The Biological Chemistry of the Elements The Inorganic Chemistry of Life

by Fraústo da Silva, J. J. R.; Williams, R. J. P.

• ISBN13: 9780198508489
• ISBN10: 0198508484
• Edition: 2nd
• Format: Paperback
• Copyright: 2001-11-01
• Publisher: Oxford University Press

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 their uptake; 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 a discussion 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 many biomolecules 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 introduction	1	(6)
PART 1 The chemical and physical factors controlling the elements of life
The chemical elements in biology	7	(22)
The element content of living systems	7	(4)
The biological elements	7	(3)
Chemical speciation: limitations of life chemistry and physics	10	(1)
An aside: some biological chemistry of hydrogen	11	(1)
The economical use of resources: abundance and availability	12	(3)
Biological environment and element availability	15	(7)
pH and redox potential considerations	15	(2)
Element concentrations in aerobic environments and in some organisms	17	(4)
Solubility products	21	(1)
Sulphide chemistry in water (anaerobes)	22	(2)
A note on homeostasis	24	(2)
Survival and evolution	26	(1)
Conclusion	26	(3)
The principles of the uptake and chemical speciation of the elements in biology	29	(54)
Introduction to chemical speciation	30	(3)
General aspects of uptake and rejection	30	(3)
The separations that biology can achieve	33	(1)
The selective uptake of metal ions	34	(4)
Effective stability constants	38	(1)
Element uptake at equilibrium: the selectivity of the uptake	39	(12)
Selection by charge type	42	(1)
Selection by ion size	43	(3)
Combination of radius and charge effect	46	(1)
Selection by liganding atom	46	(2)
Selection by preferential coordination geometry	48	(1)
Selection by spin-pairing stabilization	49	(2)
Selection by binding in clusters	51	(1)
Hydrolysis: hydroxides and oxenes	51	(2)
Selective control of oxidation states of metals	53	(1)
Selection by control of concentration of M and L	54	(4)
Availability and predicted cytoplasmic ion concentrations	56	(2)
Selection by transfer coefficients from water to proteins (or membranes)	58	(2)
Soft and hard acids, solvents, and extraction	60	(1)
Selection at surfaces and in precipitates	60	(1)
The selectivity of channels	61	(1)
Kinetic effects and control	62	(4)
The distribution coefficient D for ML1	62	(1)
Kinetics of transport	63	(1)
Insertion in pre-formed holes or chelating rings	63	(2)
Energy coupling to the selective movement of M (gates and pumps)	65	(1)
A summary of the kinetics of uptake of metal ions	65	(1)
Rejection of metal ions	66	(1)
General aspects of the uptake of essential non-metals	66	(2)
Mechanisms of selection of anions based on thermodynamic properties	68	(4)
Selection by charge and size; the hydration of anions and their binding to proteins	68	(2)
Selection of anions by differences in binding affinity for different types of cationic centres	70	(1)
Kinetic binding traps for anions, with or without accompanying redox reactions	71	(1)
Redox incorporation of anions	72	(2)
Coenzymes	74	(1)
Precipitates in compartments: cation and anion cooperativity	74	(2)
The application of equilibria and equilibrium exchange to carriers, buffers, pumps, enzymes and gene regulation	76	(3)
Carriers	76	(1)
Ion buffers and stores	77	(1)
Pumps	78	(1)
Enzymes, structural proteins and transcription factors	78	(1)
