Biochemistry CH 12 & 13

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Biochemistry CH 12 & 13
2011-10-30 20:24:16
Biochemistry 12 13

Biochemistry CH 12 & 13
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  1. Which amino acid is more likely to be on a protein's surface: Val, Gly, Trp, Ser?
    Ser - they hydroxyl group will allow for hydrogen bonding.
  2. Which of the following amino acids is most likely to be found in the interior of a globular protein: Arg, His, Asn, Asp, or Gly?
    Gly is the most likely to be located in the hydrophobic interior of a globular protein, since the other amino acids on the list are hydrophilic.
  3. How many protein subunits is myoglobin made of? How many heme groups are in this protein?
    one subunit. This leads to one heme group.
  4. How many protein residues are present in myoglobin?
    153 residues.
  5. The prosthetic group of myoglobin is heme. They participate in binding of ________.
    iron. The limited accessibility of the heme group by water is important for myoglobin's function as an oxygen carrier, since in an oxygenated solution Fe2+ is easily oxidized into Fe3+, which does not bind oxygen.
  6. In each pair of amino acid substitutions listed below which substitution would disrupt a protein structure the most?

    Leu replaced by Val or Phe
    Leu replaced by Phe.
  7. In each pair of amino acid substitutions listed below which substitution would disrupt a protein structure the most?

    Arg replaced by Trp or His
    Arg replaced by Trp
  8. In each pair of amino acid substitutions listed below which substitution would disrupt a protein structure the most?

    Asn replaced by Asp or Gln
    Asn replaced by Asp
  9. hemoglobin has a ______ structure alpha 2 - beta 2.
    Tetrameric - it contains four subunits.

    Two alpha subunits and Two beta subunits.
  10. Each subunit of hemoglobin contains ____ heme prostetic group and thus can bind one oxygen molecule. Thus, hemoglobin can transport four oxygen molecules.
    one heme group.

    Hemoglobin contains four subunits with one heme group for each units. This allows for hemoglobin may transport four oxygen molecules.
  11. T conformation dominates for oxygen free hemoglobin known also ___________. This conformation has relatively _______ affinity to oxygen.

  12. (T/F) R conformation binds oxygen two orders of magnitudes tighter than L conformation.
  13. R form hemoglobin dominants in oxygen-bound hemoglobin known as _________.

    This conformation has relatively ___ affinity to oxygen.

    High. This will bind oxygen readily.
  14. Upon hemoglobin's transition to the R state from T state, FE(II) moves into the center of the heme plane.

    The movement of Fe(II) causes the movement of alpha-helix interacts (more/less) efficiently with O2, which explains the greater affinity of oxyhemoglobin to oxygen.
    More efficient interactions will allow for greater affinity of the R conformation to bind oxygen.
  15. The T state of hemoglobin is stabilized by a network of _____ pairs and _______ bonds formed between the protein's amino acids residues.
    Ionic pairs and hydrogen bonds.
  16. Protons are released during the binding of oxygen to hemoglobin. This makes the environment more (acidic/basic).

    If pH is ______, more hemoglobin molecules undergo T to R transition. This is known as the ______.


    The Bohr effect.
  17. What is the Bohr effect?
    If pH is increased, more hemoglobin molecules undergo T to R transition. This phenomenon is also observed as the increase in the oxygen's binding by hemoglobin with increasing pH.

    This the Bohr effect.
  18. One difference between T and R states is that deoxyhemoglobin is capable of binding more ____ than oxyhemoglobin by forming carbamates.
    This increases the affinity to binding CO2.
  19. What is the following reaction displaying?

    Hb-NH2 + CO2 <-> Hb-Nh-COO-
    Deoxyhemoglobin is capable of binding more CO2 than oxyhemoglobin by forming carbamates as indicated above.
  20. (T/F) In hemoglobin, the T->R transition is that hemoglobin's subunits are so tightly coupled in the quaternary structure that changes within one subunit cannot occur without quaternary structural changes of the entire oligomer.

    No one subunit can greatly change its conformation independently of the others.
  21. (T/F) Cooperative oxygen binding of hemoglobin leads to the following:

    Binding of a single oxygen molecule switches the whole tetramer in the R state with greater affinity to oxygen. Therefore, the other three subunits bind O2 readily.
  22. What is the Hill equation?
    Fractional saturation of proteins such as myoglobin and hemoglobin.

    Y(O2) = (P(O2))^2/((P(50)^n + (P(O2))^2)

    • n = Hill constant
    • n = 1 for myoglobin
    • n = 2.8 - 3
  23. What is the P(O2) value that corresponds to Y(O2) = 0.5?
    P(50) value
  24. What is P(50) for myoglobin?
    2.8 torr (760 torr = 1 atm)
  25. Under the physiological conditions, myoglobin is almost ______ saturated with oxygen.
  26. What is P(O2) equals 100 torr in ____ arterial blood and 30 torr in ____venus blood.
    arterial and venous.
  27. (T/F) Myoglobin passes on oxygen from the capillaries to muscle cells.
  28. (T/F) The higher the affinity of a protein to a ligand the lower the dissociation constant.
  29. (T/F) Hemoglobin has a p(50) of 26 torr, which is close to venous 30 torr oxygen pressure and nearly 10 times greater than the P(50) of myoglobin.

    (T/F) This is higher p(50) is myoglobin (2.8 torr).

  30. (T'/F) The Hill constant increases with the degree of cooperativeity, which shows how the binding of one ligand molecule affects the subseque3nt bind of other ligand molecules.
  31. If n = 1, the binding is ____________.
    Positive cooperativity has n > ___.
    Negative cooperativity has n <___.
    Noncooperative. 1
  32. What is the symmetry model of allosteric regulation?
    • 1) An allosterically regulated protein consists of symmetrically oriented subunits.
    • 2) Each oligomer switches between two conformations, which coexist in equilibrium.
    • 3) The symmetry of the protein is conserved during the conformational change.
    • 4) The ligands bind to both R and T conformations with different affinities. R is designated for conformation with high affinity to the ligand, while T is designated for the conformation with a lower binding affinity.
  33. What is the sequential model for allosteric regulation?
    • 1) Protein subunits exist in different conformations. The symmetry of the oligomeric protein is not preserved.
    • 2) Upon ligand binding conformational changes are not propagated equally to all subunits. Substrate-binding induces the greatest conformational change in the subunit that has bound ligand and in adjacent subunits.