Enzymes

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lancesadams
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61990
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Enzymes
Updated:
2011-02-09 21:18:21
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Biochem S1L4
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Enzymes
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  1. Isozymes
    Different structural forms of a protein that have the same function (iso = similar or same)
  2. What does Km represent
    A small Km for an enzyme relfects a high affinity of the enzyme for the substrate

    • A Large Km has the opposite effect
    • (Km does not vary with the concentration of the enzyme!!)
  3. What does a high Km mean
    A high Km means that a lot of substrate is needed to fill half of the enzyme active sites
  4. The rate of an enzyme reaction is
    Directly proportional to the enzyme concentration at any given time
  5. Zero-order reaction:
    • Reaction rate is independent of substrate concentration: A-B; V= k
    • (All of the enzymes are saturated with substrate)
  6. First-order reaction:
    • Reaction rate depends on the concentration of one substrate.
    • A - B; V = k x [A]
  7. Second-order reaction:
    Reaction rate depends on the concentrations of two substrates.

    A+ B - C + D; V = k x [A] x [B]
  8. Pseudo-first order reaction:
    When there are two substrates but only one is rate limiting.

    Example: Hydrolysis reactions in aqueous solution.


    A + H2O - C + D; V = k x [A]
  9. Oxidoreductases (redox)
    • Catalyze oxidation-reduction reactions (NADH)
    • an enzyme that catalyzes the transfer of electrons from one molecule to another
    • A– + B → A + B–
  10. Transferases
    Catalyze transfer of functional groups from one molecule to another.
  11. Hydrolases
    Catalyze hydrolytic cleavage

    A–B + H2O → A–OH + B–H
  12. Lyases
    Catalyze removal of a group from or addition of a group to a double bond, or other cleavages involving electron rearrangement.
  13. Isomerases
    Catalyze intramolecular rearrangement
  14. Ligases
    Catalyze reactions in which two molecules are joined (ATP dependent reactions)
  15. Enzyme-Substrate
    • Nonbonding reversible reactions
    • E + S ⇌ ES → EP ⇌ E + P
  16. An important concept in biochemistry is that exergonic reactions (Delta G < 0) aka. spontaneous reaction
    drive endergonic reactions (Delta G > 0) aka. energy is absorbed
  17. When Delta G is negative,
    the reaction is spontaneous.
  18. When Delta G is positive,
    the reaction is non-spontanous.
  19. When Delta G is zero,
    the reaction is at equilibrium
  20. Many important cellular reactions must run against their thermodynamic potential ie. in direction of positive ΔG, how do they do it
    By coupling to a favorable reaction
  21. If the overall free energy change is negative
    That means that the reaction is spontaneous
  22. Coupled Reactions are
    An endergonic and an exergonic that are linked energetically; the endergonic reaction is driven by the exergonic reaction.

    Both reactions occur simultaneously and share a common intermediate which cancels out in the final sum.
  23. Delta G°’ is the
    Biochemical standard (in vitro) free energy change. This is the free energy change when the reactants and products are initially at 1.0M, at 25°C, at 1atm and the H+ concentration is pH 7.0.
  24. Delta G
    Is the actual free energy change in the cell. It depends on the actual concentrations of reactants and products.
  25. Simple enzymes
    Contain only the polypeptide portion
  26. Conjugated enzymes
    Contain the polypeptide portion & a non-protein portion; need both for activity
  27. Cofactor (prosthetic group)
    The non-protein portion of a conjugated enzyme
  28. Apoenzyme
    The protein portion of a conjugated enzyme
  29. A cofactor can be
    An organic cofactor, or a metol ion (Fe2+ , Mg2+ , Zn2+)
  30. Holoenzyme
    The complete, native, enzyme
  31. Proenzyme (zymogen)
    An inactive precursor of a native enzyme (not the same as apoenzyme) - part of polypeptide has to be removed to give native enzyme
  32. Vitamins are important
    Co Enzymes
  33. An AMP unit is
    The most common biological handle
  34. Coenzymes in general are found where in a cell
    Water soluble: located in aqueous environment and/or held in enzyme by polar/ionic forces

