BYU-I Chem481 Test 2

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BYU-I Chem481 Test 2
2013-02-02 15:12:01

Review notes for Biochemistry Test 2. Lenninger Chapter 6&7
Show Answers:

  1. Define Kcat:
    Kcat= overall rate of the reaction. Most likely approximate to the slow rate determining step.
  2. Describe an enzyme catalyzed reaction vs. a non-catalyzed reaction: 
    The Catalyzed reaction will proceed more rapidly, will have lower energy intermediates, will go through a different pathway, but will have the same starting and ending energy states.
  3. What does the enzyme stabilize in an enzyme catalyzed reaction?
    It stabilizes the transition state.
  4. T/F Prosthetic groups easily unbind with their ligand.
    False. Coenzyme Cofactors are not prosthetic groups when they easily unbind.
  5. Do enzymes affect the overall change in free energy?
    NO! While they do lower the intermediate energies required for certain transition states, they do not effect the beginning or ending energy states.
  6. Is Keq related to  or ?
    • Keq is related to
    • Not The Activation Energy.
  7. Define Specific Acid Base catalysis:
    Uses Water to shuffle protons.
  8. Define General Acid Base catalysis:
    Uses anything but water.
  9. Define Metal Ion Catalysis:
  10. How does one determine the Rate determining step for a catalyzed reaction?
    It will be the step involving the highest energy transition state.
  11. How does one determine what intermediates might be present in quantities stable enough for analysis?
    They will be the low energy troughs before the final product.
  12. What would happen if an enzyme was complementary to the substrate instead of the transition state?
    It would bind so tightly to the substrate that to move to a different conformation would require more energy than the cell could provide. The Activation energy would be increased!
  13. How are some enzymes able to lower the activation energy of their substrate, even though the same amount of work must be done to modify the substrate?
    The negative energy interactions between the enzyme and the substrate help to negate the positive energy needed to modify the substrate. This is 1 way.
  14. Define Entropy:
    • Entropy is a measure of the randomness and disorder in a system.
    • .S.
  15. Is it typical for an enzyme to increase or decrease S?
    Typically Enzymes Decrease Entropy. This is useful In Catalyzing a reaction.
  16. How can an enzyme reduce S?
    By binding to the substrate. It's binding affinity overcomes the drop in Entropy.
  17. Which interaction allow binding and recognition of a substrate for an enzyme among a sea of other substrates?
    IMF (mult weak interactions).
  18. Why would a reaction be driven forward with high [S] and backwards with high [P]?
    The leChatlier principle. Free substrate increases the binding to enzymes and pushes the reaction forward. Free product increases the probability of the reverse reaction occurring.
  19. What is V0?
    It is the Initial Rate.
  20. What are the 2 initial assumptions for Simple Enzyme Kinetics?
    • 1. V0 is what matters.
    • 2. the ES complex forms ASAP!
  21. How Fast does the ES Complex Form?
  22. Why do we assume that [P] is initially very low?
  23. Which of the following will occur fastest?

    KWill occur the fastest because all free enzyme will quickly bind to the substrate.
  24. Define the Steady State Assumption:
    [ES] is constant. Initially all free Enzyme will bind to substrate, and then as the substrate is processed into product, the Free enzyme will bind to new substrate so quickly that it will appear that all available substrate is constantly bound.

  25. Please list the above k in order of how fast they are:
    • K1 is fastest.
    • K-1 is next.
    • K2 is slowest and the rate determining step.
  26. What are the Units of a Michaelis-Menten Plot?
  27. What is the Shape of a Michealis-Menten Plot?
    rectangular hyperbola.
  28. Define the simplified Michealis-Menton equation:
  29. What does 1/2 Vmax represent on the michealis-menton plot?
  30. Determine the initial rate When [S]=Km:
    • V0=1/2Vmax
  31. Determine the initial rate When Km>>>[S]:
    • V0=0
  32. Determine the initial rate When Km<<<[S]:
    • V0=Vmax

