ChemWiki

username password
More Comments Print page Email link New page Edit page

Primary, Secondary, Tertiary, Quaternary Terms

    We use the terms primary, secondary, tertiary and quaternary at various times during the organic and biochemistry sections of the course. In each case, the terms somehow refer to the numbers 1, 2, 3 and 4, respectively. However, the exact connotations depend on the context. The purpose of this page is to bring all the meanings together, for direct comparison. The presentations here are brief; the main goal is comparison, not original presentation.

    1. 1. Carbon atoms
    2. 2. Carbocations
    3. 3. Alcohols
    4. 4. Amines
    5. 5. Protein structure
    6. 6. Nucleic acids
    7. 7. Summary
    8. 8. Contributors

    Carbon atoms

    A (saturated) carbon atom in an organic molecule is classified as primary (etc) depending on how many other C atoms are attached to it. The following table illustrates this:


    Table to show meaning of 'primary' (etc.) carbon atoms.

    Methane, CH4, is a special case. The C in methane is attached to zero other C. This C is sometimes called primary, for convenience. Alternatively, it can just be considered separate from any of these categories.

    Carbocations

    A carbocation (C atom carrying a positive charge) is classified the same way as a regular (neutral) carbon atom, above. That is, if the C of the carbocation is attached to one other C, then it is called a primary carbocation, etc.

    The book discusses this in the context of addition reactions of alkenes; acid-catalyzed addition of HX proceeds through a carbocation intermediate. Ouellette 2/e p 120.

    The same classification scheme is used for C atoms carrying a negative charge (carbanions) or carrying an unpaired electron (free radicals).

    Alcohols

    An alcohol is classified based on the C atom to which the -OH is attached. That is, if the alcohol -OH group is on a primary C, then the alcohol is a primary alcohol. Example: CH3CH2OH (ethanol) is a primary alcohol.

    Hopefully, the classification of alcohols seems logical, following from the way C atoms are classified. But caution... the next time we use these terms is for amines, and that is a quite different story.

     

    Alkyl halides are classified the same way as alcohols, discussed above. For example, CH3CH2Cl (chloroethane or ethyl chloride) is a primary alkyl halide, because the Cl is attached to a primary C. Ouellette 2/e briefly mentions this, p 204.

    Amines

    An amine is classified based on its N atom. If the N atom has 1 C attached, then the amine is primary, etc. Example: CH3NH2 (methylamine) is a primary amine, because the N has 1 C attached. The nature of the C itself is not relevant. Note that the classification of amines is not done by the same general procedure as the others discussed above. Amines are not classified by their C atoms, but rather by the N atom.

    The difference between how alcohols and amines are classified is made clear by comparing two compounds that look rather similar:

    Comparison of 2-propanol, a secondary alcohol, and 2-aminopropane, a primary amine.

     

    Amides and ammonium ions are classified the same way as amines. That is, groups based on amines are classified the same way as the amines.

    Note that it is possible to have quaternary ammonium ions, but not quaternary amines. The tetramethylammonium ion is a quaternary ammonium ion. Choline, an important molecule in biochemistry, is also a quaternary ammonium ion.

    Protein structure

    The same terms (primary, etc) are used to describe aspects of protein structure. These meanings have no relationship at all to the meanings above; they have no relationship to counting anything.

    • The term primary structure refers to the amino acid sequence in a protein.
    • The terms secondary and tertiary structure refer to the three-dimensional (3D) conformation of a protein chain. Secondary structure refers to the interactions of the backbone chain (that is, the amide linkages). Tertiary structure refers to interactions of the side chains. The distinction between secondary and tertiary is not entirely clear, and you will see various definitions. Emphasize understanding typical examples of secondary and tertiary structure, and let definitions emerge from those examples. Formal definitions are not so helpful here, unless you already understand the basic ideas.
    • Quaternary structure refers to the interaction between separate chains in a multi-chain protein. The types of interactions may be any of those found in secondary and tertiary structures.

    Nucleic acids

    The terms primary, etc., are used in essentially the same way for nucleic acids as for proteins, discussed in the previous section.

    Summary

    The following table briefly summarizes all of the usages of the terms primary (etc) discussed above. These usages fall into three general categories. Terms shown in bold are section headings above.

    Carbon atoms
    Carbocations
    Carbanions
    Carbon free radicals
    Alcohols
    Alkyl halides    		 Classified by the C atom.
    Amines
    Ammonium ions
    Amides    		 Classified by the N atom.
    Protein structure
    Nucleic acid structure     		Levels of structure

    Contributors

    This page viewed 9154 times
    The ChemWiki has 9483 Modules.

     

    Creative Commons License    UC Davis ChemWiki by University of California, Davis is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. 
    Permissions beyond the scope of this license may be available at copyright@ucdavis.edu. Terms of Use
    Powered by Mindtouch Core 2010

    You must login to post a comment.