__Biological_Physics___Energy__Information__Life

BAPPENDIX Numerical Values A single number has more genuineand permanent value than an expans ive library fu ll ofhypotheses. - Robert Mayer, 1814--1 878 Not all the values mentioned in this appendix are actually used in the text. Fundament al constan ts Boltzmann constant, kB = 1.38 . 10- 23 J K- 1. Therma l energy at roo m temper- ature (T, sa 295 K): kgT, = 4.1 pN nm = 4.1 . 10- ' 1J = 4.1 . 10- 14 erg = = =2.5 kJ mole' 1 0.59 kcal mole' 1 0.025eV. Charge on a pro ton, e = 1.6 · 10. 19 co ul. (The charge on an electron is - e.) A useful restatement is e = 40kBTr/ volt. Permittivity of vacuum, eo = 8.9 . 10- 1' F m\" ! (o r cou l'N- 1m- ' ). The combina- tion e2/ (41tfo) equals 2.3 .10- 28 J m. We treat wateras a continuum dielectric with e \"\" 80eo. Stefan- Boltzmann constant, a = 5.7 . 10- 8 W m- ' K- '. Magnitudes Sizes (sm allest to largest) hydrogen atom (rad ius), 0.05 nm. water molecule (radius), 0.135 nm. covalent bo nd length , \"\" 0.1 nm. H-bon d (distance between centers of atoms flankin g H), 0.27 nm. sugar, amino acid, nucleotide (diameter), 0.5-1 nm. electron microscope resolution , 0.7 nm. Debye screening length (of physiological Ringer's solution ), AD \"\" 0.7 nm. eoBjerrum length of water at room temperature, sa e' / (4\" ekoT,) = 0.71 nm. DNA (diameter), 2 nm. globular protein (d iameter) , 2-10 nm (lysozyme, 4 nm; RNA polymera se, 10 nm). bilayer membran e (thickness), \"\" 3 nm. F-actin (diameter) , 5 nm. 569

570 Appendix B Nume rical Values nucleo some (dia meter), 10nm . E. coli flagellum (radius), 10 nm. synaptic cleft in chemical synapse (width), 20-40 nm (neuromuscular junction , 50- 100 nm ). po lioviru s (diameter), 25 nm (sma llest viru s, 20 nm ). microtubule (diame ter), 25 nm. smallest feature that can be dr awn with electron-beam lithograph y (wid th) , 30 nm. ribo some (diameter), 30 nm. casein micelle (diameter), 100 nm. thinnest wire in Pentium processor chip (width), :::: 100 nm. eukaryotic flagellum (diameter), 100-500 nm. transistor in consumer electronics (diameter), ::::::: 180nm. optical microscope resolution, ee 200 nm. vertebrate axon (diameter), 0.2-20 /l m. wavelengt h of visible light, 400-650 nm. smallest feature that can be created by ph otolit ho graphy, 0.5 /l m. typical bacterium (diameter), I /l m (smallest, 0.5 /l m ). myofibril (diameter), 1- 2/l m. capillary (d iameter), as small as 3 /l m. E. coli flagellum (length), 10 /lm (20 000 subunits). typ ical human cell (d iameter), '\" 10 /l m (red blood cell, 7.5 /lm ). lambda phage virus DNA (conto ur length ) '\" 16.5 /l m. T4 phage DNA (contour length), 54 zz rn (160 kbp); T4 capsid (length ), '\" 100 nm. human hair (diameter), 100/lm. naked eye resolution, 200 /lm . squid «giant» axon (diameter), 1mm. E. coli genome (length if extended) , 1.4 mm. human genome (total length ), '\" 1 m. Earth (radius), 6.4· 10' m. Energies Most of the following values areexpressed as multiples of kBTn the thermal energy at room temperature. complete oxidation of one glucose, 1159kBT, . triple covalent bon d (for example, C=N) , geV = 325kBT,; double bond (for ex- ample, C= C), 240kBT,; single bond (for example C- C) , 140kBT,. visible photon (green), 120k. T,. streptavidin/biotin bond, 40ks Tr. ATP hydrolysis under normal cell conditions, 6G = - JI to - 13 kcal mole- 1 :::::: \", ao- 20kBT,/molecule. (The standard free ener gy change is = - 12.4kBT, ;

Appendix B Numerical Values 571 but cells are far from standard co nditions. } ATP productio n in hum ans. ~ 40 kg of ATP each day. generic (van der Waals, or dispersion) attraction energy between atoms, 0.6- 1.6kB T , . human resting heat output, lOOW. energy content: of glucose, 1.7 · 107 J j kg; of beer, 0.18 . 107 J j kg; of gasoline, 4.8 . 107 J j kg. peak mechan ical power of human athlete, 200 W; of bumb lebee, 0.02 W. solar energy output, 3.9 . 10' · W; power density striking Earth, 1.4 · 103 W j m' . Speciali zed valu es Viscos i ty of water at 20°(, 1.0.10- 3 Pa 5; of air, 1.7.10 - 5 Pa 5; of honey, 0.1 Pa 5; of glycerol, 1.4 Pa s. The effective viscosity of cell cytoplasm depend s on the size of the object consid- ered: For molecu les smaller than I nrn, it's sim ilar to that of wat er; fo r particles of diam eter 6 nm (such as a protein of mass 105 g mole\" ), it's abo ut 3 times that of water. For 50-500 nm particles, it's 30-300 tim es that of water; the en - tire cell behaves as tho ugh its viscosity were a mill ion times that o f water. visco us critical force: for water. 10- 9 N, for air, 2 . 10- 10 N; for glycerine, 10- 3 N. More about water energy to break an intramolecular hydrogen bond in water, 1- 2kBT, (hydrogen bond when two water molecu les co nde nse in vacuum , 8 kBTr). ele ctrostatic attractio n ene rgy of two 0.3 nm io ns in water, :::::: kBT; heat of vaporization of water. Q vap = 2.3.106 J kg- J • oil-water surface tension. L = 0 .04 J m- 2; air-water surface tension, 0 .072 J m- 2. number den sity of water m olecul es in pure water. 55 M; mass density of water at 20°(, 998 kg m- '. diffu sio n co nstant for generic sma ll mol ecu les in water, D :::: 1 .um2 rns'\" . Specifi - cally, for O2 • it's 2 .um2ms-l; for water m olecules the mselves, 2.2 .um2 rns\" : fo r glucose. 0 .67 li m2 ms\" : for globular protein in wate r, D :::::: 10- 2 .um2rns\" . heat capacity of water at room tempe rature , 4180 J kg- 1K- 1 or 0.996ca l cm- 3 K- 1• thermal cond uctivity of water at O°C, 0.56 J 5- 1 rn\" K- 1; at 1000( 6.8 J 5 - 1 m\" K- '. Ra tes The turnover number for an enzym e can vary from about 5 . 10- 2 S-I (chy- motrypsin on N- acetylglycine ethyl ester ) to I . 107 5- 1 (catalase). For acetyl- cho linesterase, it's 25000 S-I .

5 72 Appe ndix B Numerical Values Membranes (artificia l) bilayer bend stiffness (dimy ristoyl ph osphatidylcholin e, or DMP C), K 0.6 . 10- 19 J = 14kBT,. bilayer stre tch modulus (DM PC), 144 mN m- I. rupture tension (DM PC), \"\" 5 mN/m . Permeability to water, P w: DMPC, 70 u r« S- I; di alysis tubing, 11 /L m S-I . (Filtr a- tion coe fficient Lp for dialysis tubing, 3.4 . 10- 5 e m ,-I at rn\", ) Permeability of a bilayer membrane to solutes, P«: small inor ganic catio ns, like so dium o r pot assium , 10- 8 j..t m 5- 1; Cl\" , 10- 6; for glucose, 10- 3 11m 5- 1, (For sucrose through 2 mil cellophane, 1.0 /L m , - I. For glucose through dialysis tub - ing, 1.8 /L m , - I.) Membranes (cell) perm eabilit y to water of hum an red blood cell m embran e, 53 /L m , - I. filtration coefficient Lp: human red blood cell m em bran e, 91.10- 7 em , -Iatm- I; capillary blood vessel walls, 69 . 10- 7 em S-I atrn \" . Poly mers B-fonn DNA: bend per sisten ce length, \"\" 50 nm = 150 basepairs (in 10 mM NaCl) (intrinsic, o r high-salt limit, 40 om ); twist persistence length, 75-100 nm; stretch mo dulus se 1300 pN; basepair rise, 0.34 nm/bp; helical pitch in solu- tion , 10.3- 10.6 bp . Others: m icrotubule diam eter, 25 nm; persistence length , 1 mm . interm ed iate filame nt persisten ce len gth, D.l /lm ; diam eter 10 nm. actin diam eter, 7 nm; persisten ce length, 3- 10 ,urn. neurofi lament persistence length, 0.5 u.m. Mo tors • Myosin: rnyosin- n (fast skeletal muscles) spee d in vitro, 8 um 5- 1; force, 2-5 pN. myosin -v (vesicle tran sport) speed, 0.35 /L m , -I. myosin -vur and XI (cytop lasmic streaming in plants) speed, 60 /l m 5 - 1. Conventional (2-headed) kinesin: step size, 8 nm; fuel consum ption, 44 ATP S- I per head; stall force , 6-7 pN; spee d in vitro, 100 steps/s = 800 nm 5- 1; processivity, 100 steps/ release. E. coli flagellar motor: rotation rate, 100 revolutions/s (1200 protons/r evolution); torqu e, 4000 pN nm. Pi ATPase moto r: stall torque, 100 pN nm; to rque gene rated again st frictional load , \"\" 40 pN nm.

