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adenine (A): A nitrogenous base, one member of the base pair AT (adenine/ thymine). [DOE]

amino acids: Proteins glossary

base: Adenine, cytosine, guanine, thymine, and (only in RNA) uracil. Related term base pair. [DOE]  

Called bases because they are alkaline (basic) in the acidic DNA structure. Base and base pair used "fairly indiscriminately" by molecular biologists [Bains]

base pair (bp): Two bases which form a "rung of the DNA ladder." A DNA nucleotide is made of a molecule of sugar, a molecule of phosphoric acid, and a molecule called a base. The bases are the "letters" that spell out the genetic code. In DNA, the code letters are A, T, G, and C, which stand for the chemicals adenine, thymine, guanine, and cytosine, respectively. In base pairing, adenine always pairs with thymine, and guanine always pairs with cytosine. [NHGRI]  Related term uracil.

biomolecular interactions: Studies of membranes, proteins and peptides, and drug interactions with proteins and DNA, from the molecular level to the whole organism using a broad spectrum of biophysical, synthetic and biological methods. [School of Biological and Chemical Sciences, Birbeck, Univ. of  London, UK] http://www.bbk.ac.uk/bcs/research/bmi.html   Narrower terms Proteomics protein- DNA interactions, protein- protein interactions, protein-RNA interactions

biomolecules: An organic molecule, part of a living organism. Includes proteins, DNA, RNA.

biopolymers: Macromolecules (including proteins, nucleic acids and polysaccharides) formed by living organisms. [IUPAC Compendium]

carbohydrate binding proteins CBPs: http://glycomics.scripps.edu/membership.html

carbohydrates:  The largest class of organic compounds, including starches, glycogens, cellulose, gums, and simple sugars. Carbohydrates are composed of carbon, hydrogen, and oxygen in a ratio of Cn(H₂O)n. [MeSH] 

It has been estimated that about 0.5-1.0% of the translated mammalian genome participates in oligosaccharide production and function (Varki and Marth 1995). The magnitude of this genomic commitment to glycoconjugate biosynthesis is similar to that of protein phosphorylation, and may have as broad an impact on metazoan biology as the latter. In eukaryotes, protein and lipid glycosylation changes are observed during development, differentiation and importantly, numerous disease states. These differences are even being used as specific markers for diseases. Infectious diseases, and immune response are deeply imbued and dependent on carbohydrate residues.[Center for Structural Biology, Univ. of New Hampshire, US, Oct. 2000] http://glycome.unh.edu/

Related terms: glycobiology, oligosaccharide

characterization: Can include determining identity, physical chemistry data,  purity, potency, quality, stability, strength, pharmacokinetics, dose response, and efficacy. 

I am still trying to understand all the nuances of "characterize" and "characterization" of genes, genomes, proteins and proteomes and how these relate to annotation and would welcome any insights from people working in these areas.

Related terms specified biotechnology product, well characterized; characterization, protein Proteins glossary; annotation Bioinformatics glossary  

compound: A molecular compound is made of molecules bound by shared electrons (not ions). Anionic compounds are made of cations and anions (held by electrostatic forces. [Fred Senese, General Chemistry Online, Glossary, Frostburg State University, US, 2001] http://antoine.fsu.umd.edu/chem/senese/101/compounds/glossary.html

cytosine (C): A nitrogenous base, one member of the base pair GC (guanine and cytosine). [DOE]

DNA deoxyribonucleic acid: 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 genetic information 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. [ IUPAC Compendium]

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double- stranded state, yet several important biological processes transiently involve single- stranded regions. DNA, which consists of a polysugar- phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). [MeSH]

Narrower term recombinant DNA Pharmaceutical biology glossary. Related terms Sequences, DNA & beyond glossary  Related term Southern blotting Microarrays glossary

Dalton: Unit of mass equal to the unified atomic mass (atomic mass  constant). [IUPAC Compendium] After John Dalton (1766-1844) British chemist and physicist.

