Final Review Questions

1. 1For a system at equilibrium, Gibbs free energy is maximized.

   1. ATrue
   2. BFalse
2. 2The work done by biological systems is most commonly which type of work?

   1. APressure
   2. BChemical
   3. CHome
   4. DVolume
   5. EHeat
3. 3According to Le Châtelier’s principle:

   1. AA reaction always favors the formation of as much
      product as possible
   2. BReactants will only react upon the addition of
      external heat or pressure.
   3. CThe system will adjust, if more reactants are
      added, and a new equilibrium will be established to
      balance the change.
   4. DThe Gibbs free energy is always greater than the
      amount of work done plus the Helmholtz free energy
4. 4The value of ∆Go for elemental oxygen is:

   1. A–15 kJ•mol–1.
   2. B0 kJ•mol–1.
   3. CMuch larger than the free energy of elemental
      hydrogen and much less than the free energy of
      elemental uranium.
   4. DEqual to the free energy of elemental tungsten.
   5. EBoth b and d.
5. 5The cell generates ATP from ADP and Pi by coupling the
   synthesis to an energetically unfavorable process.

   1. ATrue
   2. BFalse
6. 6At equilibrium:

   1. AThere is no change in temperature over time
   2. BThe free energy of the system is minimized.
   3. CThe combined entropy of the system and
      surroundings is maximized.
   4. DOnly b and c
   5. Ea, b, and c
7. 7Gibbs free energy is used to describe systems
   with constant [blank_start]pressure and temperature[blank_end], while Helmholtz free
   energy is used to describe systems with constant [blank_start]volume and temperature[blank_end].

   1. Apressure and temperature
   2. Bvolume and temperature
8. 8The standard state has a pressure of [blank_start]1 atm[blank_end].

   1. A1 atm
9. 9The change in free energy of a process is equal to the
   [blank_start]maximum[blank_end] amount of work extracted from that
   process

   1. Amaximum
10. 10In biochemistry, the standard state for water is [blank_start]55[blank_end] M.
    Excepting H+, for all other solutions, the standard state
    is [blank_start]1[blank_end] M.

    1. A55
    2. B1

11. 11Molecules move spontaneously from regions of low
    chemical potential to regions of high concentration.

    1. ATrue
    2. BFalse
12. 12The difference in chemical potential for a region
    with 500 mM of molecule B and a region with 1 M of
    molecule B is equal to:

    1. AkBT ln(0.5)
    2. B0
    3. C1
    4. DkBT ln(500)
    5. EkBT ln(1)
13. 13The proton concentration in pure water at standard
    state (298 K) is:

    1. Aequal to 14
    2. Balways less than –7
    3. Cthe square root of the ion product
    4. D10^7
    5. E81 kJ•mol–1
14. 14The melting temperature (TM) is the temperature at
    which 100% of the protein molecules are unfolded.

    1. ATrue
    2. BFalse
15. 15Which of the following must be independent of
    temperature when properly applying the van’t Hoff
    equation?

    1. AKeq
    2. B∆So
    3. C1/T
    4. DpH
16. 16The pKa of a protein sidechain depends only on
    the chemical identity of the sidechain, not on the
    surrounding environment.

    1. ATrue
    2. BFalse
17. 17During protein folding, the entropy of water:

    1. Aincreases
    2. Bdecreases
    3. Cis equal to the protein entropy change
    4. Dis zero
18. 18A region with a high chemical potential for molecule A
    has a [blank_start]greater/higher[blank_end] concentration of molecule A than a region
    with low chemical potential.

    1. Agreater/higher
19. 19To make a buffer, add a weak acid to its conjugate [blank_start]base[blank_end].

    1. Abase
20. 20The integral of the melting curve of heat capacity versus
    temperature yields the [blank_start]enthalpy[blank_end] change of protein
    unfolding

    1. Aenthalpy
21. 21The [blank_start]free energy[blank_end] change for a reaction determines
    the direction of spontaneous change.

