describe the structure of a molecule of collagen as an example of a fibrous protein, and the arrangement of collagen molecules to form collagen fibres

Proteins – Collagen (A Key Example of a Fibrous Protein)

Learning Objective

Describe the structure of a collagen molecule and explain how collagen molecules are organised to form collagen fibres. Relate structure to function and link the topic to other areas of the Cambridge International AS & A Level Biology (9700) syllabus.

1. Protein Overview – Fibrous vs. Globular

2. Collagen – Molecular Structure

2.1 Primary Structure

• Each polypeptide chain contains ~1 000 residues.
• Repeating tripeptide motif Gly‑X‑Y (≈ 95 % of the sequence).
• X is usually proline; Y is usually hydroxyproline (post‑translationally hydroxylated).
• Why glycine every third residue? Glycine’s side‑chain is a single H atom, allowing the three chains to pack tightly at the centre of the triple helix without steric clash.

2.2 Secondary Structure of Each Chain

• Each chain adopts a left‑handed poly‑proline II helix – an extended, non‑α‑helical conformation with ~3 residues per turn.
• The helix is essentially a straight rod; there is no independent tertiary folding within a single chain.

2.3 Quaternary Structure – The Triple Helix (Tropocollagen)

• Three left‑handed helices wind around one another to form a right‑handed triple helix (≈ 300 nm long, 1.5 nm diameter).
• This arrangement is the quaternary structure of collagen and is the basis for its extraordinary tensile strength.

2.4 Stabilising Interactions

• Hydrogen bonds: carbonyl of Gly in one chain ↔ amide NH of the adjacent chain (repeating every 3 residues).
• Hydroxyproline: adds polarity, stabilises the triple helix by strengthening the H‑bond network; also raises the melting temperature.
• Covalent cross‑links (lysyl‑oxidase mediated):

  1. Lysyl‑oxidase (Cu²⁺‑dependent) oxidises specific lysine or hydroxylysine residues to aldehydes.
  2. The aldehydes react with neighbouring chains to form irreversible covalent bonds (aldol‑type cross‑links).
  3. Vitamin C is required for proline/lysine hydroxylation; deficiency → weak cross‑links (scurvy).

2.5 Dimensional Summary of a Single Collagen Molecule

3. Hierarchical Organisation – From Molecule to Tissue

1. Tropocollagen – the right‑handed triple helix (single molecule).
2. Collagen fibril – many tropocollagen molecules staggered by ~¼ of their length (the “quarter‑stagger” model). This creates a repeating banding pattern with a 67 nm periodicity called the D‑period.

   • Overlap zone (~0.45 × length) and gap zone (~0.55 × length) give rise to the characteristic electron‑microscopic striations.

3. Collagen fibre – parallel bundles of fibrils linked by extensive covalent cross‑links and surrounded by proteoglycans and glycoproteins (e.g., decorin, fibronectin).
4. Fascicle / tissue – groups of fibres embedded in a ground substance, forming tendons, ligaments, dermis, bone matrix, cartilage, etc.

3.1 Quarter‑Stagger Model (Fibril Formation)

• Each tropocollagen molecule overlaps the next by ~75 nm (≈ ¼ of its length).
• The stagger produces alternating “gap” and “overlap” zones that generate the 67 nm D‑period banding seen in transmission electron microscopy.

3.2 Cross‑linking & Mechanical Strength

• Lysyl‑oxidase creates intra‑fibrillar and inter‑fibrillar covalent bonds, dramatically increasing tensile strength.
• Cross‑link density rises with age → tissues become stiffer but less extensible.
• Insufficient cross‑linking (e.g., vitamin C deficiency) produces weak, easily torn fibres → clinical scurvy.

4. Functional Significance of the Structure

• Tensile strength: the tightly packed triple helix and extensive cross‑links resist pulling forces in tendons and ligaments.
• Scaffold for mineralisation: in bone, the orderly fibrils act as a template for hydroxyapatite deposition, providing compressive strength.
• Flexibility and resilience: the long, unbranched fibres can stretch slightly without breaking, essential for skin elasticity.
• Biomaterial applications: collagen’s biocompatibility makes it a basis for sutures, wound dressings, and tissue engineering scaffolds (link to A‑Level extension topics).

5. Integration with the Wider Syllabus

5.1 Protein Terminology (Syllabus LO 2.3)

• Primary, secondary, tertiary, quaternary structure – illustrated with collagen.
• Comparison of structural levels in a fibrous protein (collagen) versus a globular protein (e.g., haemoglobin).

5.2 Enzyme Connection (Syllabus LO 3)

• Collagen‑synthesising enzymes: prolyl‑hydroxylase, lysyl‑hydroxylase (require vitamin C, Fe²⁺, O₂, α‑ketoglutarate).
• Illustrates how protein structure determines catalytic activity – a link to enzyme kinetics.

5.3 Membrane Proteins & Transport (Syllabus LO 4)

• Contrast: collagen is an extracellular structural protein, whereas membrane proteins (e.g., channel proteins) are amphipathic and facilitate transport.
• Understanding the diversity of protein functions across the cell.

5.4 Practical Skills (Paper 3 & Paper 5)

5.5 Clinical & Genetic Links (Cross‑Topic Integration)

• Scurvy – Vitamin C deficiency → impaired hydroxylation → weak cross‑links.
• Ehlers‑Danlos syndrome (type VI) – Mutations in lysyl‑hydroxylase → reduced cross‑linking → hyper‑elastic skin.
• Osteogenesis imperfecta – Mutations in COL1A1 or COL1A2 (type I collagen) → brittle bones.
• These conditions illustrate the link between molecular genetics, protein biochemistry and disease – a key theme in the syllabus.

6. Summary Checklist (Exam‑Ready)

• Primary structure: Gly‑X‑Y repeat; Gly every third residue.
• Secondary structure: left‑handed poly‑proline II helix for each chain.
• Quaternary structure: three chains → right‑handed triple helix (tropocollagen).
• Stabilising forces: intra‑chain H‑bonds, hydroxyproline, lysyl‑oxidase‑mediated covalent cross‑links (vitamin C‑dependent).
• Dimensions: ~300 nm long, 1.5 nm diameter.
• Quarter‑stagger arrangement → 67 nm D‑period in fibrils.
• Cross‑link density ↑ with age → increased rigidity.
• Functional sites: tendons, ligaments, skin, bone matrix, cartilage.
• Key related techniques: SDS‑PAGE, X‑ray diffraction, EM, hydroxyproline assay.
• Clinical connections: scurvy, Ehlers‑Danlos, osteogenesis imperfecta.

7. Suggested Diagram (for the exam booklet)

8. Practice Exam Questions

1. Explain why glycine must occur at every third position in the collagen primary structure.
2. Describe how hydroxyproline contributes to the stability of the collagen triple helix.
3. Using a labelled diagram, illustrate the hierarchical organisation of collagen from the triple‑helix molecule to a tendon.
4. Discuss the role of vitamin C in collagen biosynthesis and the consequences of its deficiency.
5. Compare the structural differences between collagen (fibrous) and haemoglobin (globular) and relate these differences to their respective functions.
6. Outline how lysyl‑oxidase activity can be demonstrated experimentally and what the results would indicate about cross‑link formation.