Frequently used in biochemistry to express molecular mass, although the name and the symbol [Da] have not been approved by CIPM [Comité international des poids et mesures] or ISO [International Organization for Standardization]. [IUPAC Quantities] 

dimer: A molecule which consists of two similar (but not necessarily identical) subunits. The term could also be used as a verb referring to the  act of the two subunits coming together (to dimerize). 09 Oct 1997  [OMD]

double helix: The shape that two linear strands of DNA assume when bonded together. [DOE] And the title of James Watson’s first-hand account of his (and colleagues') Nobel Prize winning discovery.

drug: Drug approvals glossary

glycans: See polysaccharides.

glycobiology: The objectives of the Society for Glycobiology shall be to promote knowledge, encourage research, and to stimulate personal communications, in an inter- disciplinary sense, using as a common meeting ground an interest in the complex carbohydrates of glycoproteins, glycolipids, glycosaminoglycans, and the biological systems in which they are found. [Society for Glycobiology website] http://www.glycobiology.org/welcome.htm

Includes glycoconjugates (including glycoproteins, glycolipids, proteoglycans or free complex saccharides) or on any aspect of proteins that specifically interact with glycoconjugates (e.g. lectins, glycotransferases, glycosidases). [From the scope notes of Glycobiology, Oxford Univ. Press] http://glycob.oupjournals.org/misc/about.shtml

The biology of sugars and carbohydrates.

glycoconjugates:  A type of compound consisting of carbohydrate units covalently linked with other types of chemical constituents. [IUPAC Compendium]

glyconomics: The study of glycoproteins and glycolipds.  The term is used far less often than the related terms glycobiology and glycotechnology.See FAQ question #2 http://www.doubletwist.com/news/columns/article.jhtml?section=weekly01&name=weekly0116

glycoproteins: Glycoproteins are complexes in which carbohydrates are attached covalently to asparagine (N-glycans) or serine/ threonine (O-glycans) residues of peptides. ["Glycoproteins: How are glycoprotein sugar chains functioning within us", Glycoforum, Japan 2001] http://www.glycoforum.gr.jp/science/word/glycoprotein/GPA00E.html

glycoscience: Genes encoding a large number of glycosyltransferases involved in the synthesis of the sugar chains have been cloned, and a systematic analysis of their functions has been promoted. Under these circumstances, studies in glycoscience are being focused on examining the significance of various types of sugar chain structures and elucidating the mechanisms of biological regulation for carbohydrate synthesis In Japan, many studies on complex carbohydrates have long been accomplished by members of the research groups supported by the Ministry of Education, Science, Sports and Culture (MESSC). ["From the Genome Research Era to the Glycome: An interview with Professor Naoyuki Taniguch" Glycoforum, Japan 2000] http://www.glycoforum.gr.jp/science/now/now3E.html  Related terms carbohydrates, glycobiology, glycotechnology, oligosaccharide

GlycoWord, GlycoForum, Japan http://www.glycoforum.gr.jp/science/word/wordE.html#indexW  Up- to- the - minute guide to modern glycoscience.

glycotechnology: Related terms carbohydrates, glycobiology, glycoscience, oligosaccharide Narrower term glycotechnology- analytical

glycotechnology- analytical: Consortium for Functional Glycomics http://glycomics.scripps.edu/corec.html

guanine (G): A nitrogenous base, one member of the base pair GC (guanine and cytosine). DOE]

heterodimer: <biochemistry> A dimer in which the two subunits are different. 

isomer: Molecules with identical molecular formulas but different structural formulas. [Fred Senese, General Chemistry Glossary, Frostburg State University, 2001] http://antoine.frostburg.edu/chem/senese/101/glossary.shtml

kDA: Kilo Dalton

large molecules: Chapter on from MIT's Biology Hypertextbook  http://esg-www.mit.edu:8001/esgbio/lm/lmdir.html   Related terms macromolecule, small molecules 

macromolecular systems: Complexes or cellular systems composed of macromolecules (proteins, DNA, RNA, polysaccharides, etc.) such as RIBONUCLEOPROTEINS, CHROMATIN, MULTIENZYME COMPLEXES and other multimeric proteins. [MeSH]

macromolecule (polymer molecule):  A molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of  low relative molecular mass. Notes: 1. In many cases, especially for synthetic polymers, a molecule can be regarded as having a high relative molecular mass if the addition or removal of one or a few of the units has a negligible effect on the molecular properties. This statement fails in the case of certain macromolecules for which the properties may be critically dependent on fine details of the molecular structure. 2. If a part or the whole of the molecule has a high relative molecular mass and essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, it may be described as either macromolecular or polymeric, or by polymer used adjectivally. [IUPAC Compendium]

A molecule with a molecular weight in excess of 1,000 Daltons. [Life Sciences Dictionary]

Biological term relating to large molecules including, proteins, nucleic acids and carbohydrates, but probably not phospholipids. [OMD]

Related term: large molecules, small molecules

-mer This suffix is often used to indicate the number of nucleotides in an oligonucleotide, e.g. 30-mer, 19-mer. [ICN]  Related terms dimer, monomer, trimer, up to 10 nucleotides decamer.  Eleven and above are the number plus -mer.