    1. Afree energy
22. 22An oxidative half-reaction involves the release of
    electrons from a molecule.

    1. ATrue
    2. BFalse
23. 23Which of the following is a common consequence of a
    protein coordinating a metal:

    1. AThe free energy of the reduced and oxidized form
       of the metal are altered.
    2. BThe metal is protected from some chemical
       reactions
    3. CThe protein undergoes a conformational change
    4. DIt enables the transfer of electrons over long
       distances
    5. EAll of the above.
24. 24Standard reduction potentials in biochemistry
    correspond to solutions with [H+] = 1 M.

    1. ATrue
    2. BFalse
25. 25Which of the following conformational changes is not
    thought to occur as a K+ channel closes due to a voltage
    change:

    1. AHelix S6 becomes straighter
    2. BHelix S4 moves downward
    3. CCharged residues on helix S4 form new interactions
    4. DThe selectivity filter changes size
    5. EThe C-terminus of helix S4 forms a 3/10 helix
26. 26Most ion channels have little selectivity because ions
    are small relative to the size of the channel pore.

    1. ATrue
    2. BFalse
27. 27Which feature allows mitochondria and chloroplasts,
    unique from other organelles, to maintain large proton
    gradients:

    1. AThey contain membrane spanning proteins
    2. BThey have a second internal membrane
    3. CThere are only one of each per cell
    4. DTheir membranes consists of a lipid bilayer
28. 28Which of the following statements about the passive
    spread of a voltage perturbation in a neuron are true:

    1. AThe voltage spike is not regenerated
    2. BThe potassium conductance of the membrane
       changes locally
    3. CThe sodium conductance of the membrane remains
       constant.
    4. DIt only occurs in non-myelinated axons
29. 29The oxidized and reduced forms of a molecule are
    known as a [blank_start]redox couple[blank_end].

    1. Aredox couple
30. 30The energy from [blank_start]light[blank_end] is used to produce reduced
    compounds in photosynthesis.

    1. Alight
31. 31Sodium and potassium pumps hydrolyze [blank_start]ATP[blank_end] to
    move ions in and out of the cell.

    1. AATP
32. 32By decreasing the capacitance of the surface of the
    axon, [blank_start]myelination[blank_end] greatly facilitates the transmission
    of action potentials.

    1. Amyelination
33. 33A [blank_start]capacitor[blank_end] can build up charge on two
    conducting surfaces with an insulator sandwiched
    between them.

    1. Acapacitor
34. 34Which of the following is not a process governed by
    molecular recognition?

    1. AThe fidelity of DNA replication
    2. BPassive diffusion
    3. CActive transport.
    4. DTranslation by the ribosome
    5. ETranscription by RNA polymerase.
35. 35Noncovalent interactions, such as ionic and hydrophobic
    interactions, are generally much weaker than covalent
    interactions.

    1. ATrue
    2. BFalse
36. 36A protein binds to the DNA sequence AAAAA with a
    10-nM affinity (that is, the value of the dissociation
    constant is 10 nM). The same protein binds to the RNA
    sequence AUAAUA with a 15-nM affinity and to a lipid
    with a 10-mM affinity. Which of the following statements
    is true:

    1. AThe protein binds to RNA and DNA with high
       affinity, but low specificity
    2. BThe protein has high specificity for lipids over RNA
       and DNA
    3. CThe protein binds with low affinity for RNA and
       DNA, but high specificity
    4. DThe protein binds with low affinity and low
       specificity, for all three targets
37. 37The value of KD corresponds to:

    1. AThe reciprocal of KA
    2. BThe concentration of ligand at half saturation of
       receptor
    3. Ce^[(deltaG)/(RT)]
    4. D[P][L]/[P•L]
    5. EAll of the above
38. 38A linear ligand binding curve indicates a simple binding
    equilibrium, whereas a hyperbolic binding curve
    indicates that the system contains a receptor that
    is allosteric or contains multiple binding sites with
    different affinities.

    1. ATrue
    2. BFalse
39. 39Some inhibitors of HIV reverse transcriptase are
    nucleotide analogs that displace the natural nucleotide
    substrates in the active site.

