Cage, Calmodulin, Calpain, Carbonic anhydrase, Carbon monoxide dehydrogenases, Carboplatin, Cardiotech, Catabolism, Catalase, Catalytic antibody, CBS, CD, Central atom, Ceruloplasmin, Charge-transfer complex, Charge-transfer transition, Chaperonin, Chelation, Chelation therapy, Chemical shift, Chirality, Chlorin, Chlorophyll, Chloroplast, Chromophore, Circular dichroism, cis, Cisplatin, Clone, Cluster, Cobalamin, Codon, Coenzyme, Cofactor, Colloidal bismuth subcitrate, Comproportionation, Concanavalin A, Configuration, Conformation, Consensus sequence, Contrast agent, Cooperativity, Coordination, Corphin, Corrin, Crystal field, C-terminal amino-acid residue, Curie relation, Cytochrome, Cytochrome-c oxidase, Cytochrome P-450, Cytoplasm, Dehydrogenase, Denitrification, De-nol, Denticity, Deoxyribonucleic acid, Desferal, Desferrioxamine, dfo, Diamagnetic, Diastereoisomers, Dihydrofolate , Dinuclear, Dioxygenase, Dismutase, Dismutation, Disproportionation, Dissimilatory, Dissociation constant., DNA , Domain, Donor atom symbol, Double helix.
An aggregate of molecules, generally in the condensed phase, that surround the fragments formed by thermal or photochemical dissociation of a species.
A Ca2+ binding protein involved in metabolic regulation.
A calcium-activated neutral protease, EC 126.96.36.199.
A zinc-containing enzyme (carbonate hydro-lyase, carbonate dehydratase, EC 188.8.131.52) that catalyzes the reversible decomposition of carbonic acid to carbon dioxide and water.
Carbon monoxide dehydrogenases
Enzymes that catalyze the oxidation of carbon monoxide to carbon dioxide. They contain iron-sulfur clusters and either nickel and zinc, or molybdopterin. Some nickel-containing enzymes are also involved in the synthesis of acetyl coenzyme A from CO2 and H2.
A "second generation" platinum drug effective in cancer chemotherapy named: cis-diammine(cyclobutane-1,1-dicarboxylato)platinum(II). Carboplatin is less toxic than the "first generation" antitumor drug, cisplatin.
A species radiolabeled with 99mTc with formula [Tc(CNR)6]+(R=tert-butyl) known for imaging the heart after a heart attack.
Reactions involving the breaking down of organic substrates, typically by oxidative breakdown, to provide chemically available energy (e.g. ATP) and/or to generate metabolic intermediates used in subsequent anabolic reactions.
A hemeprotein (EC 184.108.40.206), which catalyzes the disproportionation of dihydrogen peroxide to O2 and water ; it also catalyzes the oxidation of other compounds, such as ethanol, by dihydrogen peroxide. A non-heme protein containing a dinuclear manganese cluster with catalase activity is often called pseudocatalase.
An antibody which catalyzes a chemical reaction analogous to an enzymatic reaction, such as an ester hydrolysis. It is obtained by using a hapten which mimics the transition state of the reaction. Also known as anabzyme.
Acronym for colloidal bismuth subcitrate. See de-nol.
See circular dichroism.
The atom in a coordination entity that binds other atoms or group of atoms (ligands) to itself, thereby occupying a central position in the coordination entity.
A copper protein present in blood plasma, containing type 1, type 2 and type 3 copper centers, where the type 2 and type 3 are close together, forming a trinuclear copper cluster. See also multicopper oxidases.
An aggregate of two or more molecules in which charge is transferred from a donor to an acceptor.
An electronic transition in which a large fraction of an electronic charge is transferred from one region of a molecular entity, called the electron donor, to another, called the electron acceptor (intramolecular charge-transfer) or from one molecular entity to another (intermolecular charge-transfer).
Member of the set of molecular chaperones, located in different organelles of the cell and involved either in transport of proteins through biomembranes by unfolding and refolding the proteins or in assembling newly formed polypeptides.
Chelation involves coordination of more than one sigma-electron pair donor group from the same ligand to the same central atom. The number of coordinating groups in a single chelating ligand is indicated by the adjectives didentate, tridentate, tetradentate, etc.
