Protein Structure in 3D – from Amino Acids to Quaternary Structure
BiologyCell BiologyAges 15–16
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Sign in to playA rotatable 3D model of proteins: amino acids (amine group, carboxyl group, R group) join by peptide bonds in condensation reactions to form polypeptides; α-helices and β-pleated sheets are held by hydrogen bonds; tertiary structure is held by hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions, each of which can be shown or hidden; haemoglobin has four chains and four haem groups. Students change temperature and pH, add a reducing agent or a mutation and watch the protein denature on a melting curve, compare fibrous collagen with globular haemoglobin and follow the protein secretory pathway. A 2D view is included.
Lesson: Proteins: amino acids, peptide bonds, levels of protein structure and denaturation; fibrous and globular proteins; the protein secretory pathway
What it shows
Proteins are polymers of amino acids. Each amino acid has an amine group, a carboxyl group and an R group on a central carbon atom, and condensation reactions join amino acids by peptide bonds into a polypeptide whose sequence is the primary structure. Hydrogen bonds between backbone groups fold the chain into α-helices and β-pleated sheets. Hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions between R groups give the 3D tertiary shape, and several polypeptides can form a quaternary structure, as in haemoglobin. Heat and extreme pH break these bonds and denature the protein.
How to use
Choose a tab. On Amino acids, pick an amino acid and tick Ionised (pH 7). On Peptide bonds, use the Add buttons and Hydrolyse last bond. On Tertiary, move Temperature and pH, choose a Mutation or Reducing agent, show or hide each bond type and press Record result to compare Tm values. On Quaternary, try O₂ bound, Separate subunits and the sickle-cell mutation. Switch between 3D and 2D at any time.
Parameters you can change
- Screen Amino acids, Peptide bonds, Secondary structure, Tertiary structure and denaturation, Quaternary structure (haemoglobin), Fibrous and globular proteins, Protein secretory pathway
- View 3D (rotatable), 2D (flat diagram)
- Amino acid on the Amino acids screen glycine (Gly), alanine (Ala), serine (Ser), cysteine (Cys), aspartic acid (Asp), lysine (Lys), phenylalanine (Phe)
- Draw amino acids in their ionised form (pH 7)
- Starting chain on the Peptide bonds screen (one-letter codes G, A, S, C, D, K, F; 1–10 amino acids)
- Type of secondary structure α-helix, β-pleated sheet
- Show hydrogen bonds
- Temperature 0–100 °C
- pH 1–13
- Mutation on the Tertiary screen None (wild type), Cys → Ser (no disulfide bridge), Asp → Ala (one ionic bond lost), Phe → Lys in the hydrophobic core
- Add a reducing agent (breaks disulfide bridges)
- Show ionic bonds
- Show disulfide bridges
- Show hydrophobic interactions
- Sickle-cell mutation (HbS)
Questions to explore
- How many peptide bonds and water molecules are formed when 8 amino acids join into one polypeptide?
- Why does the protein lose its function at 70 °C while its disulfide bridge stays intact?
- At pH 2, how does the Cys → Ser mutant differ from the wild-type protein, and why?
