Question

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.

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.

Added by Harper U.

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