Each amino acid has an N and a C terminus. The N terminus contains an amino group and the C terminus contains a carboxylic acid group. In order to make a peptide linkage (and eventually create a polypeptide), a bond must form between the amino and carboxylic groups, with water as a byproduct.

Basic amino acids are those containing an amine group, while acidic contain a carboxylic acid group.

The basic amino acids are lysine (the correct answer), arginine, and histidine.

The acidic amino acids are glutamic acid (glutamate) and aspartic acid (aspartate).

On the MCAT you must be able to recognize the following as basic amino acids: lysine, arginine, and histidine. Important acidic amino acids include aspartic acid (aspartate) and glutamic acid (glutamate). Important nonpolar amino acids include: methionine, alanine, isoleucine, proline, phenylalanine, tryptophan, valine, and leucine.

The resonance of the two C–O bonds that result after deprotonation of an organic acid is the major contributor to anion stability.

Every amino acid contains a carboxyl group and an amino group. These two functional groups are essential for amino acid binding and breaking.

While sulfide groups contribute to higher protein structure by forming disulfide bonds, they do not exist in every amino acid.

Phenylalanine:

Since the phenylalanine residue is at the C-terminus end of the molecule, only its carboxylic acid pKa is relevant, as its amine is involved in a peptide bond with arginine. At a pH of 7 (well above the carboxylic acid pKa of 2.58), the C-terminus carboxylic acid would be deprotonated and have a charge of .

Arginine:

For the middle amino acid, arginine, the only relevant pKa is that of its side chain since both its carboxylic acid and amino groups are involved in peptide bonds with neighboring amino acids. Since the side chain of arginine would be protonated at a pH of 7 (well below the sidechain pKa of 12.48), this amino acid would have a charge of .

Valine:

Finally, for valine, the relevant pKa to consider is the NH2 pKa of 9.72. At pH 7, this would also be protonated, resulting in a charge of .

The overall charge of the molecule at pH 7 would be .

Serine and threonine are classified as hydrophilic amino acids and contain hydroxyl (-OH) groups in their side chains. Tyrosine, although it is considered hydrophobic, does contain a hydrophilic hydroxyl group in its side chain. The answer is I, IV, and V, as all of these contain hydrophilic functional groups.

The amino acid is polar, so we do not need to worry about charges in the side chain. Since the amino acid is starting in a highly basic solution, we know that the amino acid is deprotonated at both termini. That is, the amino terminus is neutral and the carboxyl terminus is negative. This results in a net charge of -1 (at the carboxyl end). The first half equivalence point upon titration will be seen when half of the amino acids are neutral and half of the amino acids are negatively charged. The full first equivalence point will show all molecules with a neutral charge, while the second full equivalence point will show all molecules with a positive charge due to protonation of the amine.

The question states that the membrane-spanning region of the transmembrane protein is stained red; therefore, you will find only hydrophobic amino acids in this region. Recall that an amino acid has a central carbon that has a hydrogen group, carboxylic acid group, amino group, and a side chain attached. The differences between amino acids arise from the different side chains.

A hydrophobic amino acid contains nonpolar side chains. Glycine and alanine contain and side chains, respectively. Both of these amino acids will have nonpolar properties and be found in the red region of the protein. Cysteine contains , which is a polar side chain, and will be found in the blue region.

The double bond character of the carbon-nitrogen bond results in a shorter bond compared to the normal length of a pure bond ( vs. ). The double bond resonance of peptide bonds aids to increase stability, while subsequently decreasing the rotation about that bond. The partial double bond results in the amide group being planar, thus allowing for either a cis or trans conformation of a peptide bond. Due to the preference for the trans orientation over the cis orientation, there is less steric hindrance between groups attached to the alpha-carbon atoms. Thus, the correct answer is that the carbon-nitrogen bond has partial double bond character.