Genetic regulation-an introduction to control of ligand (protein) concentration	79	(1)
Concluding remarks: element handling in biological systems	80	(3)
Physical separations of elements: compartments and zones in biology	83	(25)
General aspects	84	(1)
The nature of compartments	85	(1)
The chemical solutions and physical states of compartments	86	(3)
The role and nature of membranes	89	(1)
Different types of membrane	90	(8)
Internal and external particles and their relationship to membranes	90	(2)
Lateral membrane organization and in-membrane flow	92	(2)
Transmembrane organization and flow	94	(2)
Flow of vesicles in cells	96	(2)
Special solution conditions in vesicles	98	(2)
Cooperativity of separations and localizations	100	(1)
Summary of metal ion positioning	100	(1)
Symbiosis and multicellular systems	101	(1)
Spatial distribution of bulk non-metals	101	(2)
The spatial transfer of H, C, N, S: mobile and fixed coenzymes	103	(2)
H (and O) transport	103	(1)
Phosphate transport	104	(1)
Carbon transport	104	(1)
Nitrogen transport	105	(1)
Sulphur transport	105	(1)
Summary of non-metal transport	105	(1)
Evolution of compartments and organization: summary	106	(2)
Kinetic considerations of chemical reactions, catalysis, and control	108	(27)
Introduction	108	(1)
Chemical transformations	108	(1)
The nature of acid-base reactions: hydrolysis and condensation	109	(4)
The hydrolysis of proteins, RNA, DNA, and other polymers	113	(1)
The nature of ion flow	114	(3)
Signals and controls	114	(1)
Ion migration rates: electrolytics	115	(2)
Exchange	117	(1)
On/off reactions: control systems	117	(1)
Electron-transfer reactions: electronics	118	(4)
Redox potentials of complexes	122	(1)
Atom transfer reactions	123	(2)
Group transfer	125	(1)
The nature of transition-metal centres in catalysis	125	(2)
Free radical reactions	127	(1)
Sizes of atoms, stereochemistry, and reaction paths	128	(2)
Selective binding to protein (DNA) sites in pathways	128	(2)
The creation of local small spaces: mechanical devices for transfer reactions	130	(2)
Rates of conformational changes	131	(1)
Networks: kinetic circuits	132	(1)
Control over networks of reactions	132	(1)
Summary	133	(2)
Energy in biological systems and hydrogen biochemistry	135	(19)
Introduction	135	(1)
Biological systems and light	136	(3)
Oxidative energy: mitochondria	139	(2)
Proton migration coupled to redox reactions	141	(1)
The coupling of gradients to ATP formation	142	(2)
Anaerobes in the dark	144	(3)
Compartments, energy, and metabolism	147	(1)
Organization and tension	148	(1)
Motion of organisms	148	(1)
Local storage of elements and energy	148	(2)
Primitive sources of energy	150	(1)
Sulphur compounds as energy transfer agents	151	(1)
Energy networks and summary	151	(3)
The role of biological macromolecules and polymers	154	(52)
Proteins and nucleic acids	155	(1)
Introduction	155	(1)
Protein composition and basic structure	156	(5)
The protein fold and the internal motions in solution	161	(3)
The folding process	164	(1)
The amino-acid composition of specific proteins	164	(5)
Structural proteins and mechanical devices	169	(1)
Matching of proteins and organic and inorganic ions	170	(1)
Enzymes	171	(2)
States of metal ions in proteins	173	(6)
General aspects	173	(1)
The copper blue centres	174	(1)
Metalloproteins in multiple-step reactions	175	(2)
Protein-protein assemblies and metal ions	177	(1)
Protein degradation	178	(1)
Summary of proteins: the proteome	179	(1)
