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Protien Metabolism


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Protien Metabolism

  1. 1. Protein Function Structure will determine the function of the protein
  2. 2. Key ideas and terms <ul><li>protein can bind a ligand in the binding site </li></ul><ul><li>For an enzyme, the ligand is a substrate and they bind in what is called the active site </li></ul><ul><li>ligand has to be the correct shape </li></ul><ul><li>ligand has to have the complementary charges and hydrophobicity or hydrophilicity </li></ul>
  3. 3. Lock and Key Hypothesis <ul><li>Protein and ligand have complementary shapes. </li></ul><ul><li>Interactions must also be complementary </li></ul><ul><ul><li>If enzyme charge is negative, substrate must be positive </li></ul></ul><ul><ul><li>If pocket is nonpolar, ligand must be nonpolar </li></ul></ul><ul><li>Antibodies </li></ul>
  4. 4. Induced Fit <ul><li>Induced Fit: when the protein and ligand bind, the protein may change conformation to allow for tighter binding </li></ul><ul><li>Frequently, both the ligand and the protein change conformation </li></ul>
  5. 5. Examples: O 2 binding proteins: myoglobin and hemoglobin <ul><li>oxygen is not water soluble yet needs to be transported </li></ul><ul><li>diffusion is not effective </li></ul><ul><li>myoglobin is found primarily in muscle tissue </li></ul><ul><li>Hemoglobin is in the blood </li></ul><ul><li>Both proteins contain heme </li></ul>
  6. 6. Heme Group <ul><li>consists of a Fe 2+ and a protoporphyrin ring to help stabilize the iron(II) ion </li></ul>
  7. 7. Heme Group <ul><li>the iron must be a 2+ to bind oxygen. The heme group is buried deep within the protein so that the iron is not oxidized to 3+ </li></ul><ul><li>there must be flexibility in the protein to allow for oxygen to attach and then let go </li></ul><ul><li>Iron has 6 coordination sites. </li></ul><ul><ul><li>Four of them used by porphyrin. Unshared pairs on nitrogen complex to iron </li></ul></ul><ul><ul><li>Fifth and 6 th for oxygen and protein </li></ul></ul><ul><li>Heme is planar </li></ul>
  8. 8. Myoglobin <ul><li>has heme group </li></ul><ul><li>eight alpha helical segments </li></ul><ul><li>dense hydrophobic core </li></ul><ul><ul><li>all but two polar groups on outside </li></ul></ul><ul><ul><li>room for only 4 water molecules </li></ul></ul><ul><li>flat heme in pocket </li></ul><ul><li>iron coordinated to poryphorin and H </li></ul><ul><li>As well as the heme </li></ul>
  9. 9. Myoglobin Binding Curve <ul><li>Hyperbolic binding curve </li></ul><ul><li>Relatively insensitive to small changes in oxygen concentration </li></ul>
  10. 10. Myoglobin <ul><li>The P50 (oxygen partial pressure required for half saturation) for myoglobin is very low </li></ul><ul><li>Myoglobin has a high affinity for oxygen-an important characteristic for a protein that must extract oxygen from the small amounts present in blood. </li></ul><ul><li>At the oxygen concentration existing in the capillaries, the myoglobin in adjacent tissues is nearly saturated. </li></ul><ul><li>When cells are metabolically active, their internal P O2 falls to levels where myoglobin will lose (deliver) its oxygen . </li></ul>
  11. 11. Hemoglobin <ul><li>Quaternary structure : 4 subunits </li></ul><ul><li>Each subunits is like myoglobin </li></ul><ul><li>Each subunit has heme group </li></ul><ul><li>2 alpha chains; 2 beta chains </li></ul><ul><li>Few contacts between alpha and betas, more between alphas and betas </li></ul>
  12. 12. Hemoglobin <ul><li>Exists in two states </li></ul><ul><ul><li>R state (high affinity for O 2 ) </li></ul></ul><ul><ul><li>Where would this state be favored? </li></ul></ul><ul><ul><ul><li>In the lungs </li></ul></ul></ul><ul><ul><li>T state (low affinity for O 2 ) (deoxyhemoglobin) </li></ul></ul><ul><ul><li>Where would this state be favored? </li></ul></ul><ul><ul><ul><li>In the tissue </li></ul></ul></ul><ul><ul><li>Sensitive to pressure changes </li></ul></ul><ul><ul><li>On oxygenation, one pair of subunits shifts with respect to the other by a rotation of 15 degrees. </li></ul></ul>
  13. 13. Hemoglobin <ul><li>deoxy hemoglobin (T) oxy hemoglobin (R) </li></ul>
  14. 14. Oxygen Binding to Heme in Hemoglobin <ul><li>Fe is coordinated to a histidine in helix 8 of the Hb molecule </li></ul><ul><li>In deoxy form, porphyrin is puckered and Fe is out of the plane of the heme </li></ul><ul><li>When oxygen binds the Fe (at other coordination site) the Fe is pulled into the plane of the heme </li></ul><ul><li>This pulls on the histidine, which pulls on the helix, changing the shape of the molecule. </li></ul>Fe 2+ His F8 0.6 A O 2
