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Harper Usiskin

Harper U.

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Books Assigned

Molecular Driving Forces

Molecular Driving Forces

K.Dill and… 2nd Edition
Achievement 1,978 solutions
The Molecules of Life: Physical and Chemical Principles

The Molecules of Life: Physical and…

John Kuriyan,… 1st Edition
Achievement 1,268 solutions

Viewed Questions

Binding of insulin to its receptor. Figure $27.19$ shows the binding of insulin to the insulin receptor in a detergent solution. Use the Langmuir model to estimate the binding constant.

Molecular Driving Forces

The table below lists initial velocities measured for an enzymatic reaction at different substrate concentrations in the presence and absence of an inhibitor. The enzyme concentration is identical in both reactions. a. Graph a Lineweaver-Burk plot. b. What are the apparent values of $V_{\max }$ and $K_{\mathrm{M}}$ for each experiment? c. What is the inhibition mechanism? d. If the concentration of inhibitor is $0.5 \mathrm{mM}$, what is the value of $K_{1}$ ?

The Molecules of Life: Physical and Chemical Principles

Stable states. For the energy function $V(\theta)=\cos \theta$ for $0 \leq \theta \leq 2 \pi$, find the values $\theta=\theta_{s}$ that identify stable equilibria, and the values $\theta=\theta_{u}$ that identify unstable equilibria.

Molecular Driving Forces

Questions asked

INSTANT ANSWER

UNDERSTANDING PROTEIN STABILITY CURVES (5 pts) Which of the following expressions correctly describes the curvature of the protein stability curve for a 2-state protein folding equilibrium process occurring at very high, constant pressure (ca. 6,000 atm)? Note that all the thermodynamic quantities below refer to the ‘folding’ process. In your homework sheet, provide an answer to this question by simply writing a, b, c, d or e. (a)o p o S T G −=        (b)o p o S T G +=        (c)T C T G p p o  −=        2 2 (d)T C T G p p o  +=        2 2 (e)T C T G p p o  +=        2 2 /1

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INSTANT ANSWER

DETERMINING HEAT CAPACITY CHANGES UPON PROTEIN UNFOLDING: DIFFERENTIAL SCANNING CALORIMETRY (DSC). (3 + 2 = 5 pts) a. Draw the complete DSC plot (Cp vs T) for the equilibrium unfolding of a protein that is sufficiently unstable so that both its cold- and heat-induced unfolding transitions can be observed in liquid solution by DSC. Be sure to draw lines, curves and areas with a biologically meaningful sign, based on what you know about protein folding and unfolding at equilibrium. Label Tm, Tm’, Cp,heat-unfolding and Cp,cold-unfolding on the plot. b. Draw the DSC profile for the order-disorder transition of a nonpolar lipid with Cp = 0.

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INSTANT ANSWER

TYING IT ALL UP! (1 + 1 + 1 + 1 + 1= 5 pts) Provide short answers to the following questions: a. In summary, does the hydrophobic effect stabilize or destabilize the protein native state in aqueous solution? Be sure to provide a conceptual justification for your answer. b. What do you predict will happen if you dissolve a protein in a nonpolar organic solvent (e.g., hexane) at room temperature? c. Draw a qualitative low-resolution sketch of a biological membrane, i.e., a nonpolar lipid bilayer, with polar surfaces on both ends. Now, draw a low-resolution sketch the desired basic characteristics of the native state of an integral membrane protein embedded within a lipid bilayer with some residues facing both edges of the bilayer. Assume the lipid bilayer containing the protein to be suspended in aqueous solution. Draw the protein as an oval and show the location of the majority of the polar and nonpolar amino acid side chains. d. HEPES is a well-known nonpolar buffer that is sometimes used in protein chemistry. Do you predict that this nonpolar buffer tends to stabilize or destabilize proteins, and why? e. Imagine that your best friend is a theoretical chemist able to computationally determine the partition function (QTPN) for the folded and unfolded states of protein-X at any temperature in the isothermal-isobaric ensemble. Based on the knowledge you have accumulated in this class, how would you help your friend predict the thermodynamic stability of protein-X at any temperature at P = 1 bar? TIP: no numerical calculations are required to answer this question. Just help your friend determine the folding free energyUN o G from partition functions.

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INSTANT ANSWER

DENATURING AGENTS: HOW TO SHIFT THE PROTEIN UNFOLDING EQUILIBRIUM TO THE RIGHT (5 pts) Which of the following statements about the equilibrium “m” value, for the unfolding of a biomolecule in the presence of a denaturing agent, is FALSE? In your homework sheet, provide an answer to this question by simply writing a, b, c, d or e. (a) The absolute value of the “m” value is proportional to the amount of solvent-accessible surface is very different from the conformation of the heat-unfolded  repressor. (c) Cold unfolding has a Cp of zero. (d) Cold-unfolding is characterized by a negative H0 and S0. It is likely that the value of S0 is negative mostly due to the reduced dynamics of the waters surrounding the cold-unfolded protein. (e) Cold unfolding has a negative Cp. 6. DETERMINING HEAT CAPACITY CHANGES UPON PROTEIN UNFOLDING: DIFFERENTIAL SCANNING CALORIMETRY (DSC). (3 + 2 = 5 pts) a. Draw the complete DSC plot (Cp vs T) for the equilibrium unfolding of a protein that is sufficiently unstable so that both its cold- and heat-induced unfolding transitions can be observed in liquid solution by DSC. Be sure to draw lines, curves and areas with a biologically meaningful sign, based on what you know about protein folding and unfolding at equilibrium. Label Tm, Tm’, Cp,heat-unfolding and Cp,cold-unfolding on the plot. b. Draw the DSC profile for the order-disorder transition of a nonpolar lipid with Cp = 0. - 3 - area that becomes exposed, upon denaturant-induced protein unfolding. (b) Proteins with a large and negative “m” value unfold easily in the presence of a denaturing agent. (c) At the midpoint of a denaturant-induced equilibrium unfolding curve the “m” value switches sign. (d) The “m” value is usually negative in the unfolding direction and positive in the folding direction. The absolute value of “m” is the same in both directions. (e) The unfoldin

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INSTANT ANSWER

1. THE AMAZING EFFECT OF PRESSURE ON PROTEIN UNFOLDING (0.5 + 0.5 + 0.5 + 0.5 + 1 + 2 = 5 pts) a. Write down the total differential of G as a function of its natural variables T,P and N. b. From this expression, deduce an expression for   . G    P T,N c. Modify this expression upon considering a 2-state biomolecular unfolding process (from the native state N to the unfolded state U) under standard-state conditions and write down an expression for NU   G o . This simple expression is very powerful because it explains     P T,N the effect of pressure on protein unfolding processes. d. Now, consider that all experiments performed on earth so far showed that increases in pressure shift the unfolding equilibrium to the right. In other words, high pressure unfolds proteins. Based on this observation, what is the sign of NU   G o , positive or negative?     P T,N e. Based on the results in part d, is the thermodynamic volume V of the unfolded state larger U or smaller than the thermodynamic volume of the native state N V ? f. The result of part e of this question is really interesting. Very briefly explain the origin of this amazing finding (that is: VN > VU or VN < VU) based on your reading of the article by J. Roche et al. Proc. Natl. Acad. Sci. USA 109, 6945-6950 (2012). This article has been uploaded on CANVAS.

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