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Binding and Kinetics for Molecular Biologists by James Andrew Goodrich,Jennifer F. Kugel Pdf
This handbook offers a practical guide to the principles of quantitative analysis in biological experiments. The material is primarily aimed at working molecular biologists, but the scope and clarity of presentation make it equally suitable as an introduction for students. Topics covered range from the basics — such as measuring the concentrations of macromolecules — through considerations of binding constants and the kinetics of molecular interactions. The book ends with a thorough consideration of data analysis.
Enzyme Kinetics and Mechanism by Paul F. Cook,W. W. Cleland Pdf
Enzyme Kinetics and Mechanism is a comprehensive textbook on steady-state enzyme kinetics. Organized according to the experimental process, the text covers kinetic mechanism, relative rates of steps along the reaction pathway, and chemical mechanism—including acid-base chemistry and transition state structure. Practical examples taken from the literature demonstrate theory throughout. The book also features numerous general experimental protocols and how-to explanations for interpreting kinetic data. Written in clear, accessible language, the book will enable graduate students well-versed in biochemistry to understand and describe data at the fundamental level. Enzymologists and molecular biologists will find the text a useful reference.
Introduction to Molecular Biology by S Bresler Pdf
Introduction to Molecular Biology focuses on the principles of polymer physics and chemistry and their applications to fundamental phenomena in biological sciences. It examines the structure, synthesis, and function of nucleic acids and proteins, as well as the physicochemical techniques necessary in determining the macromolecular structure, the kinetics and mechanism of enzyme action, the genetics of bacteria and their viruses, and the genetic code. It also considers the importance of precise quantitative analysis in biochemistry and biophysics, the architecture and function of biological macromolecules, and the unique mechanisms that regulate the cell's biological activity. Organized into five chapters, this book begins with an overview of proteins and their functional activity, from contractility and enzymatic catalysis to immunological activity, formation of selectively permeable membranes, and reversible binding and transport. It explains how such functions are related to molecular interactions and therefore fall within the purview of molecular biology. The book then proceeds with a discussion on the chemical structure of proteins and nucleic acids, the physicochemical techniques in measuring molecular size and shape, the mechanism of enzymatic reactions, the functions of DNA and RNA, and the mechanism of phase transition in polynucleotides. This book is intended for both biologists and non-biologists who want to be acquainted with the advances made in molecular biology, molecular genetics, and molecular biophysics during the 1950s and 1960s.
Handbook of Biochemical Kinetics by Daniel L. Purich,R. Donald Allison Pdf
Biochemical kinetics refers to the rate at which a reaction takes place. Kinetic mechanisms have played a major role in defining the metabolic pathways, the mechanistic action of enzymes, and even the processing of genetic material. The Handbook of Biochemical Kinetics provides the "underlying scaffolding" of logic for kinetic approaches to distinguish rival models or mechanisms. The handbook also comments on techniques and their likely limitations and pitfalls, as well as derivations of fundamental rate equations that characterize biochemical processes. Key Features * Over 750 pages devoted to theory and techniques for studying enzymic and metabolic processes * Over 1,500 definitions of kinetic and mechanistic terminology, with key references * Practical advice on experimental design of kinetic experiments * Extended step-by-step methods for deriving rate equations * Over 1,000 enzymes, complete with EC numbers, reactions catalyzed, and references to reviews and/or assay methods * Over 5,000 selected references to kinetic methods appearing in the Methods in Enzymology series * 72-page Wordfinder that allows the reader to search by keywords * Summaries of mechanistic studies on key enzymes and protein systems * Over 250 diagrams, figures, tables, and structures
Reversible Ligand Binding by Andrea Bellelli,Jannette Carey Pdf
Presents the physical background of ligand binding and instructs on how experiments should be designed and analyzed Reversible Ligand Binding: Theory and Experiment discusses the physical background of protein-ligand interactions—providing a comprehensive view of the various biochemical considerations that govern reversible, as well as irreversible, ligand binding. Special consideration is devoted to enzymology, a field usually treated separately from ligand binding, but actually governed by identical thermodynamic relationships. Attention is given to the design of the experiment, which aids in showing clear evidence of biochemical features that may otherwise escape notice. Classical experiments are reviewed in order to further highlight the importance of the design of the experiment. Overall, the book supplies students with the understanding that is necessary for interpreting ligand binding experiments, formulating plausible reaction schemes, and analyzing the data according to the chosen model(s). Topics covered include: theory of ligand binding to monomeric proteins; practical considerations and commonly encountered problems; oligomeric proteins with multiple binding sites; ligand binding kinetics; hemoglobin and its ligands; single-substrate enzymes and their inhibitors; two-substrate enzymes and their inhibitors; and rapid kinetic methods for studying enzyme reactions. Bridges theory of ligand binding and allostery with experiments Applies historical and physical insight to provide a clear understanding of ligand binding Written by a renowned author with long-standing research and teaching expertise in the area of ligand binding and allostery Based on FEBS Advanced Course lectures on the topic Reversible Ligand Binding: Theory and Experiment is an ideal text reference for students and scientists involved in biophysical chemistry, physical biochemistry, biophysics, molecular biology, protein engineering, drug design, pharmacology, physiology, biotechnology, and bioengineering.
