CIE AS/A Level Biology -2.3 Proteins- Study Notes- New Syllabus
CIE AS/A Level Biology -2.3 Proteins- Study Notes- New Syllabus
Ace A level Biology Exam with CIE AS/A Level Biology -2.3 Proteins- Study Notes- New Syllabus
Key Concepts:
- describe and draw the general structure of an amino acid and the formation and breakage of a peptide bond
- explain the meaning of the terms primary structure, secondary structure, tertiary structure and quaternary structure of proteins
- describe the types of interaction that hold protein molecules in shape:
• hydrophobic interactions
• hydrogen bonding
• ionic bonding
• covalent bonding, including disulfide bonds - state that globular proteins are generally soluble and have physiological roles and fibrous proteins are generally insoluble and have structural roles
- describe the structure of a molecule of haemoglobin as an example of a globular protein, including the formation of its quaternary structure from two alpha (α) chains (α–globin), two beta (β) chains (β–globin) and a haem group
- relate the structure of haemoglobin to its function, including the importance of iron in the haem group
- 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
- relate the structures of collagen molecules and collagen fibres to their function
General Structure of an Amino Acid and Peptide Bond Formation
🌱 General Structure of an Amino Acid
- Central carbon atom (alpha carbon, C).
- Amino group (-NH₂) attached to alpha carbon.
- Carboxyl group (-COOH) attached to alpha carbon.
- Hydrogen atom (H) attached to alpha carbon.
- R group (side chain) varies between amino acids, determining properties.
✍️ Diagram of a General Amino Acid
The R group varies (e.g., -CH₃ in alanine, -OH in serine).
🔗 Formation of a Peptide Bond (Condensation Reaction)
- Peptide bond is a covalent bond linking two amino acids.
- Forms between the carboxyl group (-COOH) of one amino acid and amino group (-NH₂) of another.
- Condensation reaction removes a water molecule (H₂O).
- Hydroxyl (–OH) from carboxyl and hydrogen (H) from amino combine to form water.
- The bond links carbon (C) of carboxyl to nitrogen (N) of amino group.
🔍 Peptide Bond Breakage (Hydrolysis Reaction)
- Peptide bonds can be broken by hydrolysis (addition of water).
- This splits the bond and releases individual amino acids.
- This is the reverse of condensation.
✍️ Diagram of Peptide Bond Formation
| Process | Description |
|---|---|
| Peptide Bond | Covalent bond linking amino acids via condensation (water removed) |
| Hydrolysis | Breaking peptide bonds by adding water |
| Amino Acid Parts | Central C, amino group, carboxyl group, H, R side chain |
Levels of Protein Structure
🌱 Primary Structure
- Unique linear sequence of amino acids in a polypeptide chain.
- Determined by the gene encoding the protein.
- The amino acid order dictates all higher structure levels and protein function.
🌿 Secondary Structure
- Local folding of the polypeptide chain into regular shapes.
- Formed mainly by hydrogen bonds between backbone atoms (not side chains).
- Common forms:
- Alpha (α) helix — coiled spiral shape.
- Beta (β) pleated sheet — folded sheet-like structure.
🔬 Tertiary Structure
- Overall 3D shape of a single polypeptide chain.
- Formed by interactions between amino acid R groups (side chains), including:
- Hydrogen bonds
- Ionic bonds
- Disulfide bridges (covalent bonds between cysteines)
- Hydrophobic interactions
- Determines protein specificity and function.
🧠 Quaternary Structure
- Arrangement of multiple polypeptide chains (subunits) into a functional protein complex.
- Stabilized by the same bonds as tertiary structure.
- Examples: Hemoglobin (4 subunits), insulin (2 subunits).
| Level of Structure | Description | Key Features |
|---|---|---|
| Primary | Sequence of amino acids | Peptide bonds |
| Secondary | Local folding into α-helix or β-sheet | Hydrogen bonds (backbone) |
| Tertiary | 3D shape of one polypeptide | Interactions between side chains |
| Quaternary | Multiple polypeptides forming complex | Subunit interactions |
Types of Interactions That Hold Protein Molecules in Shape
🌱 1. Hydrophobic Interactions
- Occur between non-polar (hydrophobic) side chains of amino acids.
