This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “RNA Secondary Structure Prediction Methods”.
1. At present, there are essentially two types of method of RNA structure prediction. One is the minimum free energy approach and the Second one is a comparative approach.
a) True
b) False
View Answer
Explanation: One is based on the calculation of the minimum free energy of the stable structure derived from a single RNA sequence. This can be considered an ab initio approach. The second is a comparative approach which infers structures based on an evolutionary comparison of multiple related RNA sequences.
2. Ab initio approach makes structural predictions based on ______
a) a single RNA sequence
b) comparing RNA sequences
c) evolutionary basis
d) pure phylogenetics
View Answer
Explanation: The rationale behind this method is that the structure of an RNA molecule is solely determined by its sequence. Thus, algorithms can be designed to search for a stable RNA structure with the lowest free energy.
3. In ab initio approach, generally, when a base pairing is formed, the energy of the molecule is _________ because of attractive interactions between the two strands.
a) lowered
b) increased
c) multiplied
d) kept stable
View Answer
Explanation: Here, the algorithms can be designed to search for a stable RNA structure with the lowest free energy. Thus, to search for a most stable structure, ab initio programs are designed to search for a structure with the maximum number of base pairs.
4. In ab initio methods, free energy can be calculated based on parameters empirically derived for small molecules.
a) True
b) False
View Answer
Explanation: G–C base pairs are more stable than A–U base pairs, which are more stable than G–U base pairs. It is also known that base-pair formation is not an independent event.
5. The energy necessary to form individual base pairs is not quite affected by adjacent base pairs.
a) True
b) False
View Answer
Explanation: The energy necessary to form individual base pairs is influenced by adjacent base pairs through helical stacking forces. This is known as co-operativity in helix formation.
6. The attractive interactions lead to _________ energy.
a) increased
b) higher
c) lower
d) no change in
View Answer
Explanation: If a base pair is next to other base pairs, the base pairs tend to stabilize each other through attractive stacking interactions between aromatic rings of the base pairs. The attractive interactions lead to even lower energy. Parameters for calculating the co-operativity of the base-pair formation have been determined and can be used for structure prediction.
7. If the base pair is adjacent to loops or bulges, the neighboring loops and bulges tend to ___________ the base-pair formation.
a) have no change on
b) decrease the energy
c) stabilize
d) destabilize
View Answer
Explanation: This is because there is a loss of entropy when the ends of the helical structure are constrained by unpaired loop residues. The destabilizing force to a helical structure also depends on the types of loops nearby.
8. The scoring scheme based on the combined stabilizing and destabilizing interactions forms the foundation of the ab initio RNA secondary structure prediction method.
a) True
b) False
View Answer
Explanation: Parameters for calculating different destabilizing energies have also been determined and can be used as penalties for secondary structure calculations. This method works by first finding all possible base-pairing patterns from a sequence and then calculating the total energy of a potential secondary structure by taking into account all the adjacent stabilizing and destabilizing forces.
9. Ab initio methods are energetically least favorable.
a) True
b) False
View Answer
Explanation: These methods are energetically most favorable. If there are multiple alternative secondary structures, the method finds the conformation with the lowest energy.
10. The dot matrix method and the dynamic programming method can be used in detecting self-complementary regions of a sequence.
a) True
b) False
View Answer
Explanation: A simple dot matrix can find all possible base-paring patterns of an RNA sequence when one sequence is compared with itself. In this case, dots are placed in the matrix to represent matching complementary bases instead of identical ones.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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