Nucleic-acid composition and outline structure	180	(2)
Metal-ion binding to polynucleotides	182	(3)
Cavities and metal-ion binding in DNA	183	(1)
DNA sequences and mutation	184	(1)
Completed genomes	185	(1)
Nucleic acids and proteins	185	(1)
Controlled synthesis and degradation of biopolymers	186	(1)
Genetic control	186	(8)
A note on gene expression in multicellular organisms	189	(1)
Regulation: constitutive and induced protein production using genes	190	(2)
Constitutive and induced genes for elements	192	(2)
Summary of genetic control and regulation at 'equilibrium'	194	(2)
Polysaccharides and lipids	196	(1)
Introduction	196	(1)
Introduction to polysaccharides	196	(1)
The backbones and sidechains of polysaccharides	197	(1)
Glycoproteins and cell surface packing	198	(1)
Interaction of polysaccharides with metal ions	199	(1)
Properties of lipids	200	(1)
Lipids in membranes as macromolecular assemblies	200	(1)
Composition and general functions of lipids	200	(1)
Ion association with lipid surfaces	201	(1)
The influences of selected inorganic elements	201	(1)
Potentials on membrane surfaces	202	(1)
Essential fatty acids	202	(1)
Summary of biopolymers	202	(4)
The functional value of the chemical elements in biological systems	206	(351)
Introduction	206	(2)
Major chemical properties of elements in aqueous solutions	208	(2)
Biochemical functions of the chemical elements	210	(4)
The living process	214	(3)
The chemical flow in biology	217	(7)
The synthesis and degradation of the polymers of life	217	(2)
Synthesis and degradation of monomers	219	(2)
The uptake and loss of elements	221	(1)
The flow of energy in compounds	222	(2)
Equilibria and kinetic balance	224	(1)
The integration of activity	224	(2)
The biological selection of elements	224	(1)
Self-organization and flow patterns	225	(1)
Conclusion	226	(5)
PART 2 The roles of individual element in biology
Sodium, potassium, and chlorine: osmoti control, electrolytic equilibria, and currents
Introduction	231	(1)
Passive diffusion	232	(3)
Gated channels	235	(1)
Channel selectivity and possible constructions	236	(2)
Active transport: pumps	238	(4)
The nature of selective pumps	242	(1)
Building electrolytic circuits	242	(3)
The positions of pumps and channels	242	(1)
The ATPase pumps: some general comments	243	(1)
Exchangers	244	(1)
Organic anions and cations as current carriers	245	(1)
Currents of ions and morphogenic patterns: growth	245	(1)
Simple salts and the conditions of polyelectrolytes	245	(1)
Binding to DNA	246	(1)
Enzymes requiring potassium	246	(1)
Ion genetics and networks	246	(2)
K+, Na+, Cl circuits	247	(1)
The evolution of channels	248	(1)
Summary	248	(3)
The biological chemistry of magnesium: phosphate metabolism
Introduction	251	(1)
The spatial distribution of magnesium	251	(1)
Magnesium chemistry	252	(3)
Magnesium pumping in cells	255	(2)
Very strong binding of magnesium	257	(1)
Magnesium in walls and membranes	257	(1)
Magnesium enzymes: magnesium and phosphates	257	(5)
Magnesium and muscle cells	262	(2)
Activation of tension	262	(1)
Magnesium muscle relaxation: calcium buffering	263	(1)
Magnesium and polynucleotides	264	(1)
Structures of DNA and RNA particles	264	(1)
Ribozymes	264	(1)
Competition with polyamines	265	(3)
Polymeric equilibria: tubulins, DNA, and the cell cycle	268	(1)
Magnesium outside cells	268	(1)
Sol/gel equilibria and magnesium	269	(1)
Magnesium and lipids	269	(1)
Magnesium and chlorophyll	269	(3)
Chlorophyll binding in proteins	269	(2)
