Molecular and Cellular Biophysics

520 Pages·2016·10.295 MB·English

by  Jack A. Tuszynski

Series in PURE and APPLIED PHYSICS
MOLECULAR
AND CELLULAR
BIOPHYSICS
CRC SERIES
in
Pure applied Physics
and
Dipak Basu
Editor-in-Chief
PUBLISHED Titles
Handbook of Particle Physics
M. K. Sundaresan
High-Field Electrodynamics
Frederic V. Hartemann
Fundamentals and Applications of Ultrasonic Waves
J. David N. Cheeke
Introduction to Molecular Biophysics
Jack A. Tuszynski
Michal Kurzynski
Practical Quantum Electrodynamics
Douglas M. Gingrich
Molecular and Cellular Biophysics
Jack A. Tuszynski
Series in PURE and APPLIED PHYSICS
MOLECULAR
AND CELLULAR
BIOPHYSICS
Jack A. Tuszynski
Cover image provided by Tyler Luchko.
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Acknowledgments
ThisbookgrewoutofanearliercollaborationprojectwithDr. M.Kurzyn-
ski. I am very thankful to Dr. Kurzynski for his many insights.
The author also wishes to thank his students, staff and collaborators for
their immense help in various stages of work leading to this book. In par-
ticular, the assistance of the following individuals is gratefully acknowledged:
Eric Carpenter, Torin Huzil, Tyler Luchko, Hannes Bolterauer, John Dixon,
Eberhard Unger, and Avner Priel.
Special thanks are expressed for Michelle Hanlon’s tireless work on editing
this book and organizing book material.
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List of Tables
1.1 Pattern Recognition in Networks . . . . . . . . . . . . . . . . 14
1.2 Amino Acid Sequences in Horse and Human Proteins. . . . . 56
2.1 Properties of Biologically Important Bonds . . . . . . . . . . 76
2.2 Potential Energies and Bond Distance . . . . . . . . . . . . . 83
2.3 Relative Ionization . . . . . . . . . . . . . . . . . . . . . . . . 85
2.4 Electronic Distribution . . . . . . . . . . . . . . . . . . . . . . 85
2.5 Electron Distribution for Biological Atoms . . . . . . . . . . . 86
2.6 Data for Different Types of Bonds . . . . . . . . . . . . . . . 87
2.7 The Coefficient A for Different Molecules . . . . . . . . . . . 91
2.8 Empirical Values of Coefficients A and B. . . . . . . . . . . . 92
2.9 Van der Waals Radii . . . . . . . . . . . . . . . . . . . . . . . 92
2.10 Bond Lengths for Various Bond Types . . . . . . . . . . . . . 94
2.11 Properties of Various R−H Compounds . . . . . . . . . . . 95
n
2.12 The Structure of Water in Liquid and Ice Form . . . . . . . . 98
2.13 Size of Cluster at Different Temperatures . . . . . . . . . . . 98
2.14 ChangeinThermodynamicParameterswithIntroductionofan
Organic Molecule into Water . . . . . . . . . . . . . . . . . . 99
2.15 Number of Hydrogen Bonds for a Water Molecule. . . . . . . 100
2.16 The Twenty Naturally Occurring Amino Acids . . . . . . . . 107
2.17 Energy Contributions to Native State Stabilization . . . . . . 121
2.18 The Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . 135
3.1 MajorComponentsofCytoplasm[167]inaTypicalMammalian
Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
3.2 Percentage Content and Molecular Numbers of Key Cellular
Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
3.3 The Key Biomolecular Polymers in a Cell . . . . . . . . . . . 157
3.4 The Amino Acid Sequence of human α - and β - tubulin. . . 160
1 1
3.5 Localization and Homology of Bovine β-Tubulin [200] . . . . 161
3.6 Summary of Actin-Binding Proteins . . . . . . . . . . . . . . 171
3.7 Tissue Distribution of β Tubulin Isotypes in Normal Cells . . 175
3.8 Experimental Data for Elastic Properties of MTs (and Other
Proteins) from the Literature . . . . . . . . . . . . . . . . . . 190
3.9 Tension Forces Within the Cell . . . . . . . . . . . . . . . . . 203
3.10 Concentration Ratios for Cellular Membranes and the Corre-
