1. Protein _____ defines the relation among subunits in a multisubunit lattice
    quaternary sturcture
  2. The _____ describes the relation between interatomic distances, electronic charge, solution dielectric and free energies
    van der Waals interaction
  3. Protein _____ defines the amino acid sequence
    primary structure
  4. Protein _____ defines the packing of helices, sheets, turns, etc.
    tertiary structure
  5. Protein _____ defines the motifs formed by short-range interactions between amino acids
    secondary structure
  6. A _____ interaction involves polar O, N or both and the atom for which it is named and constitutes one of the important protein stabilization elements
    hydrogen bond
  7. _____ is used to determine the sequence of a protein based on sequential chemical reactivity
    Edman degradation
  8. A _____ induces denaturation of proteins by disturbing the hydrophobic effect
    chaotropic agent
  9. Name the following protein structure:
    • R1-CH2-S-S-CH2-R2
    • disulfide bond
  10. A _____ is a graph of the conformational torsion angles Φ and Ψ for the residues in a protein or peptide, a map of the structure of the polypeptide backbone
    Ramachandran plot
  11. A _____ has two charges which neutralize each other
  12. The _____ is the primary "force" of protein structural stabilization
    hydrophobic effect
  13. The _____ is the characteristic speed of an enzyme's kinetics extrapolated to the time when a defined amount of substrate is added to the enzyme solution
    initial rate
  14. An act of _____ does not change an enzyme and lowers the transition state free energy of the associated reaction
  15. The _____ of an enzymatic catalysis reaction is the rate achieved when it is saturated with substrate
    maximum velocity
  16. The _____ equation defines parameters that are used to characterize the kinetics of an enzyme
    Lineweaver-Burh (or double reciprocal)
  17. Km is the substrate concentration when vo=vmax/2, or _____
    Michaelis-Menten constant
  18. A _____ is the enzyme-substrate combination formed during an enzyme catalysis event
    Michaelis complex
  19. The catalytic rate constant of an enzyme is abbreviated as _____
  20. _____ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme
    Competitive inhibition
  21. _____ of enzyme catalysis occurs when an inhibitor only binds to the enzyme-substrate complex
    Uncompetitive inhibition
  22. The _____ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation
    steady state approximation
  23. Internal factors that limit the velocity of an enzymatic reaction are _____ (6)
    • hydrophobic effect
    • H-bonding
    • disulfide bonds
    • van der Waals forces
    • ionic bonds (salt bridges)
    • dipole-dipole interactions (actually underlying all of the others)
  24. External factors that limit the velocity of an enzymatic reaction are _____ (7)
    • pH
    • solvent polarity
    • temperature
    • salt concentrations and types
    • presence of chaotropes
    • osmolytes
    • others
  25. What amino acid and functional group in the esterase site of acetylcholine esterase reacts with the substrate?
    • serine
    • hydroxylate
  26. Pyridine aldoximine methiodide (PAM) reactivates acetylcholine esterase, functioning as a _____
    nerve gas antidote
  27. What kind of reaction produces the reactivated enzyme?
    nucleophilic substitution
  28. The bisubstrate-enzyme _____ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progressively binding substrates
  29. An _____ works by amplifying an initial signal via several linked protease cleavage reaction stages (e.g. blood clotting)
    enzyme cascade
  30. A _____ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage
  31. A decrease in the activity of an enzyme as a result of binding of a product from the reaction in question or subsequent reactions is referred to as _____
    feedback inhibition
  32. _____ involves binding of a regulatory molecule at a site other than the active site
  33. _____ and _____ reactions, involving phosphate addition and removal respectively, regulate both glycolysis and the Krebs cycle
    • Kinase
    • Phosphatase
  34. _____ regulates entry and exit from mitosis by catalyzing a covalent modification reaction
