Nucleic Acids, Proteins and Macromolecules

Protein and nucleic acid structure

The α-carbon of an amino acid is a chiral centre whenever its four substituents (H, NH₂, COOH and the side chain R) are all different. Glycine is the only common amino acid whose α-carbon is not chiral, because its side chain is a hydrogen atom. A second stereogenic carbon in the side chain gives an amino acid two chiral centres. Isoleucine and threonine are the standard examples, since each has a β-carbon bearing four different groups, while leucine (isobutyl side chain) and serine (–CH₂OH side chain) have only the α-carbon as a stereocentre.

In the α-helix, the backbone forms an intrachain hydrogen bond between the C=O of residue i and the N–H of residue i+4. A helix of N residues therefore contains N - 4 hydrogen bonds. The notation 3.6₁₃ means 3.6 residues per helical turn, with a hydrogen-bonded ring of 13 atoms. The number of turns is N/3.6. For example, if a helix has 32 intrachain hydrogen bonds, then N = 36 and the helix has 36/3.6 = 10 turns.

A nucleotide is the basic unit of a nucleic acid and consists of three parts: a nitrogenous base, a pentose sugar (ribose or deoxyribose) and one or more phosphate groups.

• Nucleoside — base plus sugar, with no phosphate. Adding phosphate gives a nucleotide.
• Nucleoside triphosphate — a nucleotide carrying three phosphate groups, such as dATP. It is still a single nucleotide, not a polymer.
• Nucleic acid — a long polymer of many nucleotides joined by phosphodiester bonds.

In B-form DNA, adjacent base pairs are separated by a rise of about 3.4 Å along the helix axis. The number of base pairs in a molecule is therefore its length divided by 3.4 Å, and multiplying by the mass per base pair gives the total mass. Unit conversion matters here: 1\text{ m} = 10^{10} Å.

Reversible receptor–ligand binding depends on noncovalent forces such as ionic interactions (salt bridges), hydrogen bonds and hydrophobic interactions. These bonds form and break without permanently changing either molecule. Peptide bonds are covalent, and they are not broken during ligand binding, so they do not contribute to reversibility.

The three techniques that give atomic-resolution three-dimensional structures of proteins are X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy. X-ray diffraction uses protein crystals, NMR determines structures in solution from distance and angle restraints, and cryo-EM reconstructs structures from images of frozen particles. Circular dichroism is different: it reports secondary structure content and folding, but it does not give atomic coordinates.

Genetic code and codon pairing

mRNA codons and tRNA anticodons pair in an antiparallel manner, so the 5′ end of the codon pairs with the 3′ end of the anticodon. Because the mRNA is transcribed from the template (antisense) DNA strand, the template strand is complementary and antiparallel to the mRNA. Therefore, when an anticodon is given in the 3′→5′ direction, the mRNA codon is its reverse complement, and the template strand reads the same 3′→5′ as the anticodon.

The number of codons is 4^n, where n is the number of nucleotides per codon.

• Triplet code — 4^3 = 64 codons, which is the actual genetic code, including three stop codons.
• Doublet code — 4^2 = 16 codons. Such a code would be too small to specify 20 amino acids.

To estimate the molecular mass of a polypeptide from a sequence, first locate the start codon AUG, then read in frame until the first in-frame stop codon (UAA, UAG or UGA). Each codon before the stop specifies one amino acid residue. The mass is the number of residues multiplied by the average residue mass. In the typical case of a 14-residue peptide with an average residue mass of 110 Da, the mass is 14 \times 110 = 1540 Da. Only codons before the stop count, and the stop codon itself adds no residue.

Recombinant therapeutic proteins

Recombinant DNA technology allows human therapeutic proteins to be produced in engineered host cells. Each protein or agent is linked to a specific clinical condition, and these associations are frequently tested.