The judicious use of chelating (metal binding) agents for the removal of toxic amounts of metal ions from living organisms. The metal ions are sequestered by the chelating agents and are rendered harmless or excreted. Chelating agents such as 2,3-dimercaptopropan-1-ol, ethylenediaminetetraacetic acid, desferrioxamine and D-penicillamine have been used effectively in chelation therapy for arsenic, lead, iron and copper, respectively.
See nuclear magnetic resonance spectroscopy.
A term describing the geometric property of a rigid object (or spatial arrangement of points or atoms) that is non-superimposable on its mirror image; such an object has no symmetry elements of the second kind (a mirror plane, a centre of inversion, a rotation reflection axis). If the object is superimposable on its mirror image the object is described as being achiral.
2,3-Dihydroporphyrin. An unsubstituted, reduced porphyrin with two non-fused saturated carbon atoms (C-2, C-3) in one of the pyrrole rings.
Part of the photosynthetic systems in green plants. Generally speaking, it can be considered as a magnesium complex of a porphyrin in which a double bond in one of the pyrrole rings (17-18) has been reduced. A fused cyclopentanone ring is also present (positions 13-14-15).In the case of chlorophyll a, the substituted porphyrin ligand further contains four methyl groups inpositions 2, 7, 12 and 18, a vinyl group in position 3, an ethyl group in position 8 and a -(CH2)2CO2R group (R = phytyl, (2E)-(7R, 11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl) in position 17. In chlorophyll b, the group in position 7 is a -CHO group. In bacteriochlorophyll a the porphyrin ring is further reduced (7-8), andthe group in position 3 is now a -COCH3 group. In addition, in bacteriochlorophyll b, the group in position 8 is a =CHCH3 group.
The organelle of eukaryotic photosynthesis.
That part of a molecular entity consisting of an atom or group of atoms in which the electronic transition responsible for a given spectral band is approximately localized.
Circular dichroism (CD)
A spectroscopic method which measures the difference in absorbance of left- and right-handed circularly polarized light by a material, as a function of the wavelength. Most biological molecules, including proteins and nucleic acids, are chiral and show circular dichroism in their ultraviolet absorption bands, which may be used as an indication of secondary structure. Metal centers that are bound to such molecules, even if they have no inherent chirality, usually exhibit CD in absorption bands associated with ligand-based or ligand-metal charge-transfer transitions. CD is frequently used in combination with absorption and MCD studies to assign electronic transitions.
In inorganic nomenclature a structural prefix designating two groups occupying adjacent positions (not generally recommended for precise nomenclature purposes of complicated systems). See also trans.
cis-diamminedichloroplatinum(II). An antitumor drug highly effective in the chemotherapy of many forms of cancer. Of major importance in the antitumor activity of this drug is its interaction with the nucleic acid bases of DNA.
(1) A population of genetically identical cells produced from a common ancestor.
(2) Sometimes, "clone" is also used for a number of recombinant DNA molecules all carrying the same inserted sequence.
A number of metal centers grouped close together which can have direct metal bonding interactions or interactions through a bridging ligand, but are not necessarily held together by these interactions. Examples canbe found under the entries [2Fe-2S), [4Fe-4S], ferredoxin, HiPIP, iron-sulfur cluster, FeMo-cofactor, ferritin, metallothionein, nitrogenase, and Rieske iron-sulfur protein.
Vitamin B-12 or B12.A vitamin synthesized by microorganisms and conserved in animals in the liver. Deficiency or collective uptake of vitamin B-12 leads to pernicious anemia. Cobalamin is a substituted corrin-Co(III) complex in which the cobalt atom is bound to the four nitrogen atoms of the corrin ring, an axial group R and 5,6-dimethylbenzimidazole.The latter is linked to the cobalt by the N-3 nitrogen atom and is bound to the C-1 carbon of a ribose molecule by the N-1 nitrogen atom. Various forms of the vitamin are known with different R groups such as R = CN, cyanocobalamin; R = OH, hydroxocobalamin; R = CH3, methylcobalamin; R = adenosyl, coenzyme B-12.
A sequence of three consecutive nucleotides that occurs in mRNA and directs the incorporation of a specific amino acid into a protein, or represents the starting or termination signal of protein synthesis.
