Scavenger, Schiff bases, Secondary structure, Sequence, Sequence-directed mutagenesis, Serum, Siderophore, Siroheme, Site-directed mutagenesis, SOD, Soft acid, Soft base, Solvation, Solvolysis, Soret band, Speciation, Spin label, Spin-orbit coupling, Spin probe, Spin-spin coupling, Spin trapping, Square plane, Stability constant, Stable, Steady state, Stellacyanin, Stereochemical, Stereoisomeric, Stock number, Substrates, Subunit, Sulfite reductase, Superhyperfine, Superoxide dismutases, Supramolecular chemistry, Syn, Synthase, Synthetase, Tertiary structure, Tetrahedron, Tetrahydrofolates, Thalassemia, Therapeutic index, Thermolysin, Thermolysis, Thylakoids, Toxicity, Trace elements, trans, Transcription, Transduction, Transferase, Transferrin, Transition element, Translation, Trapping, Type 1,2,3 copper, Tyrosin, Urease, Vitamin B-12, Wild type, Wilson's disease, XANES, Xenobiotic, X-ray absorption near edge structure, Zinc finger, Zwitterionic compound.
A substance that reacts with (or otherwise removes) a trace component or traps a reactive reaction intermediate (as in the scavenging of radicals or free electrons in radiation chemistry).
Imines bearing a hydrocarbyl group on the nitrogen atom: R2C=NR' (R' H).
Level of structural organization in proteins described by the folding of the polypeptide chain into structural motifs such as alpha helices and beta sheets, which involve hydrogen bonding of backbone atoms. Secondary structure is also formed in nucleic acids, especially in single-stranded RNA's by internal base pairing.
The order of neighbouring amino acids in a protein or the purine and pyrimidine bases in RNA or DNA. See also primary structure.
Generic term for Fe(III)-complexing compounds released into the medium by bacteria for the purpose of scavenging iron.
A heme-like prosthetic group found in a class of enzymes that catalyze the six-electron reduction of sulfite and nitrite to sulfide and ammonia, respectively. See also sulfite reductase and nitrite reductase.
See superoxide dismutase.
See hard acid.
See hard base.
Any stabilizing interaction of a solute (or solute moiety) and the solvent or a similar interaction with solvent of groups of an insoluble material (i.e., the ionic groups of an ion-exchange resin). They generally involve electrostatic forces and Van der Waals forces, as well as chemically more specific effects such as hydrogen bond formation.
Reaction with a solvent involving the rupture of one or more bonds in the reacting solute.
A very strong absorption band in the blue region of the optical absorption spectrum of a heme protein.
Refers to the chemical form or compound in which an element occurs in both non-living and living systems. It may also refer to the quantitative distribution of an element. In biology, it refers to the origination of a new species. See also bioavailability.
A stable paramagnetic group that is attached to a part of another molecular entity whose microscopic environment is of interest and may be revealed by the electron paramagnetic resonance spectrum of the spin label. When a simple paramagnetic molecular entity is used in this way without covalent attachment to the molecular entity of interest it is frequently referred to as a "spin probe".
The interaction of the electron spin magnetic moment with the magnetic moment due to the orbital motion of the electron.
See spin label.
The interaction between the spin magnetic moments of different electrons and/or nuclei. In NMR spectroscopy it gives rise to multiplet patterns, and cross-peaks in two-dimensional NMR spectra. Between electron and nuclear spins this is termed the nuclear hyperfine interaction. Between electron spins it gives rise to relaxation effects and splitting of the EPR spectrum.
In certain solution reactions a transient radical will interact with a diamagnetic reagent to form a more "persistent" radical. The product radical accumulates to a concentration where detection and, frequently, identification are possible by electron paramagnetic resonance spectroscopy. The key reaction is usually one of attachment; the diamagnetic reagent is said to be a "spin trap", and the persistent product radical is then the "spin adduct".
An equilibrium constant that expresses the propensity of a species to form from its component parts. The larger the stability constant, the more stable is the species. The stability constant (formation constant) is the reciprocal of the instability constant (dissociation constant).
