Biological Thermodynamics

Biological Thermodynamics provides an introduction to the study of energy transformations for students of the biological sciences. Donald Haynie uses an informal writing style to introduce this core subject in a manner that will appeal to biology and biochemistry undergraduate students. The emphasis of the text is placed on understanding basic concepts and developing problem-solving skills throughout the text. The level of mathematical complexity is kept to a minimum. Each chapter provides numerous examples taken from different areas of biochemistry, as well as extensive exercises to aid understanding. Topics covered include energy and its transformation, the First Law of Thermodynamics, the Second Law of Thermodynamics, Gibbs Free Energy, statistical thermodynamics, binding equilibria and reaction kinetics, and a survey of the most exciting areas of biological thermodynamics today, particularly the origin of life on Earth. Cover......Page 1 Half-title......Page 3 Title......Page 5 Copyright......Page 6 Dedication......Page 7 Contents......Page 9 Preface......Page 13 References......Page 17 A. Introduction......Page 19 B. Distribution of energy......Page 23 C. System, boundary, and surroundings......Page 26 D. Animal energy consumption......Page 29 E. Carbon, energy, and life......Page 32 F. References and further reading......Page 33 G. Exercises......Page 34 A. Introduction......Page 39 B. Internal energy......Page 42 C. Work......Page 44 D.The First Law in operation......Page 47 E. Enthalpy......Page 50 F. Standard state......Page 53 G. Some examples from biochemistry......Page 54 H. Heat capacity......Page 58 J. References and further reading......Page 61 K. Exercises......Page 63 A. Introduction......Page 67 B. Entropy......Page 70 C. Heat engines......Page 74 D. Entropy of the universe......Page 77 E. Isothermal systems......Page 78 F. Protein denaturation......Page 80 G. The Third Law and biology......Page 81 H. Irreversibility and life......Page 82 I. References and further reading......Page 85 J. Exercises......Page 87 A. Introduction......Page 91 B. Equilibrium......Page 94 C. Reversible processes......Page 98 D. Phase transitions......Page 100 E. Chemical potential......Page 103 F. Effect of solutes on boiling points and freezing points......Page 107 G. Ionic solutions......Page 108 H. Equilibrium constant......Page 111 I. Standard state in biochemistry......Page 114 J. Effect of temperature on K......Page 116 K. Acids and bases......Page 118 L. Chemical coupling......Page 120 M. Redox reactions......Page 122 N. References and further reading......Page 126 O. Exercises......Page 128 B. Photosynthesis, glycolysis, and the citric acid cycle......Page 137 C. Oxidative phosphorylation and ATP hydrolysis......Page 141 D. Substrate cycling......Page 147 E. Osmosis......Page 148 F. Dialysis......Page 154 G. Donnan equilibrium......Page 157 H. Membrane transport......Page 158 I. Enzyme–substrate interaction......Page 162 J. Molecular pharmacology......Page 164 K. Hemoglobin......Page 169 L. Enzyme-linked immunosorbent assay (ELISA)......Page 172 M. DNA......Page 173 N. Polymerase chain reaction (PCR)......Page 177 O. Free energy of transfer of amino acids......Page 179 P. Protein solubility......Page 181 Q. Protein stability......Page 183 R. Protein dynamics......Page 189 S. Non-equilibrium thermodynamics and life......Page 191 T. References and further reading......Page 192 U. Exercises......Page 196 A. Introduction......Page 203 B. Diffusion......Page 206 C. Boltzmann distribution......Page 210 D. Partition function......Page 216 E. Analysis of thermodynamic data......Page 218 F. Multistate equilibria......Page 222 G. Protein heat capacity functions......Page 227 H. Cooperative transitions......Page 228 I. ‘Interaction’ free energy......Page 230 J. Helix–coil transition theory......Page 232 K. References and further reading......Page 235 L. Exercises......Page 238 A. Introduction......Page 241 B. Single-site model......Page 