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Structural Biology 5th Edition by Jeremy M. Berg, John L. Tymoczko, and Lubert Stryer | PDF Free Download.
JEREMY M. BERG has been Professor and Director (Department Chairperson) of Biophysics and Biophysical Chemistry at Johns Hopkins University School of Medicine since 1990.
He received his B.S. and M.S. degrees in Chemistry from Stanford (where he learned X-ray crystallography with Keith Hodgson and Lubert Stryer) and his Ph.D. in Chemistry from Harvard with Richard Holm.
He then completed a postdoctoral fellowship with Carl Pabo. Professor Berg is recipient of the American Chemical Society Award in Pure Chemistry (1994), the Eli Lilly Award for Fundamental Research in Biological Chemistry (1995), the Maryland Outstanding Young Scientist of the Year (1995), and the Harrison Howe Award (1997).
While at Johns Hopkins, he has received the W. Barry Wood Teaching Award (selected by medical students), the Graduate Student Teaching Award, and the Professor's Teaching Award for the Preclinical Sciences. He is co-author, with Stephen Lippard, of the text Principles of Bioinorganic Chemistry.
JOHN L. TYMOCZKO is the Towsley Professor of Biology at Carleton College, where he has taught since 1976. He currently teaches Biochemistry, Biochemistry Laboratory, Oncogenes and the Molecular Biology of Cancer, and Exercise Biochemistry and co-teaches an introductory course, Bioenergetics and Genetics.
Professor Tymoczko received his B.A. from the University of Chicago in 1970 and his Ph.D. in Biochemistry from the University of Chicago with Shutsung Liao at the Ben May Institute for Cancer Research.
He followed that with a post-doctoral position with Hewson Swift of the Department of Biology at the University of Chicago. Professor Tymoczko's research has focused on steroid receptors, ribonucleoprotein particles, and proteolytic processing enzymes.
LUBERT STRYER is currently Winzer Professor in the School of Medicine and Professor of Neurobiology at Stanford University, where he has been on the faculty since 1976. He received his M.D. from Harvard Medical School.
Professor Stryer has received many awards for his research, including the Eli Lilly Award for Fundamental Research in Biological Chemistry (1970) and the Distinguished Inventors Award of the Intellectual Property Owners' Association.
He was elected to the National Academy of Sciences in 1984. Professor Stryer was formerly the President and Scientific Director of the Affymax Research Institute.
He is a founder and a member of the Scientific Advisory Board of Senomyx, a company that is using biochemical knowledge to develop new and improved flavor and fragrance molecules for use in consumer products. The publication of the first edition of his text Biochemistry in 1975 transformed the teaching of biochemistry.
For more than 25 years, and through four editions, Stryer's Biochemistry has laid out this beautiful subject in an exceptionally appealing and lucid manner.
The engaging writing style and attractive design have made the text a pleasure for our students to read and study throughout our years of teaching.
Thus, we were delighted to be given the opportunity to participate in the revision of this book. The task has been exciting and somewhat daunting, doubly so because of the dramatic changes that are transforming the field of biochemistry as we move into the twenty-first century.
Biochemistry is rapidly progressing from a science performed almost entirely at the laboratory bench to one that may be explored through computers.
The recently developed ability to determine entire genomic sequences has provided the data needed to accomplish massive comparisons of derived protein sequences, the results of which may be used to formulate and test hypotheses about biochemical function.
The power of these new methods is explained by the impact of evolution: many molecules and biochemical pathways have been generated by duplicating and modifying existing ones.
Our challenge in writing the fifth edition of Biochemistry has been to introduce this philosophical shift in biochemistry while maintaining a clear and inviting style that has distinguished the preceding four editions.
How should these evolution-based insights affect the teaching of biochemistry? Often macromolecules with a common evolutionary origin play diverse biological roles yet have many structural and mechanistic features in common.
An example is a protein family containing macromolecules that are crucial to moving muscle, transmitting the information that adrenaline is present in the bloodstream, and to drive the formation of chains of amino acids.
The key features of such a protein family presented to the student once in detail, become a model that the student can apply each time that a new member of the family is encountered.
The student is then able to focus on how these features, observed in a new context, have been adapted to support other biochemical processes.
Throughout the text, a stylized tree icon is positioned at the start of discussions focused primarily on protein homologies and evolutionary origins.
To enable students to grasp the power of these insights, two completely new chapters have been added. The first, "Biochemical Evolution" (Chapter 2), is a brief tour of the origin of life to the development of multicellular organisms.
On one level, this chapter provides an introduction to biochemical molecules and pathways and their cellular context.
On another level, it attempts to deepen student understanding by examining how these molecules and pathways arose in response to key biological challenges. In addition, the evolutionary perspective of Chapter 2 makes some apparently peculiar aspects of biochemistry more reasonable to students.
