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Exercise 2.   Production of an Amino Acid Hydrophobicity Scale Using Paper Chromatography


A. Introduction

A surface model of a protein with the amino acids color-coded to show the degree of polarity.

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Amino acids are the building blocks of proteins. The structure of a protein, the structure and chemistry of it's active site, and ultimately the specific function of a protein are all determined by the sequence of amino acids in the protein's polypeptide chain. Therefore, we must understand amino acid biochemistry if we are to understand protein structure and function.

One of the most basic and important chemical characteristics of an amino acid is its polarity, that is how relatively polar or nonpolar it is. An amino acid's polarity determines how it interacts with surrounding water and how it interacts with other amino acids in the protein, and in this way serves as a major molecular force that determines how a protein folds into its stable three dimensional conformation. In fact, the single most important factor that determines the final conformation of a protein is the requirement that the interior core of the protein be densely packed and very hydrophobic. Therefore, as a protein folds, regions of the polypeptide chain that contain a relatively large number of hydrophobic amino acids tend to fold to the interior core of the protein, and regions of the polypeptide chain that have more polar amino acids tend to be displaced to the exterior of the protein, where they interact with the aqueous surroundings.

The figure to the right shows a model of a protein with the amino acids color-coded to show their relative degree of polarity. The more red the color, the more polar the amino acid. Blue depicts the nonpolar amino acids and green indicates moderately polar/nonpolar amino acids. The model shows that the more polar red, orange and yellow colored amino acids tend to be found near the hydrophilic surface of the protein while the more hydrophobic blue amino acids tend to be buried in the core of the protein.

Scientists express an amino acid's polarity in terms of its hydropathy or hydrophobicity, that is, the relative degree to which an amino acid is hydrophobic. The hydrophobicity of each of the 20 commonly-occuring amino acids has been determined using a variety of methods, and scientists have ranked the amino acids according to their hydrophobicities in a variety of hydrophobicity scales. In this exercise, we study the structure of the amino acids and review of some of the major hydropbicity scales used by protein biochemists. In lab, we will create our own amino acid hydrophobicity scale using paper chromatography.