Question

1. Which of the following statements is consistent with the structural motifs in 1OPF? This protein has tertiary structure, where each subunit is a large parallel beta barrel. This protein has quaternary structure, where each subunit is a large antiparallel beta barrel. This protein has tertiary structure, where each subunit is a large antiparallel beta barrel. This protein has quaternary structure, where each subunit is a large parallel beta barrel.

3. Given the information in the PDB entry for 1OPF, which of the following statements best predicts the properties of the beta barrels of 1OPF (See Bioinformatics Exercise 4.5)? The antiparallel beta barrels should have a nonpolar interior and a polar exterior. The antiparallel beta barrels should have a nonpolar interior and exterior. The antiparallel beta barrels should have a polar interior and exterior. The antiparallel beta barrels should have a polar interior and a nonpolar exterior.

4. How does the surface rendering of 1OPF using the hydrophobicity color scale support the predictions from Question 3? The surface rendering confirms that the exterior of the protein is hydrophilic and the interiors of the barrels are hollow and hydrophobic. The surface rendering confirms that the exterior of the protein is hydrophobic and the interiors of the barrels are hollow and nonpolar. The surface rendering confirms that the exterior of the protein is hydrophilic and the interiors of the barrels are hollow and nonpolar. The surface rendering confirms that the exterior of the protein is hydrophobic and the interiors of the barrels are hollow and hydrophilic.

5. Which of the following statements is consistent with how a lipid bilayer may interact with the OmpF porin (1OPF)? The phospholipid groups from both leaflets of the bilayer interact with the top and bottom polar regions of OmpF, while the hydrophobic core of the bilayer noncovalently interacts with the middle regions of the protein exterior through van der Waals interactions. The phospholipid groups from only one side of the bilayer interact with the polar regions of OmpF, while the hydrophobic core of the bilayer noncovalently interacts with the middle regions of the protein exterior through van der Waals interactions. The phospholipid groups from both leaflets of the bilayer interact with the top and bottom polar regions of OmpF, while the hydrophobic core of the bilayer noncovalently interacts with the middle regions of the protein exterior mainly through hydrogen bonds.lipopolysaccharide The phospholipid groups from only one side of the bilayer interact with the polar regions of OmpF, and the remaining components of the protein are exposed to the cytosol.

6. Which of the following statements is consistent with the structure shown in 2BRD? The protein has tertiary structure, where each subunit is composed of beta hairpins. The protein has quaternary structure with three identical subunits, where each subunit is composed of alpha–alpha units. This protein has tertiary structure, where each subunit is composed of alpha–alpha units. The protein has quaternary structure with three identical subunits, where each subunit is composed of beta hairpins.

7. Which of the following statements is consistent with the composition of the alpha helices in 2BRD? The alpha helices are composed of alternating nonpolar and polar amino acids. The alpha helices show no ordered arrangement of the amino acids. The alpha helices are composed mostly of nonpolar amino acids. The alpha helices are composed mostly of polar amino acids.

8. In 2BRD, what type of noncovalent interaction is likely occurring between Ile 191 and the closest lipid molecule? ion pair hydrogen bond dipole–dipole interaction London dispersion forces (induced dipole–induced dipole interactions)

9. Which of the following statements best describes the hydrophobic character of bacteriorhodopsin (2BRD)? Both the interior and exterior of the protein are hydrophobic, but the central core of the trimer is hydrophilic. Both the interior and exterior of the protein are hydrophobic, including the central core of the trimer. Both the interior and exterior of the protein are hydrophilic, including the central core of the trimer. Both the interior and exterior of the protein are hydrophilic, but the central core of the trimer is hydrophobic.

10. For any transmembrane protein structure, which of the following properties is NOT required? Polar residues at the top and bottom edges of the protein. Exterior amino acids that are hydrophobic. Interior amino acids that are hydrophobic. A secondary or supersecondary structure that forms an overall circular structure.

Answer 1

1. The statement which is consistent with the structural motifs in 1OPF is:

This protein has quaternary structure, where each subunit is a large antiparallel beta barrel.

Because 1OPF is ompf porin protein which is a homotrimeric structure (quaternary structure) with each subunit of the structure forming a barrel of antiparallel beta strands.