Magnesium insertion in chlorophyll: chelates	271	(1)
The use of maganese as a magnesium probe	272	(2)
Interference of other metal ions with Mg2+ biochemistry	274	(1)
Lithium and magnesium	274	(1)
Evolution and genetics of Mg2+ proteins and networks	274	(2)
Conclusion	276	(3)
Calcium: controls and triggers
Introduction	279	(1)
Free calcium ion levels	280	(2)
Calcium levels in pulsed cells	281	(1)
The calcium ion	282	(2)
Condensation equilibria	284	(1)
Protein ligands for calcium	284	(2)
Magnesium/calcium competition	286	(1)
The resting state of calcium in cells	287	(1)
Calcium triggering: calmodulins	288	(1)
The calcium trigger proteins	289	(2)
S-100 proteins	291	(1)
Other triggering modes: annexins and C-domains	292	(2)
Vesicular contents and their release: exocytosis	292	(2)
Calcium, filaments, and cell shape	294	(1)
Calcium and protein phosphorylation	294	(1)
Calcium buffering and calcium transport in cells	295	(1)
Calcium currents: movement through membranes, channels, gates, and pumps	296	(2)
Calcium exchangers	298	(1)
Internal calcium-induced proteases: apoptosis	298	(1)
General remarks concerning control systems in cells	298	(2)
Extracytoplasmic calcium in vesicles	300	(1)
Vesicular calcium	300	(1)
Organelle calcium	301	(1)
Extracellular calcium in circulating fluids	301	(4)
Calcium in digestion and blood-clotting	301	(3)
Calcium in cell-cell connections	304	(1)
Calcium proteins of biominerals	305	(1)
Calcium biominerals	305	(3)
Intra-and extracytoplasmic calcium balances	308	(1)
Multiple sites for calcium	308	(1)
Cell shape	308	(1)
Cell morphogenesis	309	(1)
The calcium network today	309	(3)
The genetic controls of calcium-binding proteins	312	(1)
Summary of calcium biological chemistry	312	(3)
Zinc: Lewis acid catalysis and regulation
Introduction to Lewis acids	315	(2)
Zinc in biological space	317	(1)
Availability and concentration of free Zn2+ ions	318	(1)
Types of protein associated with zinc	319	(5)
Zinc enzymes	320	(2)
Zinc proteins other than enzymes	322	(1)
Proteins for zinc distribution	322	(1)
Zinc fingers	323	(1)
Zinc exchange rates	324	(1)
The number and selectivity of ligands to zinc	324	(1)
Zinc as a catalytic group in enzymes	325	(4)
Zinc as a Lewis acid	325	(3)
Zinc and redox reactions	328	(1)
The (constrained) entatic state and probes	328	(1)
Summary of zinc proteins	329	(1)
Regulatory and control roles of zinc	330	(1)
The export of zinc enzymes: digestion and peptide messages	331	(1)
Zinc enzymes and peptide hormones	332	(1)
Zinc enzymes and peptide hormones	332	(1)
Other functions of zinc outside cells	333	(1)
Cross-linking and hardening of extracellular matrices	333	(1)
Zinc in solid-state devices	333	(1)
Zinc genetics	334	(1)
FUR and ZUR	334	(1)
Zinc and evolution	334	(1)
Summary: is zinc today a master hormone?	335	(6)
Non-haem iron: redox reactions and controls
General introduction to transition metals	341	(3)
Introduction to iron biological chemistry	344	(1)
Iron uptake	345	(3)
The non-haem iron proteins	348	(1)
The iron/sulphur proteins	348	(3)
Electron-transfer chains	351	(1)
Succinate dehydrogenese: particle II of mitochondria	351	(1)
Fe/S centres active as enzymes	351	(2)
The peculiarities of hydrogenase	352	(1)
Location of Fe/S proteins	353	(1)
Why are there Fen Sn clusters in cells?	353	(2)
Genetics of Fen Sn assembly in bacteria: genetic structure	355	(1)
The organization and selectivity of ferredoxins	355	(2)
Competition for Fe/S cluster sites by other metals	356	(1)