"a gem of a textbook which manages to produce a genuinely fresh, concise yet comprehensive guide" –Mark Leake, University of York "destined to become a standard reference.... Not just a ‘how to’ handbook but also an accessible primer in the essentials of kinetic theory and practice." –Michael Geeves, University of Kent "covers the entire spectrum of approaches, from the traditional steady state methods to a thorough account of transient kinetics and rapid reaction techniques, and then on to the new single molecule techniques" –Stephen Halford, University of Bristol This illustrated treatment explains the methods used for measuring how much a reaction gets speeded up, as well as the framework for solving problems such as ligand binding and macromolecular folding, using the step-by-step approach of numerical integration. It is a thoroughly modern text, reflecting the recent ability to observe reactions at the single-molecule level, as well as advances in microfluidics which have given rise to femtoscale studies. Kinetics is more important now than ever, and this book is a vibrant and approachable entry for anyone who wants to understand mechanism using transient or single molecule kinetics without getting bogged down in advanced mathematics. Clive R. Bagshaw is Emeritus Professor at the University of Leicester, U.K., and Research Associate at the University of California at Santa Cruz, U.S.A.
Protein-Ligand Interactions by Mark A. Williams,Tina Daviter Pdf
Proteins are the cell’s workers, their messengers and overseers. In these roles, proteins specifically bind small molecules, nucleic acid and other protein partners. Cellular systems are closely regulated and biologically significant changes in populations of particular protein complexes correspond to very small variations of their thermodynamics or kinetics of reaction. Interfering with the interactions of proteins is the dominant strategy in the development of new pharmaceuticals. Protein Ligand Interactions: Methods and Applications, Second Edition provides a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins. From the initial discovery of natural substrates or potential drug leads, to the detailed quantitative understanding of the mechanism of interaction, all stages of the research process are covered with a focus on those techniques that are, or are anticipated to become, widely accessible and performable with mainstream commercial instrumentation. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Second Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions – whether they are beginning graduate students or experts in allied areas of molecular cell biology, microbiology, pharmacology, medicinal chemistry or structural biology.
Analytical Molecular Biology illustrates the importance of simple analytical methods applied to some basic molecular biology problems, with an emphasis on the importance of biological problems, rather than the complexity of mathematics. First, the book examines crucial experimental data for a specific problem. Mathematical models will then be constructed with explicit inclusion of biological facts. From such models, predictions can be deduced and then suggest further experimental studies. A few important molecular biology problems will be discussed in the order of the complexity of the mathematical models. Based on such illustrations, the readers can then develop their own analytical methods to study their own problems. This book is for anyone who knows they need to learn how to apply mathematical models to biology, but doesn't necessarily want to, from practicing researchers looking to acquire more analytical tools to advanced students seeking a clear, explanatory text.
Chemical Relaxation in Molecular Biology by I. Pecht,R. Rigler Pdf
The development of an area of scientific research is a dynamic process with its own kinetic equations and its own physical mech anism. The study of fast chemical interactions and transformations is such an area, and while it is tempting to draw analogies or to speculate about the simplest model system, the lack of ade quately averaged observables is an annoying obstacle to such an undertaking. Sciences suffering from such conditions usually avoid quantitative models, be they primitive or complex. Instead, they prove their point by "case histories". Chemical relaxation kinetics started as an offspring of research in acoustics. In some aqueous ionic solutions anomalous acoustic absorption had been observed. A systematic study traced the cause of this absorption, showing that the covered frequency range and the intensity of the absorption were related in a predictable manner to the rate at which ions can interact and form structures differing in volume from the non interacting species. The step from this experimental observation and its correct, non trivial explanation to the discovery that all fast chemical pro cesses must reveal themselves quantitatively in the relaxation rate of a perturbed equilibrium state, and that perturbation para meters other than sound waves can be used for its exploitation, was made by MANFRED EIGEN in 1954. The foresightedness of K.F.
Driven in part by the development of genomics, proteomics, and bioinformatics as new disciplines, there has been a tremendous resurgence of interest in physical methods to investigate macromolecular structure and function in the context of living cells. This volume in Methods in Cell Biology is devoted to biophysical techniques in vivo and their applications to cellular biology. Biophysical Tools for Biologists covers methods-oriented chapters on fundamental as well as cutting-edge techniques in molecular and cellular biophysics. This book is directed toward the broad audience of cell biologists, biophysicists, pharmacologists, and molecular biologists who employ classical and modern biophysical technologies or wish to expand their expertise to include such approaches. It will also interest the biomedical and biotechnology communities for biophysical characterization of drug formulations prior to FDA approval. Describes techniques in the context of important biological problems Delineates critical steps and potential pitfalls for each method
Computer Simulation and Data Analysis in Molecular Biology and Biophysics by Victor Bloomfield Pdf
This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.
Molecular Biology and Biotechnology by Robert Allen Meyers Pdf
Articles on the theories and the techniques involved in understanding the molecular basis of life and the application of that knowledge in genetics, medicine and agriculture.
The Physical and Chemical Basis of Molecular Biology by Thomas E. Creighton Pdf
Presenting a comprehensive description of the fundamental physical and chemical phenomena that form the basis of molecular biology, this text covers topics including the fundamental thermodynamic and kinetic properties of biochemical reactions in solution and the physical properties of aqueous solutions.
Kinetics and Dynamics by Piotr Paneth,Agnieszka Dybala-Defratyka Pdf
"Kinetics and Dynamics" on molecular modeling of dynamic processes opens with an introductory overview before discussing approaches to reactivity of small systems in the gas phase. Then it examines studies of systems of increasing complexity up to the dynamics of DNA. This title has interdisciplinary character presenting wherever possible an interplay between the theory and the experiment. It provides basic information as well as the details of theory and examples of its application to experimentalists and theoreticians interested in modeling of dynamic processes in chemical and biochemical systems. All contributing authors are renowned experts in their fields and topics covered in this volume represent the forefront of today’s science.