Appe ndix B Numerical Val ues 573 RNA polym erase:stall force, 25 pN . speed: E. coliPol 1,16 basepairls; Pol II, 0.05 times as great; Pol III, 15 tim es as great; euka ryoti c polymerase, 50 bp /s ; T7 virus polymerase, 250 bp /s. DNA polymerase: sta ll force 34 pN. speed: ba cteria, 1000 n ucleotides/s; eukar yoti c cells, 100 nucl eot ides/s. HIV reverse transcriptase: 20-40 nucleo tides/s. Ribosome: 2 ami no acids/s (eukaryotic cells) or 20 5- 1 (bacteria). Ne urons pumps: '\" 10' ions/s per pump. carriers: ~ 104 ions/s per carrier. chamlels: ::::::: 106 ions/s per channel; density of so dium channels in squid axo n, ~ 300 /l m - ' ; un it cond ucta nce of open cha nne l, GN, + = 25 pS = 25 . 10- 12 [I - I . n-resting conductance per area, squid giant axo n, gt~1 ;::::::: 5 1m- 2; individual rest- ing conductances follow gK + :::::::: 25gNa+ ;:::::: 2gcl- . Duri ng an action potential, gNa+ mom entarily increases by abo ut a factor o f 500. capacitance per area . ce 1 . 10 - 2 F m- 2. n-conductivity of squid axop lasm , K :::::: 3 1m- I • human brain: power con sumption, 10 W (about 10% of whole-body resting tot al). There are se 1013 cells in the human bo dy, of which se 10 11 are nerve cells, making se 6 . 10\" synapses. Misc ellaneous acceleration o f gravity at Earth's surface, g = 9.8 m 5 - 2. typical acceleratio n in an ultracentrifuge, 3 · 106 m 5 - 2. pH : human blood, 7.35-7.45; human stomach con tents, 1.0-3.0; lemons, 2.2-2.4; drinkin g water, 6.5-8.0. Io n product of water at room temperature, 10- 14 • pK: dissociation of acetic acid , 4.76; of phosphoric acid, 2.15. deprotonation of aspartic acid , 4.4; of glutamic acid, 4.3; of histidine, 6.5; of cysteine, 8.3; of tyrosine, 10.0; of lysine, 11.0; of arginine, 12; of serine, > 13.0.



Credits COPYRIGHT PERM ISSIONS Cover: @ 1996. Used by perm ission of the Opti cal Society of America. Frontispiece: Used by permission of the Estate of Ruth Kavenoff. Part I opener: @ 1962. Used by permission of Mrs. Eric Sloane. Fig. 2.2: @ 1993. Used by permission of Sprin ger-Verlag. Fig. 2.3: @ 1993. Used by perm ission of Sprin ger-Verlag. Fig. 2.4: @ 1993. Used by permission of Springer-Verlag. Fig. 2.6: (b) @ 1980. Used by permission of Elsevier Science. Fig. 2.7: Courtesy of Dr. John Heuser. Fig. 2.8: G. F. BahrlBiological Photo Service. Fig. 2.9: Courtesy of Dr. Ju- lian Heath. Fig. 2.10: @ 1982. Used by perm ission of Jones and Bartl ett Publishers. Sudbury MA. Fig. 2.11: @ 1991 Larry Gonick. Fig. 2.14: @ 1993. Used by perm ission of Springer-Verlag. Fig. 2.15: @ 1982. American Association for th e Advancement of Science. Used by permission . Fig. 2.16: Protein Data Base accession code IEHZ (H. Shi and P. B. Moore. RNA 6 1091 (2000»). Fig. 2.17: Protein Database accession code IVII (e. j . McKnight, D. S. Doering. P. T. Matsudaira, P. S. Kim,}. Mol. BioI. 260 126 (1996»). Fig. 2.18: (c) @ 1996. Used by perm ission of Springer-Verlag. Fig. 2.20: @ 1993. Used by permission of Springer-Verlag. Fig. 2.23: @ 1993. Used by permis- sion of Springer-Verlag. Fig. 2.24: @ 1993. Used by perm ission of Springer-Verlag. Part II opener: Omikron/Photo Researchers. Inc. Fig. 3.1: @ 1991 by Larr y Gonick. Fig. 3.11: @ 1961. Used by permission of Dover Publication s. Fig. 3.13: @ 1961. Used by permission of Dover Publicatio ns. Fig. 3.14: (b) Andrew Syred/Science Photo Library/Photo Researchers, Inc. Fig. 4.1: @ 196 1. Used by perm ission of Dover Pub- lication s. Fig. 4.8: @ 1999. Used by perm ission of the American Physical Society. Fig. 5.1: @ 1972, MIT Press. Used by permission. Fig. 5.3: @ 1968. Used by permis- sion of Elsevier Science. Fig. 5.9: @ 1998. Used by permission of Elsevier Science. Fig. 6.12: @ 2000. Used by permission of Lippincott Williams and Wilkins. Fig. 7.2: @1993. Used by perm ission of Springer-Verlag. Fig. 7.4: @ 1998. American Physical Society. Used by permission . Fig. 7.12: (b)@ 1999, Philip Ball. Reprinted by permis- sion of Farr ar Straus and Girou x LLe. Epigraph to Chapter 8: @ 1936. 0gden Nash, renewed. Reprinted by permi ssion of Curtis Brown, Ltd. Fig. 8.2: @ 1949, American Associatio n for the Advancement of Science. Used by permission. Fig. 8.5: © 1992. Reprinted with perm ission from Elsevier Science. Fig. 8.10: @2 003, Miloslav Kalab; used by permission. Part III opening: @ HM Qu een Elizabeth II; reproduced by permission from the Royal Collection Pictu re Library. Fig. 9.2: @2003 Qu antomi X Ltd. Used by permission . Fig. 9.11: @ 1995, Mahlon Hoagland and Bert Dodson. Used by permission of Times Books, a divisio n of Random House , Inc. Fig. 9.12: Reprinted with permi ssion from Nature. @1 999. Macmillan Magazines Ltd. Epi- 575

576 Cred its graph to Chapter 10 appe ars tran slated in G. Gamow, Thirty years that sh ook ph ysics (New York, Dover Publication s, 1961). Used by permission of Dover Publications. Fig. 10.1: @ 1984, Prin ceton University Press. Used by permission. Fig. 10.3: @ 1993. Used by perm ission of the Bioph ysical Society. Fig. 10.4: @ 1997, American Physical Society. Used by permission. Fig. 10.5: @ 1989. Used by permission of The Rocke- feller University Press. Fig. 10.19: @ 1993. Used by permi ssion of Springer-Verlag. Fig. 10.22: Adapted with permission from Nature. @ 1999 by MacMillan Magazines Ltd. Table 10.2: @ 1999 Elsevier Science. Used by permi ssion . Fig. 11.9: @ 1993. Used by perm ission of Springer-Verlag. Fig. 11.1 0: @2 000. Used by per mission of Elsevier Science. Fig. 11.11 : Repr inted with per mission from Nature. @ 1995, Macmillan Magazines Ltd. Fig. 12.6: Reprinted by permi ssion from Nature. @ 1939, Macmillan Magazines Ltd. Fig. 12.11: @ 199 1, Sinauer Associates. Used by permis- sion. Fig. 12.13: @ 1962. Used by perm ission of The Physiological Society. Fig. 12.17: Reprinted by perm ission from Nature.@ 1980, Macmillan Magazines Ltd. Fig. 12.20: @ 1985, Oxford University Press, Inc. Fig. 12.21: @ 1993. Used by permission of Springer-Verlag. Color Figure I: Conly S. Rieder/Biological Photo Service. Color Figure 2: Co urtesy of Dr. Steve Nielsen. Color Figure 3: Courtesy of Dr. Scott Brady. Color Figure 4: @ 1999, American Association for the Advancement of Science. Used by permi ssion . Color Figure 5:@ 1993. Used by perm ission of Springer-Verlag. Color Figure 6: @ 1993. Used by permission of Springer-Verlag. GRANT SUPPORT This boo k is partially based on work supported by the United States National Science Foundation under Grants DUE-00-865 I I and DMR- 98-07156. Any opinions, find- ings, conclusions, levity, or recommendation s expressed in this book are those of the author and do not necessarily reflect the views of the National Science Foundation. The Albert Einstein Minerva Center for Theoretical Physics and the Minerva Cen- ter for Non linear Physics of Complex Systems provided additio nal support for this project.

