E to G

Contents

EC nomenclature for enzymes, EDRF, EF-Hand, Electrode potential, Electron magnetic resonance spectroscopy, Electron-nuclear double resonance, Electron paramagnetic resonance spectroscopy, Electron spin-echo envelope modulation, Electron spin-echo spectroscopy, Electron spin resonance spectroscopy, Electron transfer protein, EMR, Enantiomer, Endogenous, ENDOR, Endothelium-derived relaxing factor, Entatic state, Enterobactin, Enterochelin, Enzyme, EPR, Equilibrium constant, ESE, ESEEM, ESR, Eukaryotes, Ewens-Bassett number, EXAFS, Exogenous, Exon, Expression, Extended X-ray absorption fine structure, F-430, FeMo-cofactor, Fenton reaction, Ferredoxin, Ferriheme, Ferritin, Ferrochelatase, Ferroheme, Ferromagnetic, [2Fe-2S], [4Fe-4S], Flavin, Fluxional, Folate coenzymes, Formation constant, Fur, Gamma([[gamma]]) band, Gene, g-factor, Gold drugs, Greek letters used as entry in this glossary, Guanylate cyclase.

A classification of enzymes according to the Enzyme Commission of the International Union of Biochemistry and Molecular Biology. Enzymes are allocated four numbers, the first of which defines the type of reaction catalyzed, the next two define the substrates, and the fourth is a catalogue number. Categories of enzymes are EC 1, Oxidoreductases; EC 2, Transferases; EC 3, Hydrolases; EC 4, Lyases; EC 5, Isomerases; EC 6, Ligases (Synthetases).

EDRF

See endothelium-derived relaxing factor.

EF-Hand

A common structure to bind Ca²⁺ in calmodulin and other Ca²⁺ binding proteins consisting of a helix (E), a loop and another helix (F).

Electrode potential

The so-called electrode potential of an electrode is defined as the electromotive force (emf) of a cell in which the electrode on the left is a standard hydrogen electrode and the electrode on the right is the electrode in question. See also redox potential.

Electron magnetic resonance (EMR) spectroscopy.

See electron paramagnetic resonance spectroscopy.

Electron-nuclear double resonance (ENDOR)

A magnetic resonance spectroscopic technique for the determination of hyperfine interactions between electrons and nuclear spins. There are two principal techniques. In continuous-wave ENDOR the intensity of an electron paramagnetic resonance signal, partially saturated with microwave power, is measured as radiofrequency is applied. In pulsed ENDOR the radiofrequency is applied as pulses and the EPR signal is detected as a spin-echo. In each case an enhancement of the EPR signal is observed when the radiofrequency is in resonance with the coupled nuclei.

Electron paramagnetic resonance (EPR) spectroscopy

The form of spectroscopy concerned with microwave-induced transitions between magnetic energy levels of electrons having a net spin and orbital angular momentum. The spectrum is normally obtained by magnetic field scanning. Also known as electron spin resonance (ESR) spectroscopy or electron magnetic resonance (EMR) spectroscopy. The frequency () of the oscillating magnetic field to induce transitions between themagnetic energy levels of electrons is measured in gigahertz (GHz) or megahertz (MHz). The following band designations are used: L (1.1 GHz), S (3.0 GHz) , X (9.5 GHz), K (22.0 GHz) and Q (35.0 GHz). The static magnetic field at which the EPR spectrometer operates is measured by the magnetic flux density (B) and its recommended unit is the tesla (T). In the absence of nuclear hyperfine interactions, B and are related by : h = g _BB whereh is the Planck constant, _B is the Bohr magneton, and the dimensionless scalar g is called the g-factor. When the paramagnetic species exhibits an anisotropy, the spatial dependency of the g-factor is represented by a 3x3 matrix. The interaction energy between the electron spin and a magnetic nucleus is characterized by the hyperfine coupling constant A. When the paramagnetic species has anisotropy, the hyperfine coupling is expressed by a 3x3 matrix called a hyperfine coupling matrix. Hyperfine interaction usually results in splitting of lines in an EPR spectrum. The nuclear species giving rise to the hyperfine interaction should be explicitly stated, e.g."the hyperfine splitting due to ⁶⁵Cu". When additional hyperfine splittings due to other nuclearspecies are resolved ("superhyperfine"), the nomenclature should include the designation of the nucleus, and the isotopic number.

Electron spin-echo envelope modulation (ESEEM)

See electron spin-echo spectroscopy.

Electron spin-echo (ESE) spectroscopy

A pulsed technique in electron paramagnetic resonance, in some ways analogous to pulsed techniques in NMR. ESE may be used for measurements of electron spin relaxation times as they are influenced by neighbouring paramagnets or molecular motion. It may also be used to measure anisotropicnuclear hyperfine couplings. The effect is known as electron spin-echo envelope modulation (ESEEM). The intensity of the electron spin-echo resulting from the application of two or more microwave pulses is measured as a function of the temporal spacing between the pulses. The echo intensity is modulated as a result of interactions with the nuclear spins. The frequency-domain spectrum corresponds to hyperfine transition frequencies.

