1.) Outline the classification of proteins based on the polarity and how are they further classified based on the presence of the R-groups present in the amino acid structure?

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CLASSIFICATION OF AMINO ACIDS BASED ON POLARITY

  • There are 4 main classes of amino acids based on polarity, i.e. the interaction of the R group with water molecules at physiological pH.

Amino acids with non-polar (hydrophobic) side chain

  • These amino acids have a non–polar hydrophobic side chain. They do not provide protons or participate in hydrogen or ionic bonding. E.g.: alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan and methionine.

Amino acids with uncharged polar side chains (- R group)

  • These amino acids are more soluble in water. They are hydrophilic in nature. The functional groups can make hydrogen bonds with water. E.g.: glycine, serine, threonine, tyrosine, cysteine, asparagine and glutamine.
  • The polarity of serine, threonine is due to the presence of hydroxyl groups; the polarity of asparagine and glutamine is due to the amide group and the sulfhydryl group (thiol group) is responsible for cysteine.

Amino acids with polar, negatively charged side chain

  • These amino acids will have a net negative charge at neutral pH. E.g.: aspartic acid and glutamic acid.
  • These amino acids will have one more carboxyl group, which contribute to negative charge at neutral pH.

Amino acids with polar, positively charged side chain

  • These amino acids will have a net positive charge at pH 7. They accept protons. E.g.: lysine, arginine and histidine.
  • Lysine contains a second amino group at ε - position on the aliphatic side chain. Arginine contains a positively charged guanidino group and histidine contains an imidazole group.









points from scott mans biology text book

The Polarity and Charge of R-Groups Affect Solubility 

The nature of its R-group affects the solubility of an amino acid in in its natural environment—the aqueous interior of the cell. 

• Both polar and electrically charged R-groups interact readily with water and are hydrophilic. Hydrophilic R-groups dissolve easily in water.

 • Nonpolar R-groups lack charged or highly electronegative atoms capable of forming hydrogen bonds with water. These R-groups are hydrophobic, meaning that they do not interact with water. Instead of dissolving, hydrophobic R-groups tend to coalesce in aqueous solution. Amino acid R-groups can be grouped into three general types: charged, which includes acidic and basic; uncharged polar; and nonpolar. If given the structural formula for an amino acid at cellular pH, as in Figure 3.2, you can determine which type of amino acid it is by asking three questions: 

1. Does the R-group have a negative charge? If so, it is acidic and will lose a proton, like aspartate. 

2. Does the R-group have a positive charge? If so, it is basic and will pick up a proton, like lysine.

3. If the R-group is uncharged, does it have an oxygen atom? If so, then the highly electronegative oxygen will form a polar covalent bond in the R-group, thus making it uncharged polar like serine. (Although somewhat less electronegative, nitrogen atoms can also contribute polarity.) The overall polarity of an R-group is based on the number of highly polar covalent bonds relative to nonpolar bonds.


If the R-group in your amino acid does not have a negative charge, a positive charge, or an oxygen atom, then you are looking at a nonpolar amino acid, such as methionine.

 If you understand how the interaction between amino acids and water is affected by the side chains, you should be able to use Figure 3.2 to order the following amino acids from most hydrophilic to most hydrophobic: valine, aspartate, asparagine, and tyrosine. Explain how you determined the order of these amino acids. Now that you have seen the diversity of structures in amino acids, let’s put them together to make a protein.






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