BIOCHM E2 C6

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BIOCHM E2 C6
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2011-10-11 08:54:23
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BIOCHM E2 C6
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  1. Enzymes are undoubtedly the most important molecular machines composed of ----- OR ------.
    proteins or RNA
  2. To proceed at a viable rate, most reactions require an --------- -------- -----.
    initial energy input
  3. DEFINE activation energy (Ea)
    • A chemical reaction occurs when colliding molecules possess a minimum amount of energy called the activation energy (Ea)
    • -More commonly called free energy of activation (DG‡) in biochemistry.
  4. Catalysts increase reaction rate by lowering WHAT?
    activation energy
  5. DEFINE The free energy of activation (DG‡).
    the amount of energy to convert 1 mol of substrate (reactant) from the ground state to the transition state
  6. WHERE WOULD ONE FIND EXOTHERMIC (-DELTA G) ON THIS?
  7. Many reactions that are spontaneous (-DG) will proceed at imperceptibly ---- rates, because they do not have the energy or correct orientation.
    SLOW
  8. The likelihood of a reaction ------- with increasing the temperature or using a catalyst
    improves
  9. T OR F?
    Living systems cannot increase temperature without the risk of damaging structures, so they use catalysts (enzymes)
    TRUE
  10. Enzymes can increase reaction rate up to ----- TO ----.
    107 TO 1019
  11. T OR F?
    Enzymes are very specific for substrates AND are not permanently altered.
    TRUE
  12. Each enzyme has a ----- ------ ----- to bind the substrate
    specific active site
  13. T OR F?
    The active site also has amino acid side chains that take an active role in the catalytic process
    TRUE
  14. T OR F?
    The active site is used to optimally orient the substrate to achieve the transition state at a lower energy via charge, hydrophobic interactions, H bonds
    TRUE
  15. DEFINE HOW TO Stabilize the transition state.
    Stabilize the transition state---lowers energy barrier

    Ultimately pulls the molecule into a state that most closely resembles the transition state.
  16. T OR F ?

    Enzymes do not change the thermodynamics of a
    reaction.
    • TRUE
    • Remember, If thermodynamically unfavorable will not occur.

    IF + ΔG —enzyme can not change this aspect.
  17. NAME the t wo models that describe enzyme binding of substrate.
    • LOCK & KEY
    • INDUCED FIT
  18. T OR F?
    Many enzymes require certain non-protein components to function.
    TRUE
  19. WHAT ARE COFACTORS? NAME SOME AND THEIR FUNCTION.
    Na+, K+, Mg+2 Ca+2 ,Zn+2 (provide high positive charge)- binding small molecules, serve as electrophiles, oxidation reduction reactions.
  20. DEFINE HOLOENZYMES
    INTACT FUNCTIONAL ENZYMES WITH COFACTORS
  21. THE PROTEIN COMPONENT OF AN ENZYME IS CALLED WHAT?
    APOENZYME.
  22. NAME THE Six major enzyme categories
    • 1. Oxidoreductases ---ox/red
    • 2. Transferases---transfer structural group
    • 3. Hydrolases—break down via hydrolysis
    • 4. Lyases---groups are removed by elimination to form a double bond or added to a double bond
    • 5. Isomerases---Intramolecular rearrangement
    • 6. Ligases---Join groups/structures together
  23. WHAT IS THE FUNCTION OF THE ISOMERASES ENZYME GROUP?
    INTRAMOLECULAR REARRANGEMENT.
  24. WWHAT IS THE FUNCTION OF THE LYASES ENZYME GROUP?
    groups are removed by elimination to form a double bond or added to a double bond
  25. DEFINE DIFFUSION CONTROLED LIMIT.
    • 108 TO 109
    • CONVERT SUBSTRATE TO PRODUCT ALMOST EVERY TIME INTERACT OR CATALYTIC PERFECTION.
  26. Thermodynamics can predict whether a reaction is spontaneous, but cannot predict -------.
    RATE
  27. The rate or velocity of a reaction is the WHAT?
    The change of a concentration of reactant or product per unit of time
  28. DEFINE Initial velocity (VO)
    a velocity at the beginning of a reaction when the concentration of substrate greatly exceeds enzyme concentration (often use some sort of colored reaction to measure)
  29. Information about reaction rates is the quantitative study of enzyme catalysis, or -------- -------.
    enzyme kinetics
  30. IN ENZYME KINETICS, THIS REACTION (A -->P) IS WHAT TYPE OF ORDER?
    1ST ORDER.
  31. T OR F?
    WHEN A ENZYME KINETIC IS ZERO ORDER, THE RATE IS NOT AFFECTED BY ADDING MORE SUBSTRATE, YOU CAN KEEP ADDING BUT NO CHANGE.
    TRUE
  32. WHAT ENZYME KINETIC ORDER IS THIS AND HOW WOULD YOU CALCULATE THE RATE?
    • FIRST ORDER.
    • RATE = K = Y=MX + B
  33. NAME THIS FORMAULA AND KNOW WHAT WOULD HAPPEN IF YOU HAD A LARGE K1 VALUE.
    The Michaelis constant (Km).