    1. ATrue
    2. BFalse
40. 40Which of the following would lead to a decrease in
    binding affinity?

    1. AReleasing more protein-bound water molecules
       upon binding.
    2. BDecreasing the number of rotational degrees of
       freedom of the ligand upon binding
    3. CAdding more hydrophobic interactions to the
       ligand–protein interface.
    4. DIncreasing the number of hydrogen bonds between
       the ligand and protein.
41. 41A [blank_start]ligand[blank_end] is a small molecule that binds to a
    macromolecule receptor

    1. Aligand
42. 42In general, higher affinity is achieved by increasing the
    [blank_start]hydrophobicity[blank_end] of a ligand, while increasing specificity relies
    on increasing [blank_start]hydrogen bonds[blank_end].

    1. Ahydrophobicity
    2. Bhydrogen bonds
43. 43Because they bind to the same site as ATP, many kinase
    inhibitors are [blank_start]competitive[blank_end] with respect to ATP

    1. Acompetitive
44. 44The affinity of a macromolecular interaction reflects the
    strength of an interaction for one receptor relative to all
    other possible receptors.

    1. ATrue
    2. BFalse
45. 45Which of the following is an attribute of the FGF–FGFR
    family of interactions?

    1. AEach FGF ligand has high specificity for an FGF
       receptor
    2. BBecause there are 18 FGF and 4 FGFR genes, there
       are 72 potential interactions
    3. CSignaling specificity is enhanced through
       selective expression of only a few receptors per
       tissue type
    4. DFGFRs are soluble serine/threonine kinases.
    5. EFGF proteins have highly diverse folds.
46. 46Specificity depends on the concentration of ligand,
    whereas affinity is independent of ligand concentration.

    1. ATrue
    2. BFalse
47. 47Which of the following statements regarding interfacial
    waters is true?

    1. AThey contribute favorably to the entropy of protein–
       protein recognition
    2. BThey help to optimize the packing at the
       contact surface
    3. CThey contribute only to affinity, but not to the
       specificity of protein–protein recognition.
    4. DThere are typically fewer water-mediated hydrogen
       bonds than direct hydrogen bonds at protein–protein
       interfaces.
48. 48Interface residues that do not contribute greatly to
    binding affinity are also generally unimportant for
    specificity.

    1. ATrue
    2. BFalse
49. 49Proteins distinguish double-helical RNA and DNA by
    differences in [blank_start]groove[blank_end] shape

    1. Agroove
50. 50Which of the following can result in an allosteric
    modulation of activity?

    1. ACovalent modification such as phosphorylation or
       acetylation
    2. BOligomerization
    3. CBinding of a ligand
    4. DStabilizing an alternative conformation
    5. EAll of the above.
51. 51The transcription of a gene is controlled by a
    transcription factor binding either glucose or lactose.
    When there is 0.2 mM of either glucose or lactose in
    the cell, the gene is transcribed at about 10% of the
    maximum. When there is more than 2 mM glucose in
    the cell, the gene is fully induced. However, when there
    is 2 mM lactose in the cell, the amount of transcription
    is approximately half of the maximum. At 40 mM of
    either glucose or lactose in the cell, the gene is fully
    induced. The transcriptional regulation is likely:

    1. AUltrasensitive with respect to both glucose and
       lactose.
    2. BUltrasensitive with respect to lactose but not
       glucose
    3. CGraded with respect to glucose
    4. DUltrasensitive with respect to glucose but not
       lactose
    5. EHyperbolic with respect to glucose but not lactose
52. 52In allosteric proteins, ligand binding can only result in
    positive cooperativity

    1. ATrue
    2. BFalse
53. 53Which of the following is not a known allosteric effector
    of hemoglobin?

    1. Aoxygen
    2. Bbisphosphoglycerate
    3. Clow pH
    4. Dmyoglobin
    5. ECO2
54. 54Bacterial chemotaxis involves only random, Brownian
    movement.

    1. ATrue
    2. BFalse
55. 55Which of the following statements about the Hill
    coefficient are true?

    1. AIt is the steepness of the log-log binding isotherm
       at the half saturation point.
    2. BAllosteric systems have a Hill coefficient of exactly 1
    3. CThe maximum value for a dimeric protein is 2
56. 56Oxygen biases the equilibrium of hemoglobin towards
    the [blank_start]R[blank_end] state

    1. AR

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Bachelors BME 221 Quiz on Final Review Questions, created by Scott Laorr on 24/04/2016.

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