Nucleic Acids MCQ - IIT JAM MCQ

Nucleic acid structure cannot be determined using transmission electron microscopy or surface plasmon resonance. Both NMR and X-ray crystallography can be used to determine the structure of nucleic acids (or other biomolecules), but Wilkins, Watson and crick determined the structure of DNA using X-ray crystallography.

Endo puckering is the displacement of a specific carbon atom towards the oxygen atom, while exo puckering is displacement away from oxygen atom. In case of B-DNA (naturally occurring form), it is C-2 endo puckering.

In an endo form, sugars have carbon atoms puckered above the plane (on the side as the base) while in an exo form, the carbon atoms are puckered below this plane (on opposite side of base). C3’ endo pucker is prevalent in RNA and A-form DNA, whereas the C2’ endo pucker is characteristic of B-form DNA (C2’ endo pucker has the C2’ carbon pointed up and towards the base and in C3’ endo pucker, C3’-carbon pointed up and towards the base). The two conformations affects the overall conformation of DNA in the way that they specify different phosphate-phosphate distances along each strand (~7 Å for C2’-endo and ~6 Å for C3’-endo).

Adenine has the highest number of nitrogen atoms. Its chemical name is 6-amino purine. A purine ring has 4 nitrogen atoms and additionally there is one amino group. Hence, total 5 nitrogen atoms. While cytosine has 3 nitrogen atoms, uracil and thymine have 2 nitrogen atoms each. The number of nitrogen atoms in Guanine is also 5 (not given in option).

There are six torsion angles denoted as

rRNA is about 80% of the total cellular RNA, hence it is most abundant.

The base pair stacking interaction are the interaction between pi bonds of the adjacent base pairs.The stability of the DNA double helix depends on a fine balance of interactions including hydrogen bonds between bases, hydrogen bonds between bases and surrounding water molecules, and base-stacking interactions between adjacent bases. Inter-strand hydrogen bonding is clearly important in driving the formation of DNA double strands, but it is by no means the only contributing factor. The individual bases form strong stacking interactions which are major contributors to double strand stability, as base stacking is much more prevalent in double strands than in single strands. Base-stacking interactions are hydrophobic and electrostatic in nature, and depend on the aromaticity of the bases and their dipole moments. Base-stacking interactions in nucleic acid double strands are partly inter-strand and partly intra-strand in nature. However, it is probably more informative to consider base pairs rather than individual bases as discrete units in order to visualize the stabilising effects of base stacking.The degree of stabilization afforded by base stacking depends on the DNA sequence. Some combinations of base pairs form more stable interactions than others, so nearest neighbour base-stacking interactions are important determinants of DNA double strand stability.
Base-stacking interactions increase with increasing salt concentration, as high salt concentrations mask the destabilizing charge repulsion between the two negatively charged phosphodiester backbones. DNA double strand stability therefore increases with increasing salt concentration. Divalent cations such as Mg²⁺ are more stabilising than Na⁺ ions, and some metal ions bind to specific loci on the DNA duplex.

On reducing the humidity below 50% the naturally occurring B-DNA has propensity to form A DNA conformation. B-DNA needs around 30% water by weight, to maintain its native conformation in the crystalline state. Partial dehydration converts B DNA to A-DNA (A DNA has a shallow, wide minor groove and a narrow, deeper major groove). The transition for this transformation occurs at about 20 water molecules per base pair, with its midpoint at about 15 water molecules per base pair (at about 85% relative humidity). The B-DNA possesses a spanning water network, and it is the loss of its continuity together with the competition between hydration and direct cation coupling to the free oxygen atoms in the phosphate groups that give rise to the transition to A-DNA. This dehydration induced structural transition decreases the free energy required for A-DNA deformation and twisting, which is usefully employed by encouraging supercoiling but eventually leads to denaturation. Further dehydration results in the least hydrated D-DNA (favored by excess counter-ions that shield the DNA phosphate charges), which has a very narrow minor groove with a string of alternating water and counter-ions distributed along its edge

A-form DNA was first identified from fibre diffraction studies of DNA at ‘low’ (75%) relative humidity whereas B DNA was first identified in fibres at 92% relative humidity.
Z-DNA is a left handed DNA. and favours an alternating purine, pyrimidine sequence. There are studies that show that GC rich sequence gets converted from B to Z-DNA. However. AT rich sequences can also form Z-DNA structure.
Watson (an American biologist) and F.H.C'. Crick (a British Physicist) proposed the three-dimensional model of physiological DNA (i. e B-DNA) on the basis of X-ray diffraction data of DNA obtained by Franklin and Wilkins.
H DNA or triple stranded DNA is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. In H DNA. the third strand bind to B form DNA double helix by forming Hoogsteen base pairs. A thymine (T) nucleobase can bind to a Watson-Crick base pairing of T-A by forming a Hoogsteen hydrogen bond. The thymine hydrogen bonds with the adenosine (A) of the original double stranded DNA to create T-A*T base triplet. H DNA structure can form, when there is a homo purine stretch on one strand and consequently homo pyrimidine stretch on the other strand.
A Hoogsteen base pair (H DNA) is a variation of base-pairing in nucleic acids such as the A•T pair. A Hoogsteen base pair applies the N7 position of the purine base (as a hydrogen bond acceptor) and C6 amino group (as a donor), which bind the Watson-Crick (N3-C4) face of the pyrimidine base.