    The lower the value of Km (big k1 for instance) the greater the affinity of the enzyme for ES complex formation (fig 6.4).

    So the lower the concentration of substrate needed to achieve a given rate (fig 6.4)
  34. LABEL K1, K-1 AND K2.
  35. NAME AND DEFINE EACH UNIT:

    • [S] = substrate concentration
    • Vmax= maximum velocity
    • vo= initial velocity(ZERO ORDER STATE)
    • Km= Michaelis constant experimentally
    • determined
  36. DEFINE Catalytic perfection
    • Enzyme working at maximum capacity or at its diffusion controlled limit—i.e. how fast the substrate can get to
    • the active site (i.e. diffusion in aqueous). THINK MACROMOLECULAR CROWDING. WORKS FASTER, PROCESS COUPLED TOGTHER DUE TO SMALL SPACE.
  37. IF THE Km WAS LOWER, (STEEPER SLOPE) WHAT WOULD IT MEAN?
    • Km is substrate [conc] at Vmax/2
    • IT WOULD MEAN THAT THE SUBSTRAIT IS GOING INTO A TRANSITION STATE FASTER.
  38. WHAT IS THE Kcat VALUE?
    • The number of substrate molecules converted to product per unit time is kcat (turnover number)
    • Kcat is Vmax over total enzyme concentration (Et).
    • Kcat = Vmax/(Et).
    • THIS MEASURES THE ENZYME EFFICENCY.
  39. DEFINE SPECIFICITY CONSTANT
    Reflects the relationship between catalytic rate of enzyme and substrate binding affinity
  40. It can be used when comparing different substrates for the same enzyme since it is a measure of efficiency.
    • the specificity constant.
    • Kcat/Km

    Low Km and high kcat = high affinity and efficient.
  41. WHAT WOULD BE THE EQUATION FOR THIS LINEWEAVER-BURK LINE?
  42. THE LINEWEAVER-BURK PLOTS ARE RECIPROCAL OF WHAT?
    Michaelis-Menten equation gives a linear representation.

    DIVIDE EVERYTHING INTO 1 (1/Km)
  43. NAME THE POSITIONS OF A LINEWEAVER-BURK PLOT.
    • Slope of the line Km/Vmax
    • 1/Vmax is the Y intercept
    • -1/Km is the X intercept
  44. T OR F?
    Enzyme inhibition can be reversible or irreversible.
    TRUE
  45. NAME 3 TYPES OF REVERSIBLE ENZYME INHIBITION.
    • COMPETITIVE
    • NONCOMPTITIVE
    • UNCOMPETITIVE
  46. T OR F?
    Reversible inhibition can be counteracted by increasing substrate levels or removing the inhibitor
    TRUE
  47. Irreversible inhibition occurs when the inhibitor permanently impairs the enzyme HOW?
    Covalent interaction
  48. --------------- ----------- bind reversibly to the enzyme at the active site thus competing with substrate binding.
    Forms enzyme-inhibitor (EI) complex
    Competitive Inhibitors
  49. ------------ substrate concentration overcomes competitive inhibition
    Increasing
  50. WHAT TYPE OF GRAPH IS THIS AND LABEL BOXES.
    • Michaelis-Menten Plot of Uninhibited Enzyme Activity Versus Competitive Inhibition.
  51. Succinate dehydrogenase of the Krebs citric acid cycle is inhibited by -------.
    malonate
  52. ------ ----------- can bind reversibly to the E or ES complex at a site other than the active site of enzyme
    Noncompetitive Inhibitors
  53. WHAT TYPE OF CHART IS THIS AND LABEL BOXES.
    • Michaelis-Menten Plot of Uninhibited Enzyme Activity Versus Noncompetitive Inhibition. SHAPE CHANGES, NEVER REACHES Vmax.
  54. NAME THE TYPE OF ENZYME INHIBITOR WHO....
    Changes enzyme conformation-prevents product formation.
    Increased substrate concentration partially reverses inhibition.
    NONCOMPETITIVE INHIBITORS
  55. T OR F?
    NONCOMPETITIVE INHIBITORS HAVE DIFFERENT Vmax BUT MAY HAVE SAME OR DIFFERENT Km?
    TRUE
  56. ------------ Inhibitors: a type of noncompetitive inhibition that involves binding only the ES.
    UNcompetitive
  57. NAME THE LOCATIONS WHERE REVERSIBLE ENZYME INHIBITION CAN OCCUR.
    Competitive:bind reversibly to the enzyme at the active site.