micromolecules: Early biochemists thought small. They knew a lot about the little molecules in the cells ... Into the nineteen- twenties and after, many biochemists doubted the reality of very large molecules, even when they were using the activity of enzymes, unpurified, as practical tools to catalyze small molecular reactions.  There was no way biochemists then could discern that the molecules in the cell are all either small or very large, with nothing between - that even small macromolecular chains are forty times or more the size of even the largest, so to speak, micromolecules. [HF Judson Eighth Day if Creation, Cold Spring Harbor Laboratory Press, 1996 p. 186] Related terms small molecules, specificity Compare macromolecules  How does this word relate (if it does) to small molecules?

"Any type of molecule composed of a relatively small number of atoms. ... generally ... has a mass less than about 10 kDa. [Oxford Biochem]  

mole, mol: The mole is the amount of substance of a system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12. 2. When the mole is used, the elementary entities must be specified and may be atoms, molecules, ions, electrons, other particles, or specified groups of such particles. [Bureau International de poids et mesures, SI base units, Système International d'Unités, (International System of Units)] http://www.bipm.fr/enus/3_SI/base_units.html

molecular biology: "Molecular biology is an ambiguous terms," Crick said the first time we [he and author Horace Judson Freeman] met... "The term is used in two rather different ways. First, in a very general sense it can mean almost anything - the attempt to understand any biological problem at the level of atoms and molecules. You could talk about the molecular biology of animal behavior - and that's not so far-fetched as you might imagine,; some senior molecular biologists are getting close to that. Second there is a classical sense of the term, and this is much narrower: classical molecular biology has been concerned with the very large, long- chain biological molecules - the nucleic acids and proteins and their synthesis. Biologically, this means genes and their replication and expression, genes and the gene products. ... Several ideas underlay the classical research, Crick said, "The most basic idea is that biological information is mainly carried by the sequence of side groups on the regular backbone of a macromolecule. The genetic information is not conveyed and expressed by a large number of intricate symbols - it's not in Chinese - but in two very simple and as it were alphabetic languages. Genetically, the information is carried by nucleic acid, in the sequence of bases; but many such sequences can be translated into the other language - the amino - acid sequences of proteins - by special pieces of biochemical machinery. This machinery is rather elaborate, but the basic biological mechanisms are; nevertheless, in principle, comparatively simple, and they turn out, with minor variations, to be the same throughout nature - just as we had assumed. The simplicity and universality of these mechanisms is, I think, the main reason why molecular biology has been able to advance so rapidly. Because it is impossible to deny that molecular biology, since the discovery of the structure of DNA, has been wildly successful." [HJ Freeman Eighth Day of Creation, Cold Spring Harbor Laboratory Press, 1996 pp. 178-179]

molecular weight: See relative molecular mass. [IUPAC Compendium] 

molecule: An electrically neutral entity consisting of more than one atom (n > 1). Rigorously, a molecule, in which n > 1 must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state. See also molecular entity. [IUPAC Compendium 1998]

A group of atoms arranged to interact in a particular way; one molecule of any substance is the smallest physical unit of that particular substance. [ORD]

A chemical made up of two or more atoms. The atoms in a molecule can be the same (an oxygen molecule has two oxygen atoms) or different (a water molecule has two hydrogen atoms and one oxygen atom). Biological molecules, such as proteins and DNA, can be made up of many thousands of atoms. [CancerNet]

Smallest particle of a compound that has all the chemical properties of that compound. A single atom is usually not referred to as a molecule, and ionic compounds such as common salt are not made up of molecules. Unlike ions, molecules carry no electrical charge [encyclopedia.com] http://www.encyclopedia.com/articlesnew/08628.html

Related term compounds

multimer: A protein made up of more than one peptide chain. [FAO]

nucleic acid: A macromolecule composed of linear sequences of nucleotides that perform several functions in living cells, e.g., the storage of genetic information and its transfer from one generation to the next DNA (deoxyribonucleic acid), the expression of this information in protein synthesis (mRNA, tRNA) and may act as functional components of subcellular units such as ribosomes (rRNA).  [IUPAC Medicinal Chemistry]

Either of two kinds of molecules (DNA and RNA) formed by chains of nucleotides, that carry genetic information. [NIGMS]

nucleotide, nucleotides: Nucleosides with one or more phosphate groups esterified mainly to the 3'- or the 5'- position of the sugar moiety. Nucleotides found in cells are adenylic acid, guanylic acid, uridylic acid, cytidylic acid, deoxyadenylic acid, deoxyguanylic acid, deoxycytidylic acid and thymidylic acid. [IUPAC Bioinorganic]

