This set of Structural Biology Multiple Choice Questions & Answers (MCQs) focuses on “Ramachandran Plot”.
1. Who developed the Ramachandran plot?
a) C. N. Ramachandran
b) G. M. Ramachandran
c) C. M. Ramachandran
d) G. N. Ramachandran
View Answer
Explanation: An Indian scientist named Gopalasamudram Narayanan Ramachandran developed the Ramachandran plot. He was a physicist. He worked under Sir. C. V. Raman and contributed to the field of biophysics.
2. G. N. Ramachandran also described the structure of ___________
a) Keratin
b) Collagen
c) Hemoglobin
d) Immunoglobulin
View Answer
Explanation: In addition to the Ramachandran plot, G. N. Ramachandran also contributed to the field of biology by describing the structure of collagen. He is the first one to predict the triple helical structure of collagen.
3. What quantities are taken into consideration to plot the Ramachandran plot?
a) Phi and omega
b) Omega and psi
c) Phi and psi
d) Omega and epsilon
View Answer
Explanation: Phi and psi are the two angles taken into consideration while plotting a Ramachandran plot. Phi is taken along the X-axis of the Ramachandran plot and psi is taken along the Y-axis.
4. What is angle phi in Ramachandran plot?
a) Bond angle of the bond formed between the amino group and carboxyl carbon
b) Bond angle of the bond formed between alpha carbon and beta carbon
c) Bond angle of the bond formed between the amino group and alpha carbon
d) Bond angle of the bond formed between the alpha carbon and carboxyl carbon
View Answer
Explanation: Phi angle is one of the backbone angles used to plot the Ramachandran plot. It represents the bond angle of the bond formed between the alpha carbon of a amino acid and the amino group of the same amino acid.
5. What is angle psi in Ramachandran plot?
a) Bond angle of the bond formed between the amino group and alpha carbon
b) Bond angle of the bond formed between the alpha carbon and carboxyl carbon
c) Bond angle of the bond formed between alpha carbon and beta carbon
d) Bond angle of the bond formed between the amino group and carboxyl carbon
View Answer
Explanation: Psi angle is one of the backbone angles used to plot the Ramachandran plot. It represents the bond angle of the bond formed between the alpha carbon and carboxyl carbon of same amino acid. Unlike omega, it can be varied by various factors.
6. Angle omega is ___________
a) Bond angle of the bond formed between the amino group and carboxyl carbon
b) Bond angle of the bond formed between the amino group and alpha carbon
c) Bond angle of the bond formed between the alpha carbon and carboxyl carbon
d) Bond angle of the bond formed between alpha carbon and beta carbon
View Answer
Explanation: Omega angle is one of the backbone angles but it is not used to plot the Ramachandran plot. It represents the bond angle of the bond formed between the amino group of amino acid and the carboxyl group of another amino acid. Hence it is the bond angle of the peptide bond.
7. In most of the cases, the value of omega is ___________
a) 90°
b) 180°
c) 360°
d) 45°
View Answer
Explanation: The value of the omega is always 180°. The main reason for this is the rigidity of the peptide bond due to the partial bonds. It keeps the bond angle to be unchanged. Hence it is not included while plotting Ramachandran plot.
8. Which of the following is not a backbone angle of a polypeptide chain?
a) Phi
b) Khi
c) Omega
d) Psi
View Answer
Explanation: Backbone angles are the one which determines the primary shape of the polypeptide chain. It varies from one polypeptide to another. The bonds between NH-CO, NH-Calpha and Calpha-CO build the backbone and their angles are called as backbone angles.
9. What is angle khi?
a) Bond angle of the bond formed between the alpha carbon and beta carbon
b) Bond angle of the bond formed between the alpha carbon and carboxyl carbon
c) Bond angle of the bond formed between the amino group and alpha carbon
d) Bond angle of the bond formed between the amino group and carboxyl carbon
View Answer
Explanation: Khi angle is an angle formed between alpha carbon of the backbone and the beta carbon of the residue of an amino acid in a polypeptide chain. It is not a backbone angle and hence it is not taken into consideration while plotting the Ramachandran plot.
10. The objective of the Ramachandran plot is to ______________
a) Determine the functions
b) Determine the possible conformations
c) Determine the stable conformations
d) Determine the structures
View Answer
Explanation: Ramachandran plot is to find the stable conformations of the small polypeptides. It is done by varying the values of dihedral angles phi and psi and plotting it in the Ramachandran plot. All the polypeptide structures have a specific region in the Ramachandran plot where those structures are stable. Hence by calculating just the dihedral angles, it is possible to determine the stable conformations.
11. For computations of points used to plot Ramachandran plot, the atoms are considered as ____________
a) Hard spheres
b) Unit cell
c) Crystals
d) Nucleus
View Answer
Explanation: For computation purpose, each and every atom in the amino acid is considered as a sphere. This sphere is assumed to have corresponding Van der Waal’s radius as their Dimensions.
12. The structure of a small polypeptide obtained from an X-ray crystallography technique. It is found to have hydrogen bonds linking first and fourth amino acids. It is also found to be left-handed in nature. What will be its position in the Ramachandran plot?
a) Lower left quadrant
b) Upper right quadrant
c) Upper left quadrant
d) Lower right quadrant
View Answer
Explanation: The small polypeptide found by X-ray crystallography technique is a left-handed alpha helix. It has positive phi and psi values. These values make them energetically favourable at certain sterically allowed regions. Hence, they occupy the upper right or the first quadrant.
13. Ramachandran plot cannot be plotted for secondary structure.
a) True
b) False
View Answer
Explanation: The majority of the times, the Ramachandran plot is used for the determination of sterically allowed regions of some secondary structures like alpha helices, phi helix, 310 helix etc.
14. In some computation, the value of phi of a certain polypeptide was found to be -120° and the value of psi was 135°. And as usual, the value of omega was 180°. Which type of secondary structure is that?
a) Alpha helix
b) Collagen
c) Phi helix
d) Beta pleats
View Answer
Explanation: You can observe that the value of phi is negative and the value of psi is positive. So, it comes in the fourth quadrant. Hence it is a beta sheet. It may or may not be energetically stable.
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