    Noncompetitive: can bind reversibly to the E or ES complex at a site other than the active site of enzyme.


    Uncompetitive: binding only the ES.
  58. LINE A NORMAL ENZYME-CATALYZED RXN.
    B,C, & D ARE COMPOUNDS ADDED. IDENTIFY THE INHIBITORY ACTION.
    • B. COMPETITIVE. Km HAS ONLY CHANGED.
    • C. PURE NONCOMPETITIVE. Vmax HAS ONLY CHANGED.
    • D. UNCOMPETITIVE. BOTH Km & Vmax HAVE CHANGED.
  59. COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
    COMPETITIVE. Km HAS ONLY CHANGED.
  60. COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
    PURE NONCOMPETITIVE. ONLY Vmax HAS CHANGED.
  61. COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
    MIXED NONCOMPETITIVE.NOTICE HOW X & Y INTERSECT BELOWTHE HORIZONAL AXIS. (CAN ALSO INTERSECT ABOVE THE HORIZONAL AXIS).
  62. COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.

    MIXED NONCOMPETITIVE.NOTICE HOW X & Y INTERSECT ABOVE THE HORIZONAL AXIS. (CAN ALSO INTERSECT BELOW THE HORIZONAL AXIS).
  63. COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
    UNCOMPETITIVE. BOTH Km AND Vmax HAVE CHANGED.
  64. T OR F?
    In vitro work does not always reflect in vivo reality
    TRUE
  65. Scientists use 3 METHODS to understand the catalytic mechanism of enzymes. NAME THEM.
    • X-ray crystallography,
    • chemical inactivation,
    • modeling
  66. Essential features of catalysis are reaction between ------ & -------.
    Electron-deficient atoms (electrophiles) and electron-rich atoms (nucleophiles)

    Electrons flow from a nucleophile to an electrophile
  67. ----------- ------------ is a step-by-step description of a reaction
    Reaction mechanism
  68. Examples of reactive intermediates include WHAT? NAME 3.
    • free radicals,
    • carbocations,
    • carbanions
  69. WHAT THE HELL IS THIS AND WHAT DOES IT PRETAIN TO? WHERE WOULD YOU FIND THE PRODUCT?

    Energy Profile for a Two-Step Reaction of reactive intermediates. Products are on the bottom line of delta G on the right.
  70. T OR F?
    Mechanisms of only a few enzymes are known in significant detail
    TRUE
  71. Several factors contribute to enzyme catalysis. The most important are...NAME 3
    • 1) Proximity and Strain Effects
    • 2) Electrostatic Effects
    • 3) Acid-Base Catalysis
  72. DEFINE Proximity and Strain Effects
    ENZYME CATALYSIS. The substrate must come in close proximity to the active site. Strained enzyme substrate complex during binding induces change closer to transition state.
  73. DEFINE Electrostatic Effects OF ENZYME CATALYSIS.
    Charge distribution in the largely anhydrous active site may help position the substrate
  74. DEFINE Acid-Base Catalysis OF ENZYMES
    Proton transfer is an important factor in chemical reactions.

    Hydrolysis of an ester, for example, takes place better if the pH is raised.

    Hydroxide ion catalysis
  75. THE HYDROXIDE ION CATALYSIS IS WHAT TYPE OF CATALYSIS MECHANISM?
    ACID-BASE CATALYSIS.
  76. WHAT'S THE NEXT 2 STEPS? WHAT DOES IT REPRESENT?


    • Hydroxide Ion Catalysis.
    • --->
  77. T OR F?
    Side chains of many amino acids (e.g., histidine, lysine, and aspartate) can be used as general acids or bases OF ENZYME CATALYSIS.

    Depends on state of protonation, based on pKa of functional groups
    TRUE
  78. T OR F?
    More physiological is the use of general bases and acids (i.e. non OH- bases) FOR ENZYME CATALYSIS.
    TRUE
  79. DEFINE THE REACTION NAME THE THE NEXT 2 STEPS.
    General Base Catalysis

    --->
  80. WHAT TYPE OF CATALYSIS TYPE IS THIS AND NAME THE NEXT 2 STEPS.

