MT_K08 - NET I.D KEY 1 2 3 4 5 6 7 8 9 BIO331 MIDTERM EXAM...

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NET I . D. KEY BIO331 MIDTERM EXAM 10/23/08 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 119 TOTAL BE SURE TO PRINT LEGIBLY . IF WE CAN'T READ IT, WE CAN'T GRADE IT! (SERIOUSLY) PRINT NAME (LAST, FIRST) ON THE BACK TOP OF THE LAST PAGE (AND ONLY THE LAST PAGE) Use these pK a values: terminal COOH 4 terminal NH 3 + 9 R-GROUPS: Asp 4 Glu 4 Cys 8 Tyr 10 His 7 Lys 10 Arg 12 GAS CONSTANT R = 0.0083 kJ/mol . K
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1. (1 pt) Albert Heelicks worked day and night to purify and then sequence a small protein, which he discovered to be Leu-Glu-Asn-Ile-Lys-Gly-Val-Gln-Thr-Ala-Asn-Leu-Glu-Asn-Ile-Lys-Gly-Val-Gln-Thr-Ala-Asn. Circle how Al Heelicks can decide whether this protein is really a new discovery, or instead has already been discovered and characterized by his boss, Beth Sheetz. a. compare the primary structure of his protein to the primary structure of all sequenced proteins b. compare his protein to the structure of all the α -helices that are listed in the Pro Teen Dada Bank c. look for a short AA sequence that will transport this protein into the journal Nature d. ask the Enzyme Commissioner e. perform a reverse turn This was the joke question, but your answer should not also have been a joke! 2. (3 pts) Al Heelicks must decide if this protein is (i) embedded in a membrane, or (ii) completely surrounded by water on all sides, or (iii) an amphipathic helix. Which is correct and why? Be brief! i. NOT EMBEDDED: NO RUN OF ~ 25 NONPOLAR AA ii. POSSIBLE, BUT NO SPECIAL INDICATION FOR THIS iii. NONPOLAR AA ARE SPACED ~ EVERY 3 RESIDUES IN AN α -HELIX ON THE SURFACE 3. (8 pts) Protein Kinase A has two conserved residues, Glu91 and Lys72, which can form an ion pair. Show your work. a. At what pH value(s) would there be < 10% of these Glu-Lys that are actually in an ion pair? Circle answers. AT pH 3, ALL LYS ARE + AND 10% OF GLU ARE - SO, pH < 3 OR pH > 11 AT pH 11, ALL GLU ARE - AND 10% OF LYS ARE + 6 PTS b. At what pH value(s) would there be exactly 50% of these Glu-Lys in ion pairs? AT pH 4 AND AT pH 10 2 PTS 4. (5 pts) Draw the structure of the tripeptide Ala-Gly-Ser at pH = 7. Side chains are -CH 3 , -H, and -CH 2 -OH respectively. Show every atom. Choose one peptide bond and draw a circle around each of the 6 atoms that lie in the same plane. Label the bonds that allow free rotation with Ψ and Φ .
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V m 1 + [I]/K I K m (1 + [I]/K I ) 1/[S] 1/V 1/V 1/V -.6 -.4 -.2 0.0 0.2 0.4 0.6 1 5 . (12 pts) Kinetic studies of an enzyme are made in the absence of inhibitors, and with inhibitors A and B.
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