Within the side chain of tyrosine, there is a phenol group. However, a phenol group contains neither sulfur nor nitrogen. Methionine and cysteine are the only two amino acids that contain sulfur, which is worth memorizing. Seven amino acids contain nitrogen, including arginine and asparagine.

Quarternary structure is the association of multiple polypeptide chains into a functional protein. Not all proteins have this level of protein structure. Subunits within the quarternary structure are held together by noncovalent bonds and disulfide bonds.

Typically, nonpolar amino acids have side chains containing only carbons and hydrogens. The side chain on glycine contains only a hydrogen, and is nonpolar. The side chains on leucine and isoleucine contain nothing but carbons and hydrogens, so they are also nonpolar. Finally, the side chain on tryptophan does contain a nitrogen. However, tryptophan is large enough and contains enough carbons to balance out the increased electronegativity of the nitrogen within the side chain. Therefore, tryptophan, along with the rest of the answer choices, is nonpolar.

At physiological pH, the amino group of an amino acid is protonated and carries a charge, whereas the carboxyl group is deprotonated and carries a charge. Therefore, only side chains contribute to the overall charge (the amino and carboxyl group charges cancel out). pKa refers to the pH at which half of the side chain functional group in question will be protonated and the other half deprotonated. For acidic amino acids (aspartate and glutamate), the deprotonated form will carry a charge (protonated neutral), as it has donated a proton. For basic amino acids (histidine, arginine, and lysine), the protonated form will carry a charge (deprotonated neutral), as it has accepted a proton. At pH = 7.4, there are more protons in solution than at a pH of 12.48, so arginine will be mostly protonated . There are more protons as well than at a pH of 10.54, so Lysine will also be protonated . But there are fewer protons than at a pH of 3.90, so aspartate will be deprotonated . Therefore, the overall charge is:

"Asp" refers to aspartic acid; "Trp" refers to tryptophan; "Phe" refers to phenylalanine; and "Arg" refers to arginine.

A peptide bond is made from joining the amino group of one amino acid to the carboxyl group of another. A tetrapeptide is a peptide consisting of four amino acids, which are connected via peptide bonds. There are several ways in which these four amino acids could be joined. Any of the four could be located at the first position; any of the remaining three could be located at the second position; either of the remaining two at the third position, etc. Thus, there are possible tetrapeptides.

Asp-Trp-Phe-Arg

Asp-Trp-Arg-Phe

Asp-Arg-Phe-Trp

Asp-Arg-Trp-Phe

Asp-Phe-Trp-Arg

Asp-Phe-Arg-Trp

Phe-Asp-Trp-Arg

Phe-Asp-Arg-Trp

Phe-Trp-Asp-Arg

Phe-Trp-Arg-Asp

Phe-Arg-Trp-Asp

Phe-Arg-Asp-Trp

Trp-Asp-Phe-Arg

Trp-Asp-Arg-Phe

Trp-Phe-Arg-Asp

Trp-Phe-Asp-Arg

Trp-Arg-Phe-Asp

Trp-Arg-Asp-Phe

Arg-Asp-Phe-Trp

Arg-Asp-Trp-Phe

Arg-Phe-Trp-Asp

Arg-Phe-Asp-Trp

Arg-Trp-Phe-Asp

Arg-Trp-Asp-Phe

In phenylketonurics, the body cannot convert phenylalanine into tyrosine due to deficiency in phenylalanine hydroxylase. This can be observed by looking at the structures of these amino acids, as they only differ by the hydroxyl group on the benzene ring. Tyrosine is a necessary precursor to L-DOPA (dihydroxyphenylalanine), dopamine, catecholamine neurotransmitters, melanin, thyroid hormones, and other biologically relevant substances.

Amphoteric substances can act as an acid or a base. An example of an amphoteric substance is an amino acid. Amphipathic is the term assigned to molecules that possesses both hydrophilic and hydrophobic regions. An example of an amphipathic molecule is a phospholipid. Compounds that do not contain carbon are typically referred to as inorganic.

Denaturing a polypeptide is the process of disrupting the secondary, tertiary, and quaternary structures. This means that denaturing a protein will lead to disruption in intermolecular forces such as hydrogen bonds. Recall that hydrogen bonds occur between a hydrogen atom and either a nitrogen, oxygen, or fluorine atom; therefore, denaturing a polypeptide will cause a disruption in the intermolecular forces between nitrogen and hydrogen (hydrogen bonds).

Secondary structures can form unique structures called beta-pleated sheets or alpha helices. The beta-pleated sheets are formed when a polypeptide chain folds in such a way that it loops back to lie adjacent to an earlier segment. Alpha helices are formed when a polypeptide chain twists and forms a helical structure. Note that both of these structures involve intermolecular forces (hydrogen bonds, van der Waals, etc.) between amino acids. Denaturing a polypeptide will disrupt both of these structures.

Recall that a denatured polypeptide will not lose its peptide bonds; therefore, the polypeptide will have its original number and sequence of amino acids (primary structure). The side chains of amino acids will not change during denaturation. The intermolecular forces and disulfide bonds between adjacent amino acids will change, but the composition of each amino acid won’t change.

Only glycine is nonpolar. The rest of the answer choices are polar. Remember that being nonpolar implies that the substance is hydrophobic and, hence, insoluble in water. Besides methionine, you will notice that the rest of the nonpolar and nonaromatic amino acids have R-groups composed solely of carbon and hydrogen. Polarity of amino acids is quite important when looking at the tertiary, or three dimensional, structure of a protein.

Diethylaminoethyl (DEAE) cellulose is a positive weak ion exchanger. Any molecules with a positive charge will elute through the column first, whereas molecules with a negative charge will adhere to the DEAE column and elute after the salt wash. Since protein III has a pI greater than the pH of the column, it has a positive charge and elutes first. Protein II elutes second because its pI is less than the pH but close in value. Therefore protein II contains less of a negative charge than protein I.