biochemistry exam 2

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  1. pKa has 4 meanings
    • is equal to -logKa
    • found in Henderson/hasselbach
    • related to ionization of an acid
    • smaller the pKa the stronger the acid
  2. 2 ionizable groups AA have
    • NH3+
    • COOH
  3. some R groups have ionizable groups as well as the two on the AA
  4. if pH 7 is greater than the pKa for the C terminal it will be
  5. if the pKa is greater than pH7 on the N terminal then the
    proton will not dissociate
  6. the charge of the AA depends on the pH of the solution and the pKa of the ionizable groups
  7. isoelectric point
    is the pH at which the overall charge of the protein is 0
  8. what statement best describes the primary structure of protein
    N>C sequence of amino acids dictated by the mature mRNA
  9. low pH will cause r groups with an amine such as His, Arg, and Lys to deprotonate
  10. secondary structure refers to the
    conformation generated by interaction of amino acids that are close in sequence
  11. how are secondary structures stabilized
    hydrogen bonding
  12. 2 types of structures of secondary structures
    • regular
    • irregular
  13. 2 types of regular secondary structures
    • alpha
    • beta
  14. 2 types of irregular structures of secondary structures
    • hairpin turns
    • irregular loops
  15. proline is too floppy and glycine is to rigid to form the alpha helix structures
  16. alpha helix description
    carbonyl oxygen in each AA H bonds with the NH groups of an AA 4 residues ahead
  17. myoglobin is consisted of a great deal of helical structures
  18. amphipathic helices contain these 2
    polar and non polar amino acids
  19. what sheet has greater bonds compared to the other in the secondary structures
    beta has greater bonds
  20. the alpha helix involves the helical inside of the sheet while beta involved the back bone of the sheet
  21. 2 ways secondary beta sheets can be constructed
    • anti-parallel chains run in different directions
    • parallele chains running in the same direction
  22. in fatty acid binding protein the direction of arrows shows the directionality which is antiparallel
  23. the fatty acid binding protein is stabilized by what and contains these residues
    • hydrogen bonds
    • proline residues
  24. the fatty acid binding protein contains a hair pin loop on the ends of the strands that are running parallel
  25. what forces drive and stabilize secondary structures and what is involved?
    hydrogen bonds involving the NH and the carbonyl oxygen in the back bone
  26. tertiary structure
    arrangement of secondary structures
  27. tertiary structures are governed by
    hydrophobic interactions
  28. myoglobin contains hydrophobic and hydrophilic residues
  29. how can the tert structure be stabilized
    by covalent cross links
  30. which AA can form these types of covalent cross links
    disulfide linkages
  31. 4 forces that can stabilize tert structures
    • ionic bond
    • polypeptide backbone
    • hydrogen bond
    • disulfide linkage
    • hydrophobic interactions
  32. quaternary structure
    arrangement of secondary and tert structures in one peptide relative to the arrangement of these structures in another
  33. hemoglobin has 2 alpha and 2 beta chains
  34. the quat structure is stabilized by these 4
    • ionic interactions
    • hydrophobic interactions
    • disulfide bonds
    • hydrogen bonding
  35. 4 jobs of proteins
    • molecular
    • cell components
    • transporters
    • enzymes involved in biological processes
  36. how do proteins function molecularly
    regulators of transcription/ translation activity
  37. how to proteins function in cell components
    they are involved in cytoskeletal proteins
  38. how are proteins involved in transporters
    transporters of fatty acids, O2, Ca, NO
  39. how are proteins involved in enzymes that partake in biological proesses
    they act as carbo, lipids, and nitrogen utilization
Card Set
biochemistry exam 2
sfsu biochem
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