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Index Bold references are the defining instance of a key term. abiotic process. 324 ampe~ (unit ) , 1 9 b~, 3 1 0 absolute temperatu re scale, 205 absolute zero, 27 amphiphile, 315 , 316 ofDNA,46,47, 61 aneerobic metabolism. 488, 496 basep air, 47, 51, 52, 276, 342. 345, 386 acetic acid, 308, 310, 322 And erson, Robert, 176 acetylcholine. 5H-S4 8 An finse n, Ch ristian, 328 Bateson. Willi am , 93 acety lcholi nesterase, 548, 571 Angstrom (u n it), 566 batrachotoxin, 539 acid ,3 10 an ion , 26 1 beer, 3 actin Anson. M. i, 328 bend, 345 antibody, 38, 330 bend persistence length, ~e persi stence len gth bundl ~ 34 8 an tipo rt, 497, 503 be nd stiffness apoptos ls, 40 cortex. 54 . S6, 24 1, 407 aqueous sol utio n, 297 mem b rane. seeb ilayer m embrane fila m en tou s, 38, 54 , 56, 348, 404-406, 409. rod , 346 , 386 archea.ao Berg, Howard, 176 569 Bernstein , Julius, 52 1 globu lar. 404 Arch ibald method, 190 Bezan illa, Francisco, 545 act io n potential. 508, 52 1-537,548 Archimedes' princi ple, 159 bi layer m em br ane, 49, 55-58, 137, 322- 327, 344, mechanical analog, 519-5 21 arc lengt h, 345 speed, 530, 552, 553 arginine, 31 1 408, Co lor Figur e 2 activ ati on barrier, 26, 86, 86, 97,100,220-223, Armstrong, Clay, 539, 545 bend stiffness of, 325-327, 344, 572 Arr henius rate law, 87 , 394, 421-426, 457, see pe rmeab ility, 135-138, 324, 572 30 1, 306, 332, 403, 425, 43 1, 437.444, th ickn ess of, 569 452 also activation barrier b ilayer vesicle, see vesicle dis tribu tion of, 380, 381 Asakura, She, 25 1 bi n , 7 1, 129 effect of entropy on, 254 aspart ic acid , 3 11 b inomial d ist rib ut ion , 113, 15 1 assor t ment, 9 1 b it, 15,90, 196 effectof mechanicalloadon, 439 atm osph ere (u n it ), 567 Bjerrum len gth , 266, 569 in enzyme catalysis, 425-430 AI P, 38, 46, 48, 57, 58, 327, 486 Block, Steven, 437 blo od,338 in an ion channel, 539, 540 bou nd by kinesin , 380 Bohr, Christ ian , 376, 378 in a ratchet. 421, 422 hydrolysis of, 444, 495, see also free ene rgy. o f Bohr effect, 378 act ive tr a nsport er, 484 Boltzmann, Ludw ig, 85, 121,206 act ivity, 297, 336 ATP hydrolysis Boltz man n constan t, 27, 111,2 19, 569 Adair, G., 377 synthase, 42, 489 , 492-495 ATPase, 483 Boltzmann dist r ibution, see probability addit ion r ule, 75, 76, 218 Austin, Robert, 380, 394 adenine, 46 autoco rrelatio n fu nct ion , 387 distributio n adenosine d iphosphate, seeADP average . 73 Born-Oppenheime r approximation, 457 ade n osine mono phosph ate, seeAM P Avogadro's numbe r. 23, 33, 120 Born self-energy, 26 1. 279. 329, 50 1 adenosine triphosphate, seeATP axo n , 44 , 154,470, 507. 546 borrjeneck process, 307 AD P (adenosine diphosphat e), 46, 48 d ist ributed-dem en t model, SI S bo undary condition afterh ype rpclarization , 508, 509, 523, 534, 553 giant. 471, 523, 532. 570, 573 alcohol dehydrogenase, 466 sizes, 570 no -slip, seeno -slip boundary co nd itio n Aldrich , Richard , 545 terminal, 44, 58, 506. 548 Poisson-Boltzmann equation, su allele, q l - 94 axon hillock, 548 allom etr ic scaling expo nent, 149 axoplasm, 5 15, 573 Poisson-Boltzmann equation allosteric cont rol, 39, 378, 437 bo uto n, 44 bacter iophage. see ph age Boveri, Theodor, 93 allosteric enzyme. 378, 379 bacteriorhodopsin, 493, 497 bovi ne serum albumin, su BSA allosteric interact ions, 379, 380, 441. 447. 451 bacte rium , 40 Boyer, Paul. 495 allosteric io n channel, 540 aerobic. 138 Bragg. J. K•• 366 allostery, 376-380 coasting, 191 alpha helix, SO, 53, 364, 396, seealsohelix-coi l com pos itio n , 49 Bridges, Calvin . 95 flagellar propu lsio n, 176 Brown , Robert, 109, 119 t ransi tion Reynolds numbe r 0(, 169 Brownian motion, 109-121 , 144 , I SS, 191,258, ami no acid , 48, 50,6 1, 3 11. 3 13, 327. 328. 33 1, rotati onai d iffusionof,I 56,I 94 Baker, Pete r, 536 537 364, 435 basal metabolic rate. 3 1, 149, 191 rot ation al. 1.56, 194 amino gro u p, 48, 309 BSA (bo vin e serum albumin ), 254 amo u nt of substance, 27. 30, 335 bulk modulus, SLe modul us AMP (ad enosine monopho sph ate ). 46 , 48 Bun yan , Paul , 239 AMP-PNP (ad enosine 5' - (13 , y -im ido) - buoyant force , 159 tri phos pha te). 379, 442 <;ql

592 Index busba r, 487, 492, 497 co br a veno m, 548 Da rcy's law. 181 , 260. 283 Bustarname , Ca rlos, 351 coe n zyme, 403 Oe bye screen ing length , 270, 285 , 386, 473, 569 coe nzyme A (CoA) , 490 decay cons tan t, 136 , 222 C35 1 mole cular mo tor , Sf',' kin esin , cu iu n. 265 d ef o r m a t ion single- he aded Cole. Ken neth . 522, 532, 534 co lloidal particle, 109 ben d. see bend cab le equatio n, 517 colloidal suspe ns ion, 159, 190, 262 exte ns iona l. 345 linear, 51 7 torsional ,345 non linear. 530, 531. 552. 555 co m pe titive inhibi tion , serin h ibition degenera cy. 224, 225 com plex fluid , seefluid deg ree ofa ngle (u nit) , 20, 567 calcium pumping, 497, 546 Delbrack. Max, 17,89,99.100, 401,469 calo rie (u n it), 7. 566 co m plex system, 385 denatur at io n, 328, 33 1 co m po site state , 44 S by co ld. 329 cAMP.we cyclic AMP co ncent ratio n. 22 su rface, 331 canonicalensemble. 85 conde nsatio n react io n. 48 de nd r ite, 44 , 506, 545-548 capacitance, 29, 269, 5 10, 5 13 conducta nce den d ritic spi ne, 45, 545, 549 de ndr itic t ree, 548 membr a ne, 5 13-5 16, 534-535, 553 , 573 per a rea, 480 , 555 d ensity capacitive cur rent, see curre n t per chan nel, 555 charge, 23 capa cito r, 29, 269, 5 12, 553 rest ing , 528, 555, 573 mass, 23 capilla ry, 155, 29 1, 570, 572 co nd uc tivity carboxyl grou p. 48 eleetrical, 142. 187, 48O,5 16, 554, 573 illust rative values, 165 casein. 330. 337, 570 the rmal. 187 numbe r, 22 Castle. William, 104 confo rmatio na l substate, 225, 38 1. 394 su rface catalase, 403, 57 1 co ntinu ity equ at io n , 131 catalysis, 58, 233, 378, 402 , 403, 425, 431, 467 co ntin uu m elas ticity, 343-344 cha rge, seecha rge densi ty co nto ur length , 345. 35 1, 396 in Krebs cycle, 490 cocperativiry nu mber, 23 reversib ility of, 426, 427 an d ph ase tr an sitio ns, 363 de pletion in ter acti o n, 25 1- 254. 29 1 by RNA, 226 effect o n helix-coiltransltion, 37 1 de pletion zone. 25 1, 253 satu rat io n kine tics o f, 429, 430, 436 in hemo globin , 377 depolarization, 507 , 508 calio n, 26 1 oflink orient atio ns, 358-36 1 deproronated am ino acid resid ue, 3 11 cell wall, 37, 40 in mic elle form ation, 32 1 detergent , 3 15, 3 16, 325, 49 3 Celsius scale , 27, 205 sharpens tr an sitio ns, 373 de ter mi nistic time evol u tio n , 131 central dogma , 59 ccoperativiry paramete r. 359 , 369. 371 devi atio n , root -mean-square, o r RMS, or centr ifuge , 159, 190, 573 co rrelatio n ratchet , 463 centripetal acceleration. 28 Cc rrens, Karl, 93 standard , 74, 241, 243 cep halexin. 498 co ulomb (u nit), 19. 566 devic e, molecula r, 402 channel. 56 co un terio n, 26 1-272, 292 de Vries. Hugo, 93 co ur uerlon clou d , 265 d ielectri c con sta nt, 261 , 564 ion . u e io n chan nel co un rerio n release. 272 d iffuse charge layer, 262 . 269 co up led transpor t, 484 chan nel-inac tivat ing segment, 541, 545 co valen t bond di ffusing ratche t tp -retcbet). see ratch et ch annel inactivation . see inactivat io n length o f, 569 chaperon e, 6 1 st rength o f, 275 d iffusion , 114- 121, 127, 129, 132, 143, 152 Ch ergeff Erwin, 10 1 Crane , H. , 182 from an in itial con centration step. 152 cha rge density. 23 creep ing flow, 168 increases ent rop y. 292 Crick, Fra ncis, 18,47, SO, 59.10 1 law, un iversali ty, 117 su rface. 23. 263. 265 critical force of moment um , 187, 192 cha rge reno rrnalizarion, 286 fo r D:\"lA overstretching, 375 one-dimensional, 115, 116 cheese , 337 viscous. 164-166.57 1 two- an d thr ee-dimens ional , 116, 156 ch em ical force . 299, 304 critical micell e co ncentration , 3 18. 3 19. 325 variable-step walk, 118 che mical potential, 30. 20 1. 295-306. 40 1, 431, crossing-over, 63. 94 , 104 crowd ing agent , 254 d iffusion co nsta n t, 22, l I S. 116, 119, 123, 130, 433,463 curare. 547 22 1, 417 alter native de fin itio n s, 335 curdling. 330 ideal gas o r solutio n. 2% cu rrent illus t rative values. 154, 57 1 standa rd, see standard chem ical pot en tial ca pacit ive. 513, 534, 535 rota tion al, 156 chemiosmoti c m echan ism , 49 1-497 electric. 19, 22 d iffusion eq uat ion. 131, 5 17. 530 chi ffon pie, 33 1 Curt is. Howard . 522 fu ndam ental p ulse solu tion , 134. 143, 150, chiral mo lecu le, 25. 26. 366 cyclic AM P, 46 chlo rophyll, 38 cyclic mach ine, see mach ine l Si chlo rop last, 42 , 217, 497 cyclic process, 7 d im ensio nal analysis, 18-23, 384. 385 cho rd co nd uctance fo rmula, 512 . 5 14. 524 cysteine. 48 di me nsio nal qu an tity. 20 chromatid . 43, 94 cytop lasm, 40 di mension less qu an t ity, 19 ch ro matin, 43 cytosi ne, 46 dimer, 379, 438 chromosome, 40-4 3, 50, 93-%, 342, 406 cytosk eleto n, 54, 240, Co lor Figure I di myristoyl phospha tidy lcholi ne, see OM PC polyte ne , 96 cytosol, 42, 54, 6 1, 50 1 d in ilro phf'nol,483 chy mot rypsin, 467, 57 1 Dinsm ore. An tho ny, 253 cilia, 45. 58, 174, 175, 452 dalton (u nit) , 30 d ipal m itoyl phospha ridylcholin e. see D PPC clat hrate cage, 277. 279 Dalton, John, 25 d ip loid cell, 91 Clausius. Rudolph. 80, 206 dipo le. 273, 288 d o sed thermodynam ic system , 210 dip o le in terac tion . 309, 374, 394 d um pi ng catastro phe, 262, 496 Dische r, Den n is, 240 di screte d ist ribution . see p robability CMC. ue cri tical mi celle concen tra t ion Co A, s« coenzyme A d ist ribu tion disorder, 9-15. 100, 196-20 1. 210 , 232, 505 coagula tion, 330, 337 and che mical reactio ns, 298