    Lipid soluble: located in nonaqueous environment and/or held in enzyme by van der Waals forces (hydrophobic force)
  35. Coenzymes perform what functions
    Accomplish goals amino acid side chain units can not
  36. Chemical changes catalyzed by side chains of amino acids are limited to
    acid/base and nucleophilic/electrophilic changes
  37. Most notable use of coenzymes are in
    Reductions and oxidations
  38. What two classes of biomolecules use energy acquired from sunlight or food to be used to drive endergonic (energy-requiring) processes in the organism
    Reduced coenzymes (NADH, FADH2)

    High-energy phosphate compounds - free energy of hydrolysis more negative (-25 kJ/mol).
  39. How do you release the energy from ADP and ATP
    You simply hydrolyze them
  40. ADP and ATP are examples of
    Phosphoric acid anhydrides
  41. Large negative free energy change on hydrolysis is due to:
    Electrostatic repulsion

    Stabilization of products by ionization and resonance
  42. Some biochemical reactions are driven by the hydrolysis of UTP, GTP, or CTP. And are significant because
    These are energetically equivalent to ATP.
  43. If [ATP] is low,
    degradative pathways are stimulated.
  44. If [ATP] is high,
    degradative pathways are inhibited.
  45. Redox reactions
    Redox (shorthand for oxidation-reduction) reactions describe all chemical reactions in which atoms have their oxidation number (oxidation state) changed.

    • Oxidation is the loss of electrons
    • Reduction is the gain of electrons
  46. Redox Coenzymes Two major classes are
    Flavins and Nicotinamides
  47. H- is the same as
    H+ and two e-
  48. The two different flavins are
    • Flavin Adenine Mononucleotide
    • FMN (oxidized form); FMNH2 (reduced form)

    • Flavin Adenine Dinucleotide
    • FAD (oxidized form); FADH2 (reduced form)
    • involved mostly in the redox of C=C bonds
  49. The two types of Nicotinamides
    • Nicotinamide Adenine Dinucleotide
    • NAD+ (oxidized form); NADH (reduced form)

    • Nicotinamide Adenine Dinucleotide Phosphate
    • NADP+ (oxidized form); NADPH (reduced form)involved mostly in the redox of C=O bonds
  50. Active Site
    The region of the enzyme that binds and acts upon the substrate

    Binding = few or many weak attractions that can be reversed like, ion to ion, H-bond, van der Waals
  51. Allosteric enzymes
    are enzymes that change their conformation upon binding of an effector
  52. The shape of active site
    Generally crevice or cavern on surface of enzyme
  53. Lock-and-Key Model
    Active site has a rigid shape that is complementary to that of the substrate
  54. Breaking Reasonance has what effect on a molecule
    The molecule is less stable, therfore higher energy
  55. Induced-fit Model
    The shape of the enzyme adjusts to fit the proper substrate upon binding of the substrate
  56. A sigmoidal plot on a Rate versus Concentration of Substrate graph what does it indicate
    It is an allosteric enzyme
  57. Increasing the concentrarion of an enzyme has what effect
    It will increase the rate only to a point, then it flattens out
  58. What effect does temperature have on the rate of an ezymatic reaction
    The temp will increase the rate until the heat is so excesssive that it denatures the enzyme
  59. The Km is
    The concentration of substrate at which 1/2 of the active sites are filled
  60. The Michaelis-Menten Equation
  61. If the concentration of the substrate is very low, (below Vmax) then
    The substrate can be eliminated from the denominator of the equation
  62. Most operations in vivo are operating
    Below Km
  63. When is Vmax acheived
    Never, the enzymes are never completely used
  64. What is Kcat
    It is the direct measurement of the catylic product under saturated substrate conditions (turnover number). The maximum number of substrate molecules converted to product by the enzyme molecule per unit of time
  65. Inhibitors of enzymes are
    Generally molecules which resemble or mimic a particular enzymes substrate(s).
  66. Irreversible inhibitors generally result in
    The destruction or modification of an essential amino acid required for enzyme activity. Frequently, this is due to some type of covalent link between enzyme and inhibitor.
  67. Parathion (Insecticide)
    Inhibits acetocholinesterace
  68. Penicilin
    Inhibits the enzymes that help make bacterial cell walls
  69. Diisopropyl phosphofluoridate (Irreversible Inhibitor)
    Inhibits enzymes with active site Serine, Acetocholinesterace (degrades acetylcholine)
  70. Allopurinol (irreversible inhibitor) is used for what
    Used to treat gout, it inhibits the reaction at two places
  71. Large amounts of inhibitor
    Swamp out substrate binding, and product formation is suppressed