  33. For this reaction define Km:
  34. When does Km best approximate Kd? 
    When K2 is the rds.
  35. Define the "turnover number"
    why is it useful?
    • Vmax=Kcat[Etot]
    • This helps us to approximate the Vmax. 
    • Kcat is the actual turnover number.
    • s-1
  36. What is the specificity constant, and why is it important?
    • kcat/Km
    • This is an index of catalytic efficiency.
    • Very useful because inside cells enzymes function at very low concentrations.
  37. What is the diffusion-controlled limit?
    When the specificity constant approaches near optimal efficiency. It is near 108 to 109 1/Ms.
  38. Define the Lineweaver-Burk equation:
    It is in what algebraic form?
    • y=mx+b
  39. On a Lineweaver-Burk plot define the y and x axis:
    • y axis = 1/V0
    • x axis = 1/[S]
  40. Define the y intercept on a Lw-B Plot:
    y intercept= +1/Vmax
  41. Define the x intercept on a Lw-B Plot:
    x intercept= -1/Km
  42. Define the Slope on Lw-B Plot:
    Slope= Km/Vmax
  43. Describe Competitive inhibition:
    It is S vs. I. Both are competing for the same active site on the E. If one binds the other Cannot.
  44. Which is affected by competitive inhibition,
    Km or Vmax?
    • Km.
    • Remember equation for Km:
  45. Describe Uncompetitive Inhibition:
    ES are not allowed to proceed to E+P because they are taken up by I, forming ESI. I has its own binding local.
  46. Which is affected by Uncompetitive Inhibition, Km or Vmax?
    Both are equally affected.
  47. Describe mixed inhibition:
    The inhibitor can either compete for the substrates binding site, or it can bind to it's own binding site, or change directly between the two. It exists both as EI and ESI.
  48. Which is affected by mixed inhibition, Km or Vmax?
    Both are affected but unevenly.
  49. Competitive inhibition changes_______
    How can this be visualized on a Lw-B plot?
    • Apparent Km.
    • Moving x intercept, but solid y intercept.
    • change in Km, no change in Vmax.
  50. Uncompetitive inhibition changes_______
    How can this be visualized on a Lw-B plot?
    • Vmax and Km by same amount.
    • Moving y intercept, AND x intercept by same amounts.
    • Change in Vmax, and equal change in Km.
    • Parallel lines.
  51. Mixed inhibition changes_______.
    How can this be visualized on Lw-B plot?
    • Both Vmax and Km are changed, but not by same amount.
    • The Plot could look like anything.
  52. Describe Noncompetitive Inhibitors:
    Rare! They make the RDS even Slower.
  53. Which is affected by Noncompetitive Inhibitors, Vmax or Km?
  54. Noncompetitive Inhibition changes________
    How can this be visualized on a Lw-B plot?
    • Vmax.
    • moving y axis, stable x axis.
    • change in Vmax, no change in Km.
  55. provide an example of a Serine protease:
  56. Why are peptide bonds so stable and nonreactive?
    Resonance stabilization. 
  57. Which is the slow step in acid catalyzed hydrolysis? What characterizes this step?
    Step 2, The oxygen in water attacks the carbonyl carbon C=O+H as the double bond collapses, forming the -OH group. The Geometry changes from trigonal planar sp2 to tetrahedral sp3.
  58. Name 3 serine proteases:
    • 1. Chymotripsin.
    • 2. Trypsin.
    • 3. Elastase.
  59. The Serine Proteases are characterized by what kind of binding pocket?
    • Chymotripsin: Serine.
    • Trypsin: Aspartic Acid.
    • Elastase: Valine - Threonine.
  60. What residue(s) fit well for chymotripsins pocket?
    • Tyr
    • Arg
    • Ala, Gly
  61. Is the Catalytic Triad conserved, or nonconserved?
    It is Conserved.
  62. What residues make up the catalytic triad, and in what order?
  63. Which member of the catalytic triad is the induced nucleophile?
  64. Aspartic acids main function is to:
    • form a hydrogen bond with His, greatly increasing the pKa of Histadines R group, thus increasing the basic nature of His N.
    • pKa 6 --- pKa>12
  65. Histadines main function is to:
    Steal serines Hydrogen, inducing a H bond. making serine a strong nucleophile,
  66. How are Pre Steady State Kinetics measured?
    p-NO2-phenol is released during the fast step. It absorbs light at 400nm. Acetate is released during the slow step, therefore after steady state released. The rise in p-NO2-phenol before that point is the rate of attachement of S and E to form SE.
  67. Why dos 1/Km decrease as pH rises?
    1/km decreases, ergo Km increases because an amino terminus is ionized as the pH rises.
  68. Why does Kcat increase as pH increases?
    Because at low pH the His is protonated, as the pH rises above the pKa of Histadines R group, the residue can perform it's catalytic function.
  69. Why are phosphate groups significant?
    They are transition state analogues that have already adopted the tetrahedral geometry. They then do not change geometries and stop the mechanism. Bee and Snake venom are two examples of "irreducible complexity".
  70. What are 3 ways that proteins are "turned" on or off?
    • 1. Allosteric Control.
    • 2. Covalent Modification.
    • 3. Protein Processing.
  71. What is an Example of Allosteric Regulation?
    The Hemoglobin nonEnzyme.
  72. A sigmoid curve is indicative of:
