Part 1:

1.Calculate Energy (E) for Lysine primary amine (+) and Phosphate (-) 10 Å apart in hexane (apolar solvent) and in water.

2. How does temperature (T) influence this system? How does salt affect the system? Hydrogen bonds with water? Hydrogen bonds between bases? VDW interactions? Use the two types of pointers: → to indicate positive (increases this process) effects; ?| to indicate negative/inhibitory effects (diminishes this process).

3. What would change if the dsDNA structure contained a basepair mismatch (which state dsDNA or ssDNA is more or less likely after this change)?

4. What would happen (in terms of equilibrium balance point) if the system was in a vacuum? What would happen if the normal A, G, C, T bases were replaced with completely non-polar groups with inter-locking shapes (sterically complementary, but no possibility for H-bonding)?

5. Would substitution of A, G, C and T with completely non-polar base analogs make dsDNA more or less stable? Explain your reasoning.

6.What interactions favor the denatured state RNA and that favor the stem loop form? What will be the impact on this equilibrium if a GC basepair in the stem is replaced with an AU basepair? What will be the impact on this equilibrium situation if all salt (e.g. Mg2+, Na+, Cl- ions) is removed from the system?

7. Concept Question. Suggest a class activity for 8th graders that communicates the idea that H-bonds are less important for DNA stability and that it is really van der Waals contacts that are more important.

Important Questions:

1. (a) Name any three of the molecular interactions. (b) Rank these according to energy. (c) Name two non-covalent molecular interactions that are or can be repulsive.

2. (a) Calculate the electrostatic energy for a phosphate group (q = -1) hydrogen bonded with the primary amine of a lysine residue (q = +1). Assume an apolar solvent (D = 2). (Coulombs Law) (b) Is this a favorable (stable) or unfavorable (unstable) interaction? (c) Indicate two things that weaken this type of interaction as it would be found in a cell. (d) What is the common name for this situation?

3. Agree or disagree. The DNA double helix is primarily stabilized by hydrogen bonding. That is why GC rich DNA is more stable than AT rich DNA, since GC pairs have 3 hydrogen bonds while AT pairs have only 2. If you disagree, explain the flaw in logic?

Part 2:

1.If a glutamate residue is moved from water (polar solvent) to an apolar environment, will the pKa increase, decrease or stay the same?

2. What do we know about ?G for spontaneous reactions?

3. Concept: Is following the class on twitter @BiochemUU a spontaneous reaction?

4. Concept: Is completing extra credit problems a spontaneous reaction?

5. What would happen if the instructor contrived things so that students could only earn extra credit if they were following course on twitter?

6. Where are the instructions for protein folding stored?

Tougher Questions:

1. Indicate how many protein subunits are found in each molecular assembly. For each molecular assembly list the ligand(s) that bind with components of the assembly. (e.g. substrates, protons, allosteric effectors etc.)

Molecular assembly Number subunits Ligand(s)

(a) myoglobin
(b) alpha3beta3 (ATP synthase)
(c) c-ring (ATP synthase)
(d) ATCase
(e) hemoglobin
(f) aminoacyl-tRNA syntheses

Important:

1. The sequence of a section of polypeptide is -Val-Ser-Phe-Asn-Leu-Arg-. (a) What is the net charge of this segment at neutral pH = 7? Indicate which of these amino acid residues are hydrophobic (H) and which are polar (P). (b) What is most likely secondary structure for this sequence if it is found in contact with both aqueous exterior and hydrophobic core? (c) Draw all atoms for three consecutive residues connected by peptide bonds. Note: these three residues must come from the sequence provided.

2. (a) How are the instructions for the folding of a protein stored? (b) What thermodynamic entity opposes protein folding? (c) What is the largest contribution to the folding and stability of globular, water-soluble proteins?

3. What is fraction of glutamic acid at pH 5, pH 7, pH 7.4 (assume pKA = 5)?

4. What is degree of saturation Y for myoglobin at the lungs and at working muscle? Subtract these two Y values to obtain the theoretical oxygen transport capacity of myoglobin? How does this compare with the observed oxygen transport capacity of hemoglobin?

Tougher questions:

1. What is Y (fraction saturation) for myoglobin at 40 torr, 20 torr, and 2 torr? Hint: the P50 for myoglobin is 2 torr and y= p(o2)/p(o2) + p50 may be useful. (b) Where does oxygen bind? (c) Sketch the oxygen binding curve for myoglobin and hemoglobin. Hint: the P50 value of hemoglobin is 26 torr. (d) Will the P50 value for hemoglobin increase or decrease if 2,3 BPG is removed from the system? Briefly explain your reasoning.

2. Draw a histidine residue. Briefly describe the role(s) played by this residue in each of the following molecular situations (a) hemoglobin (b) serine protease (c) carbonic anhydrase (d) threonyl-tRNAsynthetase. For ONE of these molecular situations, draw the molecular context.