Re: Glossary terms: questions

Achim Treumann (
Tue, 9 May 1995 11:25:21 GMT

Dear all,

I've had a look at the existing chemistry entries and wanted to suggest a few
changes (all open for discussion, of course).

As a general remark: I think, it is more useful to try to explain the
relevance of certain chemical terms/groups to biochemists (with examples)
than to give a summary from an organic chemistry textbook. This makes it
often easier to keep entries short. Opinions might differ about that, of

Acid (the existing definition is correct, the Lewis acid concept, however, is
IMO not very important in biochemistry. If others think, it is, it might be
included as an entry of its own, with a crossreference to acid and vice
versa): An acid is a donator of protons (H+). Acid-base reactions involve a
conjugate acid-base pair, made up of a proton donor and acceptor. The most
important acidic goup in biochemistry is the carboxyl group (-COOH) which is
the acid group on amino acids, in the side chain of Glutamic acid and
aspartic acid and in the acids of the Krebs cycle.
Current URLs: base, amino acid, carboxy, Glu, Asp.

Compound with a -CH=O group. Important examples of aldehydes in biochemistry:
aldoses (polyhydroxy-carbonyl-compounds), several key intermediates in amino
acid metabolism.
Current URLs: carbonyl, carbohydrate.

Reaction product of an amine with a carboxylic acid. Occurs very frequently in
biochemistry, peptide bonds are amides, so is the functional group in the side
chains of Asparagine and of Glutamine.
Current URLs: amine, carbonyl, Asn, Gln, peptide bond

Organic compound containing Nitrogen. Amines are usually bases, i.e. they are
protonated in aqueous solutions. Important biochemical examples are alpha amino acids,
the side chain of lysine, and glucosamine.
Current URLs: amide, peptide bond, lysine, ornithine, glucosamine

Amino acids (again a correct entry, I believe, though, it could be shorter):
Amino acids are compounds that contain a carboxy group and an amino group. In
alpha amino acids both functional groups are on the same atom. 20 alpha
L-amino acids (of which 19 are chiral) are encoded in the genome and, linked
by peptide bonds, constitute the backbone of proteins.
Current URLs: all the aa, peptide, protein, acid, amino

Base (see my comment to acid): A base is a proton acceptor in an acid-base
reaction. Biochemically important bases are amines and purines and
pyrimidines, the bases that underly the structure of DNA.
Current URLs: acid, DNA, purines, pyrimidines

Benzene: Kekule discovered the first aromatic compound, benzene. It consists
of 6 carbons and 6 hydrogens, united into a ring. All the carbons are sp2
hybridized, joining their p electrons to form the pi-layer, which gives rise
to a ring current which can be measured using biophysical techniques. The
side chain of Phenylalanine contains a benzene ring.

Benzyl: perhaps not necessary in a protein structure glossary (?)

Benzoate: perhaps not necessary in a protein structure glossary (?)

Benzoyl: perhaps not necessary in a protein structure glossary (?)

Butyl: Four carbon atoms containing alkyl residue which is non-polar and
electron donating. Leucine and Isoleucin contain butyl side chains.

Carbohydrate: Carbohydrates are polyhydroxy-carbonyl compounds which generally
have the sum formula (CH2O)n. In biochemical systems they are used as storage
compounds, energy metabolism intermediates, structure building blocks and for
the modification of proteins.
Current synonyms: monosaccharide, sugar
Current URLs:

Carboxyate - is this a spelling error? Or does it refer to the salts of
carboxylic acids? Somebody would have to help out here.

Carboxy: Acidic functional group -COOH. Compounds that contain this group are
called carboxylic acids. Occurs in the side chain of glutamic acid and
aspartic acid, where it is usually negatively charged.
Current URLs: acid, amino acid, Glu, Asp

Chirality: (The definition is good. Maybe one would want to add on sentence)
Chiral molecules do not coincide with their mirror image (this definition is
necessary, sufficient and applies - sometimes - to imagination)
I would take out the GIF "Axial chirality" as IMO E/Z isomers are not
necessarily chiral (e.g. the examples in the URL are NOT chiral).

Configuration: The covalent linkages that make up a molecule. To change the
configuration of a molecule one has to break and make new bonds.
Current URLs: conformation, chirality, enantiomers

Glycosidic bond: there has been a discussion about this on this list which
does not seem to have affected the entry (or am I looking at the wrong

Hydrolyse: Breaking a chemical structure (e.g. an amide or a glycosidic bond)
apart by reacting it with water. Hydrolyses are often acid or base catalysed.

Hydrophilic (a TO is missing): Hydrophilic means water-loving. Hydrophilic
compounds are generally polar and more attracted to water than TO themselves,
which leads to high water solubility.

Hydrophobic: Hydrophobic means water-hating. Hydrophobic compounds are
excluded from aqueous environments and tend to stick together (due to
entropic effects). This hydrophobic effect is responsible for the observation
that in water proteins tend to adopt a conformation which minimizes the
non-polar side chain interaction with water.

Ion: definition is good - on spelling mistake: positive charge (one s)

Methyl: smallest alkyl residue, side chain of alanine.
Current URLs: alkyl, ala

Monosaccharide: replace by carbohydrate

Oligosaccharide: Oligomer consisting of carbohydrates, usually attached to a
protein as either a GPI anchor, an N-linked oligosaccharide or an O-linked
Current URLs: glycosylate, carbohydrate

Oxidation (this entry exits twice ?): replace by redox

Phosphate: (PO4)3-, the anion of phosphoric acid. Inorganic phosphate can be
transferred to many biochemically important molecules: as a phosphoric acid
anhydride (e.g. in ATP) usually for short term energy storage - energy
transfer) or as an ester (with serine, threonine or tyrosine in proteins) for
regulatory or structural purposes.
Indexing terms: phosphorylate
Current URLs: kinase, phosphatase

Phosphatase: Enzyme that takes a phosphate of a protein that has previously
been attached by a kinase. Important metabolic regulation mechanism.

Polysaccharide: Macromolecule consisting of many sugars linked via
glycosidic bonds. Polysaccharides have usually either a sorage function
(glycogen, starch) or a structural function (cellulose).

Propyl: Three carbon atoms containing alkyl residue which is non-polar and
electron donating. Valine contains a propyl side chain.

Reduction: replace by redox

Stereocentre: Atom (usually carbon atom) that is linked to four different
substituents. Such atoms are chiral and confer mostly the property of
chirality to the molecule in which they are (Anybody comes up with a better
definition? I am not very happy with it).

Sugars: replace by carbohydrate

Achim Treumann tel. +44-382-344301
Department of Biochemistry fax +44-382-322583
University of Dundee
Dundee DD1 4HN, Scotland, UK email