Stable is a term describing a system in a state of equilibrium corresponding to a local minimum of the appropriate thermodynamic potential for the specified constraints on the system. Stability cannot be defined in an absolute sense, but if several states are in principle accessible to the system under given conditions, that with the lowest potential is called the stable state, while the other states are described as metastable. Unstable states are not at a local minimum. Transitions between metastable and stable states occur at rates which depend on the magnitude of the appropriate activation energy barriers which separate them.
If during the course of a chemical reaction the concentration of an intermediate remains constant, the intermediate is said to be in a steady state. In a static system a reaction intermediate reaches a steady-state if the processes leading to its formation and those removing it are approximately in balance. The steady-state hypothesis leads to a great simplification in reaching an expression for the overall rate of a composite reaction interms of the rate constants for the individual elementary steps. Care must be taken to apply the steady-state hypothesis only to appropriate reaction intermediates. An intermediate such as an atom or a free radical, present at low concentrations, can usually be taken to obey the hypothesis during the main course of the reaction. In a flow system a steady-state may be established even for intermediates present at relatively high concentrations.
An electron transferprotein, containing a type 1 copper site, isolated from exudates of the Japanese lacquer tree.
Refers to the three-dimensional view of a molecule either as such or in a projection.
Isomerism due to difference in the spatial arrangement of atoms without any difference in connectivity or bond multiplicity between the isomers.
See oxidation number.
(1) A chemical species of particular interest, the reaction of which with some other chemical reagent is under observation (e.g. a compound that is transformed under the influence of a catalyst).
(2) The chemical entity whose conversion to a product or products is catalyzed by an enzymes.
(3) A solution or dry mixture containing all ingredients which are necessary for the growth of a microbial culture or for product formation.
(4) A component in the nutrient medium, supplying the organisms with carbon (C-substrate), nitrogen (N-substrate) etc.
An individual polypeptide chain in a protein, containing more than one polypeptide chain. Different types of subunits are frequently designated by , , , etc.
Enzymes (EC 184.108.40.206, 220.127.116.11, 18.104.22.168) which catalyze the reduction of sulfite to sulfide. All known enzymes of this type contain siroheme and iron-sulfur clusters.
See electron paramagnetic resonance spectroscopy.
Superoxide dismutases (SOD)
Enzymes (EC 22.214.171.124) which catalyze the dismutation reaction of superoxide anion to dihydrogen peroxide and dioxygen. The enzymes have active sites containing either copper and zinc (Cu/Zn-superoxide dismutase), or iron (Fe-superoxide dismutase), or manganese (Mn-superoxide dismutase).
This is defined as the chemistry of molecular assemblies and of the intermolecular bond, as "chemistry beyond the molecule", bearing on the organized entities of higher complexity that result from the association of two or more chemical species held together by intermolecular forces. Thus, supramolecular chemistry may be considered to represent a generalized coordination chemistry extending beyond the coordination of transition elements by organic and inorganic ligands to the bonding of all kinds of substrates; cationic, anionic and neutral species of either inorganic, organic or biological nature.
An enzyme that catalyzes a reaction in which a particular molecule is synthesized, not necessarily by formation of a bond between two molecules (contrast synthetase).
The overall three-dimensional structure of a biopolymer. For proteins this involves the side chain interactions and packing of secondary structure motifs. For nucleic acids this may be the packing of stem-loops or supercoiling of double helices.
Reduced folate derivatives that contain additional hydrogen atoms in positions 5, 6, 7 and 8. Tetrahydrofolates are the carriers of activated one carbon units and are important in the biosynthesis of amino acids and precursors needed for DNA synthesis. See also folate coenzymes.
A chronic inherited disease characterized by defective synthesis of hemoglobin. Defective synthesis of the chain of hemoglobin is called -thalassemia and defective synthesis of the chain ofhemoglobin is called -thalassemia. Thalassemias result in anemia that can be severe and are found more frequently in areas where malaria is endemic.
For a substance used to alleviate disease, pain or injury the therapeutic index is the ratio between toxic and therapeutic doses (the higher the ratio, the greater the safety of the therapeutic dose).
A calcium- and zinc-containing neutral protease (EC 126.96.36.199) isolated from certain bacteria.
An uncatalysed bond cleavage resulting from exposure of a compound to a raised temperature.