- Hydrophobic groups cluster inside the protein, away from water, stabilizing the 3D shape.
- Helps proteins fold by pushing hydrophobic regions inward.
🌿 2. Hydrogen Bonding
- Form between polar side chains or backbone atoms.
- A hydrogen atom is attracted to electronegative atoms like oxygen or nitrogen.
- Maintains secondary structures (α-helices and β-sheets) and stabilizes tertiary structure.
🔬 3. Ionic Bonding (Salt Bridges)
- Occurs between positively charged (basic) and negatively charged (acidic) side chains.
- Electrostatic attractions stabilize tertiary and quaternary structures.
- Sensitive to pH changes which can disrupt these bonds.
🔗 4. Covalent Bonding (Including Disulfide Bonds)
- The strongest bonds stabilizing protein structure.
- Disulfide bonds form between sulfur atoms of two cysteine residues.
- Provide strong links maintaining tertiary or quaternary structure, especially in extracellular proteins.
| Interaction | Description | Role in Protein Structure |
|---|---|---|
| Hydrophobic | Non-polar side chains cluster inside protein | Drives folding by avoiding water |
| Hydrogen bonds | Between polar groups (backbone or side chains) | Stabilizes secondary and tertiary structure |
| Ionic bonds | Between charged side chains | Stabilizes tertiary/quaternary, pH sensitive |
| Covalent bonds | Strong bonds including disulfide bonds (S–S) | Provides strong, permanent stabilization |
🧠 Key Point: Protein shape is maintained by multiple types of bonds and interactions working together, allowing precise folding and stability.
Types of Proteins: Globular vs Fibrous
🌱 Globular Proteins
- Generally soluble in water due to their compact, folded structure with hydrophilic groups on the outside.
- Have physiological roles such as enzymes, hormones, transport proteins (e.g., hemoglobin), and antibodies.
🌿 Fibrous Proteins
- Generally insoluble in water because of their long, fibrous, and repetitive structure with mostly hydrophobic amino acids exposed.
- Serve structural roles providing strength and support to cells and tissues (e.g., collagen in connective tissue, keratin in hair and nails).
| Protein Type | Solubility | Role |
|---|---|---|
| Globular | Soluble | Physiological functions (enzymes, transport, regulation) |
| Fibrous | Insoluble | Structural support (strength, protection) |
Structure of Haemoglobin: An Example of a Globular Protein
🌱 Basic Structure
- Haemoglobin is a globular protein found in red blood cells.
- Its main function is to transport oxygen from the lungs to tissues.
🌿 Subunit Composition (Quaternary Structure)
- Haemoglobin’s quaternary structure is formed by four polypeptide chains:
- Two alpha (α) chains (α-globin)
- Two beta (β) chains (β-globin)
- Each chain is a globular polypeptide folded into a specific 3D shape.
🔬 Haem Group
- Each polypeptide chain contains a haem group, a prosthetic (non-protein) group.
- The haem group has an iron (Fe²⁺) ion at its center.
- This iron ion binds oxygen molecules reversibly.
🔗 Quaternary Structure Formation
- The four polypeptide chains are held together by non-covalent interactions:
- Hydrogen bonds
- Ionic bonds
- Hydrophobic interactions
- This arrangement allows haemoglobin to change shape during oxygen binding and release, facilitating efficient oxygen transport.
| Feature | Description |
|---|---|
| Protein Type | Globular |
| Number of Polypeptide Chains | Four (2 α-globin + 2 β-globin) |
| Prosthetic Group | Haem (contains Fe²⁺ ion) |
| Function | Oxygen transport |
| Quaternary Structure | Subunits held by hydrogen, ionic, and hydrophobic bonds |
🧠 Key Point: Haemoglobin’s quaternary structure enables cooperative oxygen binding, making it an efficient oxygen carrier in blood.
Structure of Haemoglobin and Its Relation to Function
🌱 Key Structural Features of Haemoglobin
- Quaternary structure: Four polypeptide chains (2 α-globin + 2 β-globin) arranged to work cooperatively.
- Haem groups: Each chain contains one haem group with an iron (Fe²⁺) ion at the center.
- The protein’s globular shape allows it to be soluble in blood.
