شیمی بیوفیزیک ۲۰۰۹
Biophysical Chemistry 2009

1. Preface

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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