1. What causes nonpolar molecules to aggregate in water? What happens to the entropy of water when this occurs? What is the name of the driving force that causes this to happen?

2. An acid with a pKa of 8.0 is present in a solution with a pH of 6.0. What is the ratio of the protonated to the deprotonated form?

3. Identify the amino acids indicated below and give their three-letter and one-letter codes.
a. Identify two amino acids used to quantitate proteins.
b. Identify two amino acids that would be found in the core of a globular protein.
c. Name two amino acids that would be found on the surface of a protein.
d. Name an amino acid with two chiral centers.
e. Name an amino acid whose side chain is protonated at neutral pH.

4. A peptide has the sequence
Which amino acids have pKR values?
What is the net charge of the molecule at each of the following pH values: 3, 8, and 11?

5. A new protein of unknown structure has been purified. Gel filtration chromatography reveals that the native protein has a molecular weight of 300,000. Chromatography of the protein in the presence of 6 M guanidine hydrochloride yields a single peak corresponding to a molecular weight of 50,000. Chromatography of the protein in the presence of 6 M guanidine hydrochloride and 10 mM β -mercaptoethanol yields peaks corresponding to molecular weights of 30,000 and 20,000. What does this data tell you about the structure of this protein?

6. You are performing studies to test predictions about which residues are essential for a protein’s function. Which of each pair of amino acid substitutions listed below would you expect to disrupt protein structure the most? Explain your answer.
a. Val replaced by Ala or Phe.
b. Lys replaced by Asp or Arg

7. The amino acid sequence of a sugar transferring enzyme from the pathogenic bacteria Camplyobacter jejuni given below:


Copy and paste the amino acid sequence into ProtParam to compute parameters for the protein.
a) What is the pI of the protein?
b) Which amino acid residues account for this pI?
c) If you were to isolate this protein from a crude extract what type of ion exchange column would you use?

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1. Nonpolar molecules, such as alkanes or oil, do not contain polar bonds. Water molecules are polar, so they aggregate by means of dipole-dipole interaction and, particularly, hydrogen bonds. Nonpolar molecules repel from the polar ones, in this case water. Mixing of the two immiscible liquids disrupts the order established between H2O molecules, which, in turn, leads to the increase of the entropy of water due to instability. This is because nonpolar molecules are attracted to each other through van der Waals dispersion forces and not dipole-dipole interaction...

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