Principles of physical biochemistry
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| Hauptverfasser: | , , |
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Upper Saddle River, NJ
Pearson Prentice Hall
[2006]
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| Ausgabe: | Second edition, international edition |
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| Online-Zugang: | Inhaltsverzeichnis |
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| 100 | 1 | |a Van Holde, K. E. |d 1928- |e Verfasser |0 (DE-588)120099993 |4 aut | |
| 245 | 1 | 0 | |a Principles of physical biochemistry |c Kensal E. van Holde, W. Curtis Johnson, P. Shing Ho |
| 250 | |a Second edition, international edition | ||
| 264 | 1 | |a Upper Saddle River, NJ |b Pearson Prentice Hall |c [2006] | |
| 300 | |a xiii, 710, A-17, I-10 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
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| 700 | 1 | |a Johnson, W. Curtis |e Verfasser |4 aut | |
| 700 | 1 | |a Ho, Pui Shing |e Verfasser |4 aut | |
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Datensatz im Suchindex
| DE-BY-TUM_call_number | 1002 CHE 802f 2006 A 2010(2) |
|---|---|
| DE-BY-TUM_katkey | 1538034 |
| DE-BY-TUM_location | 10 |
| DE-BY-TUM_media_number | 040050488863 |
| _version_ | 1820803874809708544 |
| adam_text | Contents
Preface xiii
Chapter 1 Biological Macromolecules 1
1.1 General Principles 1
1.1.1 Macromolecules 2
1.1.2 Configuration and Conformation 5
1.2 Molecular Interactions in Macromolecular Structures 8
1.2.1 Weak Interactions 8
1.3 The Environment in the Cell 10
1.3.1 Water Structure 11
1.3.2 The Interaction of Molecules with Water 15
1.3.3 Nonaqueous Environment of Biological Molecules 16
1.4 Symmetry Relationships of Molecules 19
1.4.1 Mirror Symmetry 21
1.4.2 Rotational Symmetry 22
1.4.3 Multiple Symmetry Relationships and Point Groups 25
1.4.4 Screw Symmetry 26
1.5 The Structure of Proteins 27
1.5.1 AminoAcids 27
1.5.2 The Unique Protein Sequence 31
Application 1.1: Musical Sequences 33
1.5.3 Secondary Structures of Proteins 34
Application 1.2: Engineering a New Fold 35
1.5.4 Helical Symmetry 36
1.5.5 Effect of the Peptide Bond on Protein Conformations 40
1.5.6 The Structure of Globular Proteins 42
1.6 The Structure of Nucleic Acids 52
1.6.1 Torsion Angles in the Polynucleotide Chain 54
1.6.2 The Helical Structures of Polynucleic Acids 55
1.6.3 Higher Order Structures in Polynucleotides 61
Application 1.3: Embracing RNA Differences 64
Exercises 68
References 70
V
vj Contents
Chapter 2 Thermodynamics and Biochemistry 72
2.1 Heat, Work, and Energy—First Law of Thermodynamics 73
2.2 Molecular Interpretation ofThermodynamic Quantities 76
2.3 Entropy, Free Energy, and Equilibrium—Second Law
of Thermodynamics °
2.4 The Standard State 91
2.5 Experimental Thermochemistry yj
2.5.1 The van t Hoff Relationship 93
2.5.2 Calorimetry 94
Application 2.1: Competition Is a Good Thing 102
Exercises *04
References 105
Chapter 3 Molecular Thermodynamics
3.1 Complexities in Modeling Macromolecular Structure 1C 7
3.1.1 Simplifying Assumptions
3.2 Molecular Mechanics
3.2.1 Basic Principles 109
3.2.2 Molecular Potentials 111
3.2.3 Bonding Potentials 112
3.2.4 Nonbonding Potentials ^
3.2.5 Electrostatic Interactions */r
3.2.6 Dipole Dipole Interactions 1
3.2.7 van der Waals Interactions
3.2.8 Hydrogen Bonds 12°
3.3 Stabilizing Interactions in Macromolecules
3.3.1 Protein Structure 125
3.3.2 Dipole Interactions 129
3.3.3 Side Chain Interactions 131
3.3.4 Electrostatic Interactions
