Nucleic Acids

AQA spec ref: 3.1.3 - Nucleic acids

Nucleic acids are the molecules that store and transmit genetic information. There are two types: DNA (deoxyribonucleic acid), which stores the genetic code in the nucleus, and RNA (ribonucleic acid), which carries and expresses that information during protein synthesis. Their structure is directly adapted to their function - a recurring AQA theme.

Nucleotide Structure - The Monomer

Both DNA and RNA are polymers made of nucleotide monomers. Each nucleotide has three components joined by condensation reactions:

1. A pentose sugar - deoxyribose (in DNA) or ribose (in RNA)
2. A phosphate group - linked to the 5' carbon of the sugar
3. A nitrogenous base - linked to the 1' carbon of the sugar

The bases are divided into two structural groups:

• Purines (double-ring structure): adenine (A) and guanine (G)
• Pyrimidines (single-ring structure): cytosine (C), thymine (T) (DNA only), uracil (U) (RNA only)

Nucleotides are joined by condensation reactions between the phosphate group of one nucleotide and the 3' carbon of the pentose sugar of the next, releasing water and forming a phosphodiester bond. The resulting chain has a sugar-phosphate backbone running 5'→3', with bases projecting inward.

DNA Structure

DNA is a double-stranded polynucleotide arranged as a double helix, first described by Watson and Crick in 1953 (using Franklin's X-ray diffraction data and Chargaff's base ratios).

The Double Helix

• Two antiparallel polynucleotide strands wind around a central axis
• Antiparallel means one strand runs 5'→3' and the other runs 3'→5'. The 5' end has a free phosphate group; the 3' end has a free hydroxyl (-OH) group.
• The two strands are held together by hydrogen bonds between complementary base pairs on the inside of the helix
• The sugar-phosphate backbones are on the outside

Complementary Base Pairing

Bases pair specifically and always with their complement:

• Adenine pairs with Thymine - held by 2 hydrogen bonds
• Guanine pairs with Cytosine - held by 3 hydrogen bonds

This is Chargaff's rule: in any DNA sample, [A] = [T] and [G] = [C]. The specific pairing (A-T, G-C) is due to complementary shapes and the number of hydrogen bond donors/acceptors on each base.

The G≡C bond is stronger than the A=T bond (3 H-bonds vs 2), so DNA with a higher G+C content is more thermally stable (requires more energy to denature).

Why DNA is Double-Stranded

The double-stranded structure serves two critical functions:

• Stability - the two strands protect the base sequence; damage to one strand can be repaired using the complementary strand as a template
• Semiconservative replication - each strand acts as a template for a new complementary strand, ensuring each daughter cell receives an exact copy of the genetic information. See DNA replication and Protein synthesis.

Supercoiling and Histones

In eukaryotes, DNA is approximately 2 metres long but must fit in a nucleus ~10 μm across. DNA is wound around histone proteins to form nucleosomes, which then coil further into chromatin. This compaction is crucial for fit and for gene regulation (see Gene Expression).

In prokaryotes, DNA is circular and supercoiled but not associated with histones.

RNA Structure

RNA is a single-stranded polynucleotide. It contains:

• Ribose (not deoxyribose) - has an -OH at the 2' carbon
• Uracil instead of thymine (U pairs with A)

The single-stranded nature allows RNA to fold into complex 3D shapes stabilised by intramolecular hydrogen bonds, which is important for tRNA function.

Types of RNA

mRNA (messenger RNA)

• Single-stranded, linear molecule
• Synthesised in the nucleus during transcription - its sequence is complementary to the template strand of DNA
• Carries the genetic code from the nucleus to ribosomes in the cytoplasm as a series of codons (triplets of bases, each coding for one amino acid)
• Relatively short-lived - degraded after translation

tRNA (transfer RNA)

• Single-stranded but folds into a cloverleaf shape due to internal base pairing
• Approximately 75 - 90 nucleotides long
• Has an anticodon loop - three unpaired bases that are complementary to a specific mRNA codon
• Has an amino acid attachment site at the 3' end (sequence CCA) - the specific amino acid is attached here by aminoacyl-tRNA synthetase enzymes
• Carries amino acids to the ribosome during translation

rRNA (ribosomal RNA)

• Structural and catalytic component of ribosomes
• Combined with ribosomal proteins to form the large and small ribosomal subunits
• The catalytic activity of the ribosome (peptide bond formation) is carried out by rRNA, not protein - ribosomes are ribozymes

DNA vs RNA - Comparison Table

Nucleotides Beyond DNA and RNA

Some nucleotides function outside nucleic acids:

• ATP (adenosine triphosphate) - adenine + ribose + 3 phosphate groups. The universal energy currency. See ATP.
• NAD / FAD - coenzymes that act as hydrogen carriers in respiration. NAD is a dinucleotide (two nucleotides joined). See Respiration.

Summary

• Nucleotide=pentose sugar+phosphate group+nitrogenous base
• Nucleotides joined by condensation→phosphodiester bonds→polynucleotide chains
• DNA: double-stranded, deoxyribose, A-T (2 H-bonds) and G-C (3 H-bonds), antiparallel, double helix
• RNA: single-stranded, ribose, U instead of T; three types: mRNA (codons, carries code), tRNA (anticodon + amino acid), rRNA (ribosome)
• Chargaff's rule: [A]=[T], [G]=[C] in any DNA sample

AQA Exam Tips

• Antiparallel - always state that the two DNA strands run in opposite directions (one 5'→3', other 3'→5'). AQA mark schemes explicitly require this.
• Number of H-bonds: A=T has 2; G≡C has 3. Higher G+C content → more H-bonds → higher melting temperature → more stable DNA.
• Phosphodiester bond - formed between the phosphate group of one nucleotide and the 3' carbon (hydroxyl) of the next sugar. Don't just say "phosphate bond."
• DNA vs RNA sugar: deoxyribose lacks the -OH group at the 2' carbon that ribose has. This makes RNA less chemically stable (the 2'-OH can attack the phosphodiester bond).
• tRNA structure: cloverleaf secondary structure. Anticodon at one end, amino acid attachment (CCA sequence) at 3' end. The anticodon is complementary and antiparallel to the mRNA codon.
• Template strand vs coding strand: the template strand is read 3'→5' by RNA polymerase; the mRNA produced is identical in sequence to the coding strand (but with U instead of T).