Bmsc200 Protein structures

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Bmsc200 Protein structures
2012-10-19 20:24:58
Bmsc200 midterm1 Protein structures

Bmsc200 Protein structures
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  1. What is Native Conformation?
    the single stable shape each protein can fold into
  2. What determines the stability of a protein(stability is defined as the tendency to maintain a native conformation)?
    • -the amount of weak interactions
    • -the difference in the free energies of the folded and unfolded states.
  3. What determines the free energy of a protein?
    -in its native state the more weak interactions a protein can make with its self the lower its free energy
  4. What is a Salt Bridge?
    attractions between oppositely-charged functional groups
  5. What are Ion pairs and what makes them special?
    • -a salt bridge buried in the hydrophobic interior of a protein.
    • - they are stronger than one on the surface because it is not disrupted by water molecules
  6. How are sequences of amino's delineated?
    • -Sequences are presented N-terminus to C-terminus
    • -a pattern of N-Cα-C-N-Cα-C-N-Cα-C emerges
  7. What are the two key determinants of what secondary structure are allowable by a given primary protein structure?
    • -Favored conformations of the peptide bond.
    • -Optimization of hydrogen bonding potential.
  8. Which bond cannot be rotated around in the peptide chain?
    -Rotation around C-N(carboxyl-amino) bond is restricted due to the double-bond nature of the resonance hybrid form (no freedom of rotation).
  9. What is a Phi() bond?
    • Phi = N-Ca
    • -the bond from an alpha carbon to the nitrogen of the amino group
    • -has freedom of rotation
  10. What is a psi() bond?
    • Psi = Ca-C
    • -The bond from an alpha carbon to the carbon of the carboxyl group
    • -has freedom of rotation
  11. How is a dipole created in a peptide bond?
    Each peptide bond has a hydrogen bond donor as well as a hydrogen bond acceptor.The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge forming a dipole.
  12. How many residues per turn does an -Helix have?
  13. How are hydrogen bonds formed to create the -Helix?
    -Each C=O (residue n) forms a hydrogen bond with the amide hydrogen of  residue n+4
  14. What two aminos are unlikely to be found in an -Helix?
    Glycine, Proline
  15. What are the constraints on -Helix?
    • 1)Electrostatic repulsion (or attraction) between successive residues with charged R groups.
    • 2)The bulkiness of adjascent R groups.
    • 3)The interactions between residues spaced by three or four residues.
    • 4)The occurrence of Proline and Glycine.
    • 5)The interaction between amino acids at each end of the helix and the helix dipole.
  16. What does Amphipathic mean?
    a molecule having hydrophobic and hydrophilic regions.
  17. What are the four types of secondary protein structures?
    • -Helices
    • -Helices
    • -Sheets
    • -Strands
  18. How is tertiary structure of a protein determined?
    x-ray crystallography or NMR
  19. How are Sub units of the quaternary structure of a protein held together?
    non-covalent interactions.
  20. Where are binding sites found on Protein structures?
    Unique binding sites are produced at interface between subunits of the quaternary structures of proteins
  21. What is the primary structure of Keratin?
    a pseudo-seven repeat (a b c d e f g )  where positions a and d are hydrophobic.
  22. How are units of keratin held together?
    disulfide bonds
  23. How many residues per turn does a left handed helice have?
  24. What is the primary structure of collagen?
    Multiple repeats of Gly-X-Y where X is often proline and Y is often hydroxyproline
  25. What is the quaternary structure of Collagen?
    Formation of coiled-coils. Three left-handed helicies wrapping around each other in a right-handed fashion.
  26. What parts of the body is Collagen used for?
    • -Collagen is a major protein of vertebrates (25% of total protein).
    • -Diverse forms include tendons (ropelike fibers) and  skin (loosely woven fibers)
  27. What gives Collagen strength?
    successive linking of individual quaternary units into higher order structures linked together through covalent bonds.
  28. what amino residues undergo post translational modification to create covalent bonds in Collagen?
    • proline  hydroxyproline,
    • lysine hydroxylysine
  29. What causes the increasingly brittle character of aging connective tissueand tougher meat?
    Crosslinks between collagen units that increase with age
  30. how are 4-Hydroxyproline and 5-hydroxylysine created ?
    they are formed by enzyme hydroxylation reactions which require vit C
  31. What does vit C deficiency cause?
    -Vit C deficiency (scurvy) leads to defective post translational modification of residues in Collagen leading to defective triple helices (skin lesions, fragile blood vessels, bleeding gums).
  32. What are some genetic diseases involving Collagen?
    • -Marfans syndrome and Ehlers-Danlos syndrome
    • -Hyperextensible joints and skin
  33. What is the Primary structure of silk?
    -GSGAGA repeated
  34. What 3 dimensions are special about the structure of silk?
    • 1)Fully extended polypeptide chains (strength)
    • 2)Association of strands by hydrogen bonding (flexible)
    • 3)Association of sheets by Van der Waals and hydrophobic interactions (flexible)
  35. Who predicted -Helix, -Sheet structures and also the nature of sickle cell anemia?
    Linus Pauling