Biophysical Chemistry
eBook - PDF

Biophysical Chemistry

James P. Allen

  1. English
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eBook - PDF

Biophysical Chemistry

James P. Allen

Book details
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About This Book

" Biophysical Chemistry is an outstanding book that delivers both fundamental and complex biophysical principles, along with an excellent overview of the current biophysical research areas, in a manner that makes it accessible for mathematically and non-mathematically inclined readers."
Journal of Chemical Biology, February 2009

This text presents physical chemistry through the use of biological and biochemical topics, examples and applications to biochemistry. It lays out the necessary calculus in a step by step fashion for students who are less mathematically inclined, leading them through fundamental concepts, such as a quantum mechanical description of the hydrogen atom rather than simply stating outcomes. Techniques are presented with an emphasis on learning by analyzing real data.

  • Presents physical chemistry through the use of biological and biochemical topics, examples and applications to biochemistry
  • Lays out the necessary calculus in a step by step fashion for students who are less mathematically inclined
  • Presents techniques with an emphasis on learning by analyzing real data
  • Features qualitative and quantitative problems at the end of each chapter
  • All art available for download online and on CD-ROM

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Information

Publisher
Wiley-Blackwell
Year
2009
ISBN
9781444300734
Edition
1
Topic
Biological Sciences
Subtopic
Biochemistry
Index
Biological Sciences

