CHAPTER 7 STRUCTURE-FUNCTION RELATIONSHIPS IN PROTEINS OBJECTIVES: 1. Understand the meaning of primary, secondary, tertiary, and quaternary structure and be able to discern the difference. 2. Be able to recognize and discern between the three types of secondary structure discussed in class! 3. What is the location of the R-groups in an alpha helix? Can an alpha helix be formed from any primary sequence of amino acids? 4. What is the difference between parallel and antiparallel b-sheets? How do the R-groups protrude from the sheets? 5. What are the three names for nonregular, nonrepetitive secondary structures? 6. What is a motif? 7. What is a structural domain 8. What is a fold (fold structure or protein fold)? What is a fold family? 9. When we say that actin, heat shock protein 70, and hexokinase are homologous, what are we implying? 10. Where would you most likely find the nonpolar, polar and charged amino acids in a globular protein? 11. The LDH molecule always contains 4 polypeptide subunits and each subunit can be either a H (heart) or a M (muscle) subunit. How many isozymes are possible? Describe the isozymes in terms of the number of mers and homo or hetero. 12. What are the forces that hold the monomer units of a quaternary structure together? 13, For a ligand-protein complex that dissociates into a ligand and protein. Be able to state the dissociation constant and the association constant. 14. Using the terms ferrous iron, heme, hydrophobic pocket, histidine, alpha-helix, alpha-turns, salt bonds, hydrophobic interactions, hydrogen bonds, oxygen, and subunits, describe the myoglobin and hemoglobin molecule. 15. Be able to draw an oxygen dissociation curve for hemoglobin and myoglobin. 16. What is a ligand? 17. What is a prosthetic group? 18. Be able to explain why the oxygen saturation curve for hemoglobin is sigmoidal while the curve for myoglobin is a rectangular hyperbola. Include the terms subunits, O2, Fe2+, conformation, salt bridges, T-state, R-state. 19. Be able to describe the structure of IgG in terms of the number of chains, the number and types of domains, and the forces that hold the chains together. Which part binds to an antigen and why is it specific? What fold family do the domains belong to. 20. What determines the tertiary conformation of a protein? 21. What is denaturation? Name a few ways that proteins are denatured in humans. 22. What is a prion? 23. Explain how a prion can cause dementia and death. Include the terms PrPc, PrPsc, template, activation energy, cascade, amyloid protein, and proteolytic degradation. 24. Concerning Will Sichel: In biochemical terms, explain the development of pain during a sickle cell crises. Include the specific mutation, oxygen pressure, and protein conformation in your answer. 25. Concerning Anne Jeina: What are the three different proteins that appear in the blood following the beginning of a myocardial infarction? What are their normal cell functions? How soon can they be detected? How specific are they? 26. Concerning Amy Lloyd: What is an amyloid protein? What are the monomer units of the polymer in amyloidosis/AL? What secondary structure is found in amyloid fibers? What is an M-protein and why is it detected as a sharp peak upon serum protein electrophoresis? 27. Concerning Di Abietes, What is HbA1c? How is it made and what does it measure? 28. Understand the meaning of each of the keywords. KEYWORDS: Activation energy barrier, amyloid deposits, amyloidosis/AL, antiparallel b-strands, apoprotein, b-sheets, Bence-Jones proteins, bend, cascade, chemical modification, CK-MB, conformation, constant domains, domain, disulfide bond, fibrillar proteins, folds, g-globulins (IgG class), glycosylated hemoglobin, H chains, HbA1C, hemoglobin, homologs, heat shock proteins, heme, histidine, hydrophobic binding pocket, Ka, Kd, L chains, ligands, loop, M-component(M protein), motif, myoglobin, nonenzymatic glycosylation, pH, parallel b-strands, positive cooperativity, post translational, Prions, PrPc, PrPsc, prosthetic group, primary structure, R (relaxed) state, quaternary structure, salt bridge, secondary structure, serum protein electrophoresis, sigmoidal, solvent temperature, structural domain, T (tense) state, tertiary structure, cTN-T, turn, variable domains ASSIGNMENTS: Examine questions in chapter 6 Work questions 1-5 at the end of Chapter 6 Understand the meaning of the key words in the context of Chapter 5 Practice Questions for Chapter 7 Objectives No Other Help REFERENCE: Marks’ Basic Medical Biochemistry: A Clinical Approach, 2nd Edition, 2004, Williams and Wilkins (ISBN: 0-7817-2145-8) by Colleen M. Smith PhD, Allan D. Marks MD, and Michael A. Lieberman PhD.