HW 1 -...

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(1) Amino acid charge profiles: The table below gives the pK values for three amino acids: Amino acid pK of ! -COOH pK of ! -NH 2 pK of R group glycine 2.34 9.6 NA aspartic acid 2.09 9.82 3.86 Lysine 2.18 8.95 10.53 Estimate to within ± 0.2, the net charge of each amino acid at the following pH values: pH 2, 4, 6, 8, 10, and 12. (Examples: the net charge of a chloride ion is -1.0; the net charge of acetic acid at its pK is -0.5) Suggest a pH that would be effective for separating a mixture of the three amino acids, based on differences in their net charge. Ans: When the pH is more than 1 unit below the pK of a COOH group, the group is essentially protonated, and its contribution to the molecule charge is zero. When the pH is more than 1 unit above the pK of that group, the group is deprotonated, and its charge is -1. When the pH is the same as the pK for this group, the charge is -0.5 (the average value for a huge sample size of molecules, or the average value for a single molecule over a time frame long compared to the off-rate and on-rate of the proton). In between these reference points, you could use the Henderson-Hasselbalch equation to get a good estimate, but it is sufficient for the purposes of this problem to just do a crude linear estimate. There are probably websites out there that can do the calculation. For the NH 2 group, when the pH is more than 1 unit below the pK, the charge is +1, when the pH is more than 1 unit above the pK, the charge is zero. When the pH=pK, the charge is +0.5. Just sum up the estimates from each charged group on a molecule to get the net charge at a given pH. Note that the R group of aspartic acid is a COOH group, and the R group of lysine is a NH 2 group. pH Glycine Aspartic acid Lysine 2 +0.7 +0.5 +1.6 4 0.0 -0.5 +1.0 6 0.0 -1.0 +1.0 8 0.0 -1.0 +0.9 10 -0.6 -1.6 -0.2 12 -1.0 -2.0 -0.9 Aspartic acid is the most acidic molecule, it goes negative at the lowest pH. Lysine is the least acidic, not going negative until the pH is pretty high. Glycine is in between those two. A charge-based separation, such as electrophoresis or ion-exchange chromatography would be effective at a pH of 6, 7, or 8, as the charge for glycine is near neutral, while aspartic acid is negative and lysine is positive. (2) Harrison prob 1.3 (pH dependent charge of polyglutamic acid
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HW 1 -...

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