Biochemistry Exam 2

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Biochemistry Exam 2
2013-11-25 16:28:46
biochemistry skitty 2004

for the second biochemistry exam
Show Answers:

  1. At ten degrees above the Tm of an enzyme, what occurs?
    It is denatured
  2. The native folded structure of a protein is dictated by several factors. Which is the most important?
    the sequence of the protein
  3. Secondary, tertiary, and quaternary structures of proteins are formed and stabilized to a great extent by weak intermolecular forces.
  4. Approximately what volume of a protein is not occupied by protein atoms?
  5. Two degrees of freedom exist per residue in the peptide chain. The angle about the Ca-N bond is denoted___ and the angle about the Ca-C bond is denoted ____. A plot of one versus the other is called a ______.
    • Φ
    • ψ
    • Ramachondron plot
  6. What two amino acids are prevalent in B-turns?
    glycine and proline
  7. Residues per turn:
  8. Rise per residue:
    1.5 nm
  9. Rise per turn ((pitch):
  10. Which amino acid is termed a helix breaker?
  11. All of the information necessary for folding a peptide chain into its "native" active structure is contained in the ____ of the peptide.
  12. The arrangement if B-H and C=O groups along the helix axis creates a large net ____ moment for the helix.
  13. Pro and HyPro make up approximately 30% of the collagen triple helix. [T/F]
  14. Since the N-H and C=O moieties of the peptide backbone are highly polar, how can a peptide segment tracerse the hydrophobic core of a protein?
    The traverse as beta sheets or alpha helices to neutralize that polarity.
  15. Large globular proteins are typically made up of two or more recognizable and distinct structures termed ______ . They are compact, folded protein structures that are usually stable by themselves in aqueous solution.
  16. Provide an example of a chaotropic agent and how it can be exploited in studying protein structure. The better you example, the more credit you'll receive.
    Guanadine-HCl and Urea are chaotropic agents. You can titrate a protein with increasing concentrations of these compounds and observe changes in conformation (Unfolding).
  17. Which of the compounded proteins is not one the four structural classes of proteins?
    a-B proteins, in which B sheets predominate.
  18. What is the Vmax of an enzyme catalyzed reaction if the Km is 2mM, the [S] of substrate is .25mM, and the velocity is .2umol/min?
    1.80 umol/min
  19. Binding of a substrate to an enzyme alters the conformation of both the protein and the substrate in the induced fit hypothesis. [T/F]
  20. For enzyme catalyzed reactions at high [S], velocity becomes virtually independent of [S] and approaches a maximal limit since substrate molecules block access to the active site of the enzyme. [T/F]
  21. The effect of a catalyst is to lower the free energy of activation. [T/F]
  22. The Km is...
    equal to the substrate concentration when the velocity is half its maximal value
  23. When substrate concentration is much, much greater than Km, the rate of catalysis approaches...
  24. List the five major classes of enzymes in order.
    • Oxidoreductase
    • Transferase
    • Hydrolysase
    • Lyase
    • Isomerase
    • Ligase
  25. The slope of a Lineweacer-Burk plot for an enzyme is found to be 2.10. Its maximal velocity is 7.55 umol/min. What is the Km? Show your work, including units, and be neat.
    multiply them together. Unit will be uM
  26. Competitive inhibition
    Different Km, same Vmax
  27. Non-competitive inhibition
    Same Km, different Vmax
  28. Uncompetitive Inhibition
    Km and Vmax each change
  29. How does the binding of glucose to Hexokinase influence activity?
    It induces a conformational change that forms the catalytic site.
  30. What three amino acids make up the catalytic trio?
    • Asp
    • His
    • Ser
  31. Histidine is a versatile amino acid residue in general acid-base catalysis because it carries a net negative charge at physiological pH and acts as a base. [T/F]
  32. A good transition state analog would be an effective _____ inhibitor.
    competitive inhibitor
  33. One example mechanism of catalysis is covalent catalysis. [T/F]
  34. Formation of the ES complex results in an increase in entropy. [T/F]
  35. Transition states are bound _____ than substrates.
    More tightly
  36. Since all serine proteases share the same mechanism, why are there serine proteases that hydrolyze polypeptides at different amino acid residues? What allows that diversity?
    There is a specificity pocket that the correct amino acid residue must fit into for each serine protease, otherwise, proper proximity and orientation cannot be achieved.