Introductory Organic and Biochemistry

Terms: Primary, Secondary, Tertiary, Quaternary

Introduction
Carbon atoms
Carbocations
Alcohols
Amines
Protein structure
Nucleic acids
Summary
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Introduction

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.

Specific book references are to the Organic/Biochem (X402) textbook, Ouellette 2/e.

For brevity, the set of terms from primary to quaternary sometimes will be referred to as "primary (etc)".

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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.

Ouellette 2/e, p 71.

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.

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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). Carbanions and carbon free radicals are not encountered in this course (though they are mentioned by Ouellette 2/e, in topics that we will not cover).

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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.

Ouellette 2/e p 219.

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.

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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.

Ouellette 2/e p 291.

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.

Ouellette 2/e shows the classification of amides on pp 331 & 392.

Note that it is possible to have quaternary ammonium ions, but not quaternary amines. Ouellette 2/e introduces this, p 405. The tetramethylammonium ion is a quaternary ammonium ion. Choline, an important molecule in biochemistry, is also a quaternary ammonium ion; see Ouellette 2/e pp 349 & 377.

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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.

Ouellette 2/e discusses the levels of protein structure in Sect 15.8.

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Nucleic acids

The terms primary, etc., are used in essentially the same way for nucleic acids as for proteins, discussed in the previous section. Ouellette 2/e introduces this usage on p 452

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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

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Last update: May 26, 2011