The Fe-O-Fe cluster	357	(2)
Mononuclear non-haem/non-Fe/S iron and oxidative enzymes	359	(3)
Unusual iron enzymes	362	(1)
Iron and secondary metabolism	362	(1)
Binding ligands in non-haem/non-Fe/S proteins	363	(1)
Extracellular iron as an acid catalyst	363	(1)
Summary of non-haem iron/non-Fe/S enzymes	363	(1)
Iron buffering and carriers	364	(1)
Iron controls of metabolism	365	(1)
Iron regulation: relationship to genes and evolution	366	(4)
Haem iron: coupled redox reactions
Iron in porphyrins	370	(1)
Properties of isolated haem units	370	(3)
Classification of haem proteins by iron properties	373	(2)
Classification of haem proteins by secondary structure	375	(3)
Where are haem proteins in cells?	378	(1)
Haem protein functions I: electron-transfer	379	(5)
Simple electron-transfer proteins	379	(1)
Multihaem electron-transfer proteins	380	(1)
Electron-transfer/proton coupling: models	381	(1)
The membrane electron-transfer proteins: sidechain proton coupling	381	(2)
The membrane electron-transfer proteins: sidechain proton coupling	383	(1)
The surfaces of haem proteins	384	(1)
Haem-protein functions II: storage and transport	385	(3)
Dioxygen: storage, transport, and signalling	385	(1)
Nitric acid and haem receptors	385	(1)
Cytochrome c and cyanide	386	(2)
Haem-protein functions III: oxidases and dioxygenases	388	(4)
Cytochrome oxidase	389	(2)
Cytochrome P-450	391	(1)
Peroxidases and catalases	391	(1)
Substrates of haem enzymes and secondary metabolism	392	(2)
Haem and higher oxidation states of nitrogen and sulphur: reductive reactions	393	(1)
Haem in controls	394	(1)
The synthesis of haem and its genes	394	(3)
Genes for haem-containing proteins	395	(2)
Haem and the metallome	397	(1)
Summary of haem-iron functions	397	(3)
Manganese: dioxygen evolution and glycosylation
Introduction	400	(1)
Maganese chemistry	400	(5)
Oxidation states	400	(2)
Structures of Mn(II) complexes with organic ligands	402	(1)
Manganese (II) equilibria and biochemistry	403	(1)
The kinetics of Mn (II) complexes	404	(1)
Monomeric Mn(II) and Mn(IV) chemistry	405	(3)
Structures	405	(1)
Thermodynamics	405	(1)
Kinetics of Mn(III) and Mn(IV) reactions	406	(1)
Manganese cluster chemistry	406	(2)
The biological chemistry of manganese	408	(1)
The occurrence and availability of manganese organisms	408	(1)
The uptake of manganese	408	(1)
Pumping of manganese gradients	408	(1)
The distribution of Mn in biological systems	409	(1)
The production of dioxygen	409	(2)
Manganese and peroxide metabolism	411	(1)
Manganese and hydrolytic reactions	412	(1)
Manganese precipitates	413	(1)
Manganese control systems and genetics	414	(1)
The evolution of manganese functions	415	(1)
Summary	416	(2)
Copper: extracytoplasmic oxidases and matrix formation
Introduction	418	(1)
Copper and electron-transfer	419	(1)
Copper and dioxygen	420	(6)
Haemocyanin	420	(2)
A comment on copper of cytochrome oxidase	422	(1)
Copper and extracellular oxidases	423	(1)
Substrates of copper oxidases	424	(1)
Copper proteins and coenzyme PQQ (pyrroloquinoline quinone)	425	(1)
Copper enzymes and nitrogen oxides	426	(1)
Superoxide dismutase	426	(2)
The location	426	(1)
The reactions of superoxide dismutases	427	(1)
The transport and homeostasis of copper	428	(4)
The buffer and carrier proteins	428	(1)
The copper pumps	429	(1)
The copper carriers	430	(1)
Copper exchange rates	431	(1)
Copper genetics	431	(1)
The overall functions of copper	432	(4)
Nickel and cobalt: remnants of early life?
