Biochem exam 1.txt

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Biochem exam 1.txt
2015-02-02 00:26:34

Biochem homework questions
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  1. The "acid" in a nucleic acid nucleotide is a
    phosphate group
  2. dATP is an energy storage molecule because it contains
    mutually repelling charged groups
  3. Base pairing in DNA employs a strategy of complementary
    choices 1 and 2 (sizes, H-bond properties)
  4. The type of biomolecule with naturally occuring examples of both homopolymers and heteropolymers is ___ .
  5. A class of structures where we have NOT seen examples of a network of H-bonds within the biomolecule itself is ___ .
  6. Cellulose is a
    homopolymer of glucose
  7. Conversion of mRNA into a protein is called
  8. The formula for a carbohydrate is
    C(n) H(2n) O(n)
  9. Glyceraldehyde has the formula C3-H6-O3. It is a(an) ___ .
  10. Lauric acid has the formula C12-H24-O2. It is a(an)
    fatty acid
  11. Myosin is a ___ .
  12. Myosin is a ___ . (homopolymer or heteropolymer)
  13. Oxidation of a fatty acid during metabolism converts
    nonpolar bonds to polar bonds, and releases heat
  14. Phosphates are components of
    membrane lipids, nucleic acids
  15. A reaction joining two amino acids together creates
    an amide plus water
  16. The effect of absorption of light on the pigment retinal is
    a change in configuration at a C=C double bond
  17. The structural origin of the rigidity of cellulose is
    hydrogen bonding
  18. Every nucleotide in RNA contains a ___ component.
  19. The term which describes the reaction given below : amino acid + amino acid -> polymer + water
  20. Of the four types of biomolecules, one of them does not form polymers. This type is ___ .
  21. The exponential notation 2^3 = 8 means 2 raised to the third power (2 cubed). In molecules with n uniquely different chiral carbons, the total number of possible configurations is
  22. A linear aldose begins with an aldehyde group, ends with a -CH2-OH group, and has H-C-OH carbons in between. The chiral carbon(s) include the
    H-C-OH carbons
  23. When citric acid is bound to the enzyme aconitase, the two -CH2-COOH groups attached to the central carbon atom have ___ probabilities of interacting with groups on the enzyme
  24. The term configuration applies to ___ .
    R vs. S ; and cis vs. trans
  25. The naming system which is based on a comparison to the standard, glyceraldehyde, is the ___ system.
    D vs. L
  26. Glycerol and glyceraldehyde each have
    3 carbons
  27. Ibuprofen has one chiral carbon. The most inexpensive way to synthesize it is as a racemic mixture of R and S forms. The % of the ibuprofen molecules in the pill you buy which are physiologically active is
  28. Levo is the root word for
  29. Linear aldose sugars have their aldose group at C-1. The D carbon is always ___ .
    the highest numbered chiral carbon
  30. In chiral amino acids,the L carbon is in the
    backbone (HN-C-carbonyl)
  31. Except for glycine (which is neither D nor L), the amino acid products produced by passing a spark thru a mixture of NH3, CH4, H2O and H2 are ___ .
    50% L and 50% D
  32. A chiral carbon is viewed with its lowest priority group (4) at the rear. When the other groups in the front are considered in order 1->2->3 and they appear clockwise, the configuration is
  33. The designations which are based on the rotation of plane-polarized light of a particular wavelength are ___ .
    d and l
  34. The stereospecificity of biological reactions can be demonstrated by considering a model requiring attachment of a substrate to an enzyme at a minimum of ___ points.
  35. If a D amino acid is incorporated into the normal right-handed alpha helix of a protein, then there will be steric conflicts between the ___ .
    sidechain R group and backbone carbonyl O atom
  36. When describing acid-base equilibria, we speak of the pKa. The "a" stands for
    acid dissociation
  37. The active site of triose phosphate isomerase contains a glutamic acid (Glu) sidechain (HOOC/COO- , pKa=5) and a histidine sidechain (HN+/N:). At pH 7, the glu sidechain initially acts to
    remove an H+ from the substrate
  38. A molecule of the type (HA -> A- and H+) is best able to resist changes in pH due to either incoming H+ or incoming OH- when
    pH = pKa
  39. Buffers are composed of ___
    weak acids or bases
  40. An underwater swimmer holds his breath. CO2 from metabolism builds up in the blood. The [H+] ___ during the swim.
  41. Which of the following can function as either a conjugate acid or a conjugate base in water?
  42. The sidechain of cysteine exists as SH -> S:- plus H+ , with a pKa of 9. The dominant forms at pH 2 and pH 8 are
    SH (pH 2) ; SH (pH 8)
  43. One "equivalent" of NaOH is
    the amount of NaOH needed to fully titrate one functional group
  44. For the reaction HA -> A- + H+, Ka equals
    • Ka = dissociated products/reactants =
    • ([A-]x[H+])/[HA]
  45. One form of the Henderson Hasselbalch equation is (pKa-pH) = log (protonated/deprotonated). True or false : Another form is (pH-pKa) = log (deprotonated/protonated).
