The Biological Chemistry of the Elements The Inorganic Chemistry of Life

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Format: Hardcover
Pub. Date: 1991-10-24
Publisher(s): Oxford University Press
List Price: $90.66

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Summary

Twenty inorganic elements, mostly metal ions, are consistently found in living systems and are essential for living systems to function correctly. This text discusses, describes and explains the functional relevance of those elements: the reasons for their selection; the processes of theiruptake; transport and final localization in cells; the regulation of these processes; and the interactive network of their reactions that connects the in vivo inorganic elements to the environment and to the genome. The volume has been thoroughly revised for this second edition and includes adiscussion of the link to the genome of the uptake and transfer of inorganic elements and the regulation of homeostasis, the functional co-operative activities of the elements, the interaction with the environment, and the evolution of usage. Recent structural and mechanistic knowledge of manybiomolecules and organelles is also included.

Author Biography

J.J.R. Frausto da Silva is Professor of Analytical Chemistry, Instituto Superior Tecnico de Lisboa, Portugal R.J.P. Williams is Emeritus Professor of Chemistry, University of Oxford

Table of Contents

General introductionp. 1
The chemical and physical factors controlling the elements of life
The chemical elements in biologyp. 7
The element content of living systemsp. 7
An aside: some biological chemistry of hydrogenp. 11
The economical use of resources: abundance and availabilityp. 12
Biological environment and element availabilityp. 15
Sulphide chemistry in water (anaerobes)p. 22
A note on homeostasisp. 24
Survival and evolutionp. 26
Conclusionp. 26
The principles of the uptake and chemical speciation of the elements in biologyp. 29
Introduction to chemical speciationp. 30
The separations that biology can achievep. 33
The selective uptake of metal ionsp. 34
Effective stability constantsp. 38
Element uptake at equilibrium: the selectivity of the uptakep. 39
Hydrolysis: hydroxides and oxenesp. 51
Selective control of oxidation states of metalsp. 53
Selection by control of concentration of M and Lp. 54
Selection by transfer coefficients from water to proteins (or membranes)p. 58
Selection at surfaces and in precipitatesp. 60
The selectivity of channelsp. 61
Kinetic effects and controlp. 62
Rejection of metal ionsp. 66
General aspects of the uptake of essential non-metalsp. 66
Mechanisms of selection of anions based on thermodynamic propertiesp. 68
Redox incorporation of anionsp. 72
Coenzymesp. 74
Precipitates in comparatments: cation and anion cooperativityp. 74
The application of equilibria and equilibrium exchange to carriers, buffers, pumps, enzymes and gene regulationp. 76
Genetic regulation-an introduction to control of ligand (protein) concentrationp. 79
Concluding remarks: element handling in biological systemsp. 80
Physical separations of elements: compartments and zones in biologyp. 83
General aspectsp. 84
The nature of compartmentsp. 85
The chemical solutions and physical states of compartmentsp. 86
The role and nature of membranesp. 89
Different types of membranep. 90
Special solution conditions in vesiclesp. 98
Cooperativity of separations and localizationsp. 100
Summary of metal ion positioningp. 100
Symbiosis and multicellular systemsp. 101
Spatial distribution of bulk non-metalsp. 101
The spatial transfer of H, C, N, S: mobile and fixed coenzymesp. 103
Summary of non-metal transportp. 105
Evolution of compartments and organization: summaryp. 106
Kinetic considerations of chemical reactions, catalysis, and controlp. 108
Introductionp. 108
Chemical transformationsp. 108
The nature of acid-base reactions: hydrolysis and condensationp. 109
The hydrolysis of proteins, RNA, DNA, and other polymersp. 113
The nature of ion flowp. 114
On/off reactions: control systemsp. 117
Electron-transfer reactions: electronicsp. 118
Redox potentials of complexesp. 122
Atom transfer reactionsp. 123
Group transferp. 125
The nature of transition-metal centres in catalysisp. 125
Free radical reactionsp. 127
Sizes of atoms, stereochemistry, and reaction pathsp. 128
The creation of local small spaces: mechanical devices for transfer reactionsp. 130
Networks: kinetic circuitsp. 132
Summaryp. 133
Energy in biological systems and hydrogen biochemistryp. 135
Introductionp. 135
Biological systems and lightp. 136
Oxidative energy: mitochondriap. 139
Proton migration coupled to redox reactionsp. 141