A low-molecular-weight, non-protein organic compound (often a nucleotide) participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons.
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Colloidal bismuth subcitrate (CBS)
The reverse of disproportionation.
A protein from jack beans, containing calcium and manganese, which agglutinates red blood cells and stimulates T lymphocytes to undergo mitosis.
In the context of stereochemistry, the term is restricted to the arrangements of atoms of a molecular entity in space that distinguishes stereoisomers, the isomerism between which is not due to conformational differences.
The spacial arrangements of atoms affording distinction between stereoisomers which can be interconverted by rotations about formally single bonds.
A sequence of DNA, RNA, protein or carbohydrate derived from a number of similar molecules, which comprises the essential features for a particular function.
Paramagnetic (or ferromagnetic) metal complex or particle causing a decrease in the relaxation times (increase in relaxivity) of nuclei detected in an image, usually of water.
The phenomenon that binding of an effector molecule to a biological system either enhances or diminishes the binding of a successive molecule, of the same or different kind, to the same system. The system may be an enzyme, or a protein that specifically binds another molecule such as oxygen or DNA. The effector molecule may be an enzyme substrate or an allosteric effector. The enzyme or protein exists in different conformations, with different catalytic rates or binding affinities, and binding of the effector molecule changes the proportion of these conformations. Enhanced binding is named positive cooperativity; diminished binding is named negative cooperativity. A well-known example of positive cooperativity is in hemoglobin. In biocatalysis it was originally proposed that only multi-subunit enzymes could respond in this way. However single-subunit enzymes may give such a response (so-called mnemonic enzymes).
A coordination entity is composed of a central atom, usually that of a metal, to which is attached a surrounding array of other atoms or group of atoms, each of which is called a ligand. A coordination entity may be a neutral molecule, a cation or an anion. The ligands may be viewed as neutral or ionic entities that are bonded to an appropriately charged central atom. It is standard practice to think of the ligand atoms that are directly attached to the central atom as defining a coordination polyhedron (tetrahedron, square plane, octahedron, etc.) about the central atom. The coordination number is defined as being equal to the number of sigma-bonds between ligands and the central atom; this definition is not necessarily appropriate in all areas of (coordination) chemistry. In a coordination formula, the central atom is listed first. The formally anionic ligands appear next and they are listed in alphabetic order according to the first symbols of their formula. The neutral ligands follow, also in alphabetical order, according to the same principle. The formula for the entire coordination entity, whether charged or not, is enclosed in square brackets. In a coordination name, the ligands are listed in alphabetical order, without regard to charge, before the name of the central atom. Numerical prefixes indicating the number of ligands are not considered in determining that order. All anionic coordination entities take the ending -ate, whereas no distinguishing termination is used for cationic or neutral coordination entities.
Corphin is the F-430cofactor found in methyl-coenzyme M reductase, a nickel containing enzyme that catalyzes one step in the conversion of CO2 to methane in methanogenic bacteria. The Ni ion in F-430 is coordinated by the tetrahydrocorphin ligand. This ligand combines the structural elements of both porphyrins and corrins.
A ring-contracted porphyrin derivative that is missing a carbon from one of the mesopositions (C-20). It constitutes the skeleton C19H22N4 upon which various B-12 vitamins, cofactors and derivatives are based.
Crystal field theory is the theory which interpretes the properties of coordination entities on the basis that the interaction of the ligands and the central atom is a strictly ionic or ion-dipole interaction resulting from electrostatic attractions between the central atom and the ligands. The ligands are regarded as point negative (or partially negative) charges surrounding a central atom; covalent bonding is completely neglected. The splitting or separation of energy levels of the five degenerate d orbitals in a transition metal, when the metal is surrounded by ligands arranged in a particular geometry with respect to the metal center, is called the crystal field splitting.
C-terminal amino-acid residue
See amino-acid residue.
See magnetic susceptibility.
A heme protein that transfers electrons,and exhibits intense absorption bands (the and bands, the band having the longer wavelength) between 510 and 615 nm in the reduced form. Cytochromes are designated types a, b, c or d, depending on the position of the band, which depends on the type of heme. The iron undergoes oxidation-reduction between oxidation states Fe(II)and Fe(III). Most cytochromes are hemochromes, in which the fifth and sixth coordination sites in the iron are occupied by strong field ligands, regardless of the oxidation state of iron. Cytochromes may be distinguished by the wavelength of the band, such as cytochrome c-550. Certain specific cytochromes with particular functions, are designated with suffixes, such as cytochrome a1,b2, etc., but this practice is discouraged.
