Bio chem #2

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Bio chem #2
2012-06-11 22:44:25

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  1. Bond energies generally are larger for ______ bonds than for _______ bonds.
    • polar
    • nonpolar
  2. The bond energy for a C-C bond is 83 kcal/mole, which represents the reaction...
    C-C -> 2C
  3. The concentration of water in pure water is
    56 M
  4. When delta-G-nult is positive, K-eq ___ 1. ?
    <1 (Positive delta-G = uphill = unfav. The product is not favored, so products/reactants = small/large = <1.)
  5. The H+ gradient is created during aerobic respiration during
    electron transport
  6. The delta in delta-G, delta-H, or delta-S stands for
    product minus reactant
  7. 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.
  8. 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?
    delta-S (Delta-G = delta H - (T x delta S), so T amplifies delta-S.)
  9. delta-G-actual = delta-G-nult _____
    • + R T ln (products / reactants)
    • (At equilibrium, actual delta-G = 0. The equation then rearranges to delta-G-nult = -RT lnK.)
  10. Exothermic reactions always are favorable reactions. T or F?

    (Delta-G describes whether a reaction is favorable. It is a function of the combination of both enthalpy and entropy effects. A small favorable exothermic enthalpy effect can be overwhelmed by a large unfavorable entropy effect.)
  11. The term which describes a favorable reaction...

    (Exergonic describes negative delta-G overall. Exothermic heat release = a favorable factor, but one also must consider entropy.)
  12. 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.
    • lower
    • (Reactions run downhill to the most stable form (lowest G). The transition state at the top of the plot is the hardest point to reach.)
  13. 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
  14. The mitochondrial H+ gradient has a relatively ____ [H+] in the interior (matrix) of the mitochondrion.
  15. The prime(') in delta-G-nult-prime means ___ .
    pH 7
  16. 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
  17. Negative delta-G, negative delta-H, and negative delta-S are favorable or unfavorable?
    either of the above, depending on the quantity (G, H, or S)
  18. For the reaction heat + N2O5 (solid) -> 2 NO2 (gas) + 1/2 O2 (gas), one expects delta-S to be...
    • favorable and positive
    • (Molecules in a gas are less organized than molecules in a solid. This is favorable entropically. Increase in scrambledness = gained S in product = positive delta-S)
  19. The least stable bond in the list below is
    (C-H, O-H, O=O, C=O)
  20. The number of residues per repeating pattern of backbone structure for the alpha helix is ___ .
  21. 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
  22. A bile salt is ___
    (amphipathic, hydrophilic, hydrophobic)
    • amphipathic
    • (Bile salts are detergents. Their nonpolar surface binds to greasy nonpolar fats in food, and their polar surface favorably interacts with the aqueous solvent. This emulsifies ingested fats, converting them into small bile-coated spheres.)
  23. An example of a biological detergent is a molecule of
    bile salt
  24. The average translational kinetic energy (1/2 mv^2) of water molecules at room temperature is about ___ .
    1 kcal/mole
  25. Consider proteins contributing to the outer coating of a virus particle. The ionized protein sidechains facing the interior of the particle usually are negative. (T or F)
    • False
    • (The interior of the particle contains the genetic information molecules. The virus particle design has a favorable arrangement of charges. The
    • negative phosphate groups of the RNA or DNA genetic information inside the virus particle are stabilized by complementary positive charges on protein groups in contact with the nucleic acids.)
  26. 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
    • (You need the polar stretches to be about 3.5 residues apart (and the nonpolar stretches to be bout 3.5 residues apart), so two different polar patches will be on the same side of the folded helix facing water.)
  27. The sickle cell hemoglobin mutation changes a nonpolar residue (normal type) to a polar residue (disease type). (true or False)
    • False
    • (Exposed nonpolar surfaces in the mutant induce hemoglobin molecules to aggregate into long fibers, causing red blood cells to elongate into a fragile sickle shape.)
  28. When comparing molecules with similar molecular weights, examples of polar molecules will generally exhibit higher boiling points than nonpolar molecules.
    (True or false)
    • True
    • (Polar groups attract each other and hold molecules together in the liquid form, inhibiting their release as separated gas molecules.)
  29. A detergent is a chemical that has two sides (or ends) with opposite properties :
    nonpolar vs. polar
  30. The energy required to break C-H bonds is about....
    100 kcal/mole
  31. The energy required to break a mole of hydrogen bonds is about....
    2 to 5 kcal
  32. 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
    • (The 2 H's in H2O are both donors, and the 2 lone electron pairs on oxygen are both acceptors.)