The coupling of gradients to ATP formationp. 142
Anaerobes in the darkp. 144
Compartments, energy, and metabolismp. 147
Organization and tensionp. 148
Motion of organismsp. 148
Local storage of elements and energyp. 148
Primitive sources of energyp. 150
Energy networks and summaryp. 151
The role of biological macromolecules and polymersp. 154
A Proteins and nucleic acidsp. 155
Introductionp. 155
Protein composition and basic structurep. 156
The protein fold and the internal motions in solutionp. 161
The amino-acid composition of specific proteinsp. 164
Structural proteins and mechanical devicesp. 169
Matching of proteins and organic and inorganic ionsp. 170
Enzymesp. 171
States of metal ions in proteinsp. 173
Summary of proteins: the proteomep. 179
Nucleic-acid composition and outline structurep. 180
Metal-ion binding to polynucleotidesp. 182
Nucleic acids and proteinsp. 185
Controlled synthesis and degradation of biopolymersp. 186
Genetic controlp. 186
Summary of genetic control and regulation at 'equilibrium'p. 194
B Polysaccharides and lipidsp. 196
Introductionp. 196
Introduction to polysaccharidesp. 196
The backbones and sidechains of polysaccharidesp. 197
Glycoproteins and cell surface packingp. 198
Interaction of polysaccharides with metal ionsp. 199
Properties of lipidsp. 200
Ion association with lipid surfacesp. 201
Essential fatty acidsp. 202
Summary of biopolymersp. 202
The functional value of the chemical elements in biological systemsp. 206
Introductionp. 206
Major chemical properties of elements in aqueous solutionsp. 208
Biochemical functions of the chemical elementsp. 210
The living processp. 214
The chemical flow in biologyp. 217
The integration of activityp. 224
Conclusionp. 226
The roles of individual elements in biology
Sodium, potassium, and chlorine: osmotic control, electrolytic equilibria, and currents
Introductionp. 231
Passive diffusionp. 232
Gated channelsp. 235
Channel selectivity and possible constructionsp. 236
Active transport: pumpsp. 238
The nature of selective pumpsp. 242
Building electrolytic circuitsp. 242
Simple salts and the conditions of polyelectrolytesp. 245
Enzymes requiring potassiump. 246
Ion genetics and networksp. 246
Summaryp. 248
The biological chemistry of magnesium: phosphate metabolism
Introductionp. 251
The spatial distribution of magnesiump. 251
Magnesium chemistryp. 252
Magnesium pumping in cellsp. 255
Very strong binding of magnesiump. 257
Magnesium in walls and membranesp. 257
Magnesium enzymes: magnesium and phosphatesp. 257
Magnesium and muscle cellsp. 262
Magnesium and polynucleotidesp. 264
Competition with polyaminesp. 265
Polymeric equilibria: tubulins, DNA, and the cell cyclep. 268
Magnesium outside cellsp. 268
Magnesium and lipidsp. 269
Magnesium and chlorophyllp. 269
The use of manganese as a magnesium probep. 272
Interference of other metal ions with Mg[superscript 2+] biochemistryp. 274
Lithium and magnesiump. 274
Evolution and genetics of Mg[superscript 2+] proteins and networksp. 274
Conclusionp. 276
Calcium: controls and triggers
Introductionp. 279
Free calcium ion levelsp. 280
The calcium ionp. 282
Protein ligands for calciump. 284
Magnesium/calcium competitionp. 286
The resting state of calcium in cellsp. 287
Calcium triggering: calmodulinsp. 288
The calcium trigger proteinsp. 289
S-100 proteinsp. 291
Other triggering modes: annexins and C-domainsp. 292
Calcium and protein phosphorylationp. 294
Calcium buffering and calcium transport in cellsp. 295
Calcium currents: movement through membranes, channels, gates, and pumpsp. 296
Calcium exchangersp. 298
Internal calcium-induced proteases: apoptosisp. 298
General remarks concerning control systems in cellsp. 298
Extracytoplasmic calcium in vesiclesp. 300
Extracellular calcium in circulating fluidsp. 301
Calcium proteins of biomineralsp. 305
Calcium biomineralsp. 305
Intra- and extracytoplasmic calcium balancesp. 308
The calcium network todayp. 309
The genetic controls of calcium-binding proteinsp. 312
Summary of calcium biological chemistryp. 312
Zinc: Lewis acid catalysis and regulation
Introduction to Lewis acidsp. 315
Zinc in biological spacep. 317
Availability and concentration of free Zn[superscript 2+] ionsp. 318
Types of protein associated with zincp. 319
Zinc exchange ratesp. 324
The number and selectivity of ligands to zincp. 324
Zinc as a catalytic group in enzymesp. 325
Summary of zinc proteinsp. 329
Regulatory and control roles of zincp. 330
The export of zinc enzymes: digestion and peptide messagesp. 331
Zinc enzymes and peptide hormonesp. 332
Other functions of zinc outside cellsp. 333
Zinc geneticsp. 334
Zinc and evolutionp. 334
Summary: is zinc today a master hormone?p. 335
