)-convention, Labile, Laccase, Lactoferrin, Leghemoglobin, Lewis acid, Lewis adduct, Lewis base, Ligand, Ligand field, Ligase, Ligating, Lipoxygenase, Low-spin, Lyase.
Contents
Haber-Weiss reaction, Half life, Haloperoxidase, Hapten, Hapto, Hard acid, Hard base, Helix, Heme, Hemerythrin, Hemochromatosis, Hemocyanin, Hemoglobin, Heterolysis, Heterotrophic organisms, High-spin, HiPIP, Holoenzyme, Homolysis, Hydration, Hydrogenase, Hydrolase, Hydrolysis, Hydron, Hydrophilic, Hydrophobic interaction, Hyperfine, Imaging, Immunogold, Inert, Inhibition, Inhibitor, Insertion reaction, Intercalation compounds, Intron, Ion channel, Ionophore, Ion pumps, Iron-responsive element, Iron-responsive protein, Iron-sulfur cluster, Iron-sulfur proteins, IRP, Ischemia, Isobacteriochlorin, Isoenzymes, Isomerase, Isotropy, Kappa()-convention, Labile, Laccase, Lactoferrin, Leghemoglobin, Lewis acid, Lewis adduct, Lewis base, Ligand, Ligand field, Ligase, Ligating, Lipoxygenase, Low-spin, Lyase.
The Haber-Weiss cycle consists of the following two reactions :
H2O2 + OH. 
H2O + O2- + H+ and
H2O2 + O2- O2 + OH- + OH.
The second reaction achieved notoriety as a possible source of hydroxyl radicals. However, it has a negligible rate constant. It is believed that iron(III) complexes can catalyze this reaction: first Fe(III) is reduced by superoxide, followed by oxidation by dihydrogenperoxide. See also Fenton reaction.
For a given reaction the half life t1/2 of a reactant is the time required for its concentration to reach a value that is the arithmetic mean of its initial and final (equilibrium) value. For a reactant that is entirely consumed it is the time taken for the reactant concentration to fall to one half of its initial value. For a first-order reaction, the half life of the reactant may be called the half life of the reaction. In nuclear chemistry, (radioactive) half life is defined, for a simple radioactive decay process, as the time required for the activity to decrease to half its value by that process. See also biological half life.
A peroxidase which catalyzes the oxidative transformation of halides to XO- (X being Cl, Br or I), or organic halogen compounds. Most are hemeproteins, but some bromoperoxidases from algae are vanadium-containing enzymes .
A molecule (usually a small organic molecule) which can be bound to an antigenic determinant/epitope. Usually they are too small to give a response of their own. They become antigenic if they are coupled to a suitable macromolecule, such as a protein.
The hapto symbol, 
(Greek eta), with numerical superscript, provides a topological description for the bonding of hydrocarbons or other 
-electron systems to metals, by indicating the connectivity between the ligand and the central atom. The symbol is prefixed to the ligand name, or to that portion of the ligand name most appropriate. The right superscript numerical index indicates the number of coordinating atoms in the ligand which bind to the metal. Examples :
[PtCl2(C2H4)(NH3)] amminedichloro(2-ethene)platinum
[Fe(5-C5H5)2] bis(5-cyclopentadienyl)iron (ferrocene)
A Lewis acid with an acceptor centre of low polarizability. It preferentially associates with hard bases rather than with soft bases, in a qualitative sense (sometimes called "HSAB rule"). Conversely a soft acid possesses an acceptor centre of high polarizability and exhibits the reverse preferencefor a partner for coordination.
A Lewis base with a donor centre of low polarizability; the converse applies to soft bases. See also hard acid.
A particular rigid left- or right-handed arrangement of a polymeric chain, characterised by the number of strands,the number (n) of units per turn and its pitch (p), the distance the helix rises along its axis per full turn. Examples of single-stranded helices are the protein helices: 
-helix:n = 3.6, p = 540 pm; 310-helix: n = 3.0, p = 600 pm; -helix: n = 4.4, p = 520 pm. See also double helix.
A near-planar coordination complex obtained from iron and the dianionic form of porphyrin. Derivatives are known with substituents at various positions on the ring named a, b, c, d etc. Heme b, derived from protoporphyrin IX, is the most frequently occurring heme.
A dioxygen-carrying protein from marine invertebrates, containing an oxo-bridged dinuclear iron center.
A genetic condition of massive iron overload leading to cirrhosis and/or other tissue damage, attributable to iron.
A dioxygen-carrying protein (from invertebrates, e.g arthropods and molluscs), containing dinuclear type 3 copper sites.
A dioxygen-carrying heme protein of red blood cells, generally consisting of two alpha and two beta subunits, each containing one molecule of protoporphyrin IX.
