The Three-Dimensional Structure of Proteins

Which item is the predominant factor in protein stability?

• disulfide bonds

• the hydrophobic effect

• salt bridges

• nonpeptide covalent bonds

Answer explanation

The hydrophobic effect, derived from the increase in entropy of the surrounding water when nonpolar molecules or groups are clustered together, makes the major contribution to stabilizing the globular form of most soluble proteins.

Which statement regarding protein structure is true?

• Entropy is generally not a consideration when

       determining stability.

• Van der Waals interactions are insignificant.

• Hydrophilic side chains are never found in the interior.

• Hydrophobic side chains are usually in the interior of

  the native structure.

Answer explanation

When nonpolar groups cluster together, the extent of the solvation layer decreases, because each group no longer presents its entire surface to the solution. The result is a favorable increase in entropy. Hydrophobic amino acid side chains therefore tend to cluster in a protein’s interior, away from water.

The α helix is:

• affected by the identities of the residues near each end.

• stabilized by amino acid R-group interactions.

• a left-handed helix with 3.6 amino acids per turn.

• stabilized primarily by the hydrophobic effect.

Answer explanation

There is a net dipole along the helical axis of an α helix. The partial positive and negative charges of the helix dipole reside on the peptide NH3+ and COO− groups. For this reason, negatively charged amino acids are often found near the NH3+ terminus and positively charged amino acids are often found near the COO− terminus.

Which statement regarding the tertiary structure of proteins is false?

• Amino acid residues far apart in primary structure may

       interact with each other in the tertiary structure.

• The tertiary structure of a protein is destabilized by the

       hydrophobic effect.

• Many proteins can be classified as either globular or

       fibrous (but not both).

• Quaternary structure is the description of how the

       tertiary structures in a multisubunit protein are

       arranged with respect to each other.

Answer explanation

The tertiary structure of a protein is largely stabilized by the hydrophobic effect. In typical globular proteins, most of the hydrophobic R groups are in the interior of the molecule, hidden from exposure to water.

Quaternary structure:

• describes how oligomers are assembled into protomers.

• refers to proteins with identical subunits.

• refers to proteins with four subunits.

• refers to an arrangement of tertiary protein subunits in

    a three-dimensional complex.

Answer explanation

Some proteins contain two or more separate polypeptide chains, or subunits, which may be identical or different. The arrangement of these protein subunits in three-dimensional complexes constitutes a quaternary structure.