BioChem Enzyme Catalysts (10)

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BioChem Enzyme Catalysts (10)
2013-09-30 05:41:56

Medfoundations II
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  1. oxidoreductases
    oxidation-reduction reaction
  2. transferases
    transfer of a chemical group
  3. hydrolases
    lysis by water
  4. lyases
    a cleavage reaction NOT using water
  5. isomerases
    change of molecular configuration
  6. ligases
    joining of two compounds
  7. What enzymes are relevant for treating cystic fibrosis?
    digestive enzymes produced in the pancreas, and the presence of elastase in the lung
  8. What enzymes are relevant for the spread of breast cancer?
    hydrolytic enzymes are important for ability of cancer cells to invade into the extracellular matrix
  9. Serine proteases
    proteolytic enzymes that catalyze peptide bond hydrolysis; include pancreatic enzymes like Chymotrypsin, trypsin and elastase, and neutrophil elastase
  10. What kind of amino acid sequences does chymotrypsin bind to?
    binds bulky, hydrophobic residues
  11. What kind of amino acid sequences does trypsin bind to?
    • binds positively charged residues (eg. arginine, lysine)
    • - trypsin is composed of negatively charged amino acid, so it's attracted to positive charged ones when binding
  12. What kind of amino acid sequences does elastase bind to?
    binds residues such as glycine, alanine and valine; elastase has a small binding site so only smaller amino acids can fit
  13. What is the active site of an enzyme composed of?
    the active site contains amino acid residues that BIND the substrate and separate ones that CATALYZE a reaction; these two residues are NOT the same
  14. catalytic triad
    • how serine proteases catalyze peptide bond hydrolysis; made up of aspartic acid 102, histidine 57, & serine 195
    • the configuration of these 3 amino acids in the enzyme's active site makes serine's -OH (normally a poor nucleophile) unusually reactive
    • reactivity of serine's group is comparable to that of an ALKOXIDE (CH2O-) ion
    • it attacks peptide bonds of any properly bound substrate
  15. How does the serine protease stabilized the oxanion transition state?
    it stabilizes the oxyanion by hydrogen bonds to residues located in a pocket called the oxyanion hole
  16. List the steps of serine protease peptide bond digestion:
    • 1. binding of substrate
    • 2. attack by serine (alkoxide)
    • 3. stabilization of transition state
    • 4. release of products (& enzyme regeneration)
  17. What enzyme catalyzes the hydrolysis of peptides on the C-terminal side of phenylalanine, tyrosine and tryptophan?
  18. What amino acids make up the catalytic triad in a serine protease?
    Aspartate, histidine and serine
  19. Do enzymes change their structure after catalysis?
    No, at the end of the reaction cycle they are the same as when they started
  20. The direction in which a chemical reaction proceeds is determined by:
    • 1) the enthalpy (H, change in heat)
    • 2) the entropy (S, measure of randomness)
  21. When the Gibbs free energy (G) of a reaction is negative, that reaction is ______:
  22. When the Gibbs free energy (G) of a reaction is positive, that reaction is ______:
    non-spontaneous; endergonic
  23. When the Gibbs free energy (G) of a reaction is zero, that reaction is ______:
    at equilibrium; no further work can be done
  24. How can free energy (G) be made available to do work?
    only if the free energy of the Reactants is greater than the free energy of the Products
  25. Is G sensitive to the concentration of reactants and products?
    YES free energy is dependent on reaction and product concentrations
  26. At equilibrium, Q=Keq (=0.5 for the conversion of glucose-6-phosphate to fructose-6-phosphate)
    When Q>Keq, the reaction goes _________
    When Q<Keq, the reaction goes _________
    • When Q>Keq, the reaction goes in reverse
    • When Q<Keq, the reaction goes forward
  27. What are 4 differences between chemical and biochemical reactions:
    • 1) the only time reactions in the body are at equilibrium is at DEATH
    • 2) removal of product drives the reaction forward
    • 3) reactions proceed under non-standard conditions, hindering the accuracy of prediction G or G knot
    • 4) some processes do not take place in solution but are solid phase reactions
  28. G
    free energy of activation, associated with energy barrier to the reaction; the larger G, the slower the reaction
  29. catabolism
    fuel (food) is degraded into smaller molecules with the release of energy; burning fuel to make ATP (or storage)
  30. anabolism
    • reactions or processes that require the input of energy (burning ATP)
    • eg. biosyntheses (small molecules are rearranged into macromolecules), mechanical work (muscle contraction), and active transport (membrane potential maintenance)
