Practice Problems 3. a. What is the name of the bond formed between two amino acids? Are these bonds free to rotate?

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1 Life Sciences 1a Practice Problems 3 1. Draw the oligopeptide for Ala-Phe-Gly-Thr-Asp. You do not need to indicate the stereochemistry of the sidechains. Denote with arrows the bonds formed between the amino acids. a. What is the name of the bond formed between two amino acids? Are these bonds free to rotate? b. Circle the non-polar side chains in the oligopeptide. Put a square around the side chain that contains an alcohol. c. Circle the chiral centers in the peptide above. ow many stereoisomers are possible? d. Using the following table draw the oligopeptide for Ala-Phe-Gly-Thr-Asp in its predominant form at p 8.0. Ionizable group pka Asp side chain 4.0 Glu side chain 4.4 is side chain 6.5 Cys side chain 9.3 Tyr side chain 10.2 Lys side chain 10.9 Arg side chain 12.0 Ser side chain 13.0 Amine terminus 9.8 Carboxy terminus 2.3

2 2. The C-terminal end of the protein BRCA, a protein that is important in maintaining healthy breast cells is shown below. a. Label the secondary structural elements shown in the structure. 3. emoglobin is an oxygen-carrying protein made up of four polypeptide chains. a. The sequence of a portion of hemoglobin is shown below. Draw the peptide for the first five amino acids (boldfaced below) as they would predominantly exist at physiological p ~7.4 (refer to the pk a table). You do not need to indicate the stereochemistry of the sidechains. emoglobin - SAQVKGGKKVADALTAVAV - C b. Circle the non-polar amino acids, and put a star by the box containing an alcohol in the side chain on the above diagram.

3 c. In the native protein, the provided sequence folds into the structure shown below. What type of secondary structure is shown? d. Draw hydrogen bonds between the boxed atoms and their appropriate hydrogen bonding partners. e. In lecture we examined the interactions between amino acids that result in the folded structure of proteins. For each pair of amino acids below draw a possible interaction between their side chains at p 8.0 and identify the dominant force behind the interaction. I. Isoleucine and Valine II. Asparagine and istidine III. Lysine and Glutamate

4 4. As you will see in lab in a couple of weeks, molecules can be separated on a TLC plate based on differences in polarity. More polar molecules interact more strongly with the TLC plate than less polar molecules. This causes the more polar molecules to migrate slower than the less polar molecules. The twenty naturally occurring amino acids possess different polarities, and thus should be able to be separated by TLC. In your answers below, please draw the dominant species of each amino acid at the specified p. a. If you were to spot p7 solutions of leucine, threonine, and glutamic acid, what is the order of amino acid migration (most migration to least)? Explain. b. If you were to spot p2 solutions of leucine, threonine, and glutamic acid, would you expect to see a change in the migration of these amino acids versus the p7 solutions? Explain. c. If you were to spot p13 solutions of leucine, threonine, and glutamic acid, would you expect to see a change in the migration of these amino acids versus the p7 solutions? Explain.

5 5. Don t forget that basic principles can be reinforced by the problems in your textbooks. The answers to the Alberts problems are in the back of your book and many of the answers to the McMurry problems can also be found at the back of the book. The answers to the remaining McMurry problems can be looked up in the solution manual available at the Student Study etwork Sessions. A couple extremely useful problems are listed below and see your book for more. a. McMurry 18.70: Which would you expect to be more soluble in water, a peptide rich in aspartate and lysine, or a peptide rich in valine and alanine? Explain. b. McMurry 18.94: List the amino acids that would be capable of hydrogen bonding if included in a peptide chain. Draw an example of two of these amino acids hydrogen bonding to one another. For each one, draw a hydrogen bond to water in a separate sketch. Refer to section 8.11 for help with drawing hydrogen bonds.

6 Answers 1. Phe 2 Ala Gly Thr Asp a. The bond formed between two amino acids is called an amide bond or a peptide bond. These bonds have partial double-bond character and are not free to rotate. b. (Ala, Phe, Gly) should be circled. Thr contains alcohol-square c. There are 4 chiral alpha carbons and one chiral carbon in the sidechain of threonine. # Stereoisomers = 2 5 =32 d. Phe + 3 Ala Gly Thr - Asp - 2a. The yellow corkscrews and blue corkscrew are α-helices. The teal arrows are β-sheets. ote, not all secondary structure elements are labeled in the figure.

7 3ab cd. 3 I. Van der Waal's Ile Val II. ydrogen Bonding Asn is III. Lys Glu Ionic

8 4a Leucine Threonine - Glutamic Acid Leucine has a hydrocarbon sidechain so it is the least polar and will migrate the most. Threonine has a sidechain that is polar and it will migrate the second farthest. The most polar amino acid is glutamic acid since it has a charged sidechain so it will migrate the least. b Leucine Threonine Glutamic Acid The order will be the same Leu (the most), Thr, Glu (the least). owever, glutamic acid would migrate a little more (closer to threonine) since its sidechain will now be neutral (pka 4.25). In addition, they will all migrate a little further since the C- is now C; the loss of one charged residue will allow all three to migrate further than at p 7. c Leucine Threonine - Glutamic Acid The order will be the same, however they will all migrate slightly further than at p 7. Since the amino group will now be neutral instead of charged ( 3 + to 2 ). 5. See McMurry for answers to 18.70, and 18.94

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