ASU BCH 463 (BCH463) Biophysical Chemistry – Module 6 Homework | Questions & Answers | Latest 2026–2027

BCH 463: Biophysical Chemistry — Module 6 Homework 1. Computer simulation of the geometrical configuration of biological molecules gives a dynamic picture of the molecular movements. Which are not usually considered in the simulation if we would like to know just the protein conformational change? A. The deformation of the molecular orbitals in the electric field created by a neighboring molecule. B. Brownian motion C. Charge fluctuation of the molecule D. All of above 2. For the AMBER force field parameters, which is not included in the calculation? A. Bond length and bond angle B. Dihedral angle C. Hydrogen bond D. Metal chelation 3. Which is correct when performing molecular simulation on the biological molecules? A. Brownian motion can be correctly included in the calculations B. The precise values of the charge and permittivity can not be precisely determined C. The fluctuation of the dielectric constant of solvent is small and can be ignored D. None of above 4. In addition to the bond parameters and non-bonded interactions, there are some constraints that will also affect the potential calculation on the proteins. They are: A. Disulfide bonds B. Dielectric constant of the solvent C. Metal coordination D. All of above 5. Which of the following contributes to the free energy of a protein? A. The degrees of freedom of the peptide bond B. The rotameric state of the side chain C. Hydrogen bonding and van der Waal interaction D. All of above 6. Which of the following method can show the content of the secondary structures in a protein? A. X-ray crystallography B. Circular dichroism C. Both of them D. Mass spectroscopy 7. To obtain the subunit organization of the large size of proteins, which method can be applied for this purpose? A. Hydrodynamic measurement B. X-ray crystallography C. SDS-PAGE D. All of above 8. What is the major force to stabilize the secondary structures of a protein? A. van der Waal interaction B. Hydrogen bonding C. Covalent bonding D. Ionic bonding 9. About the Ramachandran plot, which statement is true? A. It is a plot showing the coordinates of the phi and psi angle of a protein backbone B. The torsional angle of psi is defined by N(i)-C(α)-C-N(i+1). C. The distribution of the (phi, psi) is only allowed in certain regions. D. All of above. 10. What are the common phasing methods for determining X-ray protein crystal structures? A. Molecular replacement B. Anomalous X-ray scattering C. Multiple isomorphous replacement D. All above 11. What is the structural information obtained from the 3D electron microscopy? A. Coulomb potential map of the target molecule B. Electron density map of the target molecule C. Photon density map of the target molecule D. Dipole moment of the target molecule 12. What was the challenge for electron microscopy to study structures of biological samples? A. Biological samples are always over-stained. B. Biological samples cannot be fixed. C. The object contrast is in high signal-to-noise ratio. D. Biological specimen is sensitive to radiation damage. 13. Given a crystal with lattice spacing d=2.5 Å and X-ray wavelength 1.54 Å, calculate the angle at which the first-order diffraction peak occurs. A. 17.9 degrees B. 179 degrees C. 1.79 degrees D. 30 degrees 14. In cryogenic electron microscopy (cryo-EM), why the biological sample needs to be frozen? A. To keep the sample hydrated in the EM vacuum B. To minimize the electron beam damage C. To preserve the sample in a solution state when imaged D. Above all 15. If one would like to study the structure of a molecule with 360 kDa, what method is suitable to pursue this goal? A. X-ray crystallography B. Cryo-EM C. NMR D. Dynamic light scattering