BI/CH421 Biochemistry I Name: ______________________________________ Exam 2 10/20/2014 Last Name (PRINT): First Name: Pg Topic Pts Total possible 3 Multiple 12 choice 4 Multiple 9 choice 5 Multiple 15 choice 6 Multiple 12 choice 7 Multiple 11 choice 8 True false and 18 Fill in the Blank 9 Protein folding 13 and His titration 10 Dansyl 10 chloride 11 beta sheet 5 12 ramachandran 16 13 unfolded 5 protein disguise 14 stapled 8 peptides 15 Xstallography 16 and 2D-NMR total 150 points Page of 151 Total pts for pg _________ BI/CH421 Biochemistry I Name: ______________________________________ Exam 2 10/20/2014 Instructions: READ INSTRUCTIONS BEFORE BEGINNING EXAM. 1) Carefully read question before answering. Often I highlight very important information so please make note when I do so to make sure you are answering the question correctly. 2) Write your FULL name above and at least your last name on every page. 3) Write all of your answers on the exam paper itself in the space provided. If you need additional space, you can write on the back of the SAME page. If you do this, you must write “ON BACK” so that we know where to look for your answer. 4) Your answers should be brief and legible. A correct answer that cannot be read cannot receive full credit. Additionally, extremely lengthy responses containing both correct and incorrect statements will be graded accordingly. Meaning, if you answer the question correctly but if you go on to write a “kitchen sink” response containing incorrect information, you will not receive full credit for that answer. 5) You must write your final answers in pen – no tests taken in pencil will be accepted for a regrade request 6) No use of calculators will be permitted on the exam, no exceptions. Number Log Ln 2 0.30 0.69 3 0.48 1.10 4 0.60 1.39 5 0.70 1.61 6 0.78 1.79 7 0.85 1.95 8 0.90 2.08 9 0.95 2.20 10 1 2.30 R = 8.314 J•K-1•mol-1 = 1.987 cal•K-1•mol-1 Page of 152 Total pts for pg _________ BI/CH421 Biochemistry I Name: ______________________________________ Exam 2 10/20/2014 Part I: Multiple choice –Circle the choice that best answers the question. Do not write the letter in the margin to indicate your answer, circle it. 3 points each. 1. Identify the most conservative amino acid substitution, assuming that these two residues occur at the same position in two homologous proteins. a. Leu à Val b. Leu à Pro c. Leu à Asp d. Leu à Lys e. Leu à Trp 2. The ramachandran plot for proline a. would have the all phi angles clustered around -60˚ b. would have all psi angle clustered around -60˚ c. would have all of both phi and psi angles clustered around -60˚ d. would show proline’s peptide bond is more stable in the cis conformation e. would be identical to those of the other amino acids because it is also an L-amino acid 3. You must cleave the following peptide into smaller fragments, NMTQRGCKTVNTFVAEPLKDVQNVCFLE Which of the following statements about cleaving this peptide are true? a. Cleavage with cyanogen bromide would yield two fragments of roughly equal size b. Trypsin cleavage would create 3 fragments c. Endopeptidase V8 (which cleaves on the C-terminal side of glutamate residues) would create two polypeptides and a single glutamate residue d. Elastase treatment would create two fragments e. none of the above 4. For the two conformations A and B shown below, which of the following statements about proline’s peptide bond is true? A B R R a. A and B are both in the cis conformation b. A and B are both in the trans conformation c. neither A or B show a proline peptide bond d. A is in the cis conformation and B is in the trans conformation e. A is in the trans conformation and B is in the cis conformation Page of 153 Total pts for pg _________ BI/CH421 Biochemistry I Name: ______________________________________ Exam 2 10/20/2014 5. You purified a 20 kDa protein and determined its mass spectrum and got the data shown below. Which of the following statements about the data are true? (the numbers above each peak are the m/z for that peak) a. you must have more than one protein in the sample because there is more than one peak in the mass spectrum b. the peaks with a higher m/z are more charged than those with the lower m/z c. the peak at m/z =1001.0 has a z=20 d. the protein has a mass of 1001.0 Da, not 20 kDa as you had thought. e. you cannot interpret this mass spectrum without knowing some key information not given in this question. 