  46. The "p" in pH and pKa means
    - log (base 10)
  47. The pH of blood is 7.4, and the pH of stomach gastric juice is 1.4. The blood [H+] is ____ than the gastric juice.
    a million times lower
  48. The titration curve for phosphoric acid exhibits three S-shaped curves. The first midpoint (pKa 2.15) corresponds to the reaction
    H3PO4 <=> H2PO4(-1) + H+
  49. A small pKa means a ___ Ka.
  50. The aqueous solution with the second lowest pH is
    0.1 M formic acid (pKa = 3.75)
  51. In the titration curve for glycine, the simplest amino acid, the structure in the middle of the curve is
  52. The midpoint of a titration curve (reaction HA -> H+ and A-) has HA = A- = 50% of each. This occurs when
    pH = pKa
  53. At pH 4, what are the concentrations of [H+] and [OH-]? 10^-3 M is the notation for 1 mM.
    [H+] = 10^-4 M. [OH-] = 10^-10 M
  54. Bond energies generally are larger for polar bonds than for nonpolar bonds
  55. The bond energy for a C-C bond is 83 kcal/mole, which represents the reaction
    C-C -> 2C
  56. The concentration of water in pure water is
    56 M
  57. When delta-G-nult is positive, K-eq > 1
  58. The H+ gradient is created during aerobic respiration during
    electron transport
  59. The delta in delta-G, delta-H, or delta-S stands for
    product minus reactant
  60. Consider an association reaction A + B -> AB . If water is added to a sample (already at equilibrium) to make everything more dilute, then the
    reaction will shift to the left to approach a new equilibrium.
  61. The reaction giving the melting of the double-stranded DNA double helix into two separate strands is unfavorable at low T (so DNA is a double helix) but is favorable at high temperature (so DNA is melted). Which thermodynamic factor is amplified at higher temperature?
  62. delta-G-actual = delta-G-nult _____ .
    R T ln (products / reactants)
  63. Exothermic reactions always are favorable reactions.
  64. The term which describes a favorable reaction
  65. In a free energy diagram plotting Gibbs free energy (y axis) versus the reaction pathway (x-axis), the more stable form has the ____ value of G.
  66. At the downstream end of the small intestine, at the glucose/Na+ symporter there is a relatively ___ gradient balanced against a relatively ____ gradient.
    smaller unfavorable glucose, larger favorable sodium
  67. The mitochondrial H+ gradient has a relatively ____ [H+] in the interior (matrix) of the mitochondrion.
  68. The prime(') in delta-G-nult-prime means ___
    pH 7
  69. A reaction which is thermodynamically dominated by a decrease in the randomization of locations of atoms (namely they are becoming more organized) is dominated by
    an unfavorable entropy effect
  70. Negative delta-G, negative delta-H, and negative delta-S are
    either of the above, depending on the quantity (G, H, or S)
  71. For the reaction heat + N2O5 (solid) -> 2 NO2 (gas) + 1/2 O2 (gas), one expects delta-S to be
    favorable and positive
  72. The least stable bond in the list below is
  73. The number of residues per repeating pattern of backbone structure for the alpha helix is ___ .
  74. In the NH....O=C hydrogen bonds in proteins, the carbonyl group has a partially negative ___ and a partially positive ___
    partially negative O, partially positive C
  75. A bile salt is ___ .
  76. An example of a biological detergent is a molecule of
    bile salt
  77. The average translational kinetic energy (1/2 mv^2) of water molecules at room temperature is about ___ .
    1 kcal/mole
  78. Consider proteins contributing to the outer coating of a virus particle. The ionized protein sidechains facing the interior of the particle usually are negative
  79. Protein helices have 3.6 residues per turn. A surface helix having one side facing water and one side facing the rest of the protein would have the following alternating pattern of polar (O) and nonpolar (X) residues.