The building block of DNA or RNA. Each nucleotide consists of a sugar component, a phosphate group, and an organic base. Four organic bases exist in DNA (adenine, cytosine, guanine, and thymine) and in RNA (adenine, cytosine, guanine, and uracil). [NHLBI]   Half a "rung" on the DNA ladder. [CHI SNPs]

oligo: A prefix meaning "a few" and used for compounds with a number of repeating units…The limits are not precisely defined, and in practice vary with the type of structure being considered, but are generally from 3 to 10. [IUPAC Compendium] A shortened form of oligonucleotide.

oligomer: <chemistry> A molecule consisting of just a few monomers.  [09 Oct 1997, OMD]

oligomer molecule: A molecule of intermediate relative molecular mass, the structure of which essentially comprises a small plurality of units derived, actually or conceptually, from molecules of lower relative molecular mass.   [IUPAC Compendium 1998]

oligonucleotide: An oligomer resulting from a linear sequences of nucleotides. [IUPAC Medicinal Chemistry] Macromolecules composed of short sequences of nucleotides that are usually synthetically prepared and used e.g. in site directed mutagenesis. [IUPAC Bioinorganic]

Up to 20 nucleotides [King, Lackie] 2-10 nucleotides [Oxford Biochem]

Related terms oligos, probe

oligosaccharides: Carbohydrates consisting of between two and ten MONOSACCHARIDES connected by either an alpha- or beta- glycosidic link. They are found throughout nature in both the free and bound form. [MeSH] Includes disaccharides, trisaccharides; broader term is polysaccharides.

peptides: Amides derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of  water. The term is usually applied to structures formed from a- amino acids, but it includes any amino carboxylic acid. [IUPAC Compendium]

phospholipid: A fatty compound that contains phosphate. Phospholipids make up much of the outer membranes of cells and organelles. [NIGMS]

polymers: Compounds formed by the joining of smaller, usually repeating, units linked by covalent bonds. These compounds often form large macromolecules (e.g., polypeptides, proteins, plastics). [MeSH]

polypeptides: Peptides containing ten or more amino acids. [IUPAC Compendium]

polysaccharides:  Compounds consisting of a large number of monosaccharides linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.  Also called glycans. [IUPAC Compendium]

proteins:  Naturally occurring and synthetic polypeptides having molecular weights greater than about 10,000 (the limit is not precise). [IUPAC Compendium] Related terms Proteins glossary. Narrower term peptides

proteoglycan: A subclass of protein in which the carbohydrate units are polysaccharides that contain amino sugars. The protein is glycosylated by one or more (up to about 100) glycosaminoglycans [linear polymers of up to about 2000 repeating disaccharide units. [IUPAC Compendium] Related terms Biomolecules glossary glycoscience, polysaccharides.

purine: The bases adenine and guanine in DNA and RNA.

pyrimidine: The bases cytosine, thymine and uracil in DNA and RNA.

relative molecular mass Mr: Ratio of the mass of a molecule to the unified atomic mass unit. Sometimes called the molecular weight or relative molar mass. [IUPAC Compendium]

saccharides:  Monosaccharides and di-, oligo- and polysaccharides, which are made up of n monosaccharide units linked to each other by a glycosidic bond. Considered by some to be synonymous with carbohydrates. [IUPAC Compendium]

small molecules:  Drug Discovery & Development glossary

specified biotechnology products: Was well characterized biotechnology product. More to come.

supramolecular: Composed of more than one molecule, more complex than one molecule.

thymine (T): A nitrogenous base, one member of the base pair AT (adenine/ thymine) [DOE].

uracil: A nitrogenous base normally found in RNA but not DNA; uracil is capable of forming a base pair with adenine. [DOE] Related term base pair.

well characterized biotechnology products: See specified biotechnology products.

Bibliography

[IUPAC Biotechnology] International Union of Pure and Applied Chemistry, Glossary for Chemists of terms used in biotechnology. Recommendations, Pure & Applied Chemistry 64 (1): 143-168, 1992. 200 + definitions. 

Included in [IUPAC Compendium] 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://www.chemsoc.org/chembytes/goldbook/  Does not include Glossary of Bioinorganic Chemistry (1997) or Glossary of Medicinal Chemistry (1998). 

Alpha glossary index

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