3.3.5 NucleicAcid Structure 13^
3.3.6 Base Pairing 137
3.3.7 Base Stacking 139
3.3.8 Electrostatic Interactions
3.4 Simulating Macromolecular Structure ^
3.4.1 Energy Minimization
3.4.2 Molecular Dynamics
3.4.3 Entropy 9
3.4.4 Hydration and the Hydrophobie Effect ~T
3.4.5 Free Energy Methods yr
Exercises
References 163
Contents vii
Chapter 4 Statistical Thermodynamics 166
4.1 General Principles 166
4.1.1 Statistical Weights and the Partition Function 167
4.1.2 Models for Structural Transitions in Biopolymers 169
4.2 Structural Transitions in Polypeptides and Proteins 175
4.2.1 Coil Helix Transitions 175
4.2.2 Statistical Methods for Predicting Protein
Secondary Structures 181
4.3 Structural Transitions in Polynucleic Acids and DNA 184
4.3.1 Melting and Annealing of Polynucleotide Duplexes 184
4.3.2 Helical Transitions in Double Stranded DNA 189
4.3.3 Supercoil Dependent DNA Transitions 190
4.3.4 Predicting Helical Structures in Genomic DNA 197
4.4 Nonregular Structures 198
4.4.1 Random Walk 199
4.4.2 Average Linear Dimension of a Biopolymer 201
Application 4.1: LINUS: A Hierarchie Procedure to
Predict the Fold of a Protein 202
4.4.3 Simple Exact Models for Compact Structures 204
Application 4.2: Folding Funnels: Focusing Down to the Essentials 208
Exercises 209
References 211
Chapter 5 Methods for the Separation and Characterization
of Macromolecules 213
5.1 General Principles 213
5.2 Diffusion 214
5.2.1 Description of Diffusion 215
5.2.2 The Diffusion Coefficient and the Frictional Coefficient 220
5.2.3 Diffusion Within Cells 221
Application 5.1: Measuring Diffusion of Small DNA Molecules in Cells 222
5.3 Sedimentation 223
5.3.1 Moving Boundary Sedimentation 225
5.3.2 Zonal Sedimentation 237
5.3.3 Sedimentation Equilibrium 241
5.3.4 Sedimentation Equilibrium in a Density Gradient 246
5.4 Electrophoresis and Isoelectric Focusing 248
5.4.1 Electrophoresis: General Principles 249
5.4.2 Electrophoresis of Nucleic Acids 253
Application 5.2: Locating Bends in DNA by Gel Electrophoresis 257
5.4.3 SDS Gel Electrophoresis of Proteins 259
5.4.4 Methods for Detecting and Analyzing Components on Gels 264
jjj Contents
5.4.5 Capillary Electrophoresis 266
5.4.6 Isoelectric Focusing 2
97(1
Exercises z/u
References 274
Chapter 6 X Ray Diffraction 276
977
6.1 Structures at Atomic Resolution z
6.2 Crystals 279
6.2.1 What Is a Crystal? 279
98^
6.2.2 Growing Crystals ZÖD
6.2.3 Conditions for Macromolecular Crystallization 286
Application 6.1: Crystals in Space! 289
6.3 Theoryof X Ray Diffraction 290
6.3.1 Bragg s Law 292
6.3.2 von Laue Conditions for Diffraction 294
6.3.3 Reciprocal Space and Diffraction Patterns 2
6.4 Determining the Crystal Morphology ¦ 04
6.5 Solving Macromolecular Structures by X Ray Diffraction 308
6.5.1 The Structure Factor 309
6.5.2 The Phase Problem 317
Application 6.2: The Crystal Structure of an Old
and Distinguished Enzyme
6.5.3 Resolution in X Ray Diffraction 334
6.6 Fiber Diffraction 338
6.6.1 The Fiber Unit Cell 338
6.6.2 Fiber Diffraction of Continuous Helices
6.6.3 Fiber Diffraction of Discontinuous Helices
Exercises 3
References 349
Chapter 7 Scattering from Solutions of Macromolecules
7.1 Light Scattering 351
7.1.1 Fundamental Concepts
7.1.2 Scattering from a Number of Small Particles:
Rayleigh Scattering 355
7.1.3 Scattering from Particles That Are Not Small
Compared to Wavelength of Radiation
12 Dynamic Light Scattering: Measurements of Diffusion Z~~
7.3 Small Angle X Ray Scattering 3*f
7.4 Small Angle Neutron Scattering
Application 7.1: Using a Combination of Physical Methods
