A and B

Contents

Absolute configuration, Abzyme, Achiral, Acid, Acidity constant, Acid-labile sulfide, Aconitase, Active center, Active site, Adenosine 5'-triphosphate, Adrenodoxin, Aerobe, Albumin, Allosteric effector , Allosteric enzyme, Alpha() helix, Ambidentate, Amicyanin, Amino-acid residue, Anabolism, Anemia, Anaerobe, Anation, Anisotropy, Anti, Antibody, Antiferromagnetic, Antigen, Apoprotein, Aquation, Archaea, Assimilation, Assimilative, Assimilator, Asymmetric synthesis, Asymmetry parameter, ATP, Auranofin, Autotrophic organisms, Auxotroph, Azurin, Bacteriochlorin, Bacteriochlorophyll, Base, Base pairing, Basicity constant, Beta() sheet, Beta() strand, Beta() turn, Bifunctional ligand, Binding constant, Binding site, Binuclear, Bioassay, Bioavailability, Biocatalyst, Bioconjugate, Bioconversion, Bioleaching, Biological half life, Biomass, Biomembrane, Biomimetic, Biomineralization, Biopolymers, Biosensor, Biotransformation, Bleomycin, BLM , Blotting, Blue copper protein, Bone imaging , Brain imaging, Bridging ligand, Brønsted acid, Brønsted base.

The spatial arrangement of the atoms of a chiral molecular entity (or group) and its stereochemical description.

Abzyme

See catalytic antibody.

Achiral

See chirality.

Acid

See Brønsted acid, Lewis acid, hard acid, soft acid.

Acidity constant

The equilibrium constant for splitting off a hydron from a Brønsted acid.

Acid-labile sulfide

Refers to sulfido ligands, e.g. the bridging ligands in iron-sulfur proteins, which are released as H₂S at acid pH. See also ferredoxin.

Aconitase

Trivial name for citrate (isocitrate)hydro-lyase (aconitate hydratase), EC4.2.1.3, which catalyzes the interconversion of citrate, cis-aconitate ((Z)-prop-1-ene-1,2,3-tricarboxylate) and isocitrate. The active enzyme contains a catalytic [4Fe-4S] cluster.

Active center

The location in an enzyme where the specific reaction takes place.

Active site

See active center.

Adenosine 5'-triphosphate (ATP)

Key nucleotide in energy-dependent cellular reactions, in combination with Mg(II). The reaction: ATP + water ADP + phosphate is used to supply the necessary energy.

Adrenodoxin

A [2Fe-2S] ferredoxin involved in electron transfer from NADPH⁺ (via a reductase) to cytochrome P-450 in the adrenal gland.

Aerobe

An organism that needs dioxygen for respiration and thus for growth.

Albumin

A type of protein, especially aprotein of blood plasma which transports various substances, including metal ions, drugs and xenobiotics.

Allosteric effector

Specific small molecules that bind to aprotein at a site other than a catalytic site and modulate (by activation or inhibition) the biological activity.

Allosteric enzyme

An enzymethat contains a region, separate from the region that binds the substrate for catalysis, where a small, regulatory molecule binds and affects that catalytic activity. This effector molecule may be structurally unrelated to the substrate, or may be a second molecule of substrate. If the catalytic activity is enhanced by binding, the effector is called an activator; if it is diminished, the effector iscalled an inhibitor.

Alpha() helix

See helix.

Ambidentate

Ligands, such as (NCS)^-, that can bond to a central atom through either of two or more donor atoms are termed ambidentate.

Amicyanin

An electron transfer protein containing a type 1 copper site, isolated from certain bacteria.

Amino-acid residue (in a polypeptide)

When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called anamino-acid residue. Amino-acid residues are therefore structures that lack a hydrogen atom of the amino group (-NH-CHR-COOH), or the hydroxy moiety of the carboxy group (NH₂-CHR-CO-), or both (-NH-CHR-CO-); all units of a peptide chain are therefore amino-acid residues. (Residues of amino acids that contain two amino groups or two carboxy groups may be joined by isopeptide bonds, and so may not have the formulas shown). The residue in a peptide that has an amino group that is free, or at least not acylated by another amino-acid residue (it may, for example, be acylated or formylated), is called N-terminal; it is the N-terminus. The residue that has a free carboxy group, or at least does not acylate another amino-acid residue, (it may, for example, acylate ammonia to give -NH-CHR-CO-NH₂), is called C-terminal.