243 C. Multiple independent sites......Page 244 D. Oxygen transport......Page 249 E. Scatchard plots and Hill plots......Page 253 F. Allosteric regulation......Page 258 G. Proton binding......Page 260 H. References and further reading......Page 263 I. Exercises......Page 265 A. Introduction......Page 269 B. Rate of reaction......Page 272 C. Rate constant and order of reaction......Page 273 D. First-order and second-order reactions......Page 275 E. Temperature effects......Page 277 F. Collision theory......Page 279 G. Transition state theory......Page 280 H. Electron transfer kinetics......Page 283 I. Enzyme Kinetics......Page 285 J. Inhibition......Page 289 K. Reaction mechanism of lysozyme......Page 291 L. Hydrogen exchange......Page 293 M. Protein folding and pathological misfolding......Page 296 N. Polymerization......Page 299 O. Muscle contraction and molecular motors......Page 302 P. References and further reading......Page 304 Q. Exercises......Page 306 B. What is energy?......Page 311 C. The laws of thermodynamics and our universe......Page 314 D. Thermodynamics of small systems (e.g. molecular motors)......Page 315 E. Formation of the first biological macromolecules......Page 316 Abiotic synthesis of biopolymers......Page 317 Proteins......Page 318 Nucleic acids......Page 319 F. Bacteria......Page 321 G. Energy, information, and life......Page 322 Thermodynamic optimization and biology......Page 324 Information theory and biology......Page 325 Molecular communication......Page 330 Information processing......Page 331 H. Biology and complexity......Page 332 I. The Second Law and evolution......Page 337 J. References and further reading......Page 341 K. Exercises......Page 345 Appendix A General references......Page 349 A. Introduction......Page 353 B. Differential scanning calorimetry......Page 354 C. Isothermal titration calorimetry......Page 355 E. References and further reading......Page 357 Appendix C Useful tables......Page 359 Appendix D BASIC program for computing the intrinsic rate of amide hydrogen exchange from the backbone of a polypeptide......Page 365 Glossary......Page 381 Index of names......Page 391 Subject index......Page 393 Biological Thermodynamics Provides An Introduction To The Study Of Energy Transformations For Students Of The Biological Sciences. Don Haynie Uses An Informal Writing Style To Introduce This Core Subject In A Manner Which Will Appeal To Biology And Biochemistry Undergraduate Students And Be Relevant To Their Studies. The Emphasis Is On Understanding Basic Concepts And Developing Problem-solving Skills Throughout The Text, But Mathematical Complexity Is Kept To A Minimum. Each Chapter Comprises Numerous Examples Taken From Different Areas Of Biochemistry, As Well As Extensive Exercises To Aid Understanding. Topics Covered Include Energy And Its Transformation, The First Law Of Thermodynamics, The Second Law Of Thermodynamics, Gibbs Free Energy, Statistical Thermodynamics, Binding Equilibria And Reaction Kinetics, Concluding With A Survey Of The Most Exciting Areas Of Biological Thermodynamics Today, Particularly The Origin Of Life On Earth. Counter -- Energy Transformation -- The First Law Of Thermodynamics -- The Second Law Of Thermodynamics -- Gibbs Free Energy -- Theory -- Gibbs Free Energy -- Applications -- Statistical Thermodynamics -- Binding Equilibria -- Reaction Kinetics -- The Frontier Of Biological Thermodynamics -- Appendices -- Glossary. Donald T. Haynie. Includes Bibliographical References (p. [331]-333) And Index. An accessible introduction to the study of energy transformations for biology and biochemistry undergraduate students. It is written in an informal style, with emphasis on understanding basic concepts and their relevance to biological systems, as well as developing problem-solving skills by using numerous examples and exercises Beginning perhaps with Anaximenes of Miletus (fl.c. 2550 years before present), various ancient Greeks portrayed man as a microcosm of the universe.