to Determine the Conformation of the Nucleosome
7.5 Summary 37t)
Contents ix
Exercises 376
References 379
Chapter 8 Quantum Mechanics and Spectroscopy 380
8.1 Light and Transitions 381
8.2 Postulate Approach to Quantum Mechanics 382
8.3 Transition Energies 386
8.3.1 The Quantum Mechanics of Simple Systems 386
8.3.2 Approximating Solutions to Quantum Chemistry Problems 392
8.3.3 The Hydrogen Molecule as the Model for a Bond 400
8.4 Transition Intensities 408
8.5 Transition Dipole Directions 415
Exercises 418
References 419
Chapter 9 Absorption Spectroscopy 421
9.1 Electronic Absorption 421
9.1.1 Energy of Electronic Absorption Bands 422
9.1.2 Transition Dipoles 433
9.1.3 Proteins 435
9.1.4 NucleicAcids 443
9.1.5 Applications of Electronic Absorption Spectroscopy 447
9.2 Vibrational Absorption 449
9.2.1 Energy of Vibrational Absorption Bands 450
9.2.2 Transition Dipoles 451
9.2.3 Instrumentation for Vibrational Spectroscopy 453
9.2.4 Applications to Biological Molecules 453
Application 9.1: Analyzing IR Spectra of Proteins for Secondary Structure 456
9.3 Raman Scattering 457
Application 9.2: Using Resonance Raman Spectroscopy
to Determine the Mode of Oxygen Binding to Oxygen Transport Proteins 461
Exercises 463
References 464
Chapter 10 Linear and Circular Dichroism 465
10.1 Linear Dichroism of Biological Polymers 466
Application 10.1 Measuring the Base Inclinations
in dAdT Polynucleotides 471
10.2 Circular Dichroism of Biological Molecules 471
10.2.1 Electronic CD of NucleicAcids 476
Application 10.2: The First Observation of Z form
DNAWasbyUseofCD 478
Contents
10.2.2 Electronic CD of Proteins 481
10.2.3 Singular Value Decomposition and Analyzing the
CD of Proteins for Secondary Structure 485
10.2.4 Vibrational CD 4%
Exercises
A QQ
References
Chapter 11 Emission Spectroscopy 501
11.1 The Phenomenon 501
11.2 Emission Lifetime 502
11.3 Fluorescence Spectroscopy 504
11.4 Fluorescence Instrumentation 506
11.5 Analytical Applications 507
11.6 Solvent Effects 509
11.7 Fluorescence Decay 513
11.8 Fluorescence Resonance Energy Transfer 310
11.9 Linear Polarization of Fluorescence 517
Application 11.1: Visualizing c AMP with Fluorescence 517
11.10 Fluorescence Applied to Protein 524
Application 11.2: Investigation of the Polymerization of G Actin 528
11.11 Fluorescence Applied to Nucleic Acids 530
Application 11.3: The Helical Geometry of Double Stranded
DNA in Solution 532
Exercises 533
References 534
Chapter 12 Nuclear Magnetic Resonance Spectroscopy
12.1 The Phenomenon 535
12.2 The Measurable 537
12.3 Spin Spin Interaction 540
12.4 Relaxation and the Nuclear Overhauser Effect 542
12.5 Measuring the Spectrum 544
12.6 One Dimensional NMR of Macromolecules 549
Application 12.1: Investigating Base Stacking with NMR 553
12.7 Two Dimensional Fourier Transform NMR 555
12.8 Two Dimensional FT NMR Applied to Macromolecules 560
Exercises 575
References 577
Cbapter 13 Macromolecules in Solution: Thermodynamics and Equilibria 579
13.1 Some Fundamentals of Solution Thermodynamics 58^
13.1.1 Partial Molar Quantities:The Chemical Potential
Contents xi
13.1.2 The Chemical Potential and Concentration:
Ideal and Nonideal Solutions 584
13.2 Applications of the Chemical Potential to Physical Equilibria 589
13.2.1 Membrane Equilibria 589
13.2.2 Sedimentation Equilibrium 597
13.2.3 Steady State Electrophoresis 598
Exercises 600
References 603
Chapter 14 Chemical Equilibria Involving Macromolecules 605
14.1 Thermodynamics of Chemical Reactions in Solution: A Review 605
14.2 Interactions Between Macromolecules 610