Symbols for amino acids (use of the one-letter symbols should be restricted to the comparison of long sequences) :

A	Ala	Alanine
B	Asx	Asparagine or aspartic acid
C	Cys	Cysteine
D	Asp	Aspartic acid
E	Glu	Glutamic acid
F	Phe	Phenylalanine
G	Gly	Glycine
H	His	Histidine
I	Ile	Isoleucine
K	Lys	Lysine
L	Leu	Leucine
M	Met	Methionine
N	Asn	Asparagine
P	Pro	Proline
Q	Gln	Glutamine
R	Arg	Arginine
S	Ser	Serine
T	Thr	Threonine
V	Val	Valine
W	Trp	Tryptophan
Y	Tyr	Tyrosine
Z	Glx	Glutamine or glutamic acid

Anabolism

The processes of metabolism that result in the synthesis of cellular components from precursors of low molecular weight.

Anemia

Condition in which there is a reduction in the number of red blood cells or amount of hemoglobin per unit volume of blood below the reference interval for a similar individual of the species under consideration, often causing pallor and fatigue.

Anaerobe

An organism that does not need dioxygen for growth. Many anaerobes are even sensitive to dioxygen. Obligate (strict) anaerobes grow only in the absence of dioxygen. Facultative anaerobes can grow either in the presence or in the absence of dioxygen.

Anation

Replacement of the ligand water by an anion in a coordination entity.

Anisotropy

The property of molecules and materials to exhibit variations in physical properties along different molecular axes of the substance.

Anti

In the representation of stereochemical relationships "anti" means "on opposite sides" of a reference plane, in contrast to "syn" which means "on the same side".

Antibody

A protein, belonging to the class of immunoglobulins, designed to bind a specific antigen in order to remove it from the body. They are synthesised exclusively by B-lymphocytes, in millions of forms, each with a different amino acid sequence and a specific binding site for a specific antigen (antigenic determinant or epitope). Presently a world-wide interest exists in catalytic antibodies (abzymes), elicited against transition-state analogues of chemical reactions. Such an approach has permitted the design of immunoglobulins with enzymatic activity.

Antiferromagnetic

See ferromagnetic.

Antigen

A compound (protein, polysaccharide, microorganism, virus) foreign to the body that induces the production of specific antibodies.

Apoprotein

A protein without its characteristic prosthetic group or metal.

Aquation

The incorporation of one or more integral molecules of water into another chemical species with or without displacement of one or more other atoms or groups. See also hydration.

Archaea

A group of prokaryotes, which can be subdivided into three groups (methanogenic, halophilic, thermoacidophilic), that are characterized by special constituents such as ether-bonded lipids and special coenzymes. The archaea are members of a separate kingdom that falls in between eubacterial and eukaryotic organisms.

Assimilation

To change food and other nutrients into a part of the living organism.

Assimilative

See assimilation.

Assimilator

See assimilation.

Asymmetric synthesis

A traditional term for stereoselective synthesis. A chemical reaction (or reaction sequence) in which one or more new elements of chirality are formed in a substrate molecule and which produces the stereoisomeric (enantiomeric or diastereoisomeric) products in unequal amounts.

Asymmetry parameter

In nuclear quadrupole resonance spectroscopy this parameter, , is used for describing non-symmetric fields. It is defined as = (q_xx - q_yy)/q_zz in which q_xx, q_yy andq_zz are the components of the field gradient q (which is the second derivative of the time-averaged electric potential) along the x-, y- and z-axes. By convention q_zz refers to the largest field gradient, q_yy to the next largest and q_xx to the smallest when all three values are different.

ATP

See adenosine 5'-triphosphate.

Auranofin

See gold drugs.

Autotrophic organisms

Organisms that are capable of using carbon dioxide as the sole carbon source for growth and product formation. Organisms that use light as a source of energy are said to be photoautotrophs, those that use the energy from chemical reactions are chemoautotrophs.

Auxotroph

An organism which requires a particular organic compound for growth.

Azurin

An electron transfer protein containing a type 1 copper site, isolated from certain bacteria.

Bacteriochlorin

7,8,17,18-Tetrahydroporphyrin. A reduced porphyrin with two pairs of non-fused saturated carbon atoms (C-7, C-8 and C-17, C-18) in two of the pyrrole rings. See also isobacteriochlorin.

Bacteriochlorophyll

See chlorophyll.

Base

See Brønsted base, Lewis base, hard base, soft base.

Base pairing

The specific association between two complementary strands of nucleic acidsthat results from the formation of hydrogen bonds between the base components of the nucleotides of each strand: A=T and GC in DNA, A=U and GC (and in some cases GU) in RNA (the lines indicate the number of hydrogen bonds). Single-stranded nucleic acid molecules can adopt a partially double-stranded structure through intrastrand base pairing. See also nucleosides.

Basicity constant

See acidity constant.

Beta() sheet

Preferentially called a beta pleated sheet; a regular structure in an extended polypeptide chain, stabilised in the form of a sheet by hydrogen bonds between CO and NH groups of adjacent (parallel or antiparallel) chains.

Beta() strand

Element of a beta sheet. One of the strands that is hydrogen bonded to a parallel or antiparallel strand to form a beta sheet.