    Cyclin kinase
  35. What two amino acids are modified in the reactions catalyzed by the enzyme cyclin kinase?
    tyrosine, threonine
  36. Examples of reversible factors that control the catalytic capability of an enzyme are: (3)
    • noncovalent modifications
    • pH and pKa changes
    • [salt] changes
    • possibly others
  37. Examples of irreversible factors that control the catalytic capability of an enzyme are: (3)
    • covalent modification
    • proteolysis
    • irreversible inhibitors
    • possibly others
  38. The _____ accounts for the temperature dependence of the rate of a reaction
    Arrhenius equation
  39. The two "chemical modes of catalysis"
    • acid-base
    • covalent
  40. The two "binding modes of catalysis"
    • proximity effect
    • transition-state stabilization
  41. A _____ attacks an electropositive site in it's role in a chemical (enzymatic) reaction
  42. A common process used to produce 'nucleophiles' is _____
    acid-base catalysis
  43. Probably the most common amino acid used by enzymes to carry out acid-base catalysis is _____
  44. A "catalytic triad" of amino acids is typically present in (enzyme class name) _____
    serine proteases
  45. The amino acids "collaborate" to accomplish _____
    acid-base catalysis
  46. The most typically cited currency of energy in metabolism is _____
  47. _____ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions
  48. A coenzyme is either a loosely bound cosubstrate or tightly bound _____
    prosthetic group
  49. The heavy metal molybdenum is used to facilitate the biochemical reaction in _____, a key enzyme in purine catabolism
    xanthine oxidase
  50. When ATP used in some biochemical applications it yields AMP and _____
  51. The (vitamin) _____ is required to synthesize coenzyme NAD+ for use in the metabolic redox reactions
  52. The other key redox coenzyme is abbreviated _____
  53. The coenzyme _____ often forms a Schiff base with the ε-amino group of a lysine residue in the enzyme
    pyridoxal phosphate
  54. What chemical group does coenzyme A typically carry in the course of it's biochemical function?
  55. The _____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "affinity capture" technique
  56. The coenzyme _____ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA
    N5, N10 tetrahydrofolate
  57. Our understanding of this function can be used in a strategy for (treatment technique) _____
    anti-cancer chemotherapy
  58. The coenzyme bound carbohydrate _____ and glucose are required to synthesize lactose
  59. Cis-retinal functions in _____the signal of a photon of light into a chemically recognizable form
  60. The two important straight-chain forms of carbohydrate structure are the _____ and _____
    • ketose
    • aldose
  61. The two important ring forms of carbohydrate are the _____ and _____
    • pyranose
    • furanose
  62. The two important ring conformations of β-D-glucopyranose are the _____ and _____
    • chair
    • boat
  63. The cyclohexane ring containing compound _____ is released by phospholipase C in the phospholipid signal transduction mechanism
    inositol triphosphate
  64. The acronym NAG is used to abbreviate the name of the compound _____
    N-acetyl glucosamine
  65. The key polysaccharide in starch is _____
  66. The key polysaccharide in the liver is _____
  67. The antibiotic _____ selectively inhibits cell wall peptidylglycan synthesis in bacteria
  68. Extra-cellular surface _____ regulate the osmotic pressure around cells
  69. Phospholipase C produce two different second messengers in the phospholipid signal transduction pathway. The lipid-containing second messenger is _____
  70. The compound _____ lubricates cartilage and skeletal joints
    chondroitin sulfate
  71. _____ fatty acids of the same length have a lower melting temperature (Tm)
  72. Lipid Tm values monitor the transformation from _____ to dispersed forms
    liquid crystal
  73. _____ are composed of two face-to-face monolayers while _____ form a biphasic sphere
    • Lipid bilayers
    • Lipid micelles
  74. The most popular model for a biological membrane is called the _____
    fluid mosaic model
  75. The four nucleic acid bases in RNA are
    • adenine
    • guanine
    • cytosine
    • uracil
  76. The two normal base pairs in DNA and RNA are called _____
    Watson-Crick base pairs
  77. The _____ bond in a nucleoside connects the base to the sugar
  78. The _____ can be used to determine if a double helix forms from 2 single strands of DNA or RNA
    absorbance at 260 nm
  79. The face-to-face interaction between nucleic acid bases is called _____
    base stacking
  80. Counterions bind all nucleic acids and are required to neutralize the _____
    phosphodiester phosphates
  81. The proteins called _____ serve this function in the case of most chromosomal DNAs
  82. _____ base pairs are less stable than _____ base pairs
    • A-T (or A-U)
    • G-C
  83. Differences between A and B forms of DNA are