Electron spin resonance (ESR) spectroscopy

See electron paramagnetic resonance spectroscopy.

Electron transfer protein

A protein, often containing a metal ion, that oxidizes and reduces other molecules by means of electron transfer.

EMR

Acronym for electron magneticresonance. See electron paramagnetic resonancespectroscopy.

Enantiomer

One of a pair of molecular entities that are mirror images of each other and non-superimposable.

Endogenous

Originating internally. In the description of metal ion coordination in metalloproteins, endogenous refers to internal, or protein-derived, ligands.

ENDOR

Acronym for electron-nuclear double resonance.

Endothelium-derived relaxing factor (EDRF)

The factor originally describedas EDRF is NO^., produced by a specific P-450-type of enzyme from arginine upon response of a cell to a biological signal (molecule). Different types of cells respond differently to the presence of NO^.. See also cytochrome P-450.

Entatic state

A state of an atom or group which due to its binding in a protein, has its geometric or electronic condition adapted for function. Derived from entasis (Greek) meaning tension.

Enterobactin

A siderophore found in enteric bacteria such as Escherichia coli; sometimes called enterochelin.

Enterochelin

See enterobactin.

Enzyme

A macromolecule that functions as a biocatalyst by increasing the reaction rate, frequently containing or requiring one or more metal ions. In general, an enzyme catalyzes only one reaction type (reaction specificity) and operates on only a narrow range of substrates (substrate specificity). Substrate molecules are attacked at the same site (regiospecificity) and only one or preferentially one of the enantiomers of chiral substrate or of racemic mixtures is attacked (enantiospecificity).

EPR

See electron paramagnetic resonance spectroscopy.

Equilibrium constant

See acidity constant and stability constant.

ESE

See electron spin-echo spectroscopy.

ESEEM

Acronym for electron spin-echo envelope modulation. See electron spin-echo spectroscopy.

ESR

Acronym for electron spin resonance. See electron paramagnetic resonance spectroscopy.

Eukaryotes

Organisms whose cells have their genetic material packed in a membrane-surrounded, structurally discrete nucleus, and that have well-developed cell organelles. Eukaryotes include all organisms except archaea and eubacteria. See also prokaryote.

Ewens-Bassett number

See oxidation number.

EXAFS

Acronym for extended X-ray absorption finestructure.

Exogenous

Originating externally. In the context of metalloprotein ligands, exogenous describes ligands added from an external source, such as CO or O₂.

Exon

A section of DNA which carries the coding sequence for a protein or part of it. Exons are separated by intervening, non-coding sequences (called introns). In eukaryotes most genes consist of a number of exons.

Expression

The cellular production of the protein encoded by a particular gene. The process includes transcriptionof DNA, processing of the resulting mRNA product and its translation into an active protein.

N.B. A recombinant gene inserted into a host cell by means of a vector is said to be expressed if the synthesis of the encoded polypeptide can be demonstrated. For the expression of metalloproteins usually other gene products will be required.

Extended X-ray absorption fine structure (EXAFS)

EXAFS effects arise because of electron scattering by atoms surrounding a particular atom of interest as that special atom absorbs X-rays and emits electrons. The atom of interest absorbs photons at a characteristic wavelength and the emitted electrons, undergoing constructive or destructive interference as they are scattered by the surrounding atoms, modulate the absorption spectrum. The modulation frequency corresponds directly to the distance of the surrounding atoms while the amplitude is related to the type and number of atoms. EXAFS studies are a probe of the local structure.EXAFS can be applied to systems which have local structure, but not necessarily long-range structure, such as non-crystalline materials. In particular, bond lengths and local symmetry (coordination numbers) may be derived. The X-ray absorption spectrum may also show detailed structure below the absorption edge. This X-ray absorption near edge structure (XANES) arises from excitation of core electrons to high level vacant orbitals.

F-430

A tetrapyrrole structure containing nickel, a component of the enzyme methyl-coenzyme M reductase, which is involved in the formation of methane in methanogenic bacteria. The highly reduced macrocyclic structure, related to porphyrins and corrins, is termed a corphin.

FeMo-cofactor

An inorganic clusterthat is found in the FeMo protein of the molybdenum-nitrogenase and is essential for the catalytic reduction of N₂ to ammonia. This cluster contains Fe, Mo and S in a 7:1:9 ratio. The structure of the cofactor within the FeMo protein can be described in terms of two cuboidal subunits, Fe₄S₃ and MoFe₃S₃ bridged by three S^2- ions and "anchored" to the protein by a histidine bound via an imidazole group to the Mo atom and by a cysteine bound via a deprotonated SH group to an Fe atom of the Fe₄S₃ subunit. The Mo atom at the periphery of the molecule is six-coordinate and in addition to the three sulfido ligands and the histidine imidazole is also bound to two oxygen atoms from an (R)-homocitrate molecule.

