478 INDEX
Alkali metals (Na+, K+): see also Na+/K+
ATPase and potassium (K+) ion
channels
biological functions, 1, 2t, 4t, 6, 7t, 9,
9t, 44, 190, 192, 197t
Ca2+-ATPase and, 329, 336
coordination geometry, 2t, 4t, 9, 9t
facilitated diffusion and, 197–199,
198f
homeostasis, 189–190, 192, 193–200,
198f
kinetics, 11t
passive diffusion and, 195–196
thermodynamics, 9t, 193–199
Alkaline earth metals (Mg2+, Ca2+): see
also Ca2+-ATPase, calmodulin,
troponin, ribozymes
biological functions, 2t, 4t, 44, 191,
197, 197t
Ca2+-ATPase and, 44, 95–97, 327–329
calcium-dependent molecules and,
301–302
calmodulin and, 302–326
coordination geometry, 4t
homeostasis, 193, 194–195, 199
ion channels and, 199, 204, 215
matrix metalloproteinase (MMP)
and, 120, 121f
ribozymes and, 238–301, 254f, 256f,
260f
troponin and, 3, 44, 194, 301–302,
306, 338
Allosteric, 44
Allosteric and nonallosteric enzymes,
44–46, 46f
Allosteric Interactions See
cooperativity, hemoglobin,
hemocyanin, R state/T state
Alpha helix, 34–35, 36f, 36t, 37f
Ca2+-ATPase and, 333–334, 337
calmodulin and, 303–308, 305f, 308f,
310 –311, 316, 318–319, 318f,
320–326
cytochrome bc 1 iron sulfur protein
and, 168, 393–394, 394f, 395–396,
402, 406f
cytochrome b(6)f and, 387, 387t
cytochrome c 360 and, 408, 411, 412f,
421
cytochrome c oxidase and, 429
gated channels and, 197
hemoglobin and myoglobin and, 348,
358
lysozyme and, 37–38
matrix metalloproteinase and, 120–
121, 121f
Na+/K+-ATPase and, 201
potassium ion channels and, 209, 212,
215–217, 217f, 218–234, 219f
Rieske protein and, 383
zinc fi ngers and, 63–73, 68f, 70f, 71f
American Chemical Society, 183
AMBER force fi eld, 119, 161, 166, 175,
179 –18 0
Amino Acids, 30–33, 31t, 32t
abbreviations, 31t, 32t
D/L confi guration, 332
essential, 30
structures, 31t, 32t
interactions with metal ions, 32–33,
33t
Amphipathic (amphiphilic), 37, 233,
313, 331, 334, 404
Amplifi cation, 69, 428
Anaerobic bacteria, 24, 455
Anions, 7
β-mercaptoethanol(BME) thiolate,
373
biological phosphorus and, 193
cytochrome P450 models and, 380,
381f
peroxo, 82, 349, 363, 366, 368, 372,
374, 374f, 382, 433, 433–439, 440f,
441–442, 443, 454
porphyrin(s) and, 374, 376, 378, 380
superoxide radical anion, 82, 346,
347f, 349, 363, 364, 371, 396, 428,
435, 440f, 442–443, 440f, 443, 453
trifl ate, 451
Annual Reviews,183
Antibodies, 69, 215, 218, 225, 228–229
Anticodon, 55
Antiferromagnetism:
antiferromagnetic coupling, 17
cytochrome c oxidase and, 461
cytochrome c oxidase models and,
437, 438, 440, 441, 449
hemoglobin and myoglobin and, 348