  33. 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) ____ entropy effect and a(an) ___ enthalpyeffect.
    favorable entropy ... unfavorable enthalpy
  34. The more soluble form of a molecule containing one OH vs O-, or one NH+ vs N:, is the ____ form.
  35. 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
  36. An individual molecule of water in an ice-crystal will be hydrogen-bonded to ___ other water molecules.
  37. Three atoms with similar electronegativities are
    H, C, and S
  38. The water molecules in the vicinity of an exposed nonpolar group are ___ the water molecules in the rest of the solvent.
    more organized than
  39. The dissociation of AB into A + B is a bimolecular step because both the products and the reactant involve two species (A and B).
    • false
    • (Only collision steps (associations) are bimolecular. AB is a single entity, a complex, "making up its own mind" to break apart.)
  40. For a unimolecular reaction A <=> B, a catalyst..
    reduces the time it takes to approach equilibrium.
  41. For all reactions of the type A <=> B, at equilibrium,
    delta-G-actual = 0
  42. For the dissociation reaction AB <=> A + B, the equilibrium constant K-dissoc equals
    k-dissoc / k-assoc
  43. 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. (true or false)
    • False
    • (A reaction might have a very high activation energy (high transition state barrier). If it is 30 kcal/mole at room temperature, it would take 40 years to approach equilibrium, so you probably would not wait long
    • enough to see any noticeable net changes in concentrations.)
  44. K-equilibrium for the reaction A->B is independent of ___ .
    the activation energy from A to the transition state
  45. The probability that a single molecule will undergo a chemical reaction to a different form is most closely related to a(an)
    rate constant
  46. A reaction which rapidly approaches equilibrium has a low....
    activation energy (low transition state barrier)
  47. For the reaction A + B -> AB having K-assoc = 0.2 M^-1, K-dissoc = ___ .
    • 5 M
    • (K-dissoc = (1/K-assoc). You must invert both the number and the units.)
  48. T can be positive or negative, depending upon whether you are above or below the freezing point of water. (true or false)
    • False
    • (T is in degrees Kelvin : always positive, above absolute zero.)
  49. The slope of a plot of concentration (Y axis) vs time (X axis) is most closely related to a(an)
  50. You start with 27000 radioactive atoms. After 3 half-lives, the number of remaining atoms will be...
    3375 = 27000 / 8
  51. For the reaction A <=> B, if tau(of A) is smaller than tau(of B), then G(of A) is ___ than G(of B).
    • higher
    • (A shorter lifetime for A means it is less stable, so it is more uphill (higher G) than B.)
  52. 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...
    to both k-assoc and [B]
  53. The units of k-assoc (for a reaction A + B -> AB) are
    (events/sec) M^-1
  54. The aromatic form of NAD is NADH, not NAD+ (true or false)
    • False
    • (NAD+ has N+ which has 4 electrons like carbon = benzene-like ring. Conversion of high energy NADH to resonance-stabilized NAD+ is favorable
    • and releases a lot of energy.)
  55. An example of a favorable biological reduction half reaction is..
    1/2 O2 and 2H+ and 2e- -> H2O
  56. A favorable reaction has a negative delta-G or a negative delta-E. (true or false)
    • false
    • (A favorable reaction has a negative delta-G or a positive delta-E. The signs are opposite.)
  57. iological oxidation-reduction reactions always involve ___ .
    transfer of electrons
  58. In the mnemonic (memory trick) that is OIL RIG, the letter L stands for
  59. A molecule which loses electrons is becoming
  60. 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
  61. For the reaction aldehyde -> alcohol, the more oxidized state is the aldehyde. (t or f)
    • true
    • (The aldehyde HC=O plus 2H -> alcohol CH2OH. The alcohol has gained the electrons in the 2 incoming H, as well as their nuclei. Thus the alcohol is more reduced, since gain of electrons is reduction.)
  62. A compound with a positive reduction potential is a better ___ than compounds with negative reduction potentials.
  63. The reductant is the molecule which is being reduced by something else. (true or false)
    • false
    • (reductANT = reducing AgeNT = reducing something else : being oxidized itself.)
  64. For the reaction (1/2 O2 plus 2 H+ plus 2e- -> H2O), oxygen itself is becoming ___, and therefore is the ___ .
    (becoming) reduced ; oxidant
  65. A high reduction potential corresponds to a tendency to..
    acquire electrons and become reduced
  66. The reduction potential of a compound is measured in
  67. The first carbon in the sidechain of amino acids, which is the carbon connected to the backbone, is at the ___ position.