    X O O X X O O X O O
  80. The sickle cell hemoglobin mutation changes a nonpolar residue (normal type) to a polar residue (disease type).
  81. When comparing molecules with similar molecular weights, examples of polar molecules will generally exhibit higher boiling points than nonpolar molecules.
  82. A detergent is a chemical that has two sides (or ends) with opposite properties :
    nonpolar vs. polar
  83. The energy required to break C-H bonds is about
    100 kcal/mole
  84. The energy required to break a mole of hydrogen bonds is about
    2 to 5 kcal
  85. A molecule of water in ice contributes ___ H-bond donors and ___ H-bond acceptors to the crystal structure.
    2 donor sites and 2 acceptor sites
  86. Aggregation of nonpolar molecules is thermodynamically driven by effects on solvent molecules, whose lattice network around exposed nonpolar surfaces is disrupted when those surfaces aggregate. The dominant effects therefore are a(an) ____ effect and a(an) ___ effect.
    favorable entropy ... unfavorable enthalpy
  87. The more soluble form of a molecule containing one OH vs O-, or one NH+ vs N:, is the ____ form.
  88. An organic molecule contains a titratable sulfhydryl (SH) group with a pKa = 10. Among the choices below, the best condition for achieving maximum solubility is
    pH 11
  89. An individual molecule of water in an ice-crystal will be hydrogen-bonded to ___ other water molecules.
  90. Three atoms with similar electronegativities are
    H, C, and S
  91. The water molecules in the vicinity of an exposed nonpolar group are ___ the water molecules in the rest of the solvent.
    more organized than
  92. The dissociation of AB into A + B is a bimolecular step because both the products and the reactant involve two species (A and B).
  93. For a unimolecular reaction A <=> B, a catalyst
    reduces the time it takes to approach equilibrium
  94. For all reactions of the type A <=> B, at equilibrium
    delta-G-actual = 0
  95. For the dissociation reaction AB <=> A + B, the equilibrium constant K-dissoc equals
    k-dissoc / k-assoc
  96. If a potential reaction such as A <=> B doesn't exhibit any measureable net changes over several hours, then it must have started out at equilibrium
  97. K-equilibrium for the reaction A->B is ___ .
    independent of the activation energy from A to the transition state
  98. The probability that a single molecule will undergo a chemical reaction to a different form is most closely related to a(an)
    rate constant
  99. A reaction which rapidly approaches equilibrium
    has a low activation energy (low transition state barrier)
  100. For the reaction A + B -> AB having K-assoc = 0.2 M^-1, K-dissoc = ___ .
    5 M
  101. T can be positive or negative, depending upon whether you are above or below the freezing point of water.
  102. The slope of a plot of concentration (Y axis) vs time (X axis) is most closely related to a(an)
  103. You start with 27000 radioactive atoms. After 3 half-lives, the number of remaining atoms will be
    3375 = 27000 / 8
  104. For the reaction A <=> B, if tau(of A) is smaller than tau(of B), then G(of A) is ___ than G(of B).
  105. For a molecular reaction A + B -> complex, if you are an individual molecule of A, the amount of time you must wait to undergo a reaction is
    inversely proportional to both k-assoc and [B]
  106. The units of k-assoc (for a reaction A + B -> AB) are
    (events/sec) M^-1
  107. The aromatic form of NAD is NADH, not NAD+.
  108. An example of a favorable biological reduction half reaction is
    1/2 O2 and 2H+ and 2e- -> H2O
  109. A favorable reaction has a negative delta-G or a negative delta-E.
  110. Biological oxidation-reduction reactions always involve ___ .
    transfer of electrons
  111. In the mnemonic (memory trick) that is OIL RIG, the letter L stands for
  112. A molecule which loses electrons is becoming
  113. During conversion of an aldehyde to COOH by the following reaction (aldehyde + 1/2 O2 -> COOH), electrons are moving
    from (C and H) to the new incoming O
  114. For the reaction aldehyde -> alcohol, the more oxidized state is the aldehyde.
  115. A compound with a positive reduction potential is a better ___ than compounds with negative reduction potentials.
  116. The reductant is the molecule which is being reduced by something else.
  117. For the reaction (1/2 O2 plus 2 H+ plus 2e- -> H2O), oxygen itself is becoming ___, and therefore is the ___ .
    (becoming) reduced ; oxidant
  118. A high reduction potential corresponds to a tendency to
    acquire electrons and become reduced
  119. The reduction potential of a compound is measured in