For example, the presence of ribonucleotide fragments in biochemical cofactors can be accounted for by the likely occurrence of an early world based largely on RNA. The second new chapter, "Exploring Evolution" (Chapter 7), develops the conceptual basis for the comparison of protein and nucleic acid sequences.
This chapter parallels "Exploring Proteins" (Chapter 4) and "Exploring Genes" (Chapter 6), which have thoughtfully examined experimental techniques in earlier editions.
Its goal is to enable students to use the vast information available in sequence and structural databases in a critical and effective manner.
The evolutionary approach influences the organization of the text, which is divided into four major parts. As it did in the preceding edition, Part I introduces the language of biochemistry and the structures of the most important classes of biological molecules.
The remaining three parts correspond to three major evolutionary challenges namely, the interconversion of different forms of energy, molecular reproduction, and the adaptation of cells and organisms to changing environments.
This arrangement parallels the evolutionary path outlined in Chapter 2 and naturally flows from the simple to the more complex.
PART I, the molecular design of life, introduces the most important classes of biological macromolecules, including proteins, nucleic acids, carbohydrates, and lipids, and presents the basic concepts of catalysis and enzyme action.
Here are two examples of how an evolutionary perspective has shaped the material in these chapters:
Chapter 9, on catalytic strategies, examines four classes of enzymes that have evolved to meet specific challenges: promoting a fundamentally slow chemical reaction, maximizing the absolute rate of a reaction, catalyzing a reaction at one site but not at many alternative sites, and preventing a deleterious side reaction. In each case, the text considers the role of evolution in fine-tuning the key property.
Chapter 13, on membrane channels and pumps, includes the first detailed three-dimensional structures of an ion channel and an ion pump.
Because most other important channels and pumps are evolutionarily related to these proteins, these two structures provide powerful frameworks for examining the molecular basis of the action of these classes of molecules, so important for the functioning of the nervous and other systems.
PART II, transducing and storing energy, examines pathways for the interconversion of different forms of energy. Chapter 15, on signal transduction, looks at how DNA fragments encoding relatively simple protein modules, rather than entire proteins, have been mixed and matched in the course of evolution to generate the wiring that defines signal-transduction pathways.
The bulk of Part II discusses pathways for the generation of ATP and other energy-storing molecules. These pathways have been organized into groups that share common enzymes. The component reactions can be examined once and their use in different biological contexts illustrated while these reactions are fresh in the students' minds.
Chapter 16 covers both glycolysis and gluconeogenesis. These pathways are, in some ways, the reverse of each other, and a core of enzymes common to both pathways catalyze many of the steps in the center of the pathways.
Covering the pathways together makes it easy to illustrate how free energy enters to drive the overall process either in the direction of glucose degradation or in the direction of glucose synthesis.
Chapter 17, on the citric acid cycle, ties together through evolutionary insights into the pyruvate dehydrogenase complex, which feeds molecules into the citric acid cycle, and the α-ketoglutarate dehydrogenase complex, which catalyzes one of the key steps in the cycle itself.Figure 15.34
Oxidative phosphorylation, in Chapter 18, is immediately followed in Chapter 19 by the light reactions of photosynthesis to emphasize the many common chemical features of these pathways.
The discussion of the light reactions of photosynthesis in Chapter 19 leads naturally into a discussion of the dark reactions that is, the components of the Calvin cycle in Chapter 20.
This pathway is naturally linked to the pentose phosphate pathway, also covered in Chapter 20, because in both pathways common enzymes interconvert three-, four-, five-, six-, and seven-carbon sugars.
PART III, synthesizing the molecules of life, focuses on the synthesis of biological macromolecules and their components.
Chapter 24, on the biosynthesis of amino acids, is linked to the preceding chapter on amino acid degradation by a family of enzymes that transfer amino groups to and from the carbon frameworks of amino acids.
Chapter 25 covers the biosynthesis of nucleotides, including the role of amino acids as biosynthetic precursors. A key evolutionary insight emphasized here is that many of the enzymes in these pathways are members of the same family and catalyze analogous chemical reactions. The focus on enzymes and reactions common to these biosynthetic pathways allows students to understand the logic of the pathways, rather than having to memorize a set of seemingly unrelated reactions.
Chapters 27, 28, and 29 cover DNA replication, recombination, and repair; RNA synthesis and splicing; and protein synthesis. Evolutionary connections between prokaryotic systems and eukaryotic systems reveal how the basic biochemical processes have been adapted to function in more-complex biological systems.
The recently elucidated structure of the ribosome gives students a glimpse into a possible early RNA world, in which nucleic acids, rather than proteins, played almost all the major roles in catalyzing important pathways.
PART IV, responding to environmental changes, looks at how cells sense and adapt to changes in their environments.
Part IV examines, in turn, sensory systems, the immune system, and molecular motors, and the cytoskeleton.
These chapters illustrate how signaling and response processes, introduced earlier in the text, are integrated into multicellular organisms to generate powerful biochemical systems for detecting and responding to environmental changes. Again, the adaptation of proteins to new roles is key to these discussions.
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