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# Protein Biomolecular Interactions Online Exam Quiz

Important questions about Protein Biomolecular Interactions. Protein Biomolecular Interactions MCQ questions with answers. Protein Biomolecular Interactions exam questions and answers for students and interviews.

### Which of the following is untrue about Amino acid conservation?

Options

A : a. It has been known for some time that conservation of residues at the surface of a protein family is often related to function

B : b. Conservation of residues at the core of a protein family is often related to function

C : c. This may be an enzyme active-site or binding site

D : d. Unlike hydrophobicity or electrostatic potential, displaying residue conservation on the molecular surface has no physical or chemical basis

### Which of the following is untrue about Shape Complementarity?

Options

A : a. The complementarity between two proteins or a protein and ligand can be described by surface contact or overlap

B : b. The complementarity between two proteins or a protein and ligand can be described by the overall buried surface area of two molecules in contact

C : c. The complementarity between two proteins or a protein and ligand can be described by the number of adjacent surface points (atoms or residues)

D : d. The hydrophobic effect barely has impact on protein folding

### The burial of surface area (or the maximization of surface contact) is an approximation of the effect of shape complementarity.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### Which of the following is untrue about Grid Representation?

Options

A : a. To speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements

B : b. To speed up the matching process discretizing the 3-dimensional space using a grid is done

C : c. Discretizing allows very fast computer matching using search methods such as Fourier transform

D : d. Fourier transform is hardly used in computer matching

### In Grid representation, in a translational scan the mobile molecule B moves through the grid representing the static molecule A and a signal describing shape complementarity, fc, is generated for each mapping. Mathematically the correlation function, fc, of fA and fB is given by ______ where N is the number of grid points along the cubic axes i, j, and k and ?, ?, and ? are the translational vectors of the mobile molecule B relative to the static one A.

Options

A : a. fc = $$\sum_{i=1,j=1,k=1}^N$$ (fA,i,j,k * fBi+?j+?k+?)

B : b. fc = $$\sum_{i=0,j=0,k=0}^N$$ (fA,i,j,k * fBi+?j+?k+?)

C : c. fc = $$\sum_{i=1,j=1,k=1}^N$$ (fA,0,0,0 * fBi+?j+?k+?)

D : d. fc = $$\sum_{i=0,j=0,k=0}^N$$ (f0,i,j,k * fBi+?j+?k+?)

### In Grid representation, the lowest score represents the best surface complementarity for a given translational scan.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### In Property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### Which of the following is untrue about Hydrophobicity?

Options

A : a. The hydrophobic effect plays a dominant role in the folding of proteins

B : b. Hydrophobic residues aggregate away from contact with water

C : c. Hydrophobic residues aggregate to form hydrophobic cores with more polar residues

D : d. Hydrophobic residues form the solvent accessible surface but restrict the solubility of the protein

### Oligomers are often obligate complexes meaning that the free-energy cost of dissociation is high and they exist as oligomers under physiological conditions.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### Which of the following is untrue about Electrostatic Complementarity?

Options

A : a. The electrostatic properties of biomolecules play an important role in determining interactions

B : b. The burial of charged residues at protein-protein/DNA interfaces is thought to be generally net destabilizing with the hydrophobic effect being the primary driving force

C : c. Charged groups involved in the biomolecular interface are often stabilized by other polar or oppositely charged groups on the interacting molecule

D : d. Charged groups involved in the biomolecular interface are often stabilized by similar polar or same charged groups on the interacting molecule

### Proteins are dynamic entities that undergo _______

Options

A : a. only fluctuation of flexible loop regions about equilibrium positions when in solution

B : b. only limited conformational change of amino acid side-chains when in solution

C : c. both limited conformational change of amino acid side-chains and fluctuation of flexible loop regions about equilibrium positions when in solution

D : d. illimitable or total conformational change of amino acid side-chains when in solution

### Typical motions of proteins will be primarily treated by a rigid body model for docking.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.

Options

A : a. small molecule, highly flexible

B : b. large molecule, highly flexible

C : c. large molecule, more flexible

D : d. small molecule, less flexible

### In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different _______ that are computed _____ the ligand being docked into the receptor.

Options

A : a. low-energy conformations, after

B : b. low-energy conformations, prior to

C : c. high-energy conformations, prior to

D : d. high-energy conformations, after

Options

A : a. N +1

B : b. N

C : c. N²

D : d. N/2

### In Stochastic search methods, they include methods such as Monte Carlo simulation, simulated annealing, Tabu search, genetic algorithms and evolutionary programming.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### In a Monte Carlo simulation the score (or energy) is calculated at each step and compared to the previous step. The probability of accepting the step is given by _________ where ?E is the difference in energy; kB is Boltzmann’s constant and T the temperature.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### Stochastic methods can guarantee reaching a global optimal solution and the methods are computationally costly in comparison to the other methods.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

### Which of the following is true regarding Protein flexibility?

Options

A : a. Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

B : b. Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

C : c. The Mean Field principle is rarely used in this

D : d. Methods have been described for the introduction of side-chain flexibility to protein-protein docking only