This set of Structural Biology Multiple Choice Questions & Answers (MCQs) focuses on “Potential Energy of Proteins”.

1. Potential energy of proteins are determined by ___________ methods.

a) PCR

b) Immunosorbent assay

c) Quantum mechanics

d) Electrophoresis

View Answer

Explanation: The potential energy of the proteins is determined by the quantum mechanics methods. This quantum mechanics method is time-consuming methods. Hence the determination of potential energy of even a small polypeptide requires several days of analysis and computation.

2. Which of the following is not a quantum mechanical method?

a) Ab initio method

b) Semi-empirical method

c) DFT

d) BFT

View Answer

Explanation: The quantum mechanics method utilizes the Schrödinger equations. It is mainly based on wave functions. There are three major types of quantum mechanical methods. They are ab initio wave, semi-empirical and Density Functional Theory (DFT). There is no such QM method called BFT.

3. Which one of the following QM methods has high computational cost?

a) Ab initio method

b) Dimensional method

c) Density Functional Theory

d) Semi-empirical theory

View Answer

Explanation: This method considers that the spatial arrangement of the electrons is independent of the instantaneous movement of the other electrons. And the Hartree Fock theory gives the errors in the calculation of the total energy. This low efficient Hartree Fock calculation results in high computational cost.

4. What data will be known while using the DFT method of Quantum mechanics?

a) Density

b) Density Function

c) Density Distributions

d) Total energy

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Explanation: In the Density Function theory method, the electron distribution density will be a known parameter. Hence using this data, we can find the ground state energies directly. Hence, if you compare both ab initio method and Density Function theory method, the DFT will be less complicated than the ab initio method.

5. Which method of quantum mechanics is less accurate?

a) Ab initio wave method

b) Dimensional method

c) Density Functional Theory

d) Semi-empirical theory

View Answer

Explanation: The semi-empirical theory is Less accurate when compared to the ab initio method and Density Function theory method. It can give accurate solutions only when the value of the given properties are so specific. But in most of the cases, such specifically parameterized values will not be available.

6. Which method of QM will you use if satisfactory results are expected for a large system but you have less budget and no specifically parameterized values?

a) Density Function theory method

b) Semi-empirical theory

c) Ab initio wave method

d) Ab initio method and Density Function theory method

View Answer

Explanation: In the ab initio wave method, we can get a satisfactory result for larger systems but it results in high computational costs. Hence, the ab initio wave method can’t be used. Semi-empirical theory method can be used since it has low computational cost but you don’t have specifically parameterized values. Hence, the only available method satisfying the above conditions is the Density Function theory method.

7. Choose the correct statement.

a) The protein folds into a state of high potential energy

b) The protein folds in a state of low potential energy

c) The protein folding doesn’t depend on its potential energy

d) The potential energy varies but does not affect its geometry

View Answer

Explanation: In every living cell, protein tries to be in its stable form. This conformation makes the protein to function. This potential energy depends on a variety of parameters which can be calculated and substituted in the final potential energy expression.

8. Which of the following parameters does not contribute to the potential energy of the proteins?

a) Electrostatic interactions

b) Van der Waal’s interactions

c) Charge of amino acids

d) Bond length

View Answer

Explanation: The potential energy of proteins depends on several parameters like bond length, bond angle, torsion angle, electrostatic interactions and Van der Waal’s Interactions. It doesn’t depend on the charges of the amino acids constructing a polypeptide.

9. Which one of the following is the potential energy expression for the bond length?

a) E_{bond} = ∑_{(i, j, k) E Sbond} k_{ijk}^{b} (α_{ijk} – α_{ijk}^{0})^{2}

b) E_{bond} = ∑_{(i, j) E Sbond} k_{ij}^{b} (α_{ij} – α_{ij}^{0})^{2}

c) E_{bond} = ∑_{(i, j, k, l) E Sbond} k_{ijkl}^{t} [1 + cos(n α_{ijkl} – α_{ijkl}^{0})]

d) E_{bond} = ∑_{(i, j) E Sbond} (q_{i} q_{j}) / (e_{ij} r_{ij})

View Answer

Explanation: In proteins, the two atoms should be at the fixed distance from each other. This fixed distance between the two atoms is called as the equilibrium distance. If the two atoms fail to maintain equilibrium length between them then it contributes to the potential energy of the protein.

