Disulfide bonds are disrupted by the introduction of mercaptoethanol. Disulfide bonds are created by the interaction of two cysteine amino acids on different parts of the amino acid chain during the development of tertiary protein folding. As a result, a protein with few to no cysteine amino acids would be least affected by mercaptoethanol.

Alpha-helices are linked to secondary structure, and do not involve disulfide bonds. Similarly, quaternary structure is not determined by disulfide bonds; a protein without quaternary structure could still have disulfide bonds, which would be disrupted by mercaptoethanol. Proline is not involved in disulfide bonds, and its frequency would not affect the potency of mercaptoethanol to the protein.

At low pH levels, we expect amino acids to exist in their cationic form. At a pH level equal to the isoelectric point (pI) we expect amino acids to exist as zwitterions, and at high pH levels we expect them to exist in their anionic forms.

Low pH causes protonation of the amino groups; high pH causes deprotonation of the carboxyl groups.

Polypeptides are made from individual amino acids through formation of peptide bonds.

Monosaccharides are the fundamental units for carbohydrates, while fatty acids come together to form lipids. Nucleotides and phosphates are key components of the nucleic acids, RNA and DNA.

The isoelectric point is the pH where the amino acid solution is electrically neutral. In acidic conditions, the carboxylic acid and amino terminus will both be protonated. This results in a positive charge (due to the amine being protonated). In basic conditions, both ends are deprotonated, resulting in a negative charge.

If an amino acid is basic, that means that the pH must be above 7 in order to deprotonate the amine in the side chain. Only then will the amino acid be electrically neutral. All basic amino acids (three of them) have an isoelectric point above a pH of 7. All other amino acids have an isoelectric point at a pH below 7.

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.

Only basic amino acids have an isoelectric point above a pH of 7. All others will have an isoelectric point below a pH of 7.

Since the amino acid is polar, it will have an isoelectric point below a pH of 7. Since a pH of 1 is extremely acidic, we would expect both ends of the amino acid to be protonated at that pH. As a result, a pH of 5.4 is more appropriate when predicting the amino acid's isoelectric point.

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.

Phenylalanine:

Since the phenylalanine residue is at the C-terminus end of the molecule, only its carboxylic acid pK_a is relevant, as its amine is involved in a peptide bond with arginine. At a pH of 7 (well above the carboxylic acid pK_a 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 pK_a 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 pK_a of 12.48), this amino acid would have a charge of .  

Valine:

Finally, for valine, the relevant pK_a to consider is the NH₂ pK_a 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 .

One mole is base is required to deprotonate each carboxylic acid or amine, until the amino acid exists in its most deprotonated and basic form. First, two moles of base would be needed to deprotonate the two acid groups on glutamic acid (one depicted on each end). Next, a third mole would be needed to deprotonate the amine to its neutral state. Three total moles is the correct answer. 

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