Introduction	436	(2)
The chemistry of cobalt and nickel	438	(3)
Hydrogenases	441	(1)
The reactions of vitamin B12	442	(2)
The organometallic chemistry of life	444	(1)
Hydrolytic catalysis by nickel and cobalt	444	(3)
Urease: nickel in vacuoles	445	(1)
Cobalt enzymes not using B12	446	(1)
Nickel and cobalt uptake	447	(1)
Genetic controls over nickel and cobalt uptake	447	(1)
Cobalt and nickel genes in E. coli	448	(1)
Conclusion	448	(2)
Molybdenum, tungsten, vanadium, and chromium
Introduction	450	(1)
The availabilities of molybdenum, tungsten, vanadium, and chromium	450	(1)
The molybdenum enzymes: a first overview	451	(2)
Biological chemistry of molybdenum	453	(2)
Uptake of molybdate	453	(1)
Oxidation states and redox potentials in enzymes	454	(1)
The types and rates of molybdenum reactions	454	(1)
Oxygen-atom transfer reactions	455	(1)
The structure and function of the molybdenum enzymes	455	(3)
Nitrogenase and its reaction centre: FeMoco	456	(2)
Molybdenum exchange and possible control functions	458	(1)
Molybdenum genetics	458	(1)
Molybdenum: conclusions	459	(1)
Tungsten biological chemistry	459	(2)
Vanadium chemistry and biochemistry	461	(5)
The chemistry of vanadium in biology	461	(1)
The biological forms and functions of vanadium	462	(3)
Vanadium and iron	465	(1)
Molybdenum, vanadium, and tungsten in evolution	466	(2)
The biological chemistry of chromium	468	(3)
Phosphate, silica, and chloride: acid-base non-metals
Introduction to the non-metals	471	(1)
Phosphate chemistry	472	(1)
The chemistry of phosphate	472	(1)
The forms and energies of bound phosphate	473	(7)
The energy of pyrophosphates and the resting state of cells	474	(1)
Phosphate controls	475	(1)
Phosphate messengers	476	(2)
Phosphate switches: protein phosphorylation, dephosphorylation, and time hierarchy	478	(1)
Phosphates and gene transcription	479	(1)
Phosphate minerals	480	(1)
Phosphate uptake and transport	480	(1)
Summary of phosphate functions	480	(1)
Chloride channels, pumps, and exchangers	481	(1)
Anion balance: chloride, phosphate, sulphate, and carboxylates	481	(1)
Silicon biochemistry	482	(5)
Occurrence and physical nature of silicon	482	(3)
The chemistry of silica in biology	485	(1)
Uptake and transport of silicon	486	(1)
Boron in biology	487	(1)
Halides and other non-metal trace elements	487	(2)
Sulphur, selenium, and halogens: redox non-metals
Introduction	489	(1)
Sulphur biochemistry	490	(6)
Oxidation states and redox reactions	490	(3)
Acid-base reactions	493	(1)
Group transfer reactions: coupling	494	(1)
The sulphur cycle	495	(1)
Cellular and genetic chemistry of sulphur	495	(1)
Summary of sulphur chemistry	496	(1)
The biochemistry of selenium	497	(2)
Evolution and selenium	499	(1)
Notes on the use of the halogens	499	(1)
The cellular content of sulphur, selenium, and iodine (the metallome)	500	(3)
Integrated living systems of elements
Introduction	503	(2)
The nature of systems	505	(6)
Earth as a series of equilibrated states	507	(2)
Earth as a series of non-equilibrated domains	509	(2)
Geochemical and biochemical interactions	511	(1)
The detailed steps in the evolution of earth's surface	511	(6)
The evolution of organized flow on earth: patterns	513	(1)
The persistence of patterns	514	(1)
Persistence of patterns in an enclosed space	515	(2)
Macromolecules and systems	517	(2)
The beginnings of life	519	(4)
The basic cellular flows and element homeostasis: the primitive metallome	519	(4)
Survival, reproduction and the need for a coded molecule	523	(1)
Evolution: introduction and morphological changes	523	(5)
The development of internal morphology: evolution of eukaryotes	523	(1)
The development of external morphology: evolution of multicellular organisms up to animals	524	(4)
Evolution and the metallome	528	(4)
The metallome and survival strength	529	(3)
Changes of elements in prokaryotes	532	(2)
'Anaerobic' sulphate-using bacteria and protection	534	(1)
Eukaryotes: the development of new membrane components: new lipids	534	(6)
The metallome of early 'anaerobic' eukaryotes	536	(1)
The aerobic single-cell eukaryotes and their metallome	537	(3)
Carriers	540	(2)
The metallome of extracellular and vesicular fluids of mulicellular organisms	542	(1)
The metallome of brain extracellular fluid	543	(1)
Summary of metallome content	544	(1)
Changing non-metals in the proteome and in small organic molecules	544	(4)
Changes in non-metal metabolism	547	(1)
Extracellular communication networks	548	(4)
Nerves and brain	550	(2)
Survival of systems: summary of the value of the elements	552	(5)
Index	557