6. For the portion of a peptide shown below, which of the following statements is true B O CH 3 H N N H O A C a. arrow A is pointing to the phi bond, B is pointing to the psi bond b. arrow B is pointing to the phi bond, C is pointing to the psi bond c. arrow C is pointing to the phi bond, A is pointing to the psi bond d. arrow C is pointing to the phi bond, B is pointing to the psi bond e. arrow A is pointing to the phi bond, C is pointing to the psi bond 7. Which of the following amino acid pairs would exhibit identical electron densities in a 2.0 Å crystal? a. Asp and Glu b. Asp and Val c. Asp and Gln d. A and C e. none of the above Page of 154 Total pts for pg _________ BI/CH421 Biochemistry I Name: ______________________________________ Exam 2 10/20/2014 8. Which one of the following statements about peptide bonds is FALSE. a) Peptide bonds are planar. b) Peptide bonds have about 40% double bond character. c) Peptide bonds prefer to be in the cis conformation. d) Peptide bonds are important for secondary structure formation e) Peptide bonds are also known as amide bonds. 9. Which level of protein structure is defined as "the three dimensional arrangement of polypeptides in a protein comprised of multiple polypeptides"? a) Primary b) Secondary c) Tertiary d) Quaternary e) none of the above 10. Which one of the following statements about α helices is FALSE? a. The α helix is a right handed helix b. Each residue in the α helix creates to a 100˚ turn of the helix c. An α helix has an overall macrodipole, where the C-terminus is partially positively charged and the N-terminus is partially negatively charged d. The core of the helix is tightly packed and consists of main chain atoms e. The hydrogen bonds that hold the helix together parallel to the axis of the helix. 11. If the polypeptide chain shown below were in an alpha helix, then the alpha amino group of amino acid 5 (the one with the R5 side chain) would be in a hydrogen bond with the C=O of R O R O R O R O R 1 H 3 H 5 H 7 H 9 H N N N N N N N N N N H H H H H O R O R O R O R O 2 4 6 8 a. amino acid 1 (R = R1) b. amino acid 2 (R = R2) c. amino acid 8 (R = R8) d. amino acid 9 (R = R9) e. none of the above 12. Proteins that facilitate folding of proteins into their native state inside the cell are called a. foldases b. endopeptidases c. chaperones d. prions e. amyloid Page of 155 Total pts for pg _________ BI/CH421 Biochemistry I Name: ______________________________________ Exam 2 10/20/2014 13. You cleave a peptide with chymotrypsin and sequence the resulting peptides and get the following : 1. Met-Arg-Ala-Tyr 2. Asp-Met-Leu-Phe 3. Gly-Asn The C-terminal amino acid of the starting peptide (the one cleaved with chymotrypsin) is a. Tyr b. Phe c. Asn d. all the above e. not enough information is given to answer this question 14. You cleave the SAME PEPTIDE as the one digested with chymotrypsin above with cyanogen bromide. Following sequencing, you get the resulting peptides 1. Arg-Ala-Tyr-Gly-Asn 2. Leu-Phe-Met 3. Asp-Met Using the info in this question and #13 above, the N-terminal amino acid of the original peptide is : a. Arg b. Leu c. Asp d. Met e. Asn 15. Which of the following polypeptides is most and least likely to form an alpha helix? Peptide 1: SEDNFGAPKSILW Peptide 2: QKASVEMAVRNSG a. peptide 1 will most likely form a helix, peptide 2 least likely to form a helix b. peptide 2 will most likely form a helix, peptide 1 least likely to form a helix c. both peptides have roughly the same likelihood to form a helix d. neither peptide would likely form a helix e. you cannot predict secondary structure from primary structure 16. In X-ray crystallography, the resolution of a structure a. must be at atomic resolution (below 1.2 Å) to begin to see hydrogen atoms b. is said to be very low if it is above 6 Å c. is usually in the range of 1.5 – 3 Å for typical crystal structures d.