Determining Net Charge of a Peptide: Videos & Practice Problems

In this practice problem, we analyze four tripeptides to determine their charges, nonpolar R groups, and the presence of sulfur-containing amino acids at pH 7. Understanding the ionization of amino acids is crucial for these evaluations, particularly focusing on the seven amino acids with ionizable R groups, which can be remembered using the mnemonic: "yucky crazy dragons eat knights riding horses."

To assess the charge of each tripeptide at pH 7, we first consider the amino and carboxyl groups. The pKa of the amino group is approximately 8, which is higher than the pH of 7, indicating that it will predominantly exist in its protonated form, contributing a positive charge. Conversely, the carboxyl group has a pKa of about 3.5, which is lower than the pH of 7, leading to its deprotonated form, which carries a negative charge.

Next, we evaluate the R groups of the tripeptides. For instance, tyrosine has a pKa of 10.5, meaning it remains protonated and neutral at pH 7. Lysine, also with a pKa of 10.5, contributes a positive charge. In contrast, aspartic acid, with a pKa of 3.9, contributes a negative charge at pH 7. By summing these charges, we find that the first peptide has a net charge of +1, the second peptide has a net charge of -1, the third peptide has a net charge of -2, and the fourth peptide has a net charge of 0. Therefore, the tripeptide that is most negatively charged at pH 7 is peptide 3.

For the second question regarding the largest number of nonpolar R groups, we utilize the mnemonic "GAV LIMP" to identify nonpolar amino acids. Peptide 1 contains methionine, which is nonpolar, while peptides 2 and 3 contain no nonpolar R groups. Peptide 4 includes leucine and valine, both of which are nonpolar. Thus, peptide 4 has the largest number of nonpolar R groups.

Lastly, to determine which tripeptide contains sulfur, we note that only methionine and cysteine contain sulfur atoms. Among the tripeptides, only peptide 1 includes methionine, confirming that it contains sulfur.

In summary, the answers to the questions are as follows: for part a, peptide 3 is the most negatively charged at pH 7; for part b, peptide 4 contains the largest number of nonpolar R groups; and for part c, peptide 1 contains sulfur.

In this practice problem, we explore the predominant structure and net charge of a peptide composed of asparagine, arginine, and cysteine at different pH levels. At pH 9, we begin by constructing the peptide backbone, which consists of nitrogen-carbon-carbon (NCC) sets for each amino acid. Each alpha carbon is identified as the central carbon in these sets. The carbonyl groups are then added to the backbone, and the chirality of the amino acids is considered, ensuring that L-amino acids are represented correctly with appropriate wedge and dash notations for their R groups.

Next, we incorporate the R groups of the amino acids. Asparagine, which has a non-ionizable R group, is represented by its amide structure. In contrast, arginine and cysteine possess ionizable R groups, necessitating a comparison of their pKa values with the pH to determine their ionization states. The pKa of asparagine's amino group is 8.8, which is less than the pH of 9, indicating that it exists in its deprotonated form (NH₂). For arginine, with a pKa of 12.48, the pH is lower, meaning it remains protonated (NH₂+). Cysteine's R group has a pKa of 8.18, which is also less than the pH, resulting in its deprotonated form (S^-). The carboxyl group at the C-terminus has a pKa of 1.96, which is less than the pH, indicating it is also deprotonated (COO^-).

To find the net charge of the peptide at pH 9, we sum the charges from the ionizable groups: two negative charges from cysteine's R group and the carboxyl group, and one positive charge from arginine's R group, resulting in a net charge of -1.

In part b, we analyze the peptide at pH 2. The same backbone structure is used, but the ionization states of the groups change. The amino group (pKa 8.8) is now protonated (NH₃+), as is arginine's R group (NH₂+), while cysteine's R group (pKa 8.18) remains neutral. The carboxyl group (pKa 1.96) is deprotonated (COO^-). The net charge at pH 2 is calculated as one negative charge from the carboxyl group and two positive charges from the amino and arginine groups, yielding a net charge of +1.

For part c, we determine the pH range where the net charge is approximately +1. By arranging the pKa values from smallest to largest (1.96 for the carboxyl group, 8.18 for cysteine's R group, 8.8 for the amino group, and 12.48 for arginine's R group), we find that the net charge will be +1 between the pKa of the carboxyl group (1.96) and the pKa of cysteine's R group (8.18). Thus, any pH within this range will result in a net charge of approximately +1.