Index 593 and dep letio n interaction. 254 electrotonus, see passive spread equipartinon ofenergy, 220, 237. 387 and free energy, 211 erg (u n it ), 566 a nd heat , 120. 17 1, 202- 204 eme rgent properties. 18. 206. 343 error fu nct io n. 152 a nd hydrophobic interactio n, 280 em ulsion, 3 15, 3 16, 33 1, 332 Escherichia coli, 35, 36. 60 , 176, 178. 184, 194, a nd po lymer st retch ing, 348 endocyt osis. 42 from DNA seq uence. 389 endoplasm ic ret iculu m . 4 1 252.254,406, 489, 494,497.505,570 d issipatio n. 120 endo the rm ic reactio n. 26. 300 flagellar motor. seeflagellar mot or dissipative process, 108. 158. 171 en ergy euka ryote, 40 d issociatio n, 262, 293, 308- 3 15 even function , 37 1 d ist rib ut ed netwo rk , 5 16 chemic al bond, 26 excitable m ed ium , 520 d istr ibu tion . see p roba bility dist ributio n co nserv ation of, 4 exclusive alte rn atives, 75 di sulfid e bo nd, 61 , 408 kinetic. 4 exot her mic reactio n , 26 DMPC (d imy ristoyl ph osph atidyJcho line), 327. expectation value, 73 landsc ape. 4 13, see II/SO free ene rgy landscape 572 extensio nal de fo rm at io n , see deformatio n DNA. 38, 43, SO. 342. Color Figu re 1 G cratchet. 415. 416 o ne-d imension al, 410 , 411. 552 extensive qu an ti ty. se~ entropy. extensive annealing . 374 perfect ratchet , 420 property of Bcforrn , 51. 65. 375. 399. 572 Scratcher, 416, 417 cha rge on. 310. 386 two-d ime ns ional,41 1-4 13 Pcactin, see actin, filam entous d iam eter o f. 569 mecha n ical. 4 FO and FI u n its o f AT P syn thase. 57. 452, 493, d issoc iati on . 26 1 pote ntial , 4 du plex str uctu re, 373 o f cap acitor, 29, 269 49 4 int rinsic st retch ing, 352, 362 elec tros tatic. 29, 26 1, 287. 5 11 facto r, genet ic, 91-96 melting of, 374 gravita tional, 29 FAD (flavin ade n ine di nucl eo tide), 489, 490 over str etching transitio n, 352, 375 sp ring, 28, 240, 336 falsifiable hypo thesis, 7 qual ity of, S, 9- 15, 2 16-217 farad (u n it) , 21, 566 polymer ase, see polymerase sola r, 10, 11,32,39 fat, 49 th erm al,4- 15 fatty acid. 46, 49, 280 rep licat io n. 59. 182- 184.407 ent halpy. 212, 335. 425 feed back. 39, 59, 60, 62, 227, 242, 378, 437-439, stretch ing. 350-352. 355, 358. 36 1-362, 397 en tro pic fo rce. 130. 2 13. 246 , 25 1. 286, 317, 348, supercoiling of. 399 526-529, 533 tr an scr ipt ion. 60 , 252 m Fern andez-Moran, H.•494 unzippi ng of. 375 Feynma n, Rich ard , 184 Zcfo r m, 399, 400 en tropy, 9-15.199-210,237.239,245,296 fibrin. 329 DNA helicase , 183, 184 and chemical d rive, 30 1, 335 fibrinogen , 329 Do nnan equi libr ium . 476-478. 504. 51 1 and chemical po tentia l, 295, 299. 300 fibroblast. 44 Do nnan po tential. 476 an d hydrop ho bic effect. 280 Dory, Paul. 366. 394, 396 and Le Chatelfe r's Pri nciple, 305 Fick's law. 130- 132. 138. 139, 149, reo, 187,1 90. DPPC (d ipalm itoyl phosph at idylchohnel , 49. 65 and po lymer stretch ing, 348 and qu alit y of energy, 216-2 17 205, 283, 418 Dcratch et, see ratchet and substra te bind ing, 457 seco nd , 131 and temperature. 205, 206 filo podia, 44, 54, 407 drift veloci ty, 119 , 190,338 ch ange in d epletion interaction, 251 filtra tio n coeffi cient, 157, l SI , 260, 283, 29 1, Drosophila md llllogrw a , 93, 96 conformation al, 364, 368, 397 DuBo is Reymond, Em il. 470, 521 of cc un tcrio ns, 262, 265, 269-272, 47 1 572 den sity, 233 Finkelstein , Alan , [37 du plex, see DNA extensive prop ert y. 205. 233. 235, 236 of hydrogen bo nd. 367. 397 Finzi, Lau ra. 35 1 d ut y ratio. 438 . 446 ideal gas, 200. 202, 205, 247, 292 firefly, 464 dwell tim e. 223. 227. 228 inc reases d ur ing d iffusion , 29 2 First Law, 8,10, 14. 3 1, 59, 108, 150,206,21 6 dynein, 58. 452 of mixing, 210, 308 first-o rde r rate Jaw. 307, 433, 457 small subsystem, 224 Fischer, Emil, 426 E. coli, see Eschtrichia coli trans ition state. 457 fixed poin t, 529 effective segment length , 347 FIC, see poly me r. freel y joi n ted chain model egg.315. 33 1-332. 337 envelope fu nction, 456 flagella r mot o r, 58, 176, 177. 406,452,489, eige nvalues and eigenvectors. 356-357. 390 enzyme . 38, 58-59, 402 , 459, Col or Figure 5 Einstei n, Albert, 22, 24. 26, 110, I l l , 120-121. 497-499. 572 as cyclic ma ch ine. 429. 430 flagellum 14 1. 147- 148.185. 192.537 mec han ism, 427 Einstein relatio n. 120 , 140, 191, 260, 419 prod uct , 403 bacteri al, 37, 40, 54, 175-177,406 , 489. 498, elastic respon se. 189. 343- 344 pro teol ytic, 337 570 elast ic rod model, sec po lyme r reactio n velocity, 403, 426, 434-436. 57 1 electric curr en t. St'C cu rren t substra te, 403 size o f, 570 electr ic doub le layer, 262 ep igl'net ics.63 eukaryo tic, 45, 570 electric field . 29 eq ui libratio n. 86 , 88 flashing ratchet, 463 electroc he mica l po ten tial, 297. 474, 479, 489 . equilib rium flavin ad enine d inucleo tide, see FAD che mical, 295. 300. 307 Flem min g, Walther, 93 49 1, 492, 495, 497 co m pkx.306 Flor y, Pau l. 292 grad ien t of, 482 Donnan, see Do nna n equilibrium Ilucruarion-d issipation theorem . 147 e1ectroosmot ic.476 lluid electrogenic ion pum p, seeion pu mp hydro static. 256 com plex, 384 mech an ical, 305 Ne....-tonian, 164 , 166. 344, 384 electrolyte, 269. 285. 297 therm al, 87, 199-209,220,305 e1ectronegativity. 308 equ ilibriu m cons tant, 302 , 304, 460 isotropi c. 164. 384 elect ro n volt (u nit). 485. 566 transfo rm ed , 305 viscous crit ical force o f. 165 elec t ro pho resis, 3 13. 3 14. 336. 338. 399. 400. 406 !lu x elect rop ho ret ic flux. 139 of electric charge, 23, 480 elect ro physiology, 507, 508 electrophoretic . D s electros tatic po tent ial, 29. 266 number, 23, 130 Fokker- Planck equa tion, 455

