CAPTER 29 W: AMI ACIDS + PRTEIS For all problems, consult the table of 20 Amino Acids provided in lecture if an amino acid structure is needed; these will be given on exams. Use natural amino acids (L) unless otherwise noted. GEERAL CCEPTS 1. Which amino acid is not chiral? 2. Classify each of the following amino acids as neutral, acidic or basic. A.a. Aspartic Acid Lysine Tyrosine Asparagine Threonine 2 2 (R) Type 3. Briefly explain why tryptophan is a neutral amino acid, not a basic one. 4. Briefly explain why cysteine is an acidic amino acid, yet serine and methionine are neutral. Cysteine Serine Methionine S S C3 Page 1
p-depedet AMI ACID STRUCTURE 5. Draw the three forms of serine, and list the p range where the solution is > 90% in that form. A B C p range Annotate the p scale below to show the p ranges for each form. Some p values will have a mixture of forms. p 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 6. By consulting the previous problem, in what range of p values is serine in its zwitterionic form (>90% of the solution is that form)? 7. Draw the three forms of proline, and list the p range where the solution is > 90% in that form. p range 8. Draw the four forms of glutamic acid, and list the p range where the solution is > 90% in that form. p range Page 2
9. For the amino acid arginine, a. Identify which nitrogen atom in the side chain is basic. Then explain why that nitrogen atom is basic while the other nitrogen atoms are not. 2 b. Draw the four forms of arginine, and list the p range where the solution is > 90% in that form. p range 10. For the amino acid histidine, a. Identify which nitrogen atom in the side chain is basic. Then explain why that nitrogen atom is basic while the other nitrogen atom is not. b. Draw the two forms of histidine that would be present in a buffered solution of p 5.9. Then decide which form would be in a slightly greater quantity at this p. Page 3
11. Explain why the pk a of the carboxylic acid on glycine is lower than the pk a of acetic acid. 12. Draw the primary form of these amino acids at the indicated p. Glutamine Lysine Tyrosine Aspartic acid pk a 3 + 9.1 pk a C 2 2.2 pk a 3 + 9.0 pk a C 2 2.2 pk a R 10.5 pk a 3 + 9.1 pk a C 2 2.2 pk a R 10.1 pk a 3 + 9.6 pk a C 2 1.9 pk a R 3.7 p at p 6.4 at p 4.0 at p 12.0 at p 7.0 13. Explain why the amino acid tyrosine never exists in the form shown below. 3 Page 4
DRAWIG PLYPEPTIDES For the problems in this section, don t worry about any acid-base properties (draw the structures neutral). The structural connectivity is what s important at this point. Draw the backbone of the polypeptide in its natural conformation (zigzag fashion). 14. Draw the dipeptide W E made by connecting the natural amino acids tryptophan and glutamic acid. 15. Draw the tripeptide M A D. 16. Draw the polypeptide Q R G A I C. 17. What is the amino acid sequence of each polypeptide? S C 3 2 2 Page 5
p-depedet PRTEI STRUCTURE 18. Draw the following polypeptides at the indicated p. a. S A K at p 7.4 b. M E Q W at p 1.0 c. A Y at p 7.6 Page 6
1, 2, 3 AD 4 STRUCTURE F PRTEIS 19. Briefly describe what is referred to by a protein s 1, 2, 3, and 4 structure. Type Description Primary Secondary Tertiary Quaternary 20. ow are alpha helices and beta sheets similar, and how are they different? EZYMES 21. The following is a diagram of the active site of an enzyme, with a substrate bound (in bold) and some of the enzyme s side chains shown. Fill in the boxes to label the type of interactions pointed to by each arrow. 3 3 C Page 7
22. Ketone 1 is converted to ketone 2 through an enzyme-mediated reaction. The middle structure shows key interactions between the enzyme (tyrosine-14 and aspartic acid-38) and the substrate. Enz Tyr-14 C 3 C 3 C 3 C 3 C 3 C 3 Ketone 1 Asp-38 Enz Ketone 2 a. ow does the aspartic acid sidechain (Asp-38) help the enzyme function? b. ow does the tyrosine (Tyr-14) help the enzyme function? c. If a mutation occurs such that the 14 th residue is phenylalanine (Phe-14), what effect would this have on the ability of the enzyme to function? Explain. Page 8
PRTEI DEATURATI 23. Explain how each of these conditions can denature a protein. a. Placing the protein in a solution with a different p than it is active. b. eating the protein. c. Placing the protein in an isopropyl alcohol solution. GEERAL IDEAS 24. Choose whether each statement is True or False. Statement T or F a. All proteins have quaternary structure. b. A mutation does not always cause a protein to stop functioning. c. The interior of many globular proteins is mostly nonpolar amino acids. d. The side chains of glutamine and threonine can interact in a protein through hydrogen bonding. e. The glutamine-threonine side chain interaction previously described can be altered directly by placing the protein in a more acidic environment. f. The side chains of lysine and aspartic acid interact in a protein more strongly when the protein is in a p 7 solution than when the protein is in a p 1 solution. g. Pepsin is an enzyme in the stomach that degrades proteins into shorter polypeptides. Pepsin should be denatured when placed in a p = 1 solution. Page 9