Fenton reaction

Fe²⁺ + H₂O₂ Fe³⁺ + OH^. + OH^-. This is the iron-salt-dependent decomposition of dihydrogen peroxide, generating the highly reactive hydroxyl radical, possibly via an oxoiron(IV) intermediate. Addition of a reducing agent such as ascorbate leads to acycle which increases the damage to biological molecules. See also Haber-Weiss reaction.

Ferredoxin

A protein containing more than one iron and acid-labile sulfur, that displays electron-transferactivity but not classical enzyme function. See also HiPIP.

Ferriheme

An iron(III) porphyrin coordination complex.

Ferritin

An iron storage protein consisting of a shell of 24 protein subunits, encapsulating up to 4500 iron atoms in the form of a hydrated iron(III) oxide.

Ferrochelatase

An enzyme which catalyzes the insertion of iron into protoporphyrin IX to form heme. The mammalian enzyme contains an iron-sulfur cluster.

Ferroheme

An iron(II) porphyrin coordination complex.

Ferromagnetic

If there is coupling between the individual magnetic dipole moments of a paramagnetic sample, spontaneous ordering of the moments will occur at low temperatures. If this ordering results in an electronic ground state in which the moments are aligned in the same direction (parallel), the substance is said to be "ferromagnetic". If the ordering results in an electronic ground state in which the moments are aligned in opposite directions, the substance is said to be "antiferromagnetic".

[2Fe-2S]

Designation of a two-iron, two-labile-sulfur cluster in a protein, comprising two sulfido-bridged iron atoms. The oxidation levels of the clusters are indicated by adding the charges on the iron and sulfide atoms, i.e. [2Fe-2S]²⁺; [2Fe-2S]⁺. The alternative designation, which conforms to inorganic chemical convention is to include the charges on the ligands; this is more appropriate where the ligands are other than the usual cysteine sulfurs, such as in the Rieske proteins. See also ferredoxin.

[4Fe-4S]

Designation of a four-iron, four-labile-sulfur cluster in a protein. (See [2Fe-2S]). Possible oxidation levels of the clusters are [4Fe-4S]³⁺; [4Fe-4S]²⁺; [4Fe-4S]⁺. See also ferredoxin, HiPIP.

Flavin

A prosthetic group found in flavoproteins and involved in biological oxidation and reduction.The oxidized flavin can be reduced stepwise by two electrons with the concomitant stepwise acceptance of two hydrons to give flavin semiquinone and flavin hydroquinone.

Fluxional

In inorganic chemistry this term is used to designate positional changes among ligands. A fluxional chemical species undergoes rapid (degenerate) rearrangements, generally detectable by methods that observe the behaviour of individual nuclei in a rearranged chemical species.

Folate coenzymes

A group of heterocyclic compounds that are based on the 4-(2-amino-3,4-dihydro-4-oxopteridin-6-ylmethylamino)benzoic acid (pteroic acid) and conjugated with one or more L-glutamate units. Folate derivatives are important in DNA synthesis and erythrocyte formation. Folate deficiency leads to anemia.

Formation constant

See stability constant.

Fur

The iron uptake regulating protein present in prokaryotes, which binds simultaneously Fe and DNA thereby preventing the biosynthesis of enzymes for the production of scavenger chelates (siderophores).

Gamma() band

Identical to Soret band.

Gene

Structurally, a basic unit of hereditary material; an ordered sequenceof nucleotide bases that encodes one polypeptide chain (via mRNA). The gene includes, however, regions preceding and followingthe coding region (leader and trailer) as well as (in eukaryotes) intervening sequences (introns) between individual coding segments (exons). Functionally, the gene is defined by the cis-trans test that determines whether independent mutations of the same phenotype occur within a single gene or in several genes involved in the same function.

g-factor

See electron paramagnetic resonance spectroscopy.

Gold drugs

Gold coordinationcompounds used in the treatment of rheumatoid arthritis, examples being auranofin, (tetraacetylthioglucosato-S)(triethylphosphane)gold(I), and myocrysin, disodium thiomalonatogold(I).

Greek letters used as entry in this glossary

: See helix(for alpha helix) and Cytochrome

: See beta sheet, beta strand , beta turn and Cytochrome

: See Soret band (for gamma band)

: See hapto and Asymmetry parameter

: See donor atom symbol (for kappa-convention)

: See bridging ligand (for mu-symbol)

Guanylate cyclase

An enzyme catalyzing the conversion of guanosine 5'-triphosphate to cyclicguanosine 3',5'-monophosphate, which is involved in cellular regulation processes. One member of this class is a heme-containing enzyme involved in processes regulated by nitrogen monoxide.

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