Chemistry Problem Set 2: Amino Acids and Peptides, Assignments of Biochemistry

Download Chemistry Problem Set 2: Amino Acids and Peptides and more Assignments Biochemistry in PDF only on Docsity! ANSWERS CHEM 641 Problem Set #2 assigned 9/4/07, answers posted 9/11/07 1) Draw the complete side chain structure of each of the amino acids as they occur at pH 7.0, including the 3-letter and 1-letter codes (i.e. Ala and A for alanine). Be sure that you can categorize whether an amino acid is non-polar, polar-uncharged, acidic or basic. Next, write the proton dissociation reaction demonstrating the acid-base properties of the amino acid side chains Arg, Asp, Cys, Glu, His, Lys, Ser, Thr and Tyr, which have R-group pKas of 12.5, 3.9, 8.3, 4.3, 6.0, 10.5, 13, 13, 10.1, respectively. FYI: you are going to need to learn these structures, so here is a trick that might help. After you have spent some time studying the structures, try to write all 20 amino acids down from memory. Then concentrate on the amino acids that you missed and try again. You can refer to your notes or text to check the 20 commonly occuring amino acid structures. Cα HN H2N NH2+ Arg Cα HN H2N NH Cα HN NH+ Cα HN N His Cα NH3+ Cα NH2 Lys Cα HS Cα -S Cys for pKa values above pH 7.0 + H+ + H+ + H+ + H+ Cα HO Cα -O Ser + H+ Cα CH HO Cα CH -O Thr + H+ CH3 CH3 Cα OH + H+ Cα O- Tyr for pKa values below pH 7.0 Cα + OH- Cα O O -O- O Cα OH O Asp + OH- Cα O OH Glu ANSWERS CHEM 641 Problem Set #2 assigned 9/4/07, answers posted 9/11/07 2) Starting from the acid form of a 0.1 M solution of the amino acid histidine (the carboxyl and imidazole R-group are protonated) draw the complete titration reaction showing the chemical structure after addition of each of 3 equivalents of OH-. What is the net charge of the molecule and the pH of a solution of the amino acid at 0, 0.5, 1, 1.5, 2, 2.5 and 3 equivalents of strong base added? +H3N COOH H N NH H pKa ~ 2.0pKa ~9.5 pKa = 6.0 + 1st eq. OH- +H3N COO- H N NH H + 2nd eq. OH- +H3N COO- H N NH + 3rd eq. OH- H2N COO- H N NH + + +2 charge +1 charge isoelectric zero net charge -1 charge Equivalents of OH- 0.0 0.5 1.0 1.5 2.0 2.5 3.0 pH 1.5 2.0 4.0 6.0 7.75 9.5 11.2 net charge 2.0 1.5 1.0 0.5 0.0 -0.5 -1.0 Answers given assume that you have used the pKa listed above (and mentioned in class as a good average number to know for all amino acids) for the carboxy and amino (2.0 and 9.5, respectively). Many of you correctly found the exact pKa’s for Histidine (1.8 and 9.2, respectively), and that’s okay as well. However, the numbers above will be slightly different. The 3 half equivalent points are the 3 respective pKa values. Make sure you understand why. The 1.0 equivalent point can be estimated as the average of the pKa at 2.0 and the pKa at 6.0. The 2.0 equivalent point can be estimated as the average of the pKa at 6.0 and the pKa at 9.5. The 0.0 equivalent point is calculated identically to how it was done for acetic acid in Problem set #1. Likewise, the 3.0 equivalent point for His is done the same as for acetate (1.0 equivalents added to acetic acid). Remember, here you need to use Kb (for the amino group of His) and the dissociation of a weak base. Please let me know if you need help with this.