Table of contents

  1. Preface
  2. 1 Basic thermodynamic and biochemical concepts
  3. FUNDAMENTAL THERMODYNAMIC CONCEPTS
  4. States of matter
  5. Pressure
  6. Temperature
  7. Volume, mass, and number
  8. PROPERTIES OF GASES
  9. The ideal gas laws
  10. Gas mixtures
  11. KINETIC ENERGY OF GASES
  12. REAL GASES
  13. Derivation box 1.1 Relationship between the average velocity and pressure
  14. Liquifying gases for low-temperature spectroscopy
  15. MOLECULAR BASIS FOR LIFE
  16. Cell membranes
  17. Amino acids
  18. Classification of amino acids by their side chains
  19. DNA and RNA
  20. PROBLEMS
  21. Part 1 Thermodynamics and kinetics
  22. 2 First law of thermodynamics
  23. SYSTEMS
  24. STATE FUNCTIONS
  25. FIRST LAW OF THERMODYNAMICS
  26. RESEACH DIRECTION: DRUG DESIGN I
  27. WORK
  28. SPECIFIC HEAT
  29. INTERNAL ENERGY FOR AN IDEAL GAS
  30. ENTHALPY
  31. DEPENDENCE OF SPECIFIC HEAT ON INTERNAL ENERGY AND ENTHALPY
  32. Derivation box 2.1 State functions described using partial derivatives
  33. ENTHALPY CHANGES OF BIOCHEMICAL REACTIONS
  34. RESEARCH DIRECTION: GLOBAL CLIMATE CHANGE
  35. REFERENCES
  36. PROBLEMS
  37. 3 Second law of thermodynamics
  38. ENTROPY
  39. ENTROPY CHANGES FOR REVERSIBLE AND IRREVERSIBLE PROCESSES
  40. THE SECOND LAW OF THERMODYNAMICS
  41. INTERPRETATION OF ENTROPY
  42. THIRD LAW OF THERMODYNAMICS
  43. GIBBS ENERGY
  44. RELATIONSHIP BETWEEN THE GIBBS ENERGY AND THE EQUILIBRIUM CONSTANT
  45. RESEARCH DIRECTION: DRUG DESIGN II
  46. GIBBS ENERGY FOR AN IDEAL GAS
  47. USING THE GIBBS ENERGY
  48. CARNOT CYCLE AND HYBRID CARS
  49. Derivation box 3.1 Entropy as a state function
  50. RESEARCH DIRECTION: NITROGEN FIXATION
  51. REFERENCES
  52. PROBLEMS
  53. 4 Phase diagrams, mixtures, and chemical potential
  54. SUBSTANCES MAY EXIST IN DIFFERENT PHASES
  55. PHASE DIAGRAMS AND TRANSITIONS
  56. CHEMICAL POTENTIAL
  57. PROPERTIES OF LIPIDS DESCRIBED USING THE CHEMICAL POTENTIAL
  58. LIPID AND DETERGENT FORMATION INTO MICELLES AND BILAYERS
  59. RESEARCH DIRECTION: LIPID RAFTS
  60. DETERMINATION OF MICELLE FORMATION USING SURFACE TENSION
  61. MIXTURES
  62. RAOULT’S LAW
  63. OSMOSIS
  64. RESEARCH DIRECTION: PROTEIN CRYSTALLIZATION
  65. REFERENCES
  66. PROBLEMS
  67. 5 Equilibria and reactions involving protons
  68. GIBBS ENERGY MINIMUM
  69. Derivation box 5.1 Relationship between the Gibbs energy and equilibrium constant
  70. RESPONSE OF THE EQUILIBRIUM CONSTANT TO CONDITION CHANGES
  71. ACID–BASE EQUILIBRIA
  72. PROTONATION STATES OF AMINO ACID RESIDUES
  73. BUFFERS
  74. Buffering in the cardiovascular system
  75. RESEARCH DIRECTION: PROTON-COUPLED ELECTRON TRANSFER AND PATHWAYS
  76. REFERENCES
  77. PROBLEMS
  78. 6 Oxidation/reduction reactions and bioenergetics
  79. OXIDATION/REDUCTION REACTIONS
  80. ELECTROCHEMICAL CELLS
  81. THE NERNST EQUATION
  82. MIDPOINT POTENTIALS
  83. GIBBS ENERGY OF FORMATION AND ACTIVITY
  84. IONIC STRENGTH
  85. ADENOSINE TRIPHOSPHATE
  86. CHEMIOSMOTIC HYPOTHESIS
  87. RESEARCH DIRECTION: RESPIRATORY CHAIN
  88. RESEARCH DIRECTION: ATP SYNTHASE
  89. REFERENCES
  90. PROBLEMS
  91. 7 Kinetics and enzymes
  92. THE RATE OF A CHEMICAL REACTION
  93. PARALLEL FIRST-ORDER REACTIONS
  94. SEQUENTIAL FIRST-ORDER REACTIONS
  95. SECOND-ORDER REACTIONS
  96. THE ORDER OF A REACTION
  97. REACTIONS THAT APPROACH EQUILIBRIUM
  98. ACTIVATION ENERGY
  99. RESEARCH DIRECTION: ELECTRON TRANSFER I: ENERGETICS