An enzyme,ferrocytochrome-c:dioxygen oxidoreductase, EC 220.127.116.11, cytochrome aa3. The major respiratory protein of animal and plant mitochondria, it catalyzes the oxidation of Fe(II)-cytochrome c, and the reduction of dioxygen to water. Contains two hemes and three copper atoms, arranged in three centers. Heme a3 and copper-B form a center that reacts with dioxygen;the second heme is cytochrome a; the third site, copper-A,is a dinuclear center.
General term for a group of heme-containing monooxygenases (EC 18.104.22.168). Named from the prominent absorption band of the Fe(II)-carbonyl complex. The heme comprises protophorphyrin IX, and the proximal ligand to iron is a cysteine sulfur. Cytochromes P-450 of microsomes in tissues such as liver are responsible for metabolism of many xenobiotics, including drugs. Others, such as the mitochondrial enzymes from adrenal glands, are involved in biosynthetic pathways such as those of steroids. The reaction with dioxygen appears to involve higher oxidation states of iron, such as Fe(IV)=O.
The part of protoplasm in a cell outside of and surrounding the nucleus.
An oxidoreductase which catalyzes the removal of hydrogen atoms from a substrate.
The reduction of nitrates to nitrites, nitrogen monoxide (nitric oxide), dinitrogen oxide (nitrous oxide) and ultimately dinitrogen catalyzed by microorganisms, e.g.facultative aerobic soil bacteria under anaerobic conditions.
Trade name for the potassium salt or mixed ammonium potassium salt of a bismuth citrate complex, used in the treatment of ulcers.
The number of donor groups from a given ligandattached to the same central atom.
Deoxyribonucleic acid (DNA)
A high-molecular-mass linear polymer, composed of nucleotides containing 2-deoxyribose and linked between positions 3' and 5' by phosphodiester groups; DNA contains the geneticinformation of organisms. The double-stranded form consists of a double helix of two complementary chains that run in opposite directions and are held together by hydrogen bonds between pairs of the complementary nucleotides. The way the helices are constructed may differ and is usually designated as A, B, Z, etc. Occasionally, alternative structures are found, such as those with Hoogsteen base pairing.
Chelating agent used world-wide in the treatment of iron overload conditions, such as hemochromatosis and thalassemia.
Substances having a negative magnetic susceptibility are diamagnetic. They are repelled by a magnetic field.
Diastereoisomers are stereoisomers not related as mirror images.
An oxidation product of tetrahydrofolate that appears during DNA synthesis and other reactions. It must be reduced to tetrahydrofolate to be of further use. See also folate coenzymes.
An enzyme that catalyzes the insertion of two oxygen atoms into a substrate, both oxygens being derived from O2.
An enzyme that catalyzes a disproportionation reaction.
Any chemical reaction of the type
Related to the conversion of food or other nutrients into products plus energy-containing compounds.
See stability constant.
See deoxyribonucleic acid.
An independently folded unit within a protein, often joined by a flexible segment of the polypeptide chain.
Donor atom symbol
A polydentate ligandpossesses more than one donor site, some or all of which may be involved in coordination. To indicate the points of ligation, a system is needed. The general and systematic system for doing this is called the kappa convention: single ligating atom attachments of a polyatomic ligand to a coordination centre are indicated by the italic element symbol preceded by a Greek kappa, . In earlier practice, the different donors of the ligand were denoted by adding to the end of the name of the ligand the italicized symbol(s) for the atom or atoms through which attachment to the metal occurs.
Two strands of DNAcoiled about a central axis, usually a right-handed helix. The two sugar phosphate backbones wind around the outside of the bases (A = adenine, G = guanine, T = thymine, C = cytosine) and are exposed to the solvent. The strands are antiparallel, thus the phosphodiester bonds run in opposite directions. As a result the structure has major and minor grooves at the surface. Each adenine in one strand of DNA is hydrogen bonded to a thymine in the second strand; each guanine is hydrogen bonded to a cytosine.
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