Biological ThermodynamicsBiological 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. |
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Contents
Energy transformation | 1 |
Distribution of energy | 5 |
System boundary and surroundings | 8 |
Animal energy consumption | 11 |
Carbon energy and life | 14 |
References and further reading | 15 |
Exercises | 16 |
The First Law of Thermodynamics | 21 |
Nonequilibrium thermodynamics and life | 173 |
References and further reading | 174 |
Exercises | 178 |
Statistical thermodynamics | 185 |
Diffusion | 188 |
Boltzmann distribution | 192 |
Partition function | 198 |
Analysis of thermodynamic data | 200 |
Internal energy | 24 |
Work | 26 |
The First Law in operation | 29 |
Enthalpy | 32 |
Standard state | 35 |
Some examples from biochemistry | 36 |
Heat capacity | 40 |
Energy conservation in the living organism | 43 |
Exercises | 45 |
The Second Law of Thermodynamics | 49 |
Entropy | 52 |
Heat engines | 56 |
Entropy of the universe | 59 |
Isothermal systems | 60 |
Protein denaturation | 62 |
The Third Law and biology | 63 |
Irreversibility and life | 64 |
References and further reading | 67 |
Exercises | 69 |
Gibbs free energy theory | 73 |
Equilibrium | 76 |
Reversible processes | 80 |
Phase transitions | 82 |
Chemical potential | 85 |
Effect of solutes on boiling points and freezing points | 89 |
Ionic solutions | 90 |
Equilibrium constant | 93 |
Standard state in biochemistry | 96 |
Effect of temperature on Keq | 98 |
Acids and bases | 100 |
Chemical coupling | 102 |
Redox reactions | 104 |
References and further reading | 108 |
Exercises | 110 |
Gibbs free energy applications | 119 |
Oxidative phosphorylation and ATP hydrolysis | 123 |
Substrate cycling | 129 |
Osmosis | 130 |
Dialysis | 136 |
Donnan equilibrium | 139 |
Membrane transport | 140 |
Enzymesubstrate interaction | 144 |
Molecular pharmacology | 146 |
Hemoglobin | 151 |
Enzymelinked immunosorbent assay ELISA | 154 |
DNA | 155 |
Polymerase chain reaction PCR | 159 |
Free energy of transfer of amino acids | 161 |
Protein solubility | 163 |
Protein stability | 165 |
Protein dynamics | 171 |
Multistate equilibria | 204 |
Protein heat capacity functions | 209 |
Cooperative transitions | 210 |
Interaction free energy | 212 |
Helixcoil transition theory | 214 |
References and further reading | 217 |
Exercises | 220 |
Binding equilibria | 223 |
Singlesite model | 225 |
Multiple independent sites | 226 |
Oxygen transport | 231 |
Scatchard plots and Hill plots | 235 |
Allosteric regulation | 240 |
Proton binding | 242 |
References and further reading | 245 |
Exercises | 247 |
Reaction kinetics | 251 |
Rate of reaction | 254 |
Rate constant and order of reaction | 255 |
Firstorder and secondorder reactions | 257 |
Temperature effects | 259 |
Collision theory | 261 |
Transition state theory | 262 |
Electron transfer kinetics | 265 |
Enzyme kinetics | 267 |
Inhibition | 271 |
Reaction mechanism of lysozyme | 273 |
Hydrogen exchange | 275 |
Protein folding and pathological misfolding | 278 |
Polymerization | 281 |
Muscle contraction and molecular motors | 284 |
References and further reading | 286 |
Exercises | 288 |
The frontier of biological thermodynamics | 293 |
The laws of thermodynamics and our universe | 296 |
Thermodynamics of small systems eg molecular motors | 297 |
Formation of the first biological macromolecules | 298 |
Bacteria | 303 |
Energy information and life | 304 |
Biology and complexity | 314 |
The Second Law and evolution | 319 |
References and further reading | 323 |
Exercises | 327 |
331 | |
Biocalorimetry | 335 |
Useful tables | 341 |
BASIC program for computing the intrinsic rate of amide hydrogen exchange from the backbone of a polypeptide | 347 |
Glossary | 363 |
373 | |
375 | |
Common terms and phrases
actin activity amino acid atoms bacteria binding sites biochemical Biochemistry biological Calculate calorimetry cell Chapter chemical potential Chemistry complex concentration constant denaturation depends dissociation electron energetics enthalpy enthalpy change entropy entropy change enzyme equation equilibrium example exchange experiment free energy change free energy difference function Gibbs free energy glucose heat capacity helix hemoglobin hydrogen bonds hydrolysis important increase interactions internal energy involved ions irreversible Journal of Chemical kcal kinetics Law of Thermodynamics ligand living organisms lysozyme macromolecule mathematical measured mechanism membrane metabolism mol-ยน mole molecular molecules occur oxidation oxygen panel particles phosphate phosphoryl photosynthesis physical plot polypeptide pressure properties protein folding protons reactants redox relatively residues Science Second Law side chains solution solvent spontaneously structure substrate subunits synthesis temperature theory thermal tion transfer transition unfolded universe urea York