Ch 8.3 Text

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DesLee26
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Ch 8.3 Text
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2014-10-05 20:26:03
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Sam
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Biochem
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Test two
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  1. ·         The free-energy difference between reactants and products accounts for the __, but enzymes accelerate how quickly this __ is attined. How to explain the rate enhancement in terms of thermodynamics means considering not the __ but the __
    ·         The transition state is a __ that is no longer the substrate but is not yet the product. It is the __ and __ because of its highest free energy. 
    • equilibrium of the reaction
    • equilibrium
    • end points
    • chemical pathway
    • transitory molecular structure
    • least stable
    • most-seldom occupied species
  2. o   The difference in free energy between the transition state and the substrate is __, symbolized ΔG. The activation energy does not enter into the final ΔG because __. The __ immediately suggests how an enzyme enhances the reaction rate without altering ΔG of the reaction: __ or, in other words, __
    • Gibbs free energy of activation (activation energy)
    • the energy required to generate the transition state is released when the transition state forms the product
    • activation-energy barrier
    • enzymes function to lower the activation energy, or, in other words, enzymes facilitate the formation of the transition state
  3. ·         To understand increase in reaction rates achieved by enzymes:
    o   Assume that the transition state (X) and the substrate are in equilibrium in which __ is the equilibrium constant for the formation of X and v is the __.
    §  The rate of the reaction v is proportional to the __ because only Xcan be converted into product. The concentration of Xat equilibrium is in turn related to the __; the greater the difference in free energy between these two states, the __. Thus, the overall rate of reaction V depends on ΔG.
    • K‡
    • rate of formation of product ffrom X‡
    • concentration of X‡
    • free-energy difference ΔG‡ between X‡ and S
    • smaller the amount of X‡.
  4. o   Specifically: V = v[X‡] = (kT /h) [S] e-ΔG‡/RT
    §  In this equation, k is the __, and h is __. The value of kT/h at 25oC is 6.6 x 1012 s-1
    ·         Enzymes accelerate reactions by decreasing __.
    o   The combo of substrate and enzyme creates a reaction pathway whose __ is lower than that of the reaction in the absence of enzyme. Because the activation energy is __, more molecules have the energy required to reach the transition state
    • Boltzmann’s constant
    • Planck’s constant
    • ΔG‡, the actvation energy
    • transition-state energy
    • lower
  5. ·         The __ is the first step in enzymatic catalysis
    o   Much of the catalytic power of enzymes comes from __.
    §  The substrates are bound to a specific region of the enzyme called the __. Most enzymes are highly selective in the substrates that they bind
    • formation of an enzyme-substrate complex
    • their bringing substarates together in favorable orientations to promote the formation of the transition state in enzyme-substrate complexes
    • active site
  6. o   Evidence of an ES complex? 
    First? 
    §  Observation that, at a constant concentration of enzyme, the reaction rate increases with increasing substrate concentration until a maximal velocity is reached, which uncatalyzed reactions don’t show
  7. · The fact that an enzyme catalyzed reaction has a __ suggests the __.
    o   At a sufficiently high substrate concentraiotn, what happens? 
    • maximal velocity
    • formation of a discrete ES complex
    • allt he catalytic sites are filled, or saturated, and so the reaction rate cannot increase
  8. o   Evidence of an ES complex? 
    Second and third
    §  X ray crystallography

    • §  The spectroscopic hcaracteristics of many enzymes and substrates change on the formation of an ES complex
  9. o   Active site is the region that __ and contains the __. Tehse resideues ar called the __. In essence, the interaction of the enzyme and substrate at the active site promotes the __. The active site is the region of the enzyme that most directly __, providing __
    binds the substrates and contains the residues that participate in the making and breaking of bonds

    catalytic groups

    formation of the transition state

    lowers the activation energy

    rate-enhancement
  10. o   Features of the active site:first?
    §  3D cleft formed by groups that come from different parts of the amino acid sequence; and, farther residues may interact better
  11. o   Features of the active site: second?
    §  The active site takes up a small part of the total volume of an enzyme: most amino acid residues aren’t in contact with the substrate; “extra” amino acids create the 3D active site and constitute regulatory sites or channels
  12. o   Features of the active site: third?
    §  Active sites are unique microenvironments: water, if not a reactant, is excluded; and, the cleft may have polar residues
  13. o   Features of the active site: fourth?
    §  Substrates are bound to enzymes by multiple weak attractions: noncovalent bonds are weaker than covalent bonds; and, tehse weak reversible interactions are mediated by electrostatic interactions, hydrogen bonds, and van der Waals forces, which bind only when numerous substrates come close to enzyme atoms through the hydrophobic effect
  14. o   Features of the active site: fifth?
    §  The specificity of binding depends on the precisely defined arrangement of atoms in an active site: they must have a matching shape. There was a lock and key analogy, but it is not that. It is an induced fit, which is when the active site assumes a shape that is complementary to that of the substrate only after the substrate has been bound.
  15. ·         Enzymes lower the activation energy, but where does the energy to lower the activation energy come from?
    o   Free energy is rleased by the formation of a large number of weak interactions between a complementary enzyme and its substrate.
  16. §  The fre energy released on binding is called the __.
    §  Only the correct substrate can participate in most or all of the interactions with the enzyme and thus __, accounting for the exquisite substrate specificity exhibited by many enzymes. Furthermore, the full complement of such interactions is formed only when __
    • binding energy
    • maximize binding energy
    • the substrate is converted into the transition state.
  17. · Thus, the __ is released when the enzyme facilitates the __. The energy released can be thought of as __. Paradoxically, the most-stable interaction (__) takes place between the __ and the __, the least-stable reaction intermediate. 
    • maximal binding energy
    • formation of the transition state
    • lowering the activation energy
    • maximum binding energy
    • enzyme and the transition state
  18. · However, the transition state is too __to exist for long. It collapses either __ or __, but which of the two accumulates is determined only by the __
    • unstable 
    • substrate or product
    • energy difference between the substrate and the product—that is, by the ΔG of the reaction

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