The cleavage of a bond (heterolytic cleavage or heterolytic fission) so that both bonding electrons remain with one of the two fragments between which the bond is broken.
Organisms that are not able to synthesize cell components from carbon dioxide as sole carbon source. Heterotrophic organisms use preformed oxidizable organic substrates such as glucose as carbon and energy sources, while energy is gained through chemical processes (chemoheterotrophy) or through light sources (photoheterotrophy).
See low-spin.
Formerly-used abbreviation for High-Potential Iron-sulfur Protein, now classed as a ferredoxin. An electron transfer protein from photosynthetic and other bacteria, containing a [4Fe-4S] cluster which undergoes oxidation-reduction between the [4Fe-4S]2+ and [4Fe-4S]3+ states.
An enzyme containing its characteristic prosthetic group(s) and/or metal(s).
The cleavage of a bond (homolytic cleavage or homolytic fission) so that each of the molecular fragments between which the bond is broken retains one of the bonding electrons.
Addition of water or the elements of water (i.e. H and OH) to a molecular entity. The term is also used in a more restricted sense for the process: A (gas) A (aqueous solution); cf. the use of the term in inorganic and physical chemistry to describe the state of ions of an aqueous electrolytesolution. See also aquation and solvation. 
An enzyme, dihydrogen:acceptor oxidoreductase, that catalyzes the formation or oxidation of H2. Hydrogenases are of various types. One class ([Fe]-hydrogenases) contains only iron-sulfur clusters. The other major class ([NiFe]-hydrogenases) has a nickel-containing center and iron-sulfur clusters; a variation of the latter type ([NiFeSe]-hydrogenases) contains selenocysteine.
An enzyme of EC class 3, also known as a hydro-lyase, that catalyzes the hydrolysis of a substrate.
Solvolysis by water.
General name for the ion H+ either in natural abundance, or where it is not desired todistinguish between the isotopes, as opposed to proton for 1H+, deuteron for 2H+ and triton for 3H+.
The term is used to mean "water preferring". May also be used to describe the character of interaction of a particular atomic group with the medium.
The tendency of hydrocarbons (or of lipophilic hydrocarbon-like groups in solutes) to form intermolecular aggregates in an aqueous medium, and analogous intramolecular interactions. The name arises from the attribution of the phenomenon to the apparent repulsion between water and hydrocarbons. Use of the misleading alternative term hydrophobic bond is discouraged.
See electron paramagnetic resonance spectroscopy.
A medical diagnostic technique by which useful organ images are obtained from the radiation emitted by radionuclides that are introduced into organs, or from radiation absorbed by atomic nuclei within the organs. Typical examples are imaging obtained by recording the radiation emitted by a radionuclide such as 99mTc, and the 1H-NMR imaging obtained by whole body nuclear magnetic resonance measurements. See also bone imaging, brain imaging, and magnetic resonance imaging.
A method for visualizing proteins in electron microscopy within a cell using gold particles attached to an antibody that binds specifically to that protein.
Stable and unreactive under specified conditions. See also labile.
The decrease in the rate of a reaction brought about by the addition of a substance (inhibitor).
A substance that decreases the rate of an enzyme catalyzed or other chemical reaction.
A chemical reaction or transformation of the general type X-Y-Z
Compounds resulting from inclusion, usually without covalent bonding, of one kind of molecule (the guest molecule) in a matrix of another compound (the host compound), which has a layered structure. The host compound, with a rather rigid structure, may be macromolecular, crystalline, or amorphous.
An intervening section of DNA which occurs almost exclusively within a eukaryotic gene, but which is not translated to amino-acid sequences in the gene product. The introns are removed from the pre-mature mRNA through a process called splicing, which leaves the exons untouched, to form an active mRNA.
Ion channels enable ions to flow rapidly through membranes in a thermodynamically downhill direction after an electrical or chemical impulse. Their structures usually consist of 4-6 membrane-spanning domains. This number determines the size of the pore and thus the size of the ion to be transported. See also ion pumps.
A compound which can carry specific ions through membranes of cells or organelles.
Ion pumps enable ions to flow through membranes in a thermodynamically uphill direction by the use of an energy source such as ATP or light. They consist of sugar-containing hetero-peptide assemblies, which open and close upon the binding and subsequent hydrolysis of ATP, usually transporting more than one ion towards the outside or the inside of the membrane. See also ion channel.
A specific base sequence in certain messenger RNAs that code for various proteins of iron metabolism, which allows regulation at translational level by the iron-responsive protein.
A protein that responds to the level of iron in the cell, and regulates the biosynthesis of proteins of iron metabolism, by binding to the iron-responsive element on messenger RNA.