594 Index forc.:, 28 Galvani, Luigi, 470 mechan ica l equ ivalen t o f, 7, 8, 3 1 buoyant. 5« buoyant force Gamow, Geo rge, 18 of vaporizatio n, 33, 291, 57 1 chemical, we chemical force Gau ssian cu rvatu re, 385 heavy water (HTO) , 157 damp, 439 Gaussian di stribution, we probabilit y helicase, 452 critical, sa critical force helix-ceil tra nsitio n, 364-374, 394, 3% den sit y, 256 di stribution helix-exte nsion paramete rs, 368 electrostatic , 29 Gau ssian model o f pol ymer, seepol ymer Helmholtz , Herma nn von, 7 ent rai ning, 164 , 187 Gau ss Law, 263-264, 266, 267, 473 Helmholtz free energy, 5« free energy hemog lob in , 51, 290, 328, 376-380 enrropic, see entrop ic force at a surface, 263 , 264 sickle-cell , 3 13, 3 14, 329, 338 gene ral form, 284 Heslo t, Fran cois, 375 mech an ical, 245 in bu lk, 264 hereropolyrner, 389 Gay-Lussac, Jo seph -Lou is, 25 heterozygo us genotype, 91 pro to n mot ive, seepro tc n motive force gene , 59, 93- 101 H ill, Archibald, 377 viscous, seeviscous force genome, 59, 60 , 63, 3 11, 327, 373 Hille, Ber til, 539 bacterial, 570 Hiro kawa, Nob u taka, 446, 46 1 Fourie r's law o f cond uct ion, 149 fly, 95 h istidi ne, 48 Franklin, Benjam in, 6, 23, 24, 33, 3 17, 469 HIV, 153 h istone, 43 Fran klin , Rosali nd, 10 1 h u man, 570 HIV (hu m an immu nod eficiency virus ), 37, 63, free energy, 8-15, 210-217, 243, 245, 250, 294, lambd a pha ge, 342 m itocho nd rial,497 153, 466 306, 309, 386 rep air, 97 prot ease enz yme , 430 of alpha hel ix for mat ion , 366-369, 397 genotype, 90 reverse t ra nscrip rase, 573 and chemical drive.403. 423 ger m cell, 39, 59, 9 1 Ho, Davi d, 153 and che mical po tential, 30 Gibbs d istr ib utio n , 298 Hod gkin , Alan, 482 , 483, 505, 52 1- 523, 526, an d cyclic reactio n, 429 Gibbs-Donnan relatio ns, 475, 477, 51 1 an d depletio n in teract ion , 25 1- 254, 291 Gibbs free ene rgy, seefree energy, 225 532- 534, 536, 537, SolO, S44, 554-556 an d Donnan eq uilibr iu m . 476 glob ular protein, we protein homodimer, 438 and enrropic forces, 246, 251 glucose, 46 homopolymer, 389 and ion pumping, 482. 485, 496 glutamic acid, 3 11, 313 homozygou s and pol ymer stre tchin g. 348-350 glycoge n, 5 1 and protein folding, 328-330 glycolysis, 38, 432, 488 , 490, Color Figure 5 genotype , 91 an d respi ration. 491, 492 glycosylation. 408 Hoo ke rela tio n , 17 1, 239, 240, 326, 336, 343, and su rface tensio n, 317 Golgi, Cam illo, S45 and t ra nsitio ns of two -state syste ms, 225, 227, Golgi appa rat us, 41 \"6 Gou y-Chapman laye r, 268, 270 457 grade d respo nse, 507 , 518 Hud speth , A. Jam es, 241, 244 of AT P hyd rolysis, 442, 447,465,484,486, grad ient, 149 Huggins, Mau rice, 274 grand canon ical d ist ribu tion , 298 h um iliatio n , 245 495, 570 gra nd parti tio n fu nct io n, 298 Huxley, Andrew, 50S, 52 1, 522, 526, 532 -534, bilayer ben di ng, 32S--327 gra nd po tent ial, 338 cha nge, seestandard free energy change 536, 537, 540, 544, 555 cha nge fo r B- to Z- DN A, 399 G -rat chet , see rat chet hyd rated io n, 305, 539 co unterio ns, 269, 272, 280, 2116-288, 475 hyd ra ulic perm eab ility, see filtr at io n coefficient density, 238 gr avity hyd rodynam ic resistance. Tgl of fo rrnatic n. 304 acceleration o f, 4, 20, 160, 249, 573 hydrodyn am ic scaling invar-iance, 188 G ibbs, 212, 237, 301, 302 ar ti ficial, 190 hydroge n bo nd , 47, 53, 273-280, 291, 342, 364 , Helmh oltz, 211, 300 force du e to, 3 1, 80, 118, 139, 158, 237, 255, hyd rop hobic solvat io n, 276-280, 323, 493 273, 409 367 idea l gas, 247 makes elephan ts fall, 158 d irect ion ality, 288 la nd sca pe, 421, 422, 429, 433, 447,456-458, poten tial energy d ue to, 5« en ergy, pote nt ial length, 569 sedimentation equ ilibrium d ue to, 159 st rengt h, 275, 276, 57 1 seealsoenergy lan dscape hydro lysis, 26, 48, 467 an d che m ical react ion s, 424, 425 ground state, 335 ATP, 484, 494 , we a/so free energy of ATP an d enzyme catal ysis, 425-430 GT P, 46, 452, 490, 492 o ne-d imens io nal, 432, 437 guanine, 46 hyd rolysis single-head ed kinesia. 446 guanosine t riph osp hate, 5« GT P futile , we fut ile hydrol ysis two-dim ensional, 424, 431, 437 hydron ium ion, 305 two-headed kinesin, 446 Hackn ey, Dav id, 441 hyd rophob ic effect , 278-280, 289, 315-319, 324, microsco pic system , 223-224 Haeckel, Ernst, 93 of po lar solvation, 305, 308 Hagen- Poiseuille relat ion. 181, 259 328 - 3 32 , 3 74 tr an sduct io n , 12- 15, 100, 216, 255, 308, 348, hairp in , 227, 228 Haldan e, John B. S., 426 hyd rostatic equ ilibrium, see equ ilibriu m 40 1-404, 410, 451, 452, 487, 496 Haiohacterium salinarium, 497 freely jointed chai n, 5« polyme r ha nd -o ver-han d mo del, 438 hydroxyl gro up , 309 free radical , 99 Hau rowitz , Felix, 379 hyperpo larizat io n , 507 , 508 Fricke, Hugo, 470 hypersphere , area, 234 frictio n, 4-9, 22, 89 Pi-bond, sechyd rogen bond ice, 274, 275, 288, 363 coefficient, visco us, 119 , 139, 161, 188, 3 12, head group, 49 idea l gas law, 27, 78, 80-82, 109, 110, 120, 209, 355, 356, 419 heart , 19 1, 503 heat , 4- 15 2 15,246-249,255, 537 in tram o lecu lar, 458 inactivation , 539, 54 1, 543, 544 fumarase, 404, 426 an d molecu lar mo tio n, 69, 120 lnexten sible rod , 346, 354, 36 1 fun gi, 40, 42 co nd uction , 149, seeth er mal cond uct ion inflect ion po int , 133, 143, 376 futile hyd rolysis, 459 engi ne, 2 14-2 17, 350 info rm atio n co nten t, 232 in hibition Gcactin , we act in , glob ular Gcproreins, 45 1 co mpetit ive, 437, 466, 548 no nco m pet itive, 437, 466, 467 uncornpetitive. aee