10. Which one of the following is the potential energy expression for the bond angle?

a) E_{angle} = ∑_{(i, j, k) E Sangle} k_{ijk}^{a} (α_{ijk} – α_{ijk}^{0})^{2}

b) E_{angle} = ∑_{(i, j, k, l) E Sangle} k_{ijkl}^{t} [1 + cos(n α_{ijkl} – α_{ijkl}^{0})]

c) E_{angle} = ∑_{(i, j) E Sangle} ε_{ij} [(σ_{ij} /r_{ij})^{12} – 2(σ_{ij} / r_{ij})^{6}]

d) E_{angle} = ∑_{(i, j) E Sangle} k_{ij}^{a} (α_{ij} – α_{ij}^{0})^{2}

View Answer

Explanation: Three atoms join to form two bonds. The angle between these two bonds should be equal to the fixed value called equilibrium angle. The equilibrium angle depends on the atoms taking part in the construction of chemical bonds. Even a slight change in that value adds to the potential energy of the protein.

11. Which one of the following is the potential energy expression for the torsion angle?

a) E_{torsion} = ∑_{(i, j) E Storsion} ε_{ij} [(σ_{ij} / r_{ij})^{12} – 2(σ_{ij} / r_{ij})^{6}]

b) E_{torsion} = ∑_{(i, j, k, l) E Storsion} k_{ijkl}^{t} [1 + cos(n α_{ijkl} – α_{ijkl}^{0})]

c) E_{torsion} = ∑_{(i, j) E Storsion} (q_{i} q_{j}) / (e_{ij} r_{ij})

d) E_{angle} = ∑_{(i, j) E Sangle} k_{ij}^{a} (α_{ij} – α_{ij}^{0})^{2}

View Answer

Explanation: The quartet of atoms can construct three bonds between them. In these chemical bonds, the middle bond is the one which determines the torsion angle. This torsion angle should be of fixed value to make the protein stable. This fixed value is called equilibrium torsion angle. Even a small change in that value adds to the potential energy of the protein.

12. Which one of the following is the potential energy expression for the electrostatic interactions?

a) E_{electro} = ∑_{(i, j, k, l) E Selectro} k_{ijkl}^{t} [1 + cos(n α_{ijkl} – α_{ijkl}^{0})]

b) E_{electro} = ∑_{(i, j) E Selectro} k_{ij}^{a} (α_{ij} – α_{ij}^{0})^{2}

c) E_{electro} = ∑_{(i, j) E Selectro} ε_{ij} [(σ_{ij} / r_{ij})^{12} – 2(σ_{ij} / r_{ij})^{6}]

d) E_{electro} = ∑_{(i, j) E Selectro} (q_{i} q_{j}) / (e_{ij} r_{ij})

View Answer

Explanation: In proteins, the electrostatic interaction takes place between pairs of atoms. These electrostatic interactions depend on the distance between those pairs of atoms. Hence, if the distance is not equal to its equilibrium distance then it contributes to the potential energy.

13. Which one of the following is the potential energy expression for the Van Der Wall’s interactions?

a) E_{vdw} = ∑_{(i, j) E Svdw} k_{ij}^{a} (α_{ij} – α_{ij}^{0})^{2}

b) E_{vdw} = ∑_{(i, j) E Svdw} ε_{ij} [(σ_{ij} / r_{ij})^{12} – 2(σ_{ij} / r_{ij})^{6}]

c) E_{vdw} = ∑_{(i, j) E Svdw} (q_{i} q_{j}) / (e_{ij} r_{ij})

d) E_{vdw} = ∑_{(i, j, k, l) E Svdw} k_{ijkl}^{t} [1 + cos(n α_{ijkl} – α_{ijkl}^{0})]

View Answer

Explanation: The atoms participating in the construction of proteins undergo Van Der Waal’s interactions. But it requires the atoms to be close to each other. This interaction depends on the Van der Waal’s radii. Any difference in their distance adds to the potential energy.

14. E_{total} = E_{bond} + E_{angle} + E_{torsion} + E_{electro} + E_{vdw}.

a) True

b) False

View Answer

Explanation: The total potential energy is the summation of potential energies of various parameters associated with the structure of the polypeptide. Even though the potential energy contributed by these parameters are small, it is necessary to consider all the factors.

15. The terms q_{i} and q_{j} represent atoms in the expression E_{electro} = ∑_{(i, j) E Selectro} (q_{i} q_{j}) / (e_{ij} r_{ij}).

a) False

b) True

View Answer

Explanation: In the potential energy expression for the electrostatic interactions, the terms q

_{i}represents the charge on the i

^{th}atoms. Hence, the atom in the above expression is represented by the terms i and j.

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