Non-haem iron: redox reactions and controls
General introduction to transition metalsp. 341
Introduction to iron biological chemistryp. 344
Iron uptakep. 345
The non-haem iron proteinsp. 348
The iron/sulphur proteinsp. 348
Fe/S centres active as enzymesp. 351
Location of Fe/S proteinsp. 353
Why are there Fe[subscript n] S[subscript n] clusters in cells?p. 353
The organization and selectivity of ferredoxinsp. 355
The Fe-O-Fe clusterp. 357
Mononuclear non-haem/non-Fe/S iron and oxidative enzymesp. 359
Iron and secondary metabolismp. 362
Binding ligands in non-haem/non-Fe/S proteinsp. 363
Extracellular iron as an acid catalystp. 363
Summary of non-haem iron/non-Fe/S enzymesp. 363
Iron buffering and carriersp. 364
Iron controls of metabolismp. 365
Iron regulation: relationship to genes and evolutionp. 366
Haem iron: coupled redox reactions
Iron in porphyrinsp. 370
Properties of isolated haem unitsp. 370
Classification of haem proteins by iron propertiesp. 373
Classification of haem proteins by secondary structurep. 375
Where are haem proteins in cells?p. 378
Haem protein functions I: electron-transferp. 379
The surfaces of haem proteinsp. 384
Haem-protein functions II: storage and transportp. 385
Haem-protein functions III: oxidases and dioxygenasesp. 388
Substrates of haem enzymes and secondary metabolismp. 392
Haem in controlsp. 394
The synthesis of haem and its genesp. 394
Summary of haem-iron functionsp. 397
Manganese: dioxygen evolution and glycosylation
Introductionp. 400
Manganese chemistryp. 400
Monomeric Mn(II) and Mn(IV) chemistryp. 405
The biological chemistry of manganesep. 408
The production of dioxygenp. 409
Manganese and peroxide metabolismp. 411
Manganese and hydrolytic reactionsp. 412
Manganese precipitatesp. 413
Manganese control systems and geneticsp. 414
The evolution of manganese functionsp. 415
Summaryp. 416
Copper: extracytoplasmic oxidases and matrix formation
Introductionp. 418
Copper and electron-transferp. 419
Copper and dioxygenp. 420
Copper enzymes and nitrogen oxidesp. 426
Superoxide dismutasep. 426
The transport and homeostasis of copperp. 428
The overall functions of copperp. 432
Nickel and cobalt: remnants of early life?
Introductionp. 436
The chemistry of cobalt and nickelp. 438
Hydrogenasesp. 441
The reactions of vitamin B[subscript 12]p. 442
The organometallic chemistry of lifep. 444
Hydrolytic catalysis by nickel and cobaltp. 444
Nickel and cobalt uptakep. 447
Cobalt and nickel genes in E. colip. 448
Conclusionp. 448
Molybdenum, tungsten, vanadium, and chromium
Introductionp. 450
The availabilities of molybdenum, tungsten, vanadium, and chromiump. 450
The molybdenum enzymes: a first overviewp. 451
Biological chemistry of molybdenump. 453
The structure and function of the molybdenum enzymesp. 455
Molybdenum geneticsp. 458
Molybdenum: conclusionsp. 459
Tungsten biological chemistryp. 459
Vanadium chemistry and biochemistryp. 461
Molybdenum, vanadium, and tungsten in evolutionp. 466
The biological chemistry of chromiump. 468
Phosphate, silica, and chloride: acid-base non-metals
Introduction to the non-metalsp. 471
Phosphate chemistryp. 472
The forms and energies of bound phosphatep. 473
Summary of phosphate functionsp. 480
Chloride channels, pumps, and exchangersp. 481
Anion balance: chloride, phosphate, sulphate, and carboxylatesp. 481
Silicon biochemistryp. 482
Boron in biologyp. 487
Halides and other non-metal trace elementsp. 487
Sulphur, selenium, and halogens: redox non-metals
Introductionp. 489
Sulphur biochemistryp. 490
Summary of sulphur chemistryp. 496
The biochemistry of seleniump. 497
Evolution and seleniump. 499
Notes on the use of the halogensp. 499
The cellular content of sulphur, selenium, and iodine (the metallome)p. 500
Integrated living systems of elements
Introductionp. 503
The nature of systemsp. 505
The detailed steps in the evolution of earth's surfacep. 511
Macromolecules and systemsp. 517
The beginnings of lifep. 519
Survival, reproduction and the need for a coded moleculep. 523
Evolution: introduction and morphological changesp. 523
Evolution and the metallomep. 528
Changes of elements in prokaryotesp. 532
Eukaryotes: the development of new membrane components: new lipidsp. 534
Carriersp. 540
The metallome of extracellular and vesicular fluids of mulicellular organismsp. 542
The metallome of brain extracellular fluidp. 543
Summary of metallome contentp. 544
Changing non-metals in the proteome and in small organic moleculesp. 544
Extracellular communication networksp. 548
Survival of systems: summary of the value of the elementsp. 552
Indexp. 557
Table of Contents provided by Syndetics. All Rights Reserved.

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