Structure of DNA and RNA

What are nucleic acids made of?

Nucleic acids are made of nucleotides, which consist of a nitrogen base (purine or pyrimidine), a five-carbon sugar (pentose), and one or more phosphate groups.

Name the purine bases.

Adenine (A) and Guanine (G).

Name the pyrimidine bases.

Cytosine (C), Thymine (T), and Uracil (U).

What is the sugar in DNA?

2-Deoxyribose.

What is the sugar in RNA?

Ribose.

What bond links the sugar to the nitrogen base?

N-glycosidic bond (C-1' of sugar to N-1 of pyrimidine or N-9 of purine).

What is a nucleoside?

A nitrogenous base covalently bonded to the C-1' of a sugar (no phosphate group).

What is a nucleotide?

A nucleoside with one or more phosphate groups attached, usually to the C-5' carbon.

What bond links nucleotides within a strand?

Phosphodiester bond (between 3’ OH of one sugar and 5’ phosphate of the next).

What are the complementary base pairs in DNA?

Adenine pairs with Thymine (2 hydrogen bonds); Guanine pairs with Cytosine (3 hydrogen bonds).

Why does DNA have a uniform diameter?

Both A–T and G–C pairs are of similar length, maintaining consistent spacing.

What is the backbone of DNA composed of?

Sugar-phosphate chains on the outside of the helix.

What is meant by “antiparallel” DNA strands?

One DNA strand runs 5’→3’ while the complementary strand runs 3’→5’.

What is the orientation rule when writing nucleic acid sequences?

Sequences are written 5’ to 3’ (left to right).

What is the handedness of biological DNA?

Right-handed double helix.

How many base pairs make one turn of the DNA helix?

10 base pairs (one full turn = 34 Å).

What holds the two DNA strands together?

Hydrogen bonds between complementary base pairs.

What is the structure of the DNA double helix?

Two antiparallel polynucleotide strands with bases stacked perpendicular to the helix axis.

What stabilizes the DNA helix besides hydrogen bonds?

Base stacking interactions between flat purine and pyrimidine rings.

What are the major and minor grooves in DNA?

Spaces formed by the twisting of the two strands, providing access points for proteins.

Compare the sugars in DNA and RNA.

DNA has 2-deoxyribose (no OH at 2'), RNA has ribose (OH at 2').

What makes RNA less stable than DNA?

The 2’ hydroxyl group makes RNA more prone to hydrolysis.

What are the three main forms of DNA?

A-form (right-handed, shorter, wider), B-form (right-handed, most common), Z-form (left-handed, zig-zag).

Which form of DNA is most stable under physiological conditions?

B-form DNA.

Which form of DNA is left-handed?

Z-form DNA.

What is the periodicity of B-form DNA?

10 base pairs per turn, 34 Å per helix turn.

What determines whether a helix prefers A-form or B-form?

The sugar puckering (3'-endo in RNA favors A-form; 2'-endo in DNA favors B-form).

What causes DNA denaturation?

Heat, high pH, or chemicals like urea or formamide disrupt hydrogen bonds.

What happens when denatured DNA cools?

The strands reanneal through complementary base pairing (renaturation).

Which base pairs are harder to denature and why?

G–C pairs (three hydrogen bonds) require more energy to separate.

What is Tm in DNA melting?

The melting temperature (Tm) is the temperature at which half of the DNA strands are separated.

How is Tm related to GC content?

Tm = 68.9 + 0.41(%GC); higher GC content increases Tm.

What types of secondary structures can RNA form?

Hairpins, bulges, internal loops, and multi-branched junctions.

What is tRNA’s tertiary structure?

A folded L-shaped structure that stabilizes its function in translation.

What are the three parts of a nucleotide?

Nitrogen base, sugar (pentose), and phosphate group.

What type of bond joins bases in complementary strands?

Hydrogen bonds.

What type of bond joins nucleotides within a single strand?

Phosphodiester bonds.

What does “complementary base pairing” mean?

A pairs with T (or U in RNA), and G pairs with C according to specific hydrogen-bonding rules.

Why does DNA with high GC content have higher melting temperature?

Because G–C pairs have three hydrogen bonds versus two in A–T pairs.

Who provided X-ray diffraction data critical to DNA structure discovery?

Rosalind Franklin and Maurice Wilkins.