A unit comprising two or more iron atoms and bridging sulfide ligands in an iron-sulfur protein. The recommended designation of a cluster consists of the iron and sulfide content, in square brackets, for example [2Fe-2S], [3Fe-4S]. The possible oxidation levels are indicated by the net charge excluding the ligands, for example a [4Fe-4S]2+; [4Fe-4S]1+ (or [4Fe-4S]2+;1+)cluster.
Proteins in which non-heme iron is coordinated with cysteine sulfur and usually also with inorganic sulfur. Divided into three major categories: rubredoxins; "simple iron-sulfur proteins", containing only iron-sulfur clusters, and "complex iron-sulfur proteins", containing additional active redox centers such as flavin, molybdenum or heme. In most iron-sulfur proteins the clusters function as electron transfer groups, but in others they have other functions such as catalysis of hydratase/dehydratase reactions, maintenance of protein structure, or regulation of activity.
Local deficiency of blood supply and hence dioxygen to an organ or tissue owing to constriction of the blood vessels or to obstruction.
2,3,7,8-Tetrahydroporphryin. A reduced porphyrin with two pairs of con-fused saturated carbon atoms (C-2, C-3 and C-7, C-8) in two of the pyrrole rings. See also bacteriochlorin.
Multiple forms of enzymes arising from genetically determined differences in primary structure. The term does not apply to those derived by modification of the same primary sequence.
An enzyme of EC class 5, which catalyzes the isomerization of a substrate.
Lack of anisotropy; the property of molecules and materials of having identical physical properties in all directions.
See donor atom symbol.
The term has loosely been used to describe either a relatively unstable and transient chemical species or a relatively stable but reactive species. See also inert.
A copper-containing enzyme, 1,4-benzenediol oxidase (EC 1.10.3.2), found in higher plants and microorganisms. Laccases are multicopper oxidases of wide specificity that carry out one-electron oxidation of phenolic and related compounds, and reduce O2 to water. The enzymes are polymeric and generally contain one each of type 1, type 2, type 3 copper centers per subunit, where the type 2 and type 3 are close together forming a trinuclear copper cluster.
An iron-binding protein from milk, structurally similar to the transferrins.
A monomeric hemoglobin synthesised in the root nodules of leguminous plants that are host to nitrogen-fixing bacteria. Has a high affinity for dioxygen and serves as an oxygen supply for the bacteria.
A molecular entity that is an electron pair acceptor and therefore able to react with a Lewis base to form a Lewis adduct, by sharing the electron pair furnished by the Lewis base.
The adduct formed between a Lewis acid and a Lewis base.
A molecular entity able to provide a pair of electrons and thus capable of coordination to a Lewis acid, thereby producing a Lewis adduct.
In inorganic chemistry the ligands are the atoms or groups of atoms bound to the central atom (see also coordination). The root of the word is sometimes converted into the verb to ligate, meaning to coordinate as a ligand, and the derived participles, ligating and ligated. This use should not be confused with its use to describe the action of ligases (a class of enzymes). The names for anionic ligands, whether inorganic or organic, end in -o. In general, if the anion name ends in -ide, or -ate, the final -e is replaced by -o, giving -ido, and -ato, respectively. Neutral and cationic ligand names are used without modification. Ligands bonded by a single carbon atom to metals are regarded as radical substituents, their names being derived from the parent hydrocarbon, from which one hydrogen atom has been removed. In general, the final letter -e of the name is replaced by -yl.
In biochemistry the term ligand has been used more widely: if it is possible or convenient to regard part of a polyatomic molecular entity as central, then the atoms or groups or molecules bound to that part may be called ligands.
Ligand field theory is a modified crystal field theory that assigns certain parameters as variables rather than taking them as equal to the values found for free ions, thereby taking into account the potential covalent character of the metal-ligand bond.
An enzyme of EC class 6, also known as a synthetase, which catalyzes the formation of a bond between two substrate molecules coupled with the hydrolysis of a diphosphate bond of a nucleoside triphosphate or similar co-substrate.
See ligand.
A non-heme iron enzyme (EC 1.13.11.12) which catalyzes the insertion of O2 into polyunsaturated fatty acids to form hydroperoxy derivatives.
In any coordination entity with a particular dn (1 < n < 9) configuration and a particular geometry, if the n electrons are distributed so that they occupy the lowest possible energy levels, the entity is a low-spin complex. If some of the higher energy d orbitals are occupied before all the lower energy ones are completely filled, then the entity is a high-spin complex.
An enzyme of EC class 4, which catalyzes the separation of a bond in a substrate molecule.
Return to home page for Glossary of terms used in Bioinorganic Chemistry.