Beta() turn

A hairpin structure in a polypeptide chain reversing its direction by forming a hydrogen bond between the CO group of amino-acid residue n with the NH group of residue (n+3). See also helix.

Bifunctional ligand

A ligand that is capable of simultaneous use of two of its donor atoms to bind to one or more central atoms (see also ambidentate).

Binding constant

See stability constant.

Binding site

A specific region (or atom) in a molecular entity that is capable of entering into a stabilizing interaction with another molecular entity. An example of such an interaction is that of an active site in an enzyme with its substrate. Typical forms of interaction are by hydrogen bonding, coordination, and ion pair formation. Two binding sites in different molecular entities are said to be complementary if their interaction is stabilizing.

Binuclear

Less-frequently used term for the IUPAC recommended:dinuclear. See nuclearity.

Bioassay

A procedure for determining the concentration or biological activity of a substance (e.g.vitamin, hormone, plant growth factor, antibiotic, enzyme) by measuring its effect on an organism or tissue compared with a standard preparation.

Bioavailability

The availability of a food component or a xenobiotic to an organ or organism.

Biocatalyst

A catalyst of biological origin, typically an enzyme.

Bioconjugate

A molecular species produced by livingsystems of biological origin when it is composed of two parts of different origins, e.g. a conjugate of a xenobiotic with some groups, e.g. glutathione, sulfate or glucuronic acid, to make it soluble in water or compartmentalized within the cell.

Bioconversion

The conversion of one substance to another by biological means. The fermentation of sugars to alcohols,catalyzed by yeasts, is an example of bioconversion. See also biotransformation.

Bioleaching

Extraction of metals from ores or soil by biological processes, mostly by microorganisms.

Biological half life

The time at which the amount of a biomolecule in a living organism has been reduced by one half. See also half life.

Biomass

Material produced by the growth of micro-organisms, plants or animals.

Biomembrane

Organized sheet-like assemblies consisting mainly of proteins and lipids (bilayers), acting as highly selective permeability barriers, containing specific molecular pumps and gates, receptors and enzymes.

Biomimetic

Refers to a laboratory procedure designed to imitate a natural chemical process. Also refers to a compound that mimics a biological material in its structure or function.

Biomineralization

The synthesis of inorganic crystalline or amorphous mineral-like materials by living organisms. Among the minerals synthesized biologically in various forms of life are: fluoroapatite, (Ca₅(PO₄)₃(F, OH)), hydroxyapatite, magnetite (Fe₃O₄) and calcium carbonate (CaCO₃).

Biopolymers

Macromolecules (including proteins, nucleic acids and polysaccharides) formed by living organisms.

Biosensor

A device that uses specific biochemical reactions mediated by isolated enzymes, immunosystems, tissues, organelles or whole cells to detect chemical compounds, usually by electrical, thermal or optical signals.

Biotransformation

A chemical transformation mediated by living organisms or enzyme preparations. See also bioconversion.

Bleomycin (BLM)

A glycopeptide molecule that can serveas a metal chelating ligand. The Fe(III) complex of bleomycin is an antitumor agent and its activity isassociated with DNA cleavage.

BLM

See bleomycin.

Blotting

A technique used for transferring DNA, RNAor protein from gels to a suitable binding matrix, such as nitrocellulose or nylon paper, while maintaining the same physical separation.

Blue copper protein

An electron transferprotein containing a type 1 copper site.Characterized by a strong absorption in the visible region, and an EPR signal with an unusually small hyperfine coupling to the copper nucleus. Both characteristics are attributed to coordination of the copper by a cysteine sulfur.

Bone imaging

The construction of bone tissue images from the radiation emitted by radionuclides that have been absorbed by the bone. Radionuclides such as ¹⁸F, ⁸⁵Sr and ^99mTc are introduced as complexes with specific ligands (very often phosphonate ligands) and are absorbed in the bones by metabolic activity. See also imaging.

Brain imaging

In addition to magnetic resonance imaging that is based on the absorption by the brain of electromagnetic radiation, brain images can be acquired by scintillation counting (scintigraphy) of radiation emitted from radioactive nuclei that have crossed the blood-brain barrier. The introduction of radionuclides into brain tissue is accomplished with the use of specific ^99mTc(V) complexes with lipophilic ligands. See also imaging.

Bridging ligand

A bridging ligand binds to two or more central atoms, usually metals, thereby linking them together to produce polynuclear coordination entities. Bridging is indicated by the Greek letter appearing before the ligand name and separated by a hyphen. For an example, see FeMo-cofactor.

Brønsted acid

A molecular entity capable of donating a hydron to a base (i.e., a "hydron donor") or the corresponding chemical species.

Brønsted base

A molecular entity capable of accepting a hydron from an acid (i.e., a "hydron acceptor") or the corresponding chemical species.

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