Zeon» ‘THE UNIVERSITY OF MANITOBA April 18.1994 EINAL EXAMINATION PAPER NO: __640 PAGE NO: 1 of 3 DEPARTMENT & COURSE NO: CHEMISTRY 2.463, TIME: _3- HOURS EXAMINATION: _Biochemistry of Proteins _ EXAMINER: J Neil Section 1: You must answer all of the following questions in Section 1. Your ‘can spend up to 2 hours on this part of the exam. Wherever possible use diagrams to enhance your answers. $1. Draw the peptide Ser-Glu and tabel all the dihedral angles ¢, y x. Explain what is a Ramachandran Plot and the information i Presents. 5 2. What is a helical wheel diagram? What features of protein structure are readily apparent in the diagram? 6 3, Explain the origin of the peptide dipole and its relationship t the helical macrodipole. 7 4, Describe the pslyproline helix. 12° 5, Identify the following structures. What are the main features each?40 10 10 6 ‘Using the diagram below explain the common ways in which achelices pack together. Using words and a diagram suggest how the Greek Key moti: might have arisen during evolution Use a 5 residue moving window and the table below to cale apd graph a hydropathy plot for the sequence K-T-G-I-L-V-A- Arg 15.86 Asp 9.66 Glu 7.75 Asn 7 Lys 649 Gin 648 His. 5.60 Ser 4 Thr 351 Tyr 108 Gly 0.00 Cys -0 Ala -0.87 Trp -1.39 Met -1.41 Phe -2 Val -3.10 He -3.98 Leu -3.98 How many different conformations can a 30 amino acid prot form if each amino acid can adopt only 2 different Describe the sequential framework model of protein folding, Describe the molten globule OR the hydrophobic zipper hypothesis of protein folding. With the use of the diagrams below discuss the structure of enzyme glycolate oxidase. You may add diagrams of your o- te aR2013. Section 3: 20) id 20 15. You must answer the following question in Section 2. You can spend about 1/2 hour on this question, Discuss the Intions Late and Introns Early hypotheses of protein evolution. Describe how the distance map of hemoglobin shown below was constructed, what information it conveys, and how this type of information relates to the above hypotheses. You may add diagrams of your own. Answer L of the following questions in Section 3. You can spend about 1/2 hour on this question. Suppose you wanted to study the folding pathway of a basic protein whose function is to activate an enzyme (BEA) containing 7 cys residues (3 disulfides and 1 thiol). Outline a strategy for determining the folding pathway. Explain the kinds of data you would expect to obtain and explain how you would interpret the data, Finally, propose a reasonable pathway or Describe helix formation in poly-L-proline and poly-L-glutamic acid. Explain why the helix<-->coil transition is highly cooperative in long homopolymérs. Compare this to helix formation in proteins.