sponding Nernst Potential in Equation . . . . . . . . . . . . 233
vii
viii
3.11 A Probable Cycle of Actomyosin Motion . . . . . . . . . . . . 245
3.12 FitsofSingleorDoubleGaussianProfilestotheHistogramsin
Fig. 3.58 (5 µM tilting/non-tilting and 0 ATP) . . . . . . . . 249
3.13 Key Electrostatic Properties of Tubulin . . . . . . . . . . . . 273
3.14 Concentration Data . . . . . . . . . . . . . . . . . . . . . . . 282
3.15 Data for Problem 3.18 . . . . . . . . . . . . . . . . . . . . . . 286
4.1 Diffusion Constants at Room Temperature in Water . . . . . 315
4.2 Potential Functions of Molecular Complexes as Bioelectronic
Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
4.3 CalculatedConductivityandResistanceofa1-micronPolymer
Composed of Tubulin Dimers . . . . . . . . . . . . . . . . . . 368
4.4 A Summary of Characteristic Time Estimates . . . . . . . . . 402
4.5 AListofKeyChemicalReactionsInvolvedinMicrotubuleAs-
sembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 436
4.6 TypicalParameterValuesforMicrotubuleAssemblyFollowing
[278] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437
4.7 Data for Problem 4.14 . . . . . . . . . . . . . . . . . . . . . . 464
List of Figures
1.1 Hierarchical organization of science. . . . . . . . . . . . . . . 4
1.2 General animal cell during interphase. . . . . . . . . . . . . . 6
1.3 Comparison of structures of typical animal and plant cells.. . 8
1.4 Processing genetic information. . . . . . . . . . . . . . . . . . 25
1.5 Amphiphilic molecules. . . . . . . . . . . . . . . . . . . . . . . 27
1.6 Development of the prokaryotic cell machinery. . . . . . . . . 29
1.7 Outline of the main metabolic pathways. . . . . . . . . . . . . 30
1.8 The structure of a bacterial cell. . . . . . . . . . . . . . . . . 33
1.9 Proton pumps. . . . . . . . . . . . . . . . . . . . . . . . . . . 34
1.10 Porphyrin ring. . . . . . . . . . . . . . . . . . . . . . . . . . . 35
1.11 A proton pump in purple bacteria. . . . . . . . . . . . . . . . 36
1.12 The utilization of solar energy by green sulfur bacteria. . . . 38
1.13 A proton pump using solar energy in the case of cyanobacteria. 39
1.14 Protein pump of heterotrophic aerobic bacteria. . . . . . . . . 40
1.15 A simplified phylogenetic tree of living organisms on Earth. . 41
1.16 Compartments of the eukaryotic cell. . . . . . . . . . . . . . . 44
1.17 Additional organelles of the plant cell. . . . . . . . . . . . . . 45
2.1 Examplesofthethreemostimportantkindsofcarboxylicacids
with purely carbohydrate substituents. . . . . . . . . . . . . . 62
2.2 Examples of the three most important kinds of alcohols with a
purely carbohydrate substituent. . . . . . . . . . . . . . . . . 62
2.3 Three examples of monosaccharides. . . . . . . . . . . . . . . 63
2.4 Most important examples of heterocycles. . . . . . . . . . . . 64
2.5 Some organic compounds with two functional groups. . . . . 65
2.6 Formation of the ester bond. . . . . . . . . . . . . . . . . . . 66
2.7 Formation of lipid (a) and phospholipid (b). . . . . . . . . . . 66
2.8 Example of a nucleotide, AMP. . . . . . . . . . . . . . . . . . 67
2.9 Formation of ATP from AMP . . . . . . . . . . . . . . . . . . 68
2.10 Polysaccharides. . . . . . . . . . . . . . . . . . . . . . . . . . 70
2.11 Spatial distribution of the electron probability density. . . . . 71
2.12 The spatial structure of methane, ammonia and water . . . . 72
2.13 The spatial structures of ethane, methylamine and methanol. 73
2.14 Properties related to the rotation of a single covalent bond. . 74
2.15 Conformational states. . . . . . . . . . . . . . . . . . . . . . . 75
2.16 Two enantiomers of glyceraldehyde. . . . . . . . . . . . . . . 76
ix