04 - Enzymes

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  1. What are oxidoreductases and what are some examples?
    Oxidation-reduction rxns; mostly use coenzymes such as NAD+, NADP+, FAD, coenzyme Q, or molecular oxygen as e- acceptors
  2. What are transferases and what are some examples?
    Transfer a chemical group (amino, phosphoryl, carboxyl, etc.) from a donor to an acceptor; transaminases, kinases, etc.
  3. What are hydrolases and what are some examples?
    Hydrolytic cleavage of covalent bonds between C and some other atom; peptidases, proteases, phosphatases, etc.
  4. What are lyases and what are some examples?
    Non-hydrolytic cleavage of covalent bonds between C and some other atom; decarboxylases, dehydratases, aldolases, etc.
  5. What are isomerases and what are some examples?
    Non-hydrolytic cleavage of covalent bonds between C and some other atom; decarboxylases, dehydratases, aldolases, etc.
  6. What are ligases and what are some examples?
    Formation of covalent bonds between C and other atoms such as sulfur, nitrogen or oxygen; frequently uses ATP or GTP as an energy source; carboxylases, thiokinases, etc.
  7. What are coenzymes?
    Required for enzymes to perform their function; bound very tightly by covalent or noncovalent interactions; heme, Fe, Cu, Se, etc.; many are derived from vitamins
  8. What prevalent coenzymes are derived from vitamins?
    Thiamin pyrophosphate from thiamin, FAD and FMN from riboflavin, NAD+ and NADP+ from Niacin, and Coenzyme A from pantothenic acid
  9. What are cofactors?
    Non-protein components that are not absolutely essential for enzyme activity but are needed for maximal activity of the enzymes; most common cofactors are metal ions
  10. What effects do enzymes have on the rate of a chemical reaction?
    Increase the velocity of the forward and reverse reaction at equilibrium, though it does not change the concentration of [S] or [P]; Keq remains the same
  11. What is the free energy change?
    It is the free energy of the product (GP) minus the free energy of the substrate (GS); when the free energy of the rxn (ΔG) is negative the rxn is spontaneous
  12. How is standard free energy change different from free energy change?
    The standard free energy change (ΔG°) is where the [S] and [P] are kept at 1M at the beginning of the rxn
  13. What is the free energy of activation?
    • ΔG*, Eact or ΔG, it is the free energy change
    • from S to the transition state
  14. What elements do enzymes alter on a Rxn vs. Free energy graph?
    Lower Eact but do not alter ΔG° or ΔG
  15. How do enzymes lower the free energy of activation?
    They bind the transition state in preference to the substrate while forming the ES complex
  16. What is VMAX?
    The rxn velocity at infinite [S]
  17. What is the Michaelis constant?
    Km; this is the [S] that gives a rxn velocity equal to ½ Vmax
  18. What is the Michaelis-Menten equation?
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  19. How do you calculate Km?
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  20. What is the relationship between Km and affinity of enzyme for its substrate?
    When Km­ is high the affinity of the enzyme for its substrate is low; when Km­ is low the affinity of the enzyme for its substrate is high
  21. What causes Orientals to flush?
    A genetic mutation in aldehyde dehydrogenase (Lys for Glu) which decreases the affinity of aldehyde dehydrogenase for NAD+; may be responsible for undesirable side effects of alcohol and may protect against alcoholism
  22. Lineweaver-Burk Equation/Double Reciprocal Plot
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  23. How do competitive inhibitors affect the Michaelis-Menten equation?
    • Since the inhibition is overcome by increasing the [S], Vmax­­ does not change; however it increases the Km for a given substrate, meaning that in the presence of the inhibitor, more substrate is needed to
    • achieve ½ Vmax
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  24. What effect to non-competitive inhibitors have on enzyme substrate interaction?
    • It can bind either the free enzyme or the ES complex; Km­ is unchanged; Vmax is decreased even at high substrate concentrations
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  25. Ethylene glycol ingestion
    • Antifreeze contains ethylene glycol, and some alcoholics drink this to support their drinking habit, but it is toxic; ethanol is administered to these individuals because ethanol competes for the active site on ADH and thus prevents its metabolism and the generation of its toxic metabolites (glycolic
    • acid and oxalic acid); similar for methanol (its metabolite is formic acid)
  26. What toxic metabolites are produced by ethylene glycol ingestion?
    Glycolic acid and oxalic acid
  27. What toxic metabolites are produced by methanol ingestion?
    Formic acid
  28. How do you calculate the apparent Km­ of an enzyme in the presence of a inhibitor?
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    • Remember as Km goes up the affinity of the enzyme for the substrate goes down; Ki is the inhibition constant
  29. If the Km­ for the enzyme is 2µM, and the Ki is
    0.2nM, then what would be the Kapp in the presence of 200nM of the inhibitor?
    2 (1+200/0.2)=2*1001=2002µM
  30. What are the different methods by which enzymes catalyze reactions?
    Catalysis by proximity, catalysis by strain, acid-base catalysis, and covalent catalysis
  31. How does catalysis by proximity work?
    The active site assemble subsrates to within close bond-forming distance of one another, the higher [S] the more likely they will occupy the active site in close proximity to enhance catalysis
  32. How does catalysis by strain work?
    This is typically how enzymes that break covalent bonds work; they put the bond needing to be broken in a thermodynamically unfavorable position so it will undergo cleavage
  33. How does acid-base catalysis work?
    There are ionizable functional groups at the active side which serve as acid or bases
  34. What is an example of acid-base catalysis?
    Pepsin hydrolyzes peptide bonds at the carboxyl end of large hydrophobic AAs in proteins using water; it has two aspartic acid residues at its active site which serve as acids and bases
  35. How does covalent catalysis work?
    Generates a transient covalent bond between an active side reside and one or more substrates; once the rxn is complete the intermediate disappears
  36. What is an example of covalent catalysis?
    Chymotrypsin; it is s serine protease (has a serine as a residue); it has the three residues Asp-12, His-57, and Ser-195; these three residues form a charge-relay network; they hydrolyze peptide bonds at the carboxyl end of aromatic AAs in proteins using water
  37. How are allosteric enzymes presented on a velocity vs. [Substrate] plot?
    Sigmoidal curve because the active site of one enzyme can affect the active site in the same enzyme
  38. K-class effectors of allosteric enzymes
    • Affect Km but not Vmax­; binds at an allosteric
    • site which then affects the affinity of substrate binding
  39. V-class effectors of allosteric enzymes
    Alter Vmax but not Km
  40. Equation describing sigmoidal behavior on a V vs [S] plot
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    • where n is the Hill coefficient and is equal to the number of substrate binding
    • sites on the enzyme
  41. Aspartate transcarbamoylase
    An allosteric enzyme involved it the biosynthesis of pyrimidine nucleotides; CTP is one of the end products of the biosynthetic pathway, and allosterically inhibits aspartate transcarbamoylase; ATP stimulates this pathway; both are K-class effectors
  42. Isozymes
    Enzymes which occur in more than one molecular form but catalyze the same rxn; can have different kinetic properties for Km and/or Vmax­; ΔG and ΔG° remain the same but ΔG will be different for each one
  43. How can isozymes be used for differential diagnosis?
    For example LDH exists in 5 different isoforms, with LDH1 being predominant in the heart, whereas LDH5 is predominate in erythrocytes, skeletal muscle, and liver; when tissues are destroyed the intracellular enzymes are released into blood; therefore serum levels of LDH1 vs LDH5 can be used as an indicator of where the damage occurred
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04 - Enzymes
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