    • Allosteric regulation, and Km should be replaced with K1/2.
    • This is because the substrate serves as an activator for other protein subunits.
  73. What is the difference between competitive inhibition, and competitive product inhibition?
    With one the product has no effect on inhibition, whereas the other the product concentration is the inhibitor.
  74. Covalent modifications include:
    Ubiquination, Phosphorylation. 
  75. are covalent modifications reverisble?
    YES! totally, that's why we have phosphotases and deubiquitinases.
  76. Kinases and Phosphotases help the cell:
    Communicate, produce cellular responses, modify proteins, Are critical through phosphorylation cascades.
  77. Something Very Special about phosphorylation is:
    There are examples of where it acts as a dimmer switch. More is better, less is worse. EX. Glycogen Synthase.
  78. Define Zymogen:
    Inactive Precursor that must be cleaved to form an active enzyme. Ex. Chymotrypsonogen, or Pro-"enzyme"
  79. How does the Chymotrypsin Zymogen stay inactive?
    For Chymotrypsinogen: Ile has protonated N terminus that forms salt bridge with Asp
  80. What is the difference between an Aldose and a Ketose?
    An aldose has a terminal O=CCOH. A ketose has a chain O=C.
  81. D-Glucose is:
    An AldoHexose.
  82. D-Fructose is:
    a Ketohexose.
  83. Monosaccarides are:
    • Usually Aldoses or Ketoses.
    • 3-7 carbons long.
    • Mostly D.
  84. If a monosaccaride is capable of adopting a cyclic nature, when will it do that?
    Under aqueous conditions.
  85. How can you know the max number of diastereomers possible for a certain molecule?
    • 2n Where N is the number of Stereo Centers.
  86. How is the Anomeric C group arranged on  - d-Glucopyranose?
    With the OH group UP.
  87. How is the Hemiacetal C arranged on 
    The OH group is Down.
  88. If Pure alpha or beta glucose is left to equilibrate, what ratio will it take?
    1:2 alpha:beta
  89. What 2 types of rings can the Hexoses adopt:
    • 5 membered Furanose
    • 6 membered Pyranose
  90. Which type of Hexose ring is favored at higher temperatures?
    Furanose. Specifically 
  91. Provide an Example of a modified monosaccaride:
    Chitin: it is a beta chain that has GlcNAc groups coming off of it.
  92. Describe Disaccharides:
    2 sugars held together with an O-glycosidic bond at the 1,4 carbons. May have a reducing end at the hemiacetal (C1) of sugar 2.
  93. Is Sucrose a reducing or non-reducing sugar?
    It is non-reducing
  94. What role do Amylose and Amylopectin play?
    They store energy in plants.
  95. What role does Glycogen play?
    Energy storage in Animal and Bacterial cells.
  96. What role does Cellulose play?
    Structural, it is found in plants.
  97. What role does chitin play?
    It is structural. It Forms on arthropods and yeasts.
  98. What type of linkage is found on Starch and glycogen, and is digestible?
    alpha 1,4 linkage.
  99. Why do stored sugars branch?
    to increase the number of nonreducing ends.
  100. What makes cellulose indigestible?
    It has beta 1,4 linkage, and it's linear form makes use of hydrogen bonds to strengthen the molecule, and limit the binding of water.
  101. What primarily makes up the ECM?
    Fibrous proteins, and glycoaminoglycans (GAG).
  102. Describe the structure of GAG:
    It is a Heteropolysaccharide, made up of repeating, modified subunits. It has a rod-like helix due to the buildup of (-) charge.
  103. Describe Proteoglycans:
    A proteoglycan will have a core protein with a GAG attached. They can either be tethered to the cell membrane, or be cleaved off at a Ser residue.
  104. Why role do proteoglycans play?
    They provide structural support, and Facilitate cell communication.
  105. Describe Glycoconjugates:
    It is the name given to describe the 3 classes of glycoconjugates: Proteoglycans, glycoproteins, and glycolipids.
  106. Which Glycoconjugates are associated singularly with the plasma membrane?
    • Glycoproteins,
    • Glycolipids.
    • They are also smaller than the ECM associated Proteoglycan.
  107. What are Glycoproteins involved in?
    • Modifying Polarity,
    • Destination Labels,
    • Protein Quality Control.
  108. The Sugar Code refers to what?
    • Modified Carbohydrate additions to Glycoproteins/lipids, that facilitate cell signaling. 
    • -M6P-
  109. Describe Lectins:
    • Lectins are the Membrane Bound Sugar Code Receptors. Nearly Infinite combinations.
    • They move slowly until they find what will bind to them.
  110. In glycoproteins, how is the carbohydrate most often linked?
    • N or O bonds.
    • Asn; Ser are most common.
  111. The reaction of an Aldehyde or Ketone with alcohol results in:
    a Hemeacetal or a Hemeketal. The geometry changes from sp2 to sp3, and a new chiral center is introduced.
  112. The reaction of a Hemeacetal or Hemeketal with an alcohol results in:
    An Acetal or a Ketal. If the second alcohol is part of a sugar, than a glycosidic bond can form.
  113. Define Anomer:
    An two sugars that differ only in the arrangement of the hemeacetal or hemeketal are anomers. (Alpha vs. Beta)
  114. Define Epimers:
    Two sugars that differ only in the arrangement of 1 carbon.