Problem Set 4: Chapter 4: The three dimensional structure of proteins

1) Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a
protein, and describe one condition or reagent that interferes with each type of stabilizing force.
Ans: Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen
bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with these forces
are (a) mercaptoethanol or dithiothreitol, (b) pH etremes, (c) detergents and urea, and (d) changes in
pH or ionic strength, respectively.
!) "escribe three of the important features of the #helical polypeptide structure predicted by
$auling and %orey. $rovide one or two sentences for each feature.
Ans: &he #helical structure of a polypeptide is tightly wound around a long central ais' each turn of
the right#handed heli contains (.) residues and stretches *.+ , along the ais. &he peptide NH is
hydrogen#bonded to the carbonyl oygen of the fourth amino acid along the se-uence toward the
amino terminus. &he . groups of the amino acid residues protrude outward from the helical
bac/bone.

() 0ach of the following reagents or conditions will denature a protein. 1or each, describe in one or
two sentences what the reagent2condition does to destroy native protein structure.
(a) urea
(b) high temperature
(c) detergent
(d) low pH
Ans: (a) 3rea acts primarily by disrupting hydrophobic interactions. (b) High temperature provides
thermal energy greater than the strength of the wea/ interactions (hydrogen bonds, electrostatic
interactions, hydrophobic interactions, and van der 4aals forces, brea/ing these interactions. (c)
"etergents bind to hydrophobic regions of the protein, preventing hydrophobic interactions among
several hydrophobic patches on the native protein. (d) 5ow pH causes protonation of the side chains
of Asp, 6lu, and His, preventing electrostatic interactions.
+) 7nce a protein has been denatured, how can it be renatured8 9f renaturation does not occur, what
might be the eplanation8
Ans: :ecause a protein may be denatured through the disruption of hydrogen bonds and hydrophobic
interactions by salts or organic solvents, removal of those conditions will reestablish the original
a-ueous environment, often permitting the protein to fold once again into its native conformation. 9f
the protein does not renature, it may be because the denaturing treatment removed a re-uired
prosthetic group, or because the normal folding pathway re-uires the presence of a polypeptide chain
binding protein or molecular chaperone. &he normal folding pathway could also be mediated by a
larger polypeptide, which is then cleaved (e.g., insulin). "enatured insulin would not refold easily.