ini tiat io n pa ramete r, 369 lamb da p hage, 342 , 35 1, 355 Index 595 ino rgan ic p hos ph ate , 46 , 48 lamellipod ia, 44, 54, 407 insu lin, 64 lami nar flow, 163, 165- 168, 179, 180, 191 Mic haelis-Menten rule, 435-440, 445, 446. 460, integral memb ran e p rote in, 5&-58, 325 Langevi n, Pau l, 155 466 integra te-a nd -fire model, 548 Langevin fu nctio n, 243 in ten sive q uan tity, 205 Laplace's fo rm ula, 25 1 Michaelis constan t, 434 intermedia te filame nt , 572 LeChatelier's Pri nciple, 289, 305, 336, 367, m icrosco p ic systems, 2 17 in terna l co nstr a int, 206 m icrostate, 199 invertase, 467 37. m icro tub ule, 54-58, 3 15, 329, 368, 379, 406-409, ion , 39, 98, 139, seeabo colon, countenon ion channel, 17, 57, 499,501,536 lecith in, 3 16, 332 443,447, 452, Co lo r Figu res I , 3, and 4 Lehn inger, Albe rt, 489 diameter of, 570, 572 co nduct ance, 555 Leibnitz, Go ttfried, 4 mic rov illi, 45, 54 ligand-ga ted , 54- 3, 544, 547, 549 Levinthal, Cyru s, 182 midpoint tem per atu re, 368 voltage-ga ted, 506, 527-549, 573 Le....i s. Gilbert, 274 mil k, 159, 16 1,192,330,337 ionopho re, 498 , 499 m iJIime terof mercury, or m m of Hg [unit ], 567 ion product of water, 309 ligand-gated ion chan nel, we ion cha nnel Mirsky, A. E., 328 ion pump, 17, 56, 59, 402, 45 1, 482, 483, 502, M iss Muffet, 330 ligase , 399 Mitch ell, Pete r, 491 504,511 linear cab le equation, seecable equation mitocondrion, 4Q-4 2, 57, 407, 489, 494 calciu m, 497 Lineweave r-Burk plot , 435, 436, 440 geno me, 497 electrogenic, 484 linked gene s, 93-95,104 mitosis. 39, 43, 92, 315, 452 ncnelectrogeni c.us-t linking numbe r, 399, 400 MM rul e, seeMich aelis-Men ten ru le proto n, 477 , 497 Liou ville's theorem, 235 mo bility, electropho ret ic, 3 14 sodium-calcium exchanger, 497 lipid b ilayer, 57 m o d u l us sodium-potassium, 57,48 1,484,485, 502, Lis/rna mOIlOC)'/ogrrlt'$, 408, 409 b ulk, 342 lite r (u nit) , 566 she ar, 171, 342 503,5 10, 5 11, 553 liverwu rst, 356 mo lar (u nit) , 250 , 297, 567 Iso, K., 366, 394, 396 lo llipo ps , 494 mo lar m ass, 25 isoelec tric po in t, 3 13 lym phocy te, 36 mo le (un it) , 24, 30, 567 iso me rization , 25, 22 1, 299, 30 1, 337, 423, 460 lysine, 3 1I mo lecular crowd ing, 251 isotope, 30 lysis, 251 , 476 mo lecular d evice, 402 isot ropy lysozyme, 569 mo lecu lar machine, 402 molecular moto r, 14, 175,379, 402, 404-409, o f a flu id , 164, 384 ma ch ine o f a n elastic rod , 387 cyclic, 214. 402, 404-407, 429 43 1-432,437-45 1 o ne-s hot, 402 . 407-409, 4 15 mo me ntu m , 28 Janssen s, Frans-Alfons, 94 osmotic, sec os m otic mach ine mon olaye r, 23, 3 16 monom er, 100 jou le (unit], 19, 566 Macki nn o n , Rod erick , 540 mo nom er ic fo rm of a protein, 407 Jou le, James, 7, 31 macro ion, 26 1-263, 309-313, 477 mo nova lent ion . 265, 47 1 macro mo lecul e, 100, 474 Mo rgan , Tho ma s H. , 93, 104 Katz, Ber na rd, 482, 483, 505, 522, 523, 532, 537, macroscop ic system , 236 most p rob able value, 74, 84 554 magneti sm, 359 mo tilit y assay. 404, 406, 438, 439, Co lor Figur e 4 ma gneti zat ion , 240 mo tor , see molecul ar mot or Kauzr uann, Walter, 280, 289, 328 Maier, Bcrenlk e, 125 m RNA, secRNA, m essenger Kelvin, see Th omson, Will iam Marko . jo hn, 390, 392 Muller, Herm a nn . 95-98, 100, 104 , 105, 469 Kelvin scale, 205 Ma rmout, George, 532, 534 mu ltip licatio n rul e, 76, 84, 85, 115, 143, 223, 387 Kenn ed y, Eugen e, 489 Mass Act io n, 304-3 11, 3 19, 336, 376 mu lt iplicity, 225 kern el,390 mat rix, 356, 390 multis table be havior, 423 Keynes, Richard, 482 muscle fibe r, 405 KIFIA, sec ki nesin, sing le-heade d of m itocho nd rio n , 42, 57, 489 mu tagenesis, 97-99 kine matic viscosity, 187, 19 1 sym me t ric, 357 mutat io n, 63, 92 tran sfer, 360 Mycoplasma genitillium , 60 kincsin. 56, 58, 402, 406 , 43 1,437-451, Colo r matrix p rod uct , 358 , 391 myelin sheath , 506 max imum velocity, o f enzy me, 434 myofibril, 36, 40 5, 464, 570 Figu res 1 and 3 Maxwell, James Cle rk, 84, 121, 148,2 10 myo globin, 65, 159, 160,37&-38 1 allo steric cha nge, 379 McBain , Ja mes, 3 18 myosi n, 38, 64, 404-406, 452, 464, 547 fami ly, 406 McClintock, Barba ra, 95 neck linker doma in, 379 mea n, 73 fam ily, 406 sing le-headed, 446-45 1, Color Figu re 4 mean-field approximation, 265, 266, 292, 359 kine tic energy, 28 mea n cu rva ture, 385 NAD (n icot inam ide ad en ine d inu cleotid e), 489, kink, 519 mechan ical equ ivalen t of heat , see heat 490 , 493 Kinosita , lr., Kazuhi ko. 495 mechanoch emical cou pling, 375, 380, 43 1 Kirchoff's first law. 5 10, 5 11, 513 me iosis, 39, 9 1-94, 104 na tive con form atio n, 328 , 33 1, 380, 38 1 Koltwff, Nikola i, 96 membrane Navier-Sto kes equat ion, 188 Krame rs, Hendnk. 359, 458 bilaye r, seebila yer membrane neck linker, 379-380, 441 , 44 3 Kratk y-Porod model, seepo lymer, elastic rod pe rmeability, seebila yer membra ne Neher. Erwin, 537 semipermeable , 13, 248, 249, 252, 255. 257, Nemst-Planc k form ula, 140 , 142, 160,4 18 model Nerns t relatio n , 140, 141, 159, 220, 221,297, Krebs cycle, 404 , 490-492 259,260, 284 Kufflee, Stephe n, 547 Mendel, Grego r, 90 47Q-4 74, 480, 486, 5 14 Kuhn length, 347 messenger RNA, set RNA neurofilamen t,572 metabolism , 3 1. 39 neu ro m uscul ar ju nct ion, 547, 570 lacto glo bulin, 330 micelle, 3 1&-321, 325, 330, 377 n euron, 36, 43, 44 , 128, 505 lacto se permease, 497 Lagrange multiplier, 232 all- ot -no thi ng respo nse, 508