Glycosyl bond conformation in A and B form of DNA is ‘Anti’, whereas in Z form of DNA, it is Anti for pyrimidines and syn for purines.

Rise of helix per base pair is 3.4 angstrom, 2.6 and 3.7 angstrom for B-DNA, A-DNA and Z-DNA respectively. Hence Z-DNA is the longest and A DNA is the shortest in length.

The average molecular weight of a nucleotide pair is 660 dalton while that of a nucleotide is 325, hence the ratio of molecular weights of DNA and RNA will be 2:1.

Option (a) is correct.
In secondary conformation, naturally occurring RNA mostly adopt local pairing of complementary base pairs.
Option (b) is incorrect.
During DNA denaturation, double stranded DNA unwinds and separates into single strands. The temperature at which the DNA strands are half  denatured is called the melting temperature (T_m).

Option (c) is incorrect.
The DNA molecules are not always double stranded helical structures. Sometimes they occur in single stranded form also called as single stranded DNA (ssDNA). DNA in ssDNA form is present in very few viruses.
Option (d) is incorrect.
RNA is a genetic material in many viruses. Human diseases caused by RNA viruses [virus that has RNA as genetic material] include rabies, common cold, hepatitis C.

Option (a) is correct. B DNA has 10.5 base pairs per helical turn and helix rise per base pair in B DNA is 3.4 Aº. Therefore rise per turn in B DNA will be 34 Å.
Option (b) is correct.
Z DNA is formed by DNA sequences in which pyrimidines alternate with purines especially alternating C and G. Hence Z DNA has GC as repeating unit.    
Option (c) and (d) are incorrect as B DNA is formed in excess of humidity (92%). A DNA has 3’ endo sugar puckering.

Statement b and d are correct as the formation of H-DNA occurs due to flipping of purines from anti-orientation to syn orientation. As the hoogsteen and watson-crick faces are opposite to each other flipping of one of the base results in new possibilities of hydrogen bond formation. This allows the formation of hydrogen bonds such C…G…...C instead of conventional CG pairing. This allows the formation of triple helical DNA or tetra helical DNA.

DNase are known to depend upon the divalent ions such as magnesium ions, which can be sequestered (blocked) in solution by addition of chelating agents such as EDTA. Hence, EDTA is added to DNA storage solution from preventing it from DNase mediated degradation.

Statement c and d are not part of chargaff’s rule. While statement a is part of 1st parity rule and statement b is part of second parity rule.

Option (a) is correct.
Palindromic DNA/RNA sequences can form alternative structures with intrastrand base pairing. When only single DNA/RNA strand is involved, hairpin structure is formed. When both strands of duplex DNA are involved, it is called cruciform.
Option (b) is correct.
N-7, O⁶ and N⁶ of purines are the atoms that participate in the hydrogen bonding of triplex DNA resulting in Hoogsteen pairing, thereby forming triplex DNAs.
Option (c) is correct.
Increase in absorption that accompanies the denaturation of double stranded nucleic acid is called hyper chromic effect which can be measured by monitoring absorption of UV light.
Option (d) is correct.
GC pair has 3 hydrogen bonds unlike AT pair which has 2 hydrogen bond. It is easier to break 2 hydrogen bond than 3.

No. of bp per turn = 10
Rise per base pair = 3.4Å
Rise per turn = 3.4Å x 10 = 34Å

1 turn = 10 base pairs
2 turns = 20 base pairs

Provided that there are 500 base pairs, which means 1000 bases, and if 20% are G, i.e. 200 are G hence, C will also be 200. Remaining 600 will be A and T (300 A and 300 T), so total number of AT pairs = 300 and total GC pairs = 200. Each AT pair has two hydrogen bonds and Each GC pair has 3 hydrogen bonds. So, total number of hydrogen bonds will be (300 x 2) + (200 x 3) = 1200.

Linking number is sum of twist and writhe. Lk = Tw + Wr
Twist = number of times one strand crosses other i.e. total number of base pairs/bp per turn
i.e 1000/10 = 100 = Lk
Writhe = –20 (negative sign for negative supercoil, positive sign for positive supercoil)
So, linking number = 100 – 20 = 80.

A 200 amino acids large, peptide will be encoded by 200 x 3 = 600 bp. (Each amino acid is encoded by a triplet of base pairs called codon)
Rise per base pair in B DNA = 3.4Å or 0.34 nm
So, 600 bp DNA will form helix of length = 0.34 × 600 = 204 nm