. Their names and affiliations are listed separately. Our team—authors and editors—put forth great effort to detect and root out errors and ambiguities. We undertook an arduous process of editing and revising several drafts of each chapter in manuscript stage, as well as copyediting, proofreading, and accuracy, reviewing multiple rounds of page proofs in an effort to ensure the highest level of quality control.

Throughout this process, as in our previous writing, we have been most grateful for the patience, good judgment, and emotional support provided by our wives—Maureen Appling, Yvonne Anthony-Cahill, and Kate Mathews. We expect them to be as relieved as we are to see this project draw to a close, and hope that they can share our pleasure at the completed product.

Dean R. Appling
Spencer J. Anthony-Cahill
Christopher K. Mathews