2.3 Proteins

· Proteins are polymers made from amino acids joined by peptide bonds.
· Each amino acid has a central carbon bonded to an amine group (NH₂), carboxyl group (COOH), hydrogen atom, and variable R group.
· The R group differs between amino acids and affects protein properties, folding, and function.
· Proteins show a strong structure–function relationship: the precise amino acid sequence determines folding, shape and biological role.

This diagram shows the general structure shared by all amino acids. The R group changes between amino acids and influences how the protein folds and functions. Source

Peptide Bonds

· A peptide bond forms when the carboxyl group of one amino acid reacts with the amine group of another amino acid.
· This is a condensation reaction because a molecule of water is released.
· A dipeptide contains two amino acids joined by one peptide bond.
· A polypeptide contains many amino acids joined by peptide bonds.
· A peptide bond is broken by hydrolysis, where water is added.
· Exam phrase: condensation forms peptide bonds; hydrolysis breaks peptide bonds.

Educational caption: This diagram shows condensation between two amino acids. The peptide bond forms between the carbon of the carboxyl group and the nitrogen of the amine group. Source

Protein Structure Levels

· Primary structure = the sequence of amino acids in a polypeptide chain.
· Secondary structure = local folding into α-helices or β-pleated sheets, held by hydrogen bonds.
· Tertiary structure = the overall 3D shape of one polypeptide, caused by interactions between R groups.
· Quaternary structure = arrangement of two or more polypeptide chains into one functional protein.
· Changes in primary structure can alter folding, 3D shape, and therefore function.

Bonds and Interactions Holding Proteins in Shape

· Hydrophobic interactions occur when non-polar R groups cluster away from water inside the protein.
· Hydrogen bonds form between slightly positive and slightly negative groups in the polypeptide.
· Ionic bonds form between oppositely charged R groups.
· Covalent bonds are strong bonds; the key example is a disulfide bond between sulfur-containing R groups.
· These interactions maintain the protein’s specific 3D shape, which is essential for function.

Globular and Fibrous Proteins

· Globular proteins are generally soluble and usually have physiological roles.
· Fibrous proteins are generally insoluble and usually have structural roles.
· Haemoglobin = example of a globular protein.
· Collagen = example of a fibrous protein.
· Exam contrast: globular = compact, soluble, functional/physiological; fibrous = long, insoluble, structural.

Haemoglobin: Globular Protein Example

· Haemoglobin has quaternary structure because it contains four polypeptide chains.
· It is made from two α-globin chains and two β-globin chains.
· Each chain is associated with a haem group.
· Each haem group contains an iron ion (Fe²⁺).
· The iron ion binds reversibly with oxygen, allowing haemoglobin to transport oxygen.
· Structure–function link: haemoglobin’s globular shape, four subunits, and haem groups allow efficient oxygen transport in blood.

Haemoglobin is a globular protein with quaternary structure. Its four polypeptide chains and haem groups allow oxygen to bind and be transported. Source

Collagen: Fibrous Protein Example

· Collagen is a fibrous protein with a long, strong structure.
· A collagen molecule is made from three polypeptide chains wound together into a triple helix.
· Many collagen molecules are arranged together to form collagen fibres.
· Collagen fibres have high tensile strength, meaning they resist stretching.
· Structure–function link: collagen’s triple helix and fibre arrangement make it strong and suitable for support in tissues such as tendons, skin and bone.

This diagram shows collagen’s triple helix. The arrangement of three polypeptide chains gives collagen strength, making it suitable for structural support. Source

Common Exam Command Words and Answers

· Describe amino acid structure: mention amine group, carboxyl group, hydrogen, R group, and central carbon.
· Describe peptide bond formation: say condensation, water released, and bond forms between COOH and NH₂ groups.
· Explain protein structure levels: define primary, secondary, tertiary, and quaternary accurately.
· Relate haemoglobin to function: mention four polypeptide chains, haem groups, iron, and oxygen binding.
· Relate collagen to function: mention triple helix, collagen fibres, and tensile strength.