Proton Acidity. (b) For the following reaction, draw the arrowhead properly to indicate the position of the equilibrium: HA + K + B -

Transcription

1 Proton Acidity A01 Given that acid A has a pk a of 15 and acid B has a pk a of 10, then: (a) Which of the two acids is stronger? (b) For the following reaction, draw the arrowhead properly to indicate the position of the equilibrium: A + K + B - K + A - + B (c) Calculate the equilibrium constant for this reaction as it is drawn. A02 Circle or draw in the most acidic hydrogen(s) in the following molecules. (a) (b) (c) 2 2 C 3 (d) (e) (f) A03 Formic acid has a dissocation constant K a = 1.77x10-4. What is its pk a? Calculate the approximate concentration of formate ions in a solution nominally 0.1 M in formic acid. A04 In each of the following pairs, which is the stronger base? Explain briefly. (a) C 3 C 2 - or C 3 C - 2 C 3 CClC - 2 (b) ClC 2 C 2 C 2 - or

2 (c) Cl - or C 3 C 2 - (d) FC 2 C 2 - or F 2 CC 2 - (e) ClC 2 C 2 C 2 - or C 3 C 2 C 2 C 2 -

3 Protein tructure B01 Draw the amino acid cysteine as it exists in aqueous solution at p=1. When treated with sodium ethoxide, cysteine s acidic protons can be removed. Draw the product of each stepwise deprotonation reaction. B02 In addition to the now-established mechanism for peptidyl-prolyl isomerization, an earlier mechanism based on limited data had been proposed. It had been observed that chemical modification of a cysteine in FKBP significantly reduced its rotamase activity. (a) Considering the properties of the cysteine sidechain, propose an alternative mechanism for cis-trans proline isomerization. Consider especially how cysteine s sulfur could facilitate the rotation about the peptide bond. (b) In your mechanism, if the cysteine were replaced by an alanine, would you expect the activity of the enzyme to be increased, decreased, not affected, or abolished? Explain. B03 Enzymes can accelerate reactions dramatically. For example, the rate of the reaction below is very slow (10-9 mol/s) at room temperature in water. owever, when a very small amount of the enzyme chymotrypsin is added, the rate of the reaction increases significantly (10-2 mol/s). C 3 C 3 2 Ph + 2 Ph In general, how does the enzyme produce such rate accelerations? B04 The values observed for ω are usually 0 and 180 in polypeptides. That is, the peptide bond is normally planar.

4 R 1 R 2 R R 1 2 (a) What is the reason for the planarity of the peptide bond? (b) For mono--substituted amides, the trans configuration (180 ) is usually favored over the cis (0 ) configuration. Explain. (c) The ΔG between the cis and trans forms is less in proline than in the other amino acids. Rationalize this result based on the structure of proline. (d) Based on your knowledge of allylic strain, redraw the above peptide on the left in a conformation which favors β-pleated sheets. B05 The following molecule is called glutathione, a very common small peptide in a wide variety of organisms. It is made up of the amino acids glutamate, cysteine, and glycine. 3 + C - - glutathione (a) There are two amide bonds in glutathione. Please circle these bonds and indicate for each amide bond whether it is in a cis- or trans-conformation. (b) There is a feature in this molecule that is not normally observed in the proteins we looked at so far. In the space below briefly describe the unusual aspect of this structure compared to a normal protein structure. (c) Draw a trans-amide bond between the carboxyl group of cysteine and the amino group of glycine. ext to that, draw an important amide resonance form for your peptide bond. Amide resonance enforces a preference for planarity of the amide bond. Circle all the atoms in your dipeptide that are normally held in this plane. (d) Circle the most acidic proton in each of the following compounds aspartic acid serine

5 B06 ickle cell anemia, characterized by the aggregation of hemoglobin, results from a single mutation in the gene that encodes hemoglobin. pecifically, a Glu on the surface of the protein is mutated to Val. Please discuss how this change could cause aggregation. B07 Protein folding usually occurs in an aqueous environment. Please give a short explanation why folding may not occur in an organic solvent such as hexane. B08 Draw the amino acid arginine as it exists in aqueous solutions of the following p: (a) 0.5 (b) 5.5 (c) 11.0 B09 The spontaneous conversion of a polypeptide into a properly folded protein is, by definition, thermodynamically favorable. The ΔG for this process is in the neighborhood of -5 to -15 kcal/mol. (a) f the intramolecular forces we discussed in lecture, which provides the greatest driving force for the folding? B10 (b) Given that ΔG = Δ - TΔ, what is the greater driving force for protein folding enthalpy or entropy? Explain your reasoning. The strength of a glutamate-arginine salt bridge was measured over a range of p values. The interaction was found to be the greatest at or near neutral p; the strength of the interaction dropped significantly under acidic or basic conditions. Give a brief explanation of this phenomenon. B11 The residues of naturally occurring peptides are linked together by amide bonds as illustrated in 1. It is possible to construct non-natural peptides (2) instead containing thioester bonds. Please answer each of question in just one or two sentences, using drawings to illustrate your answer if necessary.

6 R 1 R 2 R 3 R 4 natural peptides; all amide linkages 1 R 1 R 2 R 3 R 4 non-natural peptides; all thioester linkages 2 (a) Which molecule (1 or 2) is more stable towards hydrolysis with 0.1 a? Why? (b) Which molecule (1 or 2) is more stable towards protease enzymes? Why? (c) Which of the two molecules shown above would be expected to form b- pleated sheets? Why? B12 In the lab, a fragment of a protein was isolated which had the sequence EVKFDCR (Glu Val Lys Phe Asp Cys Arg). (a) Is this peptide more likely to be part of an α-helix or a β-sheet? Why? (b) Draw the structure of this peptide. (c) If you wanted to change the folding propensity of this peptide, what changes would you make to this sequence and why?