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Molecular and Cellular Biophysics PDF

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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. CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2008 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Version Date: 20160411 International Standard Book Number-13: 978-1-4200-1172-2 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmit- ted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright. com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com 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. TThhiiss ppaaggee iinntteennttiioonnaallllyy lleefftt bbllaannkk 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

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