  100. Derivation box 7.1 Derivation of the Marcus relationship
  101. ENZYMES
  102. Enzymes lower the activation energy
  103. Enzyme mechanisms
  104. RESEARCH DIRECTION: DYNAMICS IN ENZYME MECHANISM
  105. MICHAELIS–MENTEN MECHANISM
  106. LINEWEAVER–BURK EQUATION
  107. ENZYME ACTIVITY
  108. RESEARCH DIRECTION: THE RNA WORLD
  109. REFERENCES
  110. PROBLEMS
  111. 8 The Boltzmann distribution and statistical thermodynamics
  112. PROBABILITY
  113. BOLTZMANN DISTRIBUTION
  114. PARTITION FUNCTION
  115. STATISTICAL THERMODYNAMICS
  116. RESEARCH DIRECTION: PROTEIN FOLDING AND PRIONS
  117. PRIONS
  118. REFERENCES
  119. PROBLEMS
  120. Part 2 Quantum mechanics and spectroscopy
  121. 9 Quantum theory: introduction and principles
  122. CLASSICAL CONCEPTS
  123. EXPERIMENTAL FAILURES OF CLASSICAL PHYSICS
  124. Blackbody radiation
  125. Photoelectric effect
  126. Atomic spectra
  127. PRINCIPLES OF QUANTUM THEORY
  128. Wave–particle duality
  129. Schrödinger’s equation
  130. Born interpretation
  131. GENERAL APPROACH FOR SOLVING SCHRÖDINGER’S EQUATION
  132. INTERPRETATION OF QUANTUM MECHANICS
  133. Heisenberg Uncertainty Principle
  134. A quantum-mechanical world
  135. RESEARCH DIRECTION: SCHRÖDINGER’S CAT
  136. REFERENCES
  137. PROBLEMS
  138. 10 Particle in a box and tunneling
  139. ONE-DIMENSIONAL PARTICLE IN A BOX
  140. PROPERTIES OF THE SOLUTIONS
  141. Energy and wavefunction
  142. Symmetry
  143. Wavelength
  144. Probability
  145. Orthogonality
  146. Average or expectation value
  147. Transitions
  148. RESEARCH DIRECTION: CAROTENOIDS
  149. TWO-DIMENSIONAL PARTICLE IN A BOX
  150. TUNNELING
  151. RESEARCH DIRECTION: PROBING BIOLOGICAL MEMBRANES a 0
  152. RESEARCH DIRECTION: ELECTRON TRANSFER II: DISTANCE DEPENDENCE
  153. REFERENCES
  154. PROBLEMS
  155. 11 Vibrational motion and infrared spectroscopy
  156. SIMPLE HARMONIC OSCILLATOR: CLASSICAL THEORY
  157. Potential energy for the simple harmonic oscillator
  158. SIMPLE HARMONIC OSCILLATOR: QUANTUM THEORY
  159. Derivation box 11.1 Solving Schrödinger’s equation for the simple harmonic oscillator
  160. PROPERTIES OF THE SOLUTIONS
  161. Forbidden region
  162. Transitions
  163. VIBRATIONAL SPECTRA
  164. RESEARCH DIRECTIONS: HYDROGENASE
  165. REFERENCES
  166. PROBLEMS
  167. 12 Atomic structure: hydrogen atom and multi-electron atoms
  168. SCHRÖDINGER’S EQUATION FOR THE HYDROGEN ATOM
  169. Derivation box 12.1 Solving Schrödinger’s equation for the hydrogen atom
  170. Separation of variables
  171. Angular solution
  172. Radial solution
  173. PROPERTIES OF THE GENERAL SOLUTION
  174. Angular momentum
  175. Orbitals
  176. s Orbitals
  177. p Orbitals
  178. d Orbitals
  179. TRANSITIONS
  180. RESEARCH DIRECTION: HYDROGEN ECONOMY
  181. SPIN
  182. Derivation box 12.2 Relativistic equations
  183. MULTI-ELECTRON ATOMS
  184. Empirical constants
  185. Self-consistent field theory (Hartree–Fock)
  186. HELIUM ATOM
  187. SPIN–ORBITAL COUPLING
  188. PERIODIC TABLE
  189. REFERENCES
  190. PROBLEMS
  191. 13 Chemical bonds and protein interactions
  192. SCHRÖDINGER’S EQUATION FOR A HYDROGEN MOLECULE
  193. VALENCE BONDS
  194. THE HÜCKEL MODEL
  195. INTERACTIONS IN PROTEINS
  196. Peptide bonds
  197. Steric effects
  198. Hydrogen bonds
  199. Electrostatic interactions
  200. Hydrophobic effects
  201. SECONDARY STRUCTURE
  202. DETERMINATION OF SECONDARY STRUCTURE USING CIRCULAR DICHROISM