    Likewise large amounts of substrate swamp out inhibitor binding.
  72. In the body Methanol is metabolized by the enzyme alcohol dehydrogenase producing highly toxic formaldehyde. How can you fix consumption of such
    Ethanol competes for the same enzyme. Therefore administration of ethanol occupies the enzyme thereby delaying methanol metabolism long enough for clearance through the kidneys.
  73. Ki values are used
    To characterize and compare the effectiveness of inhibitors relative to Km.
  74. In general, the lower the Ki value,
    The tighter the binding, and hence the more effective an inhibitor is.
  75. As the amount of inhibitor increases, there is more competition at the active site therefore
    The enzyme does not bind the substrate as well in the presence of inhibitor and therefore “Km” increases
  76. Noncompetitive Inhibition
    • Inhibitor and substrate DO NOT have common shape

    • Binding is NOT at active site but causes a change in the substrate binding site

    • Large amounts of inhibitor prevent access of substrate to binding site

    • Large amounts of substrate CANNOT overcome inhibitory effect
  77. NonCompetetive Inhibitors can inhibit the enzyme
    Whether there is a substrate or not
  78. What is the difference between competetive inhibitors and allosteric inhibitors
    Allosteric inhibitors bind on a different chain then the active site
  79. Allosteric enzymes
    • Allosteric enzymes are enzymes that change their conformation upon binding of an effector.
    • Do not follow Michaelis-Menten Kinetics
  80. Heterotropic Allosteric Effectors
    A molecule separate from the substrate, activating and inhibiting effectors that bind at allosteric sites
  81. Homotropic effectors
    Substrates acting as effectors are said to be homotropic effectors.

    Substrate itself induces distant allosteric effects when it binds to the catalytic site
  82. Catalytic Mechanisms
    1. Bond Strain: Strains substrate bonds, which facilitates attaining the transition state.

    2. Proximity and Orientation: Binding brings molecules into proximity and helps to properly orient reactive groups.

    3. Acid/Base Catalysis: Required catalytic proton donors (acids) or acceptors (bases) are supplied by catalyst.

    4. Covalent Catalysis: The reaction is facilitated by formation of a covalent intermediate between the enzyme (or coenzyme) and the substrate.
  83. The Serine Protease Family have catalytic center composed of
    A serine, a histidine, and aspartic acid, regardless of specificity of cleavage.
  84. Lysozyme Mechanism
    Peptidoglycan hydrolysis, part of ‘innate’ immunity (breaks down cell walls of bacteria). Lysozyme is found in tears, saliva, nasal secretions and lysosomes.
  85. Chymotrypsin
    Digestive enzyme, activated by proteolysis
  86. Chymotrypsin has an affinity for
    Large bulky amino acids like Phenylalanine
  87. Histidine is the only amino acid that has
    Both acid and base qualities, where it can either donate or recieve a proton
  88. A catalytic triad
    Three amino acid residues found inside the active site of certain protease enzymes: serine (S), aspartate (D), and histidine (H). They work together to break peptide bonds on polypeptides.
  89. The catylitic triad initiates
    The hydrolysis of the serine proteases like Chymotrypsin
  90. One-third of all known enzymes need what to function
    Metal ions
  91. Metal ion catalysts like (Fe++, Cu++, Zn++, ect) participate in one of three ways:
    a. They bind substrates to orient them for catalysis

    b. Through redox reactions gain or loss of electrons.

    c. Electrostatic stabilization or negative charge shielding
  92. What is essentially a catalyticaly perfect enzyme, why
    Carbonic Anhydrase, because the Kcat/Km is very high
  93. Carbonic Anhydrase and Carbonic Dehydrase occur where in the body
    In the lungs and capillaries respectively
  94. The statin drugs (Cholesterol) like mevacor act as potent competitive inhibitors because:
    The statins have Ki values several orders of magnitude lower than the Km for the substrate
  95. A cofactor is
    a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity.
  96. loosely-bound cofactors termed
    coenzymes
  97. Tightly-bound cofactors termed
    Prosthetic groups
  98. The term "holoenzyme" can also be applied to enzymes that
    Contain multiple protein subunits
  99. Vmax is dependent only on
    The amount of available enzyme

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