    A: 3'endo sugar conformation, Base pairs tilted 20° from helix axis, "Doughnut hole" in center of helix, Shorter squatter helix

    • B: 2'endo sugar, Base pairs perpendicular to helix axis, Base pairs
    • cross center of helix, Longer narrower helix
  84. The 2'-hydroxyl group catalyzes _____ of RNA, a good example of anchiomeric assistance in a non-protein biomolecular mechanism
    alkaline hydrolysis
  85. An antisense oligoculeotide functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____ binding
    tRNA anticodon
  86. Name the two most prevalent of the four classes of RNA
    ribosomal RNA and transfer RNA
  87. Distinctive features of most eukaryotic mRNAs are _____ (4)
    • m7G+ (5'-5') cap
    • monocistronic
    • contains introns and exons
    • poly(A) tail
  88. A _____ is used to detect the presence of a specific complementary nucleic acid sequence
    DNA probe
  89. _____ are required to produce, manipulate and clone specific pieces of DNA
    Restriction endonucleases
  90. The two functional end of transfer RNA are the _____ and _____
    • anticodon
    • amino acid acceptor
  91. The three most central catabolic pathways of intermediary metabolism are:
    • glycolysis
    • Krebs cycle
    • electron transport/oxidative phosphorylation
  92. The four major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are:
    • ATP
    • NADH
    • FADH2
    • Coenzyme QH2
  93. The _____ corrects for deviations from standard state concentrations (1 M)
    mass action ratio (Q)
  94. _____ steps in glycolysis control most of the flux through the pathway under actual cellular conditions
    metabolically irreversible (3)
  95. In contrast to metabolically irreversible reactions, the rest of the reactions are _____
    near equilibrium
  96. The kinetics of an enzyme reaction are most easily controlled when Km is approximately equal to _____
    the actual concentration of the reactant
  97. The enzyme triose phosphate isomerase converts _____ into _____
    • dihyroxyacetone phosphate
    • glyceraldehyde-3-phosphate
  98. When citrate negatively regulates (discourage) the phosphofructokinase-1 reaction, the general name for this phenomenon is _____
    feedback inhibition
  99. When fructose-1,6-bisphosphate stimulates the pyruvate kinase reaction, the general name for this phenomenon is _____
    feedforward activation
  100. What are the 3 possible catabolic fates of pyruvate?
    • acetyl CoA
    • ethanol
    • lactate
  101. The enzyme alcohol dehydrogenase converts _____ to _____
    • acetaldehyde
    • ethanol
  102. _____ uses the coenzyme lipoic acid in "fueling" the Krebs cycle
    dihydrolipoamide acetyl transferase
  103. What "symport" reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzed the reaction?
    pyruvate translocase
  104. The two "oxidative decarboxylation" reactions of the Krebs cycle are catalyzed by _____ and _____
    • isocitrate dehydrogenase
    • α-ketoglutarate dehydrogenase
  105. List the reactions, coenzymes, cofactors, and enzymes involved in the "substrate-level phosphorylation" reaction of the Krebs cycle
    • succinyl CoA to succinate
    • Enzyme: succinyl CoA synthetase
    • Cofactors: Pi (bonded to histidine), GDP or ADP-->GTP or ATP CoA-SH
  106. The enzymes _____ and _____ "fix" a carbonyl group on succinate in the production of oxaloacetate
    • fumarase
    • malate dehydrogenase
  107. What crucial 2 carbon compound is "fixed" to oxaloacetate?
  108. What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals?
    • alanine
    • lactate
  109. What energy sources are used to produce the "protomotive force"?
    • NADH
    • FADH2
    • CoQH2
  110. What enzyme complex uses protomotive force as the driving energy for ATP synthesis in oxidative phosphorylation?
    • f0f1 ATP synthase (or ATPase)
    • ("synthetase" not accepted)
  111. How does electron transport drive production of the protomotive force?
    • exports H+ from mitochondrion
    • (which creates a gradient, making them predisposed to flowing back in)
  112. How many reactions does each round of β-oxidation of a fatty acid require?
    • four
    • (oxidation 1, hydration, oxidation 2, thiolysis)
  113. What are the products of one round of β-oxidation?
    • and What's the tally in terms of ATP equivalents of energy conserving products?
    • 1 CoQH2=1.5 ATP
    • 1 NADH=2.5 ATP, H+
    • 1 acetyl CoA=10 ATP
    • 1 fatty acid (minus 2 Cs)
  114. What are the 4 cofactors involved in the "siphon" of β-oxidation?
    • CoA
    • FAD/FADH2
    • Fe-S2+/3+
    • CoQ/CoQH2
  115. A set of coupled cofactor regeneration cycles siphon off _____ then fix them into _____ in reactions that are coupled to the first _____ step of fatty acid β-oxidation
    • reducing equivalents
    • coenzyme Q
    • oxidative
  116. Which 3 steps of the Kreb's cycle do the first 3 steps of the fatty acid β-oxidation cycle resemble?
    • succinate dehydrogenase
    • fumarase
    • malate dehydrogenase
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