596 Index neuro n doctrine, 545 gra nd, 298 po lym er, 50, 100, 122 neu roto xin, 482 par tial, 225 elasticity, 348 neu ro tran smitter, 39, 42,1 33,154, 543- 549 pa scal (un it) , 80, 566 clastic rod model , 346 , 355, 361, 385-393, ne utr al p H, 310 passive spread. 507, 518, 531 397- 3 99 Newlo n's law of cooling, 149 Pasteu r, l o u is, 25 extensible, 362 newton (unit] , 19, SM pa tch d amp, 537-540 freely jo inte d chain model (FIe) , 122, Newto n. Isaac, 4, 8, 164, 185 Pau ling, l inu s, 17, 3 13, 3 14, 338.4 30 347-348, 355, 358, 36 1, 386-389, 396 Newt o nian fluid , su fluid PC, sa phosp ha tid ylchol ine Gaussian model , 144, 151 n icot inam id e ade n ine d inu cleo tide, seeNAlJ Peeler numbe r, 178 on e-d imensi o nal coo pe rative chai n model, 1100(', of a reaction graph. 423 PEG ( po lyethylene glycol), 254 355, 359 non -Newtonian fluid , secflu id, com ple x pen icillin,498 non competitive inhi bition , see inhi bitio n pep tid e bo nd , 48, 467 semil1exible, s« semi l1exib le po lyme r non ergod ic be havior, 233 peptid oglycan layer, 54, 176, 452 non linear cable eq uatio n. S{!( cable eq uation Perelsnn, Alan, 153 poly me rase no npolar mole cule , 273, 278, 279, 289, 309 DNA, 59, 65, 183, 184, 407, 452,573 no rma lization con dition perfect ratche t, secratche t RNA, 60, 407, 452, 569, 573, Co lo r Figur e 6 co nti nuo us d istr ibuti on . 72 pe riphe ral membrane prote in , 56 polynudcotidcs.S n di screte di str ibu tion . 7 1 pcriplasrnic space. 176 po lypeptide, 48, 50. 6 1 no -slip bou nd ar y co nd itio n, 169. 180 permeability, 135- 138, 156, 283, sec alsob ilayer polysaccharides, 51 NT P,46 polytene ch ro mo some, see ch romosome NT P ( nucleoside tr iph o spha te ), 46, 6 1 memb rane po rtal mot o r, 452 nuclear pore . 41 hydrau lic, sa filtra tio n coefficient pos tsyna pt ic neuron , 54 5 Nudeic Acid Databa se. 65 per meabil ity mat rix, 283 pote ntial energy,$('t ene rgy nuclooid, 37 pe rmeatio n, 156, SOl po te ntial of m ean force, 458 nucleoside triphosphate. sec NTP permittivity, 21, 29, 26 1, 263. 273. 569 po wer st roke, 09, 448 nucleosome, 43, 50, 65 ,570 Per rin, Jean , 112, 121. 155 PP;, sa pyrop ho spha te nucleotid e, 46 , 6 1 persistence len gth pressu re, 28, 79, 2 12 nucleus, 40 bend, 346-348, 386 presynap t ic neu ro n . 545 numbe r-averaged chain length, 394 twist, 346 primary str uct u re, 50, 33 1 num ber de nsit y, 22 Pa ut z, Max, 17, 378 primordial so up, 307 nu mber flux, 23 Pfetfer, Wilhelm , 290 pr ion , 63. 233 p H, 309-3 15. 328, 330, 338, 408 proba bil ity, 70 odd fu nct ion, 37 1 and l1agellar mot or , 497 probabil ity de nsity. 71 Od ijk, Th eo, 362 a nd ox id ative p hos pho rylat ion. 493 proba bil ity dis t ribut io n. 447 O hm 's law, 29, 142, ISO, 18 1, 187,480. 482 illustra tive values, 573 o hm (u nit) , 566 neut ral, 310 binomial, 1I 3,1 51 O hm ic hypot hesis, 480-482. 486, 504, 510, 512, wate r, 3 10, 337 Boltzman n, 82-85, 88, 89, 106, 144, 147, p hage , 35, 37 5 14, 524, 527 p hase tr an sit ion , 363 218-224, 247, 258, 293, 369, 387, 389 Okada, Yasushi, 440, 40 1 p heno me no logica l parame ter s, 343 and Nerns t relation , 14 1, 474 o ligoden d roglia. 44 ph eno type, 90 an d Po isso n equat io n, 266, 267, 284 one-shot action pote nti al m odel . 52 1, 527-532 p he nylalan ine, 52 in ratchet, 419 o ne -shot ma ch ine. $ce mach ine p ho sph atid ylcholine 65, 137, 310, 323 co n tinuo us, 7 1-73 O nsager, Lars. 284 phos phoglycerate kinase, 432, Color Figure 5 di me nsion s of, 71 Oosawa, Furnio, 25 1 phos pholipid, 49, 55, 3 \\ 5, 316, 3H-326, 332, d iscrete, 70-7\\ open the rmody nam ic system, 210 Gau ssian, 72-73, 127 o ptical ro tatio n. 364-369, 393 Colo r Figure 2 Gibbs, 298 opt ical tweezer, 226, 35 1, 404, 406. 438, 439 ph ot on , 26, 105 in Dcratchct . 448 o rganel le. 40. 327 physical Law, 184 u nifor m . 72 p K, 302, 310-3 14. 338 p rocess, of a cell, 44 tran spo rt of, 452 p rocessivity. 438 o smor egu latio n, 478 . 496 deprotonation o f am ino ac id s, 573 p rod uct, o f enzym e, 403 os moti c 110w, 12. 13, 207,249,257.259. 283 illust rativ e values, 573 p roka ryotes . 40 osm ot ic mach ine , 13, 14. 249. 299. 306 , 402, 4 14 Planck, Max, 1411 proltne. a t i osmot ic p ressu re, 248-2 60. 318. 3 19, 476 Planckconstant , 26, 148, 20 I, 234 pron uclei.vd osteoblast, 44 plasm alemma, 503 propagation parameter, 368 o ubain. 503, 512 plasma membrane, 40. 55-58. 327 p rosthetic grou p. 403 oxidation, 487 plasmid. 400 protease in hibi to r, 430, 466 oxid ative ph osph o rylat ion , 489, 492-494 po ise (u nit), 16 1, 567 protei n, 39. SO, 6 1 po ison da rt frog . 539 foldi ng, 328 Pi' sa ino rga nic pho sph ate Poisson- Boltzma nn equ atio n, 267-270, glob ula r, SO, 124, 2SO,254, 29 1 p.m.f see pro ton mo t ive force regula to ry, 59 Painter, T heophilus, 96 284- 2 87 repressor, 59, Co lo r Figure 6 palm itic acid, 48 bou nda ry co nd ition, 267, 268 size o f, 569 pancreatic carboxypept idase , 435. 436 Poisson eq uatio n , 266, 267 syn thesis, 48 Paramecium, 175 po larimeter, 365 Prot ein Data Ban k, 64 part ition coe fficient , 137, 324. 50 I po lar ity, o f a m icro tubu le, 441 . 444 , 447 proton, 46 part ition fun ction , 224, 243, 360, 390 polarizable mediu m , 273 cha rge o n, 569 pol arized light, $('1' op tical rotation p rotonared form of a residu e, 3 11 and ent rop ic forc es, 246-249, 352, 353, 359 pol ar m olecule. 273 . 279, 280. 309 p rotonmcnve force, 49 1, 498 and t ransfe r m atri x, 360, 369, 372, 390 po lydi spe rsh y, 317. 370, 394 pseudo-first -o rde r rate consta n t, 460 po lyelectrolyt e, 396 pseudopodia, 44 , 407 po lyethylene glycol. see PEG

Index 597 pseudoscalar, 385 charged , 31 1, 3 14. 329. 331 semipe rmeable me mb rane . see me mbrane p ump. 5ec ion pu m p hyd rop hob ic, 328. 331 septat io n, 498 pure nu mbe r, 19 protonated and deprotonated fo rms. 3 11, 312 seru m albumi n, 124 purines. 46 resistance Shan no n's formula, 197, 224 Pu rki nje cell. 546 electrical. 142 Shaw. T. I., 536 py ra m ida l cell, 546 hydro d ynam ic. 181 py rim id ines. 46 resistivity, 554 shear. 163. 164 pyrop ho sph at e. 48 respiration , 486 . 491 shea r modulus, see mod ulu s pyr uvate. 488 resting po tent ial. 39. 476-477, 48~ 86. 504. shear strain. 5('1.'strain pyr uvate deh yd rogenase, 38, 490 shear stress. 172 507, 51D-5 12. 554 sickle-odl anem ia, 313, 3 14, 329 quasi- steady state. 135,433, 434.460 , 479. 512. and hyperpolarization. 508, 509 sid e group. 48, 53, 311 reverse os mo sis, 13, 14.257,259,260 siem ens (un it), 480 . 566 srs Reynolds. Osbo rne , 168 Siggia, Eric, 390. 392 Reynolds num be r. 166. 168, 188 sigmo id. 370 , 374. 376 q uasist atic proc ess. 215 cr itical, 11l1l Silverm an , Michael. 176 q uatern ary struc ture, 51, 379 ribonu clease, 313 Simon, Melvin . 176 ribose, 46 site-di rected mutagenesis, 329 Racker, Efraim, 493, 494 ribosom e, 38. 52, 6 1. 252. 403 . 452. 570 Si u nits, I 8 radi a n (u nit) , 567 ribozy me, 65. 403 Ritz variati on al app roximat ion , 39 1. 398 Skou , lens. 483 rad ius of gyration . 124. 126, 148 RMS deviat io n , we deviat ion slime mold. 549 Rad ler, Joach im , 125 RNA,50 Ramo n y Cajal , Santi ago, 545. 546 ed it ing. 63 slippi ng.41 1--413 rando m coil. 122-1 26. 16 1, 192.396 fold ing an d unfoldi ng. 52. 226-229 Sm ith , Steve n, 35 1 random walk. I J0- 117 messenger (m RNA), 60, 6 1, 252. 452 Smoluc howski, Marian Ritter von , 455 polymerase. we po lymerase Smcluchows kl equatio n, 4 19-422, 433, 447, 458 on e-d imen siona l. I J6 transfer (tRNA), 38, 52. 61, 65, 452 sod iu m an om aly, 477 room temperat ure, 205 sodium-calcium exchanger, 497 po lymer co nfo rmatio n as. see ran dom coi l rubbe r, 34R-350, 396 rumes.44 sodium channel. see ion channel. voltage-gated rota tiona l. 156 self-avoiding, 124, 125,292-293 Rumford, sec Thompson, Benjamin sod ium dod ecyl sulfate . 5« SDS three -dimemional, 122, 124, 388--389 sod iu m- po tassium pu mp, see io n p u mp two- d ime ns iona l. I l l , 112. 155 SdccharomY«$ «rrvisitt', 40 with dr ift , 117, 119, 178 Saito, Nobuhiko. 390 soft condensed matter, 385 rap id isomerizatio n , 444. 460 Sakmann. Bert. 537 so lar energy. see energy RasMo l. 64 Sakur-Tet rod e formu la, 201, 203, 205. 209. 212, ratch et solub ility, 276, 278 d iffusing t o -ratchet). 446-451 . 46 1--463. 502 2 14.233 F-, 465 sarco me re, 405 solubilizatio n o f mem b ran e prot ein s, 325, 329. Gilbe rt 's (G-ratehet) , 4 13--416. 419 per fect, 417--421. 433, 438 satura t ion kinetics. 404. 422. 429. seealso m Sullivan's {Sv rarchet},414-423, 432, 444 ra te-coding scheme, 548 catal ysis solu tio n rate -limiting process, 307 sauce bea maise, 317 rate constant , 22 1, 306 scalar qua ntit y, 345 aq ueo us. 297 pseud o-fi rst -o rder.aeo scale height. 159, 160 entro py of. 210 react ion coo rdinat e, 424. 425 scaling exponent. 123-125,148, 16 1 react ion diag ra m, 222, 434 solvation , hyd rophobic, 278. 289, SCI.' also free fully co nnected, 424 allo me tri c, 149 en erg y o f hydrophobic solvation spa rsely co n nec ted. 423, 424 Sche llmall , John. 366 reacti on quotient , 302. 444 Sch nitzer. Mark , 437 so ma, « , 546 reaction velocity. seeenzy me Schrcdlngcr. Erwi n. 89. 97 recepto r, 56 Schwen n cell. 44 somatic cell, 43. 9 1 recipr ocal mot io n, 174 SOS (sod iu m dcdecyl sulfate), 315-318, 323. 329 span' damp, 532- 533 reco mb ina tion. 94 seco nd ary struct u re, 50 space constant, of axon , 517 rect ificati o n Second Law, 9- 10, 28, 162, 185, 206-210, 216. o f elect ric cu rre n t. 50 I spasrnonerne, 179 o f rando m motion , 255-259, 4011, 4 J5, 465, 239. 348. 4 14. specific op tical rotatio n, seeopt ical rotation and dir ection of che m ical reactions, 299- 302 spl'ctrin, 58 502 a nd machine efficiency. 217 sper m. 36 red blood cell, 36, 5 1. 58, 59, 157, 240, 241. 250. a nd oil-water sepa ratio n. 273 sp herocytosis. 478 a nd open systems. 211-2 14 sp ring, po tenti al energy of. 5« energy, po tentia l 25 1, 28 1,3 13,324,376, 478, 570. 572 and ratchet s, -tl S, 465 squid \"giant\" axon, 5« axon red uctio n, 487 as LeChatcher's Principle, 305 S-ratc het, we ratchet reference concent ration. 296 . 302. 303 second o rder rate law. 307 secre tor y vesicle. SCI.'vesicle stack ing, 5« un stackin g of DNA bases speci al biochem ical co nventio ns. 304 sed imentat ion. 190 standa rd chemical po tentia l, 297, 304 refracto ry pe riod, 509, 521 sedim entat ion t ime scale, 123, 160 regu lato ry protein, see prot ein scff-assembly , 56, 254 , 280, 3 15- 330. Co lor standard free ene rgy change, 30. 303-305, 445. relaxation to eq uilibrium , 136. 222, 38 1, 543, 4 91 Figure 2 544 seff-avoid ing walk, 5« random walk tr ans formed . 305 rep lication, 5« ONA self-lim iting property, 52 1 statistical fluct uation . 132. 217 repressor pro tein , see protein serniflexiblc polymer, 348 Statistical Postulate, 199-203. 209-210, 218, res idue , 48 , 53, 61, 263. 31 1. 327, 376, 397, 435. 232-235 467 stat istical system. 232 isolated , 200 Staud inger, Her man n. 100 steady state. 32, 138, 4 17. 467,479,48 1. 485, 504 , 511,512,528 Stefan-Boltzma n n constant, 32, 569 ste reoc ilia, 241-243 ste reospecific bind ing , 263. 441 Stir ling's form ula, 113. 197

