Biochemistry I Fall Term, 2000

Lecture 4: Structure & Properties of Amino Acids

Assigned reading in Campbell: Chapter 3.1-3.3.

Self-guided tour of the amino acids:
http://www.bio.cmu.edu/courses/03231/BBlocks/AAVFrameset.htm
Amino Acid Identification Quiz (Chime Images):
http://www.bio.cmu.edu/courses/BiochemMols/aaIDCQz/aaQCMain.htm
Amino Acid Structure Quiz (GIF images):
http://www.bio.cmu.edu/Courses/BiochemMols/PQuiz/PQInst.html

Amino acids are the building blocks of proteins. Proteins play essential roles in:

• Chemical reactions (enzymes)
• Immune system (antibodies)
• Mechanical structure (tendons)
• Generation of force (muscles)
• Nerve conduction (ion channels)
• Vision (eye lens)
• . . . and much more!

Nomenclature

Properties of Amino acids

Charged Residues are seldom buried in the interior of a folded protein. They are normally found on the surface of the protein where they interact with water and with other important biological molecules. Note that these groups can be important in the recognition (binding) of oppositely charged groups on molecules that interact with proteins.

Nonpolar residues do not interact favorably with water. The central core of most proteins is composed almost exclusively of nonpolar residues, stabilized by numerous van der Waals interactions. However, a significant number of nonpolar residues are also found on the surface of the protein.

Spectral properties of amino acids Trp, Tyr, and Phe contain conjugated aromatic rings. Consequently, they absorb light in the ultraviolet range (UV). The extinction coefficients (or molar absorption coefficients) of these three amino acids are:

The amount of light absorbed by a solution of concentration [X] is given by the Beer-Lambert Law:

where

A is termed the "absorbance" of the sample;

I₀ is the intensity of the incident light;

I is the intensity of the light that leaves the sample;

e is the molar extinction coefficient at a specific wavelength, e.g. at l_max;

[X] is the concentration of the absorbing species; and

l is the path length (usually 1 cm).

The above table shows that Trp absorbs UV light the strongest. Furthermore, since both Trp and Tyr show the maximum light absorbance at approximately 280 nm the absorption maximum of most proteins is around 280 nm. In contrast, the absorption maximum for nucleic acids is approximately 260 nm.

Optical Activity

Amino acids have one or more chiral centers. In all amino acids (except glycine) the a-carbon is chiral. In some amino acids, additional chiral centers are present. These are chiral centers because all four groups attached to the carbon are different. Thus, there are two possible configurations (enantiomers) of amino acids. Enantiomers ("stereoisomers" in Campbell) have the following attributes:

• Identical physical properties
• Opposite rotation of polarized light

The absolute configuration of amino acids is defined by the Cahn-Ingold-Prelog system.

1. Groups attached to the chiral carbon are assigned letters W, X, Y, Z with W being the highest atomic number (the amino group in this case)
2. The molecule is oriented such that the Z group (lowest atomic number, H, the proton in the case of amino acids.) is pointing away from the viewer.
3. If WXY describes a counter-clockwise direction, the configuration of the group is (S).
4. If WXY describes a clockwise direction the configuration, of the group is (R)

Most common amino acids have an S configuration. An older, but much used, notation is D and L (related to the rotation of polarized light):

An L configuration is identical to an S configuration. Most amino acids are L-amino acids; all of the amino acids in ribosome-synthesized proteins are L-amino acids.

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