🔍 How Structure Supports Function
| Structural Feature | Functional Importance |
|---|---|
| Four subunits | Allows cooperative binding: binding of oxygen to one subunit increases affinity at others, enhancing oxygen uptake and release. |
| Haem group with Fe²⁺ ion | The iron ion binds oxygen reversibly, enabling haemoglobin to pick up oxygen in the lungs and release it in tissues. |
| Globular shape | Solubility in blood plasma allows efficient oxygen transport. |
| Flexible quaternary structure | Changes shape when oxygen binds (oxyhaemoglobin) and releases (deoxyhaemoglobin), optimizing oxygen delivery. |
🧠 Importance of Iron (Fe²⁺) in the Haem Group
- The Fe²⁺ ion is the active site for oxygen binding.
- It binds one oxygen molecule (O₂) per haem group, so each haemoglobin molecule can carry up to four oxygen molecules.
- The reversible binding is crucial for oxygen loading in lungs and unloading in tissues.
📌 Summary:
Haemoglobin’s structure – with multiple subunits and haem-bound iron – is perfectly adapted to efficient oxygen transport.
The iron ion in haem is essential for oxygen binding, making haemoglobin vital for respiration.
Haemoglobin’s structure – with multiple subunits and haem-bound iron – is perfectly adapted to efficient oxygen transport.
The iron ion in haem is essential for oxygen binding, making haemoglobin vital for respiration.
Structure of Collagen: An Example of a Fibrous Protein
🌱 Basic Structure of a Collagen Molecule
- Collagen is a fibrous protein providing structural support in connective tissues.
- Its basic unit is a tropocollagen molecule made of three polypeptide chains (called α-chains).
- These three chains are left-handed helices twisted together into a right-handed triple helix.
- Each chain is rich in the amino acids glycine, proline, and hydroxyproline.
- Glycine appears at every third position, allowing the chains to pack tightly.
- Hydroxyproline helps stabilize the triple helix via hydrogen bonds.
🌿 Arrangement of Collagen Molecules
- Many tropocollagen molecules line up in a staggered, overlapping manner to form collagen fibrils.
- Fibrils are stabilized by cross-links (covalent bonds) between lysine residues in adjacent molecules, increasing tensile strength.
- Multiple fibrils bundle together to form collagen fibres, which are visible under a microscope.
- This hierarchical structure provides high tensile strength and flexibility.
| Level | Description |
|---|---|
| Tropocollagen | Triple helix of 3 α-polypeptide chains |
| Fibrils | Staggered, cross-linked tropocollagen molecules |
| Fibres | Bundles of collagen fibrils |
| Function | Provides strength and support in connective tissue |
🧠 Key Point: The triple helix structure and cross-linking give collagen its exceptional tensile strength, making it ideal for structural roles in skin, tendons, and bones.
Relationship Between Structure and Function of Collagen Molecules and Fibres
🌱 Structural Features of Collagen
| Structure Level | Key Features |
|---|---|
| Collagen Molecules | Triple helix formed by three α-chains, rich in glycine, proline, and hydroxyproline. Tight packing and hydrogen bonding provide stability. |
| Collagen Fibrils | Staggered arrangement of molecules with covalent cross-links between lysine residues increases tensile strength. |
| Collagen Fibres | Bundles of fibrils form thick, strong fibres with flexibility and durability. |
🔍 How Structure Relates to Function
| Structural Feature | Functional Benefit |
|---|---|
| Triple helix structure | Provides high tensile strength and resistance to stretching forces. |
| High glycine content | Allows tight packing of chains for a compact, strong structure. |
| Hydrogen bonds and cross-links | Stabilize the molecule and fibrils, enhancing durability and mechanical strength. |
| Fibril staggered arrangement | Distributes mechanical stress evenly, preventing damage. |
| Bundle formation into fibres | Produces tough, flexible connective tissue structures (e.g., tendons, ligaments, skin). |
🧠 Summary: The triple helix and covalent cross-links give collagen its strength and stability, crucial for supporting tissues under tension.
The hierarchical organisation from molecules to fibres allows collagen to resist pulling forces while maintaining flexibility, making it essential for structural support in animals.
The hierarchical organisation from molecules to fibres allows collagen to resist pulling forces while maintaining flexibility, making it essential for structural support in animals.