    • GENERAL ACID CATALYSIS.
  81. T OR F?
    In order to participate in catalysis, the amino acid has to be charged or polar. For example, chymotrypsin.
    TRUE
  82. ----------- side groups function to orient substrate or stabilize transition state whereas charged catalytic groups function in the reaction
    Noncatalytic
  83. The active sites of enzymes are lined with ----- ----- that create a microenvironment conducive to catalysis
    AMINO ACIDS
  84. DEFINE AND NAME Alkali metals OF ENZYME CATALYSIS.
    • Alkali metals are usually loosely bound and play structural roles.
    • Na+, K+, Mg2+, and Ca2+
  85. DEFINE AND NAME Transition metals.
    Transition metals usually play a functional role in catalysis as part of a functional group.

    Zn2+, Fe2+, and Cu2+
  86. T OR F?
    Metals are good Lewis acids (accept charge) and effective electrophiles.
    TRUE
  87. WHAT THE HELL IS......
    1.Contain functional groups that amino acid side chains do not
    2.Can be tightly or loosely bound and their structures are often changed by the catalytic process
    3. Most are derived from vitamins
    COENZYMES
  88. NAME THE 3 COENZYME GROUPS.
    • 1. electron transfer (NAD+),
    • 2. group transfer (coenzyme A),
    • 3. high energy transfer potential (nucleotides)
  89. DEFINE Coenzymes
    a group of organic molecules that are attached to enzyme and are essential for function.
  90. IN ENZYME CATALYSIS,Temperature- the higher the temperature, the faster the reaction rate. WHY?
    increased number of collisions.
  91. DEFINE pH optimum
    pH- hydrogen ion concentration affects enzyme function; therefore there is a pH optimum
  92. T OR F?
    Catalytic activity is related to ionic state of the active site
    TRUE
  93. T OR F?
    Changes in ionizable groups could change structure of the enzyme: increase or decrease activity—remember bonds that stabilize tertiary structure—H bonds, salt bridges
    TRUE
  94. WHAT THE HELL IS Chymotrypsin?
    It's basically,serine protease of 27kD

    Serine proteases have a triad of amino acids in their active site (e.g., Asp 102, His 57, and Ser 195)

    Hydrolyzes peptide bonds adjacent to aromatic amino acids—such tyrosine (Y), tryptophan (W), and phenylalanine (F) (carboxyl side).

    Used to digest food.
  95. Enzyme regulation is necessary for...NAME 3
    • Maintenance of ordered state
    • Conservation of energy
    • Responsiveness to environmental changes
  96. ENZYME CATALYSIS REACTIONS ARE CONTROLED HOW?
    • Control is accomplished by:
    • genetic control,
    • covalent modification,
    • allosteric regulation,
    • compartmentalization
  97. Genetic Control happens at the ----level and can lead to repression or induction of enzyme synthesis
    DNA
  98. Several covalent modifications in enzyme structure cause changes ------ ------.
    IN FUNCTION
  99. Types of covalent modification include NAME 3
    • phosphorylation,
    • methylation,
    • acetylation
  100. THROUGHT COLVALENT MODIFICATION,Some enzymes produced and stored as ----- OR --------.
    • proenzymes or
    • zymogens (inactive precursor)
  101. WHAT ARE allosteric sites?
    Sites other than active site—can induce a conformation change and thus alter enzyme activity.
  102. The Rate of An Enzyme-Catalyzed Reaction As a Function of Substrate Concentration PRODUCE WHAT TYPE OF LINE ON A GRAPH?
    Sigmoidal curve, unlike Michaelis-Menten kinetics
  103. Most allosteric enzymes are ---------- ------------.
    multisubunit enzymes
  104. NAME THE allosteric enzymes 2 theoretical models.
    concerted and sequential
  105. DEFINE THE concerted model OF THE ALLOSTERIC ENZYMES.
    In the concerted model, all subunits are changed at once from taut (T) to relaxed (R) or vice versa with first binding of effector (e.g. activator or inhibitor). An activator shifts the equilibrium in favor of the R form; an inhibitor shifts in favor of the T form
  106. DEFINE THE sequential model OF THE ALLOSTERIC ENZYMES.
    In the sequential model binding of the ligand to one subunit, it triggers a conformational change that is passed to subsequent subunits
  107. T OR F?
    ENZYMES ARE EFFECTED BY Diffusion barriers—pathways connected do not need to wait for substrate to diffuse through crowded cell
    TRUE
  108. Diagnostic Enzymes
    NAME ONE PROCEDURE.
    myocardial infarction (MI) leads to heart muscle cell death.
  109. ---------- AND ---------have been used to diagnose MI replaced by cTnI (troponin assay for muscle damage
    Lactate dehydrogenase and creatine kinase

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