Volume 3, No. 4 
October 1999


Dr. Claff
 


 


 

 

 
 
 
 
 
 
 
 
 
Translation Journal
 
Factory
 



 
 


A Translator’s Guide to Organic Chemical Nomenclature

Part XVII


by Chester E. Claff, Jr., Ph. D.
 
 

 
Polypeptides in the news

 

IX. a-Amino Acids, (Poly)peptides, and Proteins (continued)

One-letter system for long peptide sequences

The three-letter system for polypeptide representation described in Part XVI is customarily used in texts and reports. However, a one-letter system has been developed for documents and files in which brevity is important or computerization is intended. The listing below shows the correlation of the two systems:

A (Ala), C (Cys), D (Asp), E (Glu), F (Phe), G (Gly), H (His), I (Ile), K (Lys), L (Leu), M (Met), N (Asn), P (Pro), Q (Gln), R (Arg), S (Ser), T (Thr), V (Val), W (Trp), and Y (Tyr).

The polypeptide illustrated in Part XVI:

Ala-Ser-Asp-Leu-Glu-Phe-Val

when converted to the one-letter system becomes:

A S D L E F V.
 

Protein and polypeptide conformation (folding)

Protein chains in their natural state spontaneously assume four levels of conformational structure, the terminology of which can present problems in translation. The four levels of conformation are:
   1. The primary structure - the sequence of amino acid residues that make up the protein chain, as already discussed.
   2. The secondary structure - the coiled or folded conformation assumed by a protein chain in its native environment.
   3. The tertiary structure - the overall folded form assumed by a protein chain that has already folded or coiled into its secondary structure.
   4. The quaternary structure - the aggregation pattern of multiple protein chains.
 

Secondary structure of protein chains

The three principal forms of secondary structure of protein chains are the a helix, the b sheet, and the b turn. Some (but by no means all) of the terms that may be encountered in this discipline are properly translated as follows:

a helix
b turn
b sheet
b-pleated sheet structure
amino acid sequence
antiparallel b-pleated sheet
coiled peptide chain
denatured protein
disordered region
fibrous protein
globular protein
microfibril
native structure
protein folding
protofibril
sheeted peptide chain
supracoiling

Fortunately it is not necessary to understand fully the meanings of these terms to translate them properly! The terminology of proteins is constantly evolving; new terms are invented every day.
   All natural proteins are derived from a-amino acids. Currently being explored are synthetic polypeptides made up of b-amino acid residues. Their interactions with living systems, their conformations, their pharmacology, and their possible use in medicine are being examined.
 

X. Other compounds of nitrogen
 
Nitriles (cyano compounds)
 
The loss of water from an amide leads to a nitrile, in which a nitrogen atom is triple-bonded to carbon:

RC(=O)NH2 ® RCºN + H2O

The names of simple nitriles are derived from the root of the trivial name of the related carboxylic acid. Alternatively, they can be named as cyano-substituted hydrocarbons, as in the following examples:

CH3CN = acetonitrile, ethanenitrile, or cyanomethane
C2H5CN = propionitrile, propanenitrile, or cyanoethane
n-C3H7CN = butyronitrile, butanenitrile, or 1-cyanopropane
(CH3)2CHCN = isobutyronitrile, 2-methylpropanenitrile, or 2-cyanopropane
CH2(CN)2 = malononitrile, dicyanomethane, or methanedicarbonitrile
CH2=CHCN = acrylonitrile

Numerous alternatives are available for many cyano-substituted compounds. Some examples of commonly-used names are:

CH2=CHC(=O)OCH2CH2CN = cyanoethyl acrylate
CH2=C(CN)C(=O)OCH2CH3 = ethyl a-cyanoacrylate
HOCH2CH2CN = ethylene cyanohydrin or 3-hydroxypropionitrile
NCCH2CO2H = cyanoacetic acid
HN(CH2CH2CN)2 = bis(2-cyanoethyl)amine or dicyanoethylamine
 

Ureas and related compounds

The history of organic chemistry dates to 1828 when Friedrich Wöhler heated ammonium cyanate, an inorganic salt, and obtained urea, previously believed to originate only from life processes:

   NH4+OCN-   ®   H2NC(=O)NH2

Derivatives of urea abound. Urea when heated with diethyl malonate yields barbituric acid:

CH2(CO2C2H5)2 + CO(NH2)2   ®

   Substituted malonic esters in this reaction lead to barbiturates, the use or abuse of which may have effects ranging from sedation to anesthesia to death.
   Replacing the oxygen atom of urea with sulfur leads to thiourea H2NC(=S)NH2.
   Urea-formaldehyde resins are manufactured in large tonnages for textile treatment, laminating compositions, fertilizers, and other uses. Their production may proceed through dimethylolurea [HOCH2NHC(=O)NHCH2OH] to give linear and/or branched and/or crosslinked polymers of the form HO[CH2NHC(=O)NH]nH, with branching occuring at the nitrogen atoms.
   The myriad types of organic compounds of nitrogen, when combined with their oxygen and sulfur derivatives, prohibit comprehensive discussion. They will be treated individually below as they arise. Their nomenclature is complex, individualistic at times, and even well-versed chemists frequently have to refer to the literature for help. When in doubt, an Internet search can often confirm or reject a presumed translation in this area.
 

XI. Aromatic compounds

Aromatic hydrocarbons

In Part XIII with regard to cyclic compounds, we reserved consideration of cyclohexatriene as a special case. The structure of this compound, C6H6, can be written in two ways that differ only in the positions of the double bonds:



In such a case, as explained in detail in 1944 by George Wheland (The Theory of Resonance and its Application to Organic Chemistry, John Wiley and Sons, New York), neither of the two so-called Kekulé structures shown above corresponds to the actual compound, benzene. The molecule is in fact intermediate between the two Kekulé structures, and all six carbon-to-carbon bonds are identical. This "resonance" between different electron distributions as illustrated classically occurs whenever a molecule can be depicted in two or more ways differing only in the distribution of electrons, and with little or no displacement of atoms. Resonance contributes greatly to stability. For example, it is much more difficult to hydrogenate benzene than cyclohexadiene. The electrons of benzene are termed "p-electrons" and are delocalized and distributed uniformly around the ring. This resonance stabilization is called "aromaticity." The term derives from the original discovery of the stability of these compounds and their characteristic, generally pleasant, odors. The aromatic nature of a ring system is often shown as a hexagon containing a circle representing the delocalized electrons:
   

   Benzene rings can be fused to one another or joined in series. The fused systems are called binuclear, trinuclear, etc. They are also resonance-stabilized. Examples of fused-ring systems are:
Naphthalene Anthracene Phenanthrene

   Examples of series-connected systems are:
BiphenylFluorene

   Part XVIII will continue the discussion of aromatic hydrocarbons.