Peptide bonds
278
Steric effects
278
Hydrogen bonds
279
Electrostatic interactions
280
Hydrophobic effects
280
Secondary structure
282
Determination of secondary structure using circular dichroism
284
Research direction: modeling protein structures and folding
284
References
289
Problems
289
14 Electronic transitions and optical spectroscopy
291
The nature of light
291
The Beer–Lambert law
293
Measuring absorption
294
Transitions
296
Derivation box 14.1 Relationship between the Einstein coefficient and
electronic states
298
Lasers
300
Selection rules
301
The Franck–Condon principle
302
The relationship between emission and absorption spectra
303
The yield of fluorescence
305
Fluorescence resonance energy transfer
306
Measuring fluorescence
306
Phosphorescence
307
Research direction: probing energy transfer using two-dimensional
optical spectroscopy
307
Research direction: single-molecule spectroscopy
310
Holliday junctions
312
References
315
Problems
315
15 X-ray diffraction and extended X-ray absorption fine structure
317
Bragg’s law
319
Bravais lattices
320
Protein crystals
322
Diffraction from crystals
323
Derivation box 15.1 Phases of complex numbers
325
Phase determination
328
Molecular replacement
328
Isomorphous replacement
329
Anomalous dispersion
329
Model building
331
Experimental measurement of X-ray diffraction
332
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