14.3 Binding of Small Ligands by Macromolecules 615
14.3.1 General Principles and Methods 615
14.3.2 Multiple Equilibria 622
Application 14.1: Thermodynamic Analysis of the
Binding of Oxygen by Hemoglobin 641
14.3.3 Ion Binding to Macromolecules 644
14.4 Binding to Nucleic Acids 648
14.4.1 General Principles 648
14.4.2 Special Aspects of Nonspecific Binding 648
14.4.3 Electrostatic Effects on Binding to Nucleic Acids 651
Exercises 654
References 658
Chapter 15 Mass Spectrometry of Macromolecules 660
15.1 General Principles: The Problem 661
15.2 Resolving Molecular Weights by Mass Spectrometry 664
15.3 Determining Molecular Weights of Biomolecules 670
15.4 Identification of Biomolecules by Molecular Weights 673
15.5 Sequencing by Mass Spectrometry 676
15.6 Probing Three Dimensional Structure by Mass Spectrometry 684
Application 15.1: Finding Disorder in Order 686
Application 15.2: When a Crystal Structure Is Not Enough 687
Exercises 690
References 691
Chapter 16 Single Molecule Methods 693
16.1 Why Study Single Molecules? 693
Application 16.1: RNA Folding and Unfolding Observed at
the Single Molecule Level 694
16.2 Observation of Single Macromolecules by Fluorescence 695
xii Contents
16.3 Atomic Force Microscopy 699
Application 16.2: Single Molecule Studies of Active Transcription
by RNA Polymerase 701
16.4 OpticalTweezers 703
16.5 Magnetic Beads 707
Exercises 708
References 709
Answers to Odd Numbered Problems A l
Index 1 1
|
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| author | Van Holde, K. E. 1928- Johnson, W. Curtis Ho, Pui Shing |
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| dewey-ones | 572 - Biochemistry |
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| discipline | Chemie / Pharmazie Physik Biologie |
| edition | Second edition, international edition |
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| id | DE-604.BV019879357 |
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| indexdate | 2024-12-23T18:18:09Z |
| institution | BVB |
| isbn | 013201744X |
| language | English |
| lccn | 2005042993 |
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| physical | xiii, 710, A-17, I-10 Seiten Illustrationen, Diagramme |
| publishDate | 2006 |
| publishDateSearch | 2006 |
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| publisher | Pearson Prentice Hall |
| record_format | marc |
| spellingShingle | Van Holde, K. E. 1928- Johnson, W. Curtis Ho, Pui Shing Principles of physical biochemistry Biochemie gtt Biochimie physique Bioquímica larpcal Fysische chemie gtt Physical biochemistry Biophysikalische Chemie (DE-588)4291844-3 gnd |
| subject_GND | (DE-588)4291844-3 |
| title | Principles of physical biochemistry |
| title_auth | Principles of physical biochemistry |
| title_exact_search | Principles of physical biochemistry |
| title_full | Principles of physical biochemistry Kensal E. van Holde, W. Curtis Johnson, P. Shing Ho |
| title_fullStr | Principles of physical biochemistry Kensal E. van Holde, W. Curtis Johnson, P. Shing Ho |
| title_full_unstemmed | Principles of physical biochemistry Kensal E. van Holde, W. Curtis Johnson, P. Shing Ho |
| title_short | Principles of physical biochemistry |
| title_sort | principles of physical biochemistry |
| topic | Biochemie gtt Biochimie physique Bioquímica larpcal Fysische chemie gtt Physical biochemistry Biophysikalische Chemie (DE-588)4291844-3 gnd |
| topic_facet | Biochemie Biochimie physique Bioquímica Fysische chemie Physical biochemistry Biophysikalische Chemie |
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