Protein Structure

Proteins are the most functionally diverse group of biological molecules. They serve as enzymes, structural components, antibodies, transport molecules, hormones, receptors, and much more. All proteins are polymers of amino acids linked by peptide bonds, but the enormous variety of protein functions arises from the different sequences and three-dimensional arrangements of these amino acids.

---

Amino Acid Structure

Key Definition: An amino acid is the monomer of a protein. It consists of a central carbon atom (the α-carbon) bonded to four groups: an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and a variable R group (side chain).

There are 20 different amino acids used by living organisms to build proteins. Each has a different R group, which determines:

• The chemical properties of the amino acid (polar, non-polar, charged, uncharged).
• How the amino acid interacts with other amino acids and with water.
• The overall shape and function of the protein.

Examples of R groups:

• Glycine: R = H (the simplest amino acid).
• Alanine: R = CH₃ (non-polar, hydrophobic).
• Serine: R = CH₂OH (polar, hydrophilic).
• Cysteine: R = CH₂SH (can form disulphide bridges with another cysteine).
• Aspartate: R = CH₂COO⁻ (negatively charged at physiological pH).
• Lysine: R = (CH₂)₄NH₃⁺ (positively charged at physiological pH).

---

Peptide Bonds

Key Definition: A peptide bond is a covalent bond formed between the amino group (–NH₂) of one amino acid and the carboxyl group (–COOH) of another, through a condensation reaction that releases one molecule of water.

• Two amino acids joined by a peptide bond form a dipeptide.
• Three or more amino acids joined form a polypeptide.
• A protein may consist of one or more polypeptide chains, sometimes with additional non-protein components (prosthetic groups).

The bond is broken by hydrolysis (addition of water), which occurs during digestion (catalysed by proteases and peptidases).

Biuret Test for Proteins

The Biuret test detects the presence of peptide bonds:

1. Add the sample to a test tube.
2. Add an equal volume of sodium hydroxide (NaOH) solution.
3. Add a few drops of dilute copper(II) sulphate (CuSO₄) solution and mix gently (do not shake).
4. Positive result: the solution turns from blue to purple/violet. Cu²⁺ ions form coordinate bonds with the nitrogen atoms in peptide bonds.
5. Negative result: the solution remains blue.

Exam Tip: The Biuret test requires at least two peptide bonds to give a positive result, so dipeptides (with one peptide bond) and single amino acids give a negative result in the standard test.

---

Levels of Protein Structure

Primary Structure

The primary structure is the specific sequence of amino acids in the polypeptide chain, held together by peptide bonds. It is determined by the base sequence of the gene that codes for the protein.

• Even a single amino acid change can dramatically alter protein function (e.g., in sickle cell anaemia, a single substitution of valine for glutamic acid at position 6 of the β-globin chain causes the haemoglobin molecules to polymerise under low oxygen conditions, distorting red blood cells into a sickle shape).

Secondary Structure

The polypeptide chain folds into regular, repeating structures stabilised by hydrogen bonds between the C=O group of one amino acid and the N–H group of another amino acid in the peptide backbone (not between R groups).

Two main types:

• α-helix: the polypeptide coils into a right-handed helix. Hydrogen bonds form between every fourth peptide bond (between the C=O of residue n and the N–H of residue n+4). Common in fibrous proteins such as keratin.
• β-pleated sheet: the polypeptide folds back on itself, forming a sheet-like structure. Hydrogen bonds form between adjacent parallel or antiparallel strands. Common in silk fibroin and parts of many globular proteins.

Tertiary Structure

Key Definition: The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, resulting from interactions between the R groups of amino acids.

The following bonds and interactions maintain the tertiary structure: