Chem 135 Fall 2009 PS1 - Chem 135 Fall 2009 Problem Set 1...

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Unformatted text preview: Chem 135 Fall 2009 Problem Set 1 Due Friday, September 11, 2009 in class 1. Draw the following peptide as an organic molecule (including stereochemistry) at pH 11. H2N‐Y‐E‐G‐T‐A‐K‐R‐D‐N‐V‐W‐H‐Q‐CO2H a. What is its net charge? b. What is its net charge at pH 3 and pH 7? 2. The glutamic acid side chain usually has a pKa of 4.2 in aqueous solution. However, in a certain folded protein, the pKa of a Glu side chain was found to be 6.1. a. Draw the equilibrium reaction for the dissociation of a proton from the Glu sidechain in a polypeptide (i.e. a linear, unfolded protein). Use “R” groups to represent the remainder of the peptide connected to the amino and carboxyl groups of the Glu residue that you draw. b. In which direction has the above equilibrium shifted in the folding of the polypeptide (assume pKa of Glu is normally 4.2) to the final protein mentioned above? c. Briefly suggest two possible causes for this pKa alteration. 3. As discussed in class, the planar amide bond can be considered to be trans or cis with respect to the peptide backbone substituents (shown here as “R” groups). For most amino acids, the trans:cis ratio is 10000:1. In contrast, peptide bonds involving proline display a trans:cis ratio of only 80:20. 4. In order to track the localization of a specific protein in a living cell, a common practice is the attachment of fluorescent dye molecules. This can be conveniently achieved through the labeling of cysteine residues using maleimide reagents: a. Draw the trans and cis conformations of an Ala‐Pro dipeptide and explain why the cis conformation is more accessible for proline than for other amino acids. Do not use the “R” groups to abbreviate your structures. b. Suppose you encounter a peptide that forms a single α–helix. What effect would a proline residue have if it were introduced into the middle of the sequence? a. What is the pKa of a cysteine residue? b. Provide a detailed arrow‐pushing mechanism for this protein modification reaction. c. Would you expect this reaction to proceed faster or slower when carried out at pH 7? Explain your answer. 5. The following question pertains to an important class of DNA‐binding proteins characterized by the unusually large number of leucine residues in their sequences (see figure on next page). a. What is the chemical structure of a leucine residue? b. These sequences fold into a single, uninterrupted alpha helix. Sketch a Ramachandran plot that you would expect to obtain for such a structure. Be sure to label your x‐ and y‐axes. c. Suppose this alpha helix was synthesized with the enantiomers of the 20 natural amino acids. The same general fold is observed, but it is the mirror image of the helix. Sketch a Ramachandran plot for this protein. d. When placed under the right conditions, two identical copies of this alpha helix made with the natural enantiomers of the 20 amino acids come together to form a dimer: This dimerization is an example of which hierarchical level of protein structure? e. On the figure in part c, sketch where you would expect to find most of the leucine residues. Briefly explain why you chose this location. f. Once the dimer has been formed, this protein binds double stranded DNA and alters the levels of gene expression: Considering that DNA is a polymer linked by a phosphate backbone, name two residues that you would expect to find in abundance in the DNA binding region? 6. In 1994, the structure was reported of the tail spike of bacteriophage P22, a virus that infects various species of Salmonella bacteria as its host. The structure revealed a series of β‐ sheets coiled together to form a β‐helix. Note that the structure is not hollow. The location of the tail spike is indicated by the arrow in a transmission electron micrograph (Figure 1), and the corresponding structural cartoon is shown in Figures 2‐4. The letters “N” and “C” denote the N‐ and C‐termini, respectively. The following questions pertain to this structure. a. Based on your inspection of the figure, is the β‐helix right‐ or left‐handed? b. Are the strands organized in a parallel or an antiparallel fashion? Draw two segments consisting of three amino acids each that would be found on two adjacent strands of the helix. Clearly indicate the pattern of hydrogen bonds between them. c. The protein segment forming the structure in Figures 3 and 4 has 17 glycine residues in the primary sequence of 106 amino acids. Speculate on the role glycine is playing, and indicate where you would expect to find these residues. d. Assuming that this spike extends into an aqueous environment, what pattern do you think the rest of the amino acid sequence would have? (Hint: Think about the nature of the side chains.) 7. Hemoglobin (Hb), the red blood pigment, is a protein whose main role is to transport oxygen throughout the body. The functional unit of hemoglobin is an α2β2 tetramer, consisting of two identical α polypeptide chains and two identical β polypeptide chains. Hemoglobin tetramers are contained within red blood cells (RBCs). As they travel through the circulatory system, red blood cells must squeeze through capillary blood vessels with a diameter smaller than the diameter of the cell. In individuals with sickle‐cell disease, the RBCs take on an elongated, rigid crescent shape, impeding blood flow and causing tissue damage and excruciating pain. A single amino acid mutation on the surface of the β chain of hemoglobin, Glu β6 Val, is responsible for sickle‐cell anemia. This mutation is benign under normal oxygen levels, but leads to the formation of long, rigid fibers that deform the RBC under the lower oxygen levels typical of capillaries. Figure 3. Figure 2. Electron micrograph of an Hb fiber Figure 1. Sickled RBCs Hb tetramer. a. Which hierarchical levels of protein structure are affected by the mutation at normal oxygen concentrations? Which levels are affected at low oxygen concentrations? b. On the α subunit, Phe 85 and Leu 88 form a hydrophobic pocket that is required for fiber formation. What role do you think this pocket plays in fiber formation? Both normal Hb and sickle‐cell Hb (HbS) possess this pocket, but fibers are only formed with HbS. Why? c. In contrast to the consequences of the Glu Val mutation, most Hb surface mutations cause little change. Glu β26 Lys, for example, is the most common Hb mutant after HbS, possessed by up to 10% of the population in Southeast Asia. Why doesn’t this mutation lead to fiber formation? ...
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