  31. the _________ of food yields ___
    the CATABOLISM of food yields ATP
  32. Enzymes couple ATP (or GTP/CTP) hydrolysis to:
    bond synthesis
  33. What levels of substrate are suitable for assays of ENZYME concentration?
    High, saturating substrate levels are, since the velocity is the highest (as well as being directly proportional to the amount of enzyme and one does not need to be concerned about endogenous substrate of a sample)
  34. What levels of substrate are suitable for assays of SUBSTRATE concentration?
    Low substrate levels are best for assays of substrate concentration, since the initial enzyme velocity is directly proportional to the amount of substrate (eg. linearly dependent)
  35. True or False: all exothermic reactions are spontaneous?
    False. Delta G can be negative (indicating a spontaneous reaction) even when delta H is positive. This occurs when delta S (the change in entropy) is positive.
  36. True or False: reactions in the body are in equilibrium
  37. How do enzymes affect the energy of reactions?
    Enzymes lower the activation energy. They accelerate the rate of reactions, but do not change the potential energy of the substrates or products.
  38. How does the activation energy affect the speed of a reaction?
    In general, the larger the activation energy the slower the reaction
  39. velocity (v) of a reaction
    the number of product molecules (P) made per unit time(or the disappearance of substrate (S) with time)
  40. How can one determine reaction velocity?
    By measuring the amount of product formed per unit time
  41. What kinetic parameters can be extracted from a Michaelis-Menten kinetics graph?
    Vmax, the maximum velocity of the catalyzed reaction, and Km, the substrate concentration required to achieve half the maximum velocity
  42. When is Km equal to the substrate concentration in a Michaelis-Menten Kinetics graph?
    When the substrate concentration is at half of Vmax
  43. A small Km indicates ______ affinity of enzyme for a substrate, while a large Km reflects a ____ affinity of enzyme for the substrate.
    • small Km = HIGH affinity
    • large Km = LOW affinity
  44. Lineweaver-Burk Plot (double-reciprocal plot)
    • y-intercept = 1/Vmax
    • x-intercept = -1/Km
    • Slope = Km/Vmax
    • used because the graph of v against [S] is asymptotic, making it difficult to determine Vmax
  45. Delta G for ATP hydrolysis (ATP + H2O -> ADP + Pi) is -7.3 kcal/mole. How much energy is required to perform the reverse reaction?
    +7.3 kcal/mole
  46. cofactor
    small molecules that help promote catalysis; many vitamins act as cofactors
  47. Which enzyme is deficient in individuals with methylmalonic acidemia?
    Methylmalonyl mutase
  48. What is the cofactor for methylmalonyl mutase?
    Vitamin B12
  49. What are the substrates and products of methylmalonyl mutase?
    The enzyme converts methylmalonyl CoA to succinyl CoA
  50. True or False: generally, the atoms in an enzyme that bind to a substrate are different than the atoms that participate in the catalysis of a reaction?
  51. What is an oxyanion hole and what is its function?
    It is a structural pocket in an enzyme that stabilizes an oxyanion (i.e. stabilizes the transition state)
  52. The initial enzyme velocity is proportional to what?
    The amount of substrate
  53. The y-intercept in Lineweaver-Burk plots corresponds to what kinetic parameter?
  54. The x-intercept in Lineweaver-Burk plots corresponds to what kinetic parameter?
  55. The slope in Lineweaver-Burk plots corresponds to what kinetic parameter?
  56. Methylmalonyl acidemia is a profound metabolic disease, characterized by accumulation of a metabolite, methylmalonic acid, in blood and urine. The methylmalonyl mutase enzyme binds two substrates - a coenzyme (coenzyme B12; which is derived from Vitamin B12) and methylmalonylCoA. MethylmalonylCoA is produced during catabolism of certain lipids and amino acids. Sequencing of an infant's enzyme indicates a defect in the substrate binding pocket for Vitamin B12, but not for methylmalonyl CoA. Treatment to alleviate the "failure to thrive" symptoms would therefore most likely include:
    C. limiting dietary protein and increased Vitamin B12