Enclosed membrane structures inside chloroplasts and photosynthetic bacteria.
The action of poisons (including xenobiotics) on biochemical reactions or processes in living organisms or ecological systems. A study of this action is the subject matter of toxicology.
Elements required for physiological functions in very small amounts that vary for different organisms.Included among the trace elements are Co, Cu, F, Fe, I, Mn, Mo, Ni, Se, V, W, and Zn. Excess mineral intake may produce toxic symptoms.
In inorganic nomenclature a structural prefix designating two groups directly across a central atom from each other (not generally recommended for precise nomenclature purposes of complicated systems). See also cis.
The process by which the genetic information encoded in a linear sequence of nucleotides in one strand of DNA is copied into an exactly complementary sequence of RNA.
(1) The transfer of genetic information from one bacterium to another by means of a transducing bacteriophage. When the phage is grown on the first host, a fragment of the host DNA can be incorporated into the phage particles. This foreign DNA can be transferred to the second host upon infection with progeny phage from the first experiment.
(2) In cell biology the transduction of a signal (mechanical signal, hormone, etc.) to cells or tissues summarizes the chain of events between the primary reception of the signal and the final response (change in growth and/or metabolism) of the target cells or tissues. Inorganic substances (e.g., calcium ions) are frequently involved in the transduction of signals.
An enzyme of EC class 2, which catalyzes the transfer of a group from one substrate to another.
An iron-transport protein of blood plasma, which comprises two similar iron-binding domains with high affinity for Fe(III). Similar proteins are found in milk (lactoferrin) and eggs (ovotransferrin).
A transition element is an element whose atom has an incomplete d-sub-shell, or which gives rise to a cation or cations with an incomplete d-sub-shell. The First Transition Series of elements is Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu. The Second and Third Transition Series are similarly derived: these include the lanthanoids (lanthanides) and actinoids (actinides) respectively which are designated inner (or f) transition elements of their respective Periods in the Periodic Table.
The unidirectional process that takes place on the ribosomes whereby the genetic information present in an mRNA is converted into a corresponding sequence of amino acids in a protein.
The interception of a reactive moleculeor reaction intermediate so that it is removed from the system or converted into a more stable form for study or identification.
Type 1,2,3 copper
Different classes of copper-binding sites in proteins, classified by their spectroscopic properties as Cu(II). In type 1, or blue copper centers the copper is coordinated to at least two imidazole nitrogens from histidine and one sulfur from cysteine. They are characterized by small copper hyperfine couplings and a strong visible absorption in the Cu(II) state. In type 2, or non-blue copper sites, the copper is mainly bound to imidazole nitrogens from histidine. Type 3 copper centers comprise two spin-coupled copper ions, bound to imidazole nitrogens.
A copper protein containing an antiferromagnetically coupled dinuclear copper unit (type 3 like site) which oxygenates the tyrosine group to catechol and further oxidizes this to the quinone.
A nickel enzyme, urea amidohydrolase (EC 188.8.131.52), that catalyzes the hydrolysis of urea to ammonia and carbon dioxide. The active site comprises two Ni(II) ions, bridged by a carbamate.
The most frequently encountered genotype in natural breeding populations.
An inherited condition in which copper fails to be excreted in the bile. Copper accumulates progressively in the liver, brain, kidney and red blood cells. As the amount of copper accumulates hemolytic anaemia, chronic liver disease and a neurologic syndrome develop. See also chelation therapy.
Acronym for X-ray absorption near edge structure. See extended X-ray absorption fine structure.
A xenobiotic (Greek, xenos "foreign"; bios "life") is a compound that is foreign to a living organism. Principal xenobiotics include: drugs, carcinogens and various compounds that have been introduced into the environment by artificial means.
X-ray absorption near edge structure (XANES)
See extended X-ray absorption fine structure.
A domain, found in certain DNA-binding proteins, comprising a helix-loop structure in which a zinc ion is coordinated to 2 - 4 cysteine sulfurs, the remaining ligands being histidines. In many proteins of this type the domain is repeated several times.
A neutral compound having electrical charges of opposite sign, delocalized or not, on adjacent or non-adjacent atoms.