  15. 15. Hemoglobin <ul><li>Conformational changes in hemoglobin alter its binding ability </li></ul><ul><li>Binding of oxygen in one subunit causes conformational changes in the next subunit </li></ul><ul><li>This is called cooperative binding </li></ul><ul><li>This can happen because it is composed of 4 independent subunits </li></ul><ul><li>produces a different binding curve that is sigmoidal </li></ul><ul><li>The modulation of the affinity of a site for a ligand by ligand binding at another site is called Allostery . </li></ul>
  16. 16. Hemoglobin Binding Curve
  17. 17. Bohr Effect <ul><li>Hemoglobin's affinity for oxygen is decreased in the presence of carbon dioxide and at lower pH. </li></ul><ul><li>Carbon dioxide reacts with water to give bicarbonate, carbonic acid free protons via the reaction: </li></ul><ul><ul><li>CO 2 + H 2 O ---> H 2 CO 3 ---> H + + HCO 3 - </li></ul></ul><ul><li>Protons bind at various places along the protein and carbon dioxide binds at the alpha-amino group forming carbamate. </li></ul><ul><li>This causes a conformational change in the protein and facilitates the release of oxygen. </li></ul>
  18. 18. Bohr Effect <ul><li>Blood with high carbon dioxide levels is also lower in pH (more acidic). (recall the equilibrium) </li></ul><ul><li>Conversely, when the carbon dioxide levels in the blood decrease (i.e. around the lungs), carbon dioxide is released, increasing the oxygen affinity of the protein. </li></ul>
  19. 19. Bohr Effect Summary <ul><li>High CO 2 in tissues </li></ul><ul><li>Higher H+ </li></ul><ul><li>Lower pH </li></ul><ul><li>Affinity for O 2 decreases </li></ul><ul><li>O 2 released to tissues </li></ul><ul><li>T state favored </li></ul><ul><li>Low CO 2 in lungs </li></ul><ul><li>Lower H+ </li></ul><ul><li>Higher pH </li></ul><ul><li>Affinity for O 2 increases </li></ul><ul><li>O 2 binds hemoglobin </li></ul><ul><li>R state favored </li></ul>
  20. 20. Hemoglobin and CO poisoning <ul><li>Other ligands can compete with oxygen for binding to hemoglobin </li></ul><ul><li>The binding of oxygen is affected by molecules such as carbon monoxide (CO) (For example from tobacco smoking, cars and furnaces). CO competes with oxygen at the heme binding site. </li></ul><ul><li>Hemoglobin binding affinity for CO is 200 times greater than its affinity for oxygen, meaning that small amount of CO can dramatically reduces hemoglobin’s ability to transport oxygen. </li></ul><ul><li>Hemoglobin also has competitive binding affinity for Nitrogen Dioxide and Hydrogen sulfide . </li></ul>
  21. 21. Oxygen and Carbon Monoxide <ul><li>Oxygen and carbon monoxide same size and shape. </li></ul><ul><li>Carbon monoxide, however has formal charge </li></ul><ul><li>Sticks to Fe better </li></ul><ul><li>Blocks oxygen binding </li></ul>
  22. 22. Hemoglobin and 2,3 DPG <ul><li>In people acclimated to high altitudes, the concentration of 2,3-diphosphoglycerate (2,3-DPG) in the blood is increased, which allows these individuals to deliver a larger amount of oxygen to tissues under conditions of lower oxygen tension. </li></ul><ul><li>This phenomenon, where molecule Y affects the binding of molecule X to a transport molecule Z, is called a heterotropic allosteric effect . </li></ul>
  23. 23. Sickle Cell Anemia <ul><li>Sickle cell disease is caused by an abnormal adult hemoglobin, called hemoglobin S. People with sickle cell disease make hemoglobin S instead of hemoglobin A. </li></ul><ul><li>Single amino acid substitution </li></ul><ul><ul><li>glutamate changed to valine </li></ul></ul><ul><li>To show condition, have to have mutation in both genes (Homozygous) </li></ul>
  24. 24. Sickle vs normal hemoglobin <ul><li>first 9 amino acids of normal hemoglobin beta chain </li></ul><ul><ul><li>v h l t p e e k s </li></ul></ul><ul><li>first 9 amino acids of sickle hemoglobin beta chain </li></ul><ul><ul><li>v h l t p v e k s </li></ul></ul><ul><ul><li>Notice the single amino acid change? </li></ul></ul>
  25. 25. Sickle Cell Anemia <ul><li>Position 6 is on outside of molecule </li></ul><ul><li>Glutamate is polar </li></ul><ul><li>Valine substitution causes “sticky spot” on outside of hemoglobin </li></ul><ul><li>Causes hemoglobin molecules to stick together </li></ul><ul><li>Forms long chains which cause red blood cell to sickle </li></ul>