Proteins: Amino Acids, Peptide Bonds and Four Levels of Structure

One letter, one disease

Hemoglobin, the oxygen-carrying protein in your red blood cells, has 574 amino acids in four chains. In people with sickle cell disease, just one amino acid in each β chain is different: at position 6, glutamic acid (charged, hydrophilic) is replaced by valine (non-polar, hydrophobic). That single change makes hemoglobin molecules stick together when oxygen is low, bending red blood cells into stiff sickle shapes that can block small blood vessels.

Proteins are the cell's workers: enzymes, transporters, receptors, hormones, antibodies, motors and structural fibres. Every one of them depends on folding into exactly the right shape.

Amino acids

Every amino acid has the same backbone: a central α carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and an R group. At cell pH, the amino group is usually –NH₃⁺ and the carboxyl –COO⁻.

The R group is what makes each of the 20 amino acids different. Biochemists sort them into four groups:

• Non-polar (hydrophobic): R is mostly hydrocarbon. Examples: glycine (R = H, the smallest), alanine (–CH₃), valine, leucine, phenylalanine.
• Polar (uncharged, hydrophilic): R has –OH, –SH or an amide. Examples: serine, threonine, asparagine, glutamine, cysteine.
• Acidic (negative at pH 7): R has a carboxyl group. Examples: aspartic acid, glutamic acid.
• Basic (positive at pH 7): R has an amino group. Examples: lysine, arginine, histidine (histidine is only partly charged at pH 7).

The peptide bond

The carboxyl group of one amino acid reacts with the amino group of the next in a condensation reaction, forming a peptide bond (C–N) and releasing water. Repeating this gives a polypeptide with a free amino end (N-terminus) and a free carboxyl end (C-terminus). Ribosomes always build chains from N to C. Digestive proteases break peptide bonds by hydrolysis.

Four levels of protein structure

1. Primary structure: the sequence of amino acids, such as Gly–Ala–Cys–Lys… It is coded by a gene (Molecular Genetics). The sequence decides everything else.
2. Secondary structure: parts of the chain coil into an α-helix or line up side by side as a β-pleated sheet. Both are held by hydrogen bonds between backbone atoms: the C=O of one peptide bond and the N–H of another. R groups are not involved.
3. Tertiary structure: the whole polypeptide folds into a specific 3-D shape. This level is held by interactions between R groups:

• hydrophobic interactions: non-polar R groups cluster in the core, away from water;
• hydrogen bonds between polar R groups;
• ionic bonds between acidic (–COO⁻) and basic (–NH₃⁺) R groups;
• disulfide bridges: strong covalent –S–S– links between cysteines.

1. Quaternary structure: two or more polypeptides (subunits) fit together, held by the same kinds of bonds. Hemoglobin has four subunits: two α and two β, each holding an iron-containing heme group. Not every protein has quaternary structure.

Many proteins fold on their own, but some get help from chaperone proteins, which shield them while they fold.

Denaturation

A protein is denatured when its secondary, tertiary or quaternary structure falls apart. The peptide bonds are not broken, so the primary structure remains, but the shape and function are lost.

• Heat makes the chain vibrate until hydrogen bonds and hydrophobic interactions break (frying an egg white turns clear liquid albumin into a white solid).
• pH changes alter the charges on acidic and basic R groups, breaking ionic bonds and hydrogen bonds.
• Heavy-metal ions, salts, alcohol and detergents disrupt R-group interactions.

Some small proteins can refold when conditions return to normal, which showed that the primary structure alone contains all the information for the shape. Many larger proteins, like a cooked egg, never recover.