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Pharmaceutical biology glossary & taxonomy
Evolving terminologies for emerging technologies

Suggestions? Comments? Questions? Mary Chitty  mchitty@healthtech.com
Last revised November 07, 2013  


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Genomic biology term index:  Finding guide to terms in these glossaries  Site Map   Related glossaries include Biologics  Drug discovery & developmentDrug discovery informatics  Drug & disease targets      Chemistry

active center: The location in an enzyme where the specific reaction takes place. IUPAC Bioinorganic

active site: See active center.

affinity: The tendency of a molecule to associate with another. The affinity of a drug is its ability to bind to its biological target (receptor, enzyme, transport system, etc.) For pharmacological receptors it can be thought of as the frequency with which the drug, when brought into the proximity of a receptor by diffusion, will reside at a position of minimum free energy within the force field of that receptor. [IUPAC Medicinal Chemistry]

A powerful method of protein purification in which a ligand is chemically attached to a solid support and used to absorb the relevant protein from solution. After washing to remove all other proteins, those bound tightly are eluted by adding soluble ligand or by changing the conditions to decrease the affinity of the protein for the bound ligand [ICN] Related term/narrower?: antibody affinity

antigenic mimicry: See under molecular mimicry

antisense (molecule): An oligonucleotide or analog thereof that is complementary to a segment of RNA or DNA and that binds to it and inhibits its normal function. [IUPAC Medicinal Chemistry]

Many scientists are still confused by the terms ‘sense’ and antisense’ when referring to DNA because the terminology has changed over the years. Because there are good logical threads that allow one to rationalize how each strand could be designated as the sense strand of DNA, the terms become intrinsically confusing…It became apparent that Richard Moldwin’s rmoldwin@midway.uchicago.edu proposal is probably the best solution to the problem. ..that the terminology for the strands of DNA with respect to transcription should therefore be formalized and the use of sense strand for DNA be avoided in future literature. One strand of DNA acts as the template for transcription and the other does not. When referring to DNA, the terms should be "transcribed strand"… and "non- transcribed strand"… The term antisense would be best reserved for RNA...Whether the members’ decision will be taken seriously and whether it will be come the existing standard remains to be seen. [PA Hengen, Is there any sense in antisense terminology? Trends in Biotechnology 21: 153-154 April 1996] Is this a moot point by now?

Molecular biologists describing DNA sequences or referring to one of the two strands of double- stranded DNA frequently use complementary pairs of terms, such as coding/ non- coding, sense/ nonsense or transcribing/ non- transcribing. Unfortunately none of these pairs is defined in a universally accepted way…Of the three pairs of terms mentioned, NC- IUB and JCBN believe coding/ non- coding to be preferable. Moreover, as the word 'coding' refers to the relationship between nucleic acids and proteins, rather than the mere transcription of DNA into RNA, it is logical to call the strand with the mRNA sequence the coding strand, as in the first example. When DNA sequences are described by giving the sequence of only one strand, this is usually the strand with the same sequence as the RNA (messenger, ribosomal, transfer, etc.) and should therefore be called the coding strand. [JCBN/ NC- IUB Newsletter, Joint Commission on Biological Nomenclature and Nomenclature Commission of IUB, 1989]  http://www.chem.qmw.ac.uk/iubmb/newsletter/misc/DNA.html  Narrower terms: antisense DNA, antisense oligonucleotides, antisense RNA, Related terms: Biologics antisense therapy; RNAi; SNPs & other genetic variations missense mutation, nonsense mutation; Sequences DNA & beyond ribozymes

antisense DNA: DNA that is complementary to the sense strand. (The sense strand has the same sequence as the mRNA transcript. The antisense strand is the template for mRNA synthesis.) Synthetic antisense DNAs are used to hybridize to complementary sequences in target RNAs or DNAs to effect the functioning of specific genes for investigative or therapeutic purposes. MeSH, 1991

antisense oligonucleotides: Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize. MeSH, 1991Related terms  antisense, antisense DNA, antisense RNA, morpholinos

antisense RNA: RNA
aptamers: Technologies overview

binding site:  Drug & disease target
 

enzymes: Macromolecules, mostly of protein nature, that function as (bio) catalysts by increasing the reaction rates. In general, an enzyme catalyses only one reaction type (reaction specificity) and operates on only one type of substrate (substrate specificity). Substrate molecules are attacked at the same site (regiospecificity) and only one or preferentially one of the enantiomers or chiral substrates is attacked (stereospecificity). [IUPAC Compendium]

A substance (usually a protein) that speeds up, or catalyzes, a chemical reaction without being permanently altered or consumed. [NIGMS]

Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however catalytic RNA (RNA, CATALYTIC) and catalytic DNA (DNA, CATALYTIC) molecules have also been identified. MeSH   Related terms: substrate, Metabolic engineeringPharmacogenomics enzyme kinetics Narrower term: immobilized enzymes