......l. j ;; ; ~~~ \"'~ ··\" !5 98~< lridex _,.~\\ \"6 : • Stoeckeni'U~, ' \\'alther.493 to rsio nal sp ring co nstant. 399 wate r, 16 1 stoic hiome tric coe fficie n ts, 303 tors io nal stress, set st ress tr ait. genet ic. 90 visco us critica l force. see critica l fo rce Stokes fo rmula, 119 , 16 1, 187. 19 1.3 12 t ra nsc rip l,60 visco us d rag, 187, 439, 49 5 \" str ain , shl;d{ \\ 72;' 192 t ra nsc rip tion, see DN A visco us force rul e. 164, 17 1. 192, 344 , 384 \" '. . _-- ' ',;> t ra nsfer matrix, 360 general geo metr y, 194 • st ~ess ~ .' ,'-: ' ..r tr ansfe r RNA, see RNA viscous friction coefficien t, see friction shear, 172 , tr ans it ion sta te, 424-427, 459 coeffici en t to rsiona l, 399-400 ana log , 430 viscous res po n se, 189 translatio n, 6Q-6 3, 25 2 Vissch er. Koen , 437 st retch , 345, 346 tr ansloc atio n vitalism , 10 Vologods kii, Alexan d er. 390 st retc h modulus o f bi layer, 572 o f io ns, 484 volt (u n it ), 566 of macro mo lec ules, 407. 408. 41 4 Vo h a, Alessa ndro, 470 stre tch stiffness, 346, 362 tr an spo sable ele me nt , 95 voltage-gated io n cha nnel, see ion chan nel t raveling wave. 134. 135 , 5 18-52 1. 524, 530 voltage-gat ing hypothesis, 527- 53 1, 536, 540 Sturtev ant , Alfred . 94, 104 t ricar bo xylic aci d cycle. set Kreb s cycle triglyceride, SO simp lified. 526, 534 sub state, see co nforma tional substate tritium, 30, 157 voltage cla mp. 498, 499 , 533. 535 IRNA. see RNA volume Bo w ra te. 22 subs trate, o f enzym e, 403 tubulin, see m icro tubul e volume flux, 18 1 sucrose, 46 tu rb ule nce, 18 1 volume fract io n. 192.250. 253 su pe rcoiling,399 tur b ulen t flow, 163. 165 vo n Haller, Alb rech t, 470 turnover nu mber. 40 4, 57 1 vo n Tsche r mak, Er ich, 93 superpo sition pro pe rt y, 5 18 tweezer, optical, seeoptical tweezer twist density, 345 wait ing ti me, sa dwelltime su rface attraction , electrostatic, 272 twist stiffness, 346 twist- stretch co u pling . 346 , 385 Walker, John , 495 su rface cha rge d ensily, set charge density two -stat e syste m. 2 19-225 w annie r, G rego ry, 359 wa te r su rface numbe r de nsity. seedensity ult rafi ltration . 14 un its. 18-23 Bjer rum length in. 569 surface repulsio n, elect rostatic, 269 un myelinated axon , S06 d iffu sio n co nstants in, 57 1 unstacking of D NA bases, 330, 374 heat ca pacity o f. 571 su rface tensio n, 33, 250, 279, 327, 363, 57 1 uracil. 46 heat of vapo riza tio n. 57 1 Ussing, Ha ns, 482 numbe r and m ass density o f. 57 1 surfacta n t, 3 15. 3 16 permeab ilit y o f mem bra nes 10, 572 vacuole, 4 1, 42. 503 per mitt ivity of. 569 Sutt on , Walter, 93 valence. 474 , 563 pH of. 3 10.573 val ine, 48, 3 13 size of mo lecu le. 569 svedbe rg (u n it) , 160, 566 van Benede n, Edoua rd , 93 sur face ten sio n o f, 57 1 va n der Waals att ract io n , 289. 374 thermal co nd uct ivity o f. 57 1 symport, 497 viscos ity, 571 st rength o f. 275, 57 1 wa terston, Joh n. 33 synapse , 43, 44 , 545. 547 va n ' I Ho ff. Jacobus. 290 Watson . James, 18. 47, 50,10 1 va n ' t Ho ff relatio n, 249 . 258, 259 , 266, 29 1, 318 , watt [un it}, 566 excitat o ry a nd in h ibitory, S-48 weak ac id . 3 10 31. weight -averaged chain length, 394 synapt ic cleft , 545 , 546-548, 570 varia nce, 74 white blood cell. 36 vascul ar network. 179 Wilkin s, Mau rice, 17 synapt ic vesicle, s« vesicle velocity o f catalyzed react io n. wee nzyme work. 7. 28 ves icle, 42, 56. 253, 269 , 323, 325, 327. 406 , 493 wo rmlike chain model, set po lyme r. elasric rod syn th ase, 40 2 sec relo ry. 42 model Taylo r. Geoffrey, 162 synaptic , 42, 58. 133, 546-548 Wu. Hsie n, 328 temperature. 80, 202-206, 235 fusion , 43. 547 X-ray mutagenesis. seem utagenesis m id po int. see m id po int tem pe ratu re virus, 38 roo m , see room tem perat u re yeast, 36. 4Q-4 2 tensio n, su rfa ce, see surfa ce tensio n H IV. see H IV yog ur t, 330 tert iary st ru ct ure, 50 p hag e, 37 Yos h ida, M nsasuke, 495 tctr ame r, 377 size, 570 ther mal co nduc t io n, 149, 187, 200, 202 viscoelas tic ma ter ial, 189 Ze h ran, K.. 482 th ermal eq u ilibrium, see equ ilib riu m viscosit y, 119, 16 1- 164 , 194 Ze roth Law. 203, 206. 2 11. 2 18 th ermal rese rvoi r, 2 11 illu strative val ues. 165. 57 1 zeroth o rde r rate law. 307 the rmody na mica lly co nju gate variables, 283 int rinsic. o f a po lym er. 192. 193 Zimm, Br un o, 366, 394 th eta so lvent , 148, 192, 193 polymer sol ution. 192 Thom pso n , Benjamin (Co u nt Ru m fo rd ), 6. 3 1 Th o mson, William (Lord Kelvin ), 206 th reshold st im ulus, 509, 518 . 520, 529, 53 1. S49 thrombin , 64 thym ine. 46 tigh t co upl ing, 431. 432, 437. 438 , 449, 483 ti me co nstan t, o f axon, 5 17 nme reversel. jes- tzz Tim ofee ff Nikolai, 98, 100, 105 tip lin k, 242, 243 titin , 375 titra tion , 312 to noplast, 503 to po iso m er, 399 , 400 tc poiso rnerase, 184 to po logical invariant, 399 tor qu e. 28 tors ion al deformatio n . set deformation