  203. RESEARCH DIRECTION: MODELING PROTEIN STRUCTURES AND FOLDING
  204. REFERENCES
  205. PROBLEMS
  206. 14 Electronic transitions and optical spectroscopy
  207. THE NATURE OF LIGHT
  208. THE BEER–LAMBERT LAW
  209. MEASURING ABSORPTION
  210. TRANSITIONS
  211. Derivation box 14.1 Relationship between the Einstein coefficient and electronic states
  212. LASERS
  213. SELECTION RULES
  214. THE FRANCK–CONDON PRINCIPLE
  215. THE RELATIONSHIP BETWEEN EMISSION AND ABSORPTION SPECTRA
  216. THE YIELD OF FLUORESCENCE
  217. FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET)
  218. MEASURING FLUORESCENCE
  219. PHOSPHORESCENCE
  220. RESEARCH DIRECTION: PROBING ENERGY TRANSFER USING TWO-DIMENSIONAL OPTICAL SPECTROSCOPY
  221. RESEARCH DIRECTION: SINGLE-MOLECULE SPECTROSCOPY
  222. HOLLIDAY JUNCTIONS
  223. REFERENCES
  224. PROBLEMS
  225. 15 X-ray diffraction and extended X-ray absorption ‱ne structure
  226. BRAGG’S LAW
  227. BRAVAIS LATTICES
  228. PROTEIN CRYSTALS
  229. DIFFRACTION FROM CRYSTALS
  230. Derivation box 15.1 Phases of complex numbers
  231. PHASE DETERMINATION
  232. Molecular replacement
  233. Isomorphous replacement
  234. Anomalous dispersion
  235. MODEL BUILDING
  236. EXPERIMENTAL MEASUREMENT OF X-RAY DIFFRACTION
  237. EXAMPLES OF PROTEIN STRUCTURES
  238. RESEARCH DIRECTION: NITROGENASE
  239. EXTENDED X-RAY ABSORPTION FINE STRUCTURE
  240. REFERENCES
  241. PROBLEMS
  242. 16 Magnetic resonance
  243. NMR
  244. Chemical shifts
  245. Spin–spin interactions
  246. Pulse techniques
  247. Two-dimensional NMR: nuclear Overhauser effect
  248. NMR spectra of amino acids
  249. RESEARCH DIRECTION: DEVELOPMENT OF NEW NMR TECHNIQUES
  250. Determination of macromolecular structures
  251. RESEARCH DIRECTION: SPINAL MUSCULAR ATROPHY
  252. MRI
  253. ELECTRON SPIN RESONANCE
  254. Hyperfine structure 2
  255. Electron nuclear double resonance
  256. Spin probes
  257. RESEARCH DIRECTION: HEME PROTEINS
  258. RESEARCH DIRECTION: RIBONUCLEOTIDE REDUCTASE
  259. REFERENCES AND FURTHER READING
  260. PROBLEMS
  261. Part 3 Understanding biological systems using physical chemistry
  262. 17 Signal transduction
  263. BIOCHEMICAL PATHWAY FOR VISUAL RESPONSE
  264. SPECTROSCOPIC STUDIES OF RHODOPSIN
  265. BACTERIORHODOPSIN
  266. STRUCTURAL STUDIES
  267. COMPARISON OF RHODOPSINS FROM DIFFERENT ORGANISMS
  268. RHODOPSIN PROTEINS IN VISUAL RESPONSE Halorhodopsin Bacteriorhodopsin
  269. REFERENCES AND FURTHER READING
  270. PROBLEMS
  271. 18 Membrane potentials, transporters, and channels
  272. MEMBRANE POTENTIALS
  273. ENERGETICS OF TRANSPORT ACROSS MEMBRANES
  274. TRANSPORTERS
  275. ION CHANNELS
  276. REFERENCES AND FURTHER READING
  277. PROBLEMS
  278. 19 Molecular imaging
  279. IMAGING IN CELLS AND BODIES
  280. GREEN FLUORESCENT PROTEIN
  281. Mechanism of chromophore formation
  282. Fluorescence resonance energy transfer
  283. Imaging of GFP in cells
  284. IMAGING IN ORGANISMS
  285. Radioactive decay
  286. PET
  287. Parkinson’s disease
  288. REFERENCES AND FURTHER READING
  289. PROBLEMS
  290. 20 Photosynthesis
  291. ENERGY TRANSFER AND LIGHT-HARVESTING COMPLEXES
  292. ELECTRON TRANSFER, BACTERIAL REACTION CENTERS, AND PHOTOSYSTEM I Exciton transfer (a)
  293. WATER OXIDATION
  294. REFERENCES AND FURTHER READING
  295. PROBLEMS
  296. Answers to problems
  297. Index
  298. Fundamental constants
  299. Conversion factors for energy units
  300. The periodic table