1. You need 0.5 liter of a 0.1 M buffer for a biochemical reaction that you plan to perform at pH 2.0. On the shelf in your laboratory you have available phosphoric acid, and the amino acids aspartate, glycine, glutamate, tyrosine, and histidine (all you have available are the fully deprotonated forms of the molecules); these are the only buffer materials you have available. (The pKå values for these compounds are given below.) For phosphoric acid, pKa1 = 2.12, pKa2 = 7.21, and pKa3 = 12.32 For aspartate, pKaCOOH = 1.88, pKaNH3+ = 9.60, pKa sidechain = 3.65 For glycine, pKaCOOH = 2.34, pKaNH3+ = 9.60 For glutamate, pKaCOOH = 2.19, pKaNH3+ = 9.67, pKa sidechain = 4.25 For histidine, pKaCOOH = 1.82, pKaNH3+ = 9.1 pKa sidechain = 6.00 For tyrosine, pKɑCOOH = 2.20, pKɑNH3+ = 9.11, pKa sidechain 10.07 a. Of these possible buffers, which is likely to yield the greatest resistance to pH change from the starting pH of 2.0, assuming that you were going to run a biochemical reaction that absorbed 0.003 moles of protons from 0.5 L of your buffer? (I recommend performing the calculations and showing a table of the pH change for reasonable candidate buffer species.) b. Of these possible buffers, which is likely to yield the greatest resistance to pH change from the starting pH of 2.0, assuming that you were going to run a biochemical reaction that released 0.003 moles of protons into 0.5 L of your buffer? (I recommend performing the calculations and showing a table of the pH change for reasonable candidate buffer species.) c. How many moles of NaOH or HCl would you have to add to make 0.5 liter of a 0.1 M buffer (pH 2.0) using the most effective of the possible buffer molecules? (If there is more than one "most effective" please perform the calculations for each of the better choices.)

An organic chemist is generally happy with 95% yields. If you synthesized a polypeptide and realized a 95% yield with each amino acid residue added, what would be your overall yield after adding 10 residues (to the first amino acid)? After adding 50 residues? After 100 residues? Would these low yields be biochemically “satisfactory”? How are low yields avoided, biochemically?

20. The dissociation constant of protein Z for ligand Y is: 10 micromolar. What fraction of the ligand is bound at ligand concentration = 5 micromolar?

A purified protein fraction has a total sample volume of 360 µL.  The sample has a corrected A280 of 0.484, and the blank corrected A280 was 0.052.  (Both values were measured with a path length of 1.00 cm.)  If 5.00 µL of the sample was used in a reaction, calculate the mass of protein in the reaction (in µg).

The enzyme phospholipase A2 has an optimal pH of 5.5. If a biochemist wants to set up an in vitro assay to screen inhibitors of this enzyme, which buffer system would be BEST?

The oligopeptide GEHRKDYWCM was isolated from blood plasma. Calculate its net charge to the nearest 0.01 at pH 7.6. Show all calculations