  68. The sulfur-containing amino acid which is capable of making disulfide bridges is
  69. The only amino acid with a sidechain pKa of 7.0 (when incorporated into a protein chain) is
  70. The amino acid with the greatest number of sidechain nitrogens is
  71. In the list below, the tripeptide which contains the most sulfur atoms is
  72. In the diagram -CHR-NH-CO-CHR-NH-CO- the sequence runs left to right. (true or false)
    • False
    • (Boxing off one amino acid (with CHR in the middle) gives -CHR-NH-[CO-CHR-NH]-CO- . Within this box, the sequence from the amino end to carbonyl end [ <- CO-CHR-NH <- ] is right to left. )
  73. Immunoglobulins have multiple chains joined together by disulfides made after translation. There are __heavy chains and ___ light chains
    • 2 heavy chains and 2 light chains
    • (The four chains give two antigen binding sites, each comprised of the variable regions of one H chain and one L chain.)
  74. The peptide alanyl-glycyl-asparagine contains three amino acids, two backbone amide (peptide) bonds, and one amide sidechain group (in asparagine). It therefore is a
  75. Proteins which are made in biological cells are synthesized ___ .
    starting from the amino-terminal end
  76. One of the hydrophobicity scales is based on the delta-G for transfer of an amino acid from water to octanol. In this scale, phenylalanine is assigned a negative value. (true or false)
  77. If you cut a soluble cytoplasmic protein in half (like a grapefruit) and view the cross-section, a type of amino acid which is found both buried on the inside and also equally often exposed to water on the outside is ___ .
  78. The amino acid lacking a backbone NH hydrogen when it is incorporated in a protein chain is
  79. ____ is a molecule containing a long flexible carbon chain with several C=C bonds which is added to some proteins as a membrane anchor.
  80. Two amino acids which are negatively charged at pH 7 are
    asp and glu
  81. The class of amino acids which may be phosphorylated is
    alcohols (ser, thr, and tyr)
  82. The amino acid with the most restricted rotation at the bond between the backbone N atom and the backbone alpha carbon is
  83. Thyroxine is a hormone containing benzene rings to which O's and iodines are attached. It is made from
    tyrosine in the thyroid gland.
  84. Protein phosphorylation, disulfide formation, and zymogen activation are called ____ modifications.
  85. The amino acid with the strongest absorbance in the near UV region (240 to 300 nm) is...
    • tryptophan at 280 nm
    • (Tyrosine has the second highest absorbance in this region, also near 280 nm.)
  86. An example of a zymogen is
    • chymotrypsinogen
    • (and trypsinogen)
  87. The evolutionary origin of the Bowman-Birk protease inhibitor, which exhibits internal homology, is most likely the consequence of gene duplication and ___ .
    loss of a stop codon
  88. The Bowman-Burk double-headed protease inhibitor binds
    one trypsin and one chymotrypsin
  89. Which of the following pairs of amino acids would constitute conservative substitutions?
    asp vs glu
  90. Edman degradation processes a protein by cutting off one amino acid at a time, starting from the C-terminal end. (true or false)
    • false
    • (Residue 1 (the protein's N-terminus) is the first residue removed.)
  91. The phrase "______ homology" describes the case of a single protein chain containing two genetically related segments within itself.
  92. Residues 70-79 in cytochrome c form a long stretch that is invariant (nomutations) in 35 different species of animals and plants. That sequence occurs on the outside surface of functional cytochrome c. It's primary purpose probably is to ___ .
    bind another protein in the electron transport chain
  93. Cytochrome c's heme group contains an iron (like the iron in the heme of hemoglobin). That Fe atom undergoes oxidation/reduction (Fe+2 vs Fe+3). Cytochrome c is part of the ___ pathway in metabolism.
    electron transport
  94. The cytochrome c sequence from the giant grey swimming killer whale is most likely to resemble the sequence from the...
    small brown friendly dog
  95. An example of a strong nucleophile is a
    deprotonated serine O:-
  96. A 25-residue protein is digested by trypsin. After all possible cleavages occur, there are three fragments 1-10, 11-15, and 16-25. Lys or arg must be found at...
    10 or 15, and may be found at 25
  97. In cytochrome c, a type of site with a high mutation frequency is a
    polar surface residue not involved in interactions with other cell components
  98. Chymotrypsin cleaves at the ______ side of large nonpolar residues