Stony Brook University

• BIO 361

BIO 361 Exam 1, Summer 2020 Exam Answer Key An annotated version with answer explanations will be available in the next few days 1. You have observed that many of your colleagues who are studying enzymes keep them in an ice bucket, rather than at room temperature. You have just discovered that the enzyme you are studying appears to unfold when chilled, but it remains active at room temperature or somewhat above. An explanation for your observation could be: a. the deltaH for unfolding of this enzyme is so positive that the unfolding process proceeds spontaneously even at ice temperatures. b. the deltaH for unfolding of this enzyme is so negative that unfolding proceeds spontaneously at cold temperatures even though the value of deltaS for unfolding of enzymes is generally zero. c. the deltaS for unfolding of this enzyme is so intrinsically temperature dependent that, regardless of the temperature, it predicts that the enzyme will unfold spontaneously. *d. the deltaH for unfolding is negative, but the deltaS for unfolding is also negative and the overall Gibbs free energy change will be dominated by the contribution of deltaH at low temperatures and by the contribution of deltaS at high temperatures. e. this observation cannot be explained by thermodynamic parameters – it must reflect kinetic parameters. 2. You have measured the temperature dependence of the equilibrium between reactants and products in a biochemical reaction. In a van’t Hoff plot: a. the x-intercept gives you an idea of the sign of deltaS *b. the sign of the y-intercept alone may give you an idea of whether the change in entropy is positive or negative. c. the slope gives you an idea of whether the change in entropy is positive or negative d. the value of deltaH can be obtained, but not the value of deltaS e. if the line that best fits the data does not cross any point on the y-axis, then the change in enthalpy for the reaction must cancel out the change in entropy. 3. You are trying to account for the apparent conflict between the observations that addition of either sodium dodecyl sulfate (SDS) or urea results in the unfolding of the protein you are studying but there is only evidence for a molecular interaction between SDS and the protein: a. Part of the explanation is related to the fact that SDS stabilizes the protein in a hairpin shape covered with dodecyl sulfate molecules; but, urea stabilizes the protein in a globular shape with a water shell covered with urea molecules b. Part of the explanation is that hydrogen bonds form between water molecules and SDS molecules; but, hydrogen bonds form only between water and protein molecules. *c. Part of the explanation is that urea dilutes selectively, and thereby destabilizes, the ordered phase of hydrogen bonded water even when hydrophobic side chains of a protein are exposed to the water, while dodecyl sulfate molecules on a protein surface cause water molecules to have the positive ends of their dipoles pointed to the dodecyl sulfate anions. d. Part of the explanation is that dodecyl sulfate oligomers coat the protein surface as aggregates while urea molecules are too small to be detected when they coat the protein surface as hydrogen-bonded shells. e. Addition of urea solubilizes the protein in its native state whereas addition of SDS solubilizes the unfolded state of the prot