Enzyme nomenclature list
, IUPAC, 1992 print edition & supplements http://www.chem.qmul.ac.uk/iubmb/enzyme/ See also Nomenclature Enzyme nomenclature for more detailed explanation.

enzymes and coenzymes: Biological catalysts and their cofactors. MeSH 2004

homologue: Used to describe a compound belonging to a series of compounds differing from each other by a repeating unit, such as a methylene group, a peptide residue, etc. IUPAC Medicinal Chemistry

This is different from homolog/ homologue defined in the Functional genomics

hormone: A substance produced by endocrine glands, released in very low concentration into the bloodstream, and which exerts regulatory effects on specific organs or tissues distant from the site of secretion. [IUPAC Medicinal Chemistry] 

Chemical substances having a specific regulatory effect on the activity of a certain organ or organs. The term was originally applied to substances secreted by various endocrine glands and transported in the bloodstream to the target organs. It is sometimes extended to include those substances that are not produced by the endocrine glands but that have similar effects. MeSH Related term: receptor.

immobilized enzymes: Enzymes which are immobilized on or in a variety of water- soluble or water- insoluble matrices with little or no loss of their catalytic activity. Since they can be reused continuously, immobilized enzymes have found wide application in the industrial, medical and research fields. MeSH, 1977

ligand: Drug & disease targets  
mechanism of action: Pharmacogenomics
metabolism, metabolite, metabolite profiling, metabonomics: Metabolic profiling
NF-kappa B: Drug & disease targets 

optical isomers: See under enantiomers
paratope:
Wikipedia http://en.wiktionary.org/wiki/paratope  Related term: binding sites, antibody  MeSH

pathways: Metabolic profiling

permeability:  Ability of a compound to diffuse across biological membranes. "Reducing the investment made in likely drug development failure" CHI's Genome Link 15.1 http://www.chidb.com/newsarticles/issue15_1.asp  Christopher  Lipinski talks about improving permeability.  Related terms: bioavailability, biological availability

pharmacophore: Drug & disease targets 

prodrug: Drugs that, once administered, must be chemically modified by metabolic processes in order to become pharmaceutically active.

Any compound that undergoes biotransformation before exhibiting its pharmacological effects. Prodrugs can thus be viewed as drugs containing specialized non- toxic protective groups used in a transient manner to alter or to eliminate undesirable properties in the parent molecule. [IUPAC Medicinal Chemistry]

receptor: Drug & disease targets

recognition site: 1. A nucleotide sequence to which a protein binds specifically. 2. An amino acid sequence in an antibody molecule to which the specific antigen binds specifically. [IUPAC Biotech]  Related term: molecular recognition. Drug discovery & development

recombination: See genetic recombination SNPs & Genetic variations

solubility: The analytical composition of a saturated solution, expressed in terms of the proportion of a designed solute in a designated solvent is the solubility of that solute. The solubility may be expressed as a concentration, molality, mole fraction, mole ratio, etc. [IUPAC Compendium 1997]

Ability of a compound to dissolve.

"Reducing the investment made in likely drug development failure" CHI's Genome Link 15.1 http://www.chidb.com/newsarticles/issue15_1.asp  Christopher  Lipinski talks about improving solubility.  Related terms:  molality, molarity; Cheminformatics rule of five

substrate: A chemical species, 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). The term should be used with care. Either the context or a specific statement should always make it clear which chemical species in a reaction is considered the substrate. IUPAC Compendium 

How does this definition compare with substrate Microarrays & protein arrays  Related term enzyme.

substrate specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts. MeSH, 1978

Bibliography
IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms used in Bioinorganic Chemistry, Recommendations, 1997. 450+ definitions. http://www.chem.qmw.ac.uk/iupac/bioinorg/
IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms used in Biomolecular Screening 2011 http://iupac.org/publications/pac/83/5/1129/IUPAC  International Union of Pure and Applied Chemistry, Compendium of Chemical Terminology: Recommendations, compiled by Alan D. McNaught and Andrew Wilkinson, Blackwell Science, 1997. "Gold Book" 6500+ definitions. http://goldbook.iupac.org/
IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms used in Computational Drug Design, H. van de Waterbeemd, R.E. Carter, G. Grassy, H. Kubinyi, Y. C.. Martin, M.S. Tute, P. Willett, 1997. 125+ definitions. http://www.iupac.org/reports/1997/6905vandewaterbeemd/glossary.html
IUPAC International Union of Pure and Applied Chemistry, Glossary of Medicinal Chemistry, 1998. 100+ terms. http://www.chem.qmw.ac.uk/iupac/medchem/

Alpha glossary index

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

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