02.10 Proteins
Overview of Proteins
Proteins are essential macromolecules that constitute over 50% of the dry mass of most cells. They perform a vast array of functions crucial to biological processes, including enzymatic activities, structural support, transport, hormonal regulation, immunity, movement, and storage of nutrients.
Types of Proteins Based on Shape
Proteins are categorized into two main types based on their three-dimensional shapes: globular proteins and fibrous proteins. This classification is fundamental to understanding their diverse roles in biological systems.
1. Globular Proteins
Characteristics:
- Shape: Compact and spherical.
- Solubility: Typically soluble in water and aqueous environments.
- Structure:
- Hydrophilic R Groups: Face outward, interacting with the surrounding water.
- Hydrophobic R Groups: Cluster inside, stabilizing the protein’s structure by avoiding water.
Functions:
- Metabolic Processes: Enzymes catalyze biochemical reactions.
- Transport: Molecules like haemoglobin and myoglobin carry oxygen.
- Hormonal Regulation: Proteins such as insulin and glucagon act as hormones.
- Immunity: Antibodies protect against pathogens.
- Movement: Proteins like actin and myosin enable muscle contraction.
Examples:
- Haemoglobin:
- Function: Transports oxygen in red blood cells.
- Structure: Comprises four polypeptide chains (two α and two β chains) arranged nearly spherically.
- Enzymes:
- Function: Act as biological catalysts, accelerating biochemical reactions without being consumed.
- Structure: Typically globular, enabling the formation of active sites where substrates bind and reactions occur.
2. Fibrous Proteins
Characteristics:
- Shape: Long, thin, and thread-like structures.
- Solubility: Typically insoluble in water.
- Structure:
- Composed of long polypeptide chains with repetitive amino acid sequences.
- Chains align side-by-side to form strong fibers.
Functions:
- Structural Support: Provide strength, flexibility, and support to cells and tissues.
- Protection: Form protective layers in various organisms.
Examples:
- Collagen:
- Function: Provides structural support in tendons, skin, bones, and other connective tissues.
- Structure: Consists of three helical polypeptide chains wound together in a “triple helix.”
- Keratin:
- Function: Forms hair, nails, and the outer layer of skin, providing protection and resilience.
- Structure: Similar to collagen, keratin forms strong, fibrous structures through repeated amino acid sequences and extensive cross-linking.
Key Functions of Proteins
- Enzymatic Activity:
- Role: All enzymes are proteins that catalyze biochemical reactions, increasing reaction rates without being consumed.
- Structural Role:
- Examples: Collagen provides strength to tissues such as bone and artery walls.
- Transport:
- Examples: Haemoglobin and myoglobin carry oxygen throughout the body.
- Hormonal Function:
- Examples: Insulin and glucagon regulate blood sugar levels.
- Immunity:
- Examples: Antibodies defend against pathogens.
- Movement:
- Examples: Actin and myosin enable muscle contraction.
- Storage:
- Examples: Casein in milk and ovalbumin in eggs store nutrients.
- Protection and Structure:
- Example: Keratin in hair, nails, and the skin’s surface layer provides structure and protection.
Amino Acids: The Building Blocks of Proteins
Basic Structure of Amino Acids
Each amino acid consists of:
- Central Carbon Atom (α-carbon): Bonds to four different groups.
- Amino Group (–NH₂): Acts as a base.
- Carboxylic Acid Group (–COOH): Acts as an acid.
- Hydrogen Atom (–H): Attached to the central carbon.
- R Group (Side Chain): Varies among different amino acids, imparting specific properties.
Example:
- Glycine: Has a simple hydrogen atom as its R group.
Diversity of Amino Acids
- Number of Common Amino Acids: 20
- Unique R Groups: Each of the 20 amino acids has a distinct R group, leading to diverse properties and functions in proteins.
Formation of Proteins: Peptide Bonds
Peptide Bond Formation:
- Process: Condensation reaction between two amino acids.
- Loss of –OH: From the carboxylic group of one amino acid.
- Loss of –H: From the amino group of another amino acid.
- Result: Formation of a peptide bond (C–N link) and release of a water molecule (H₂O).
- Product: Dipeptide; multiple peptide bonds form a polypeptide chain.
Polypeptides and Proteins:
- Polypeptide: A long chain of amino acids linked by peptide bonds.
- Protein: Can consist of one or multiple polypeptide chains.
Breaking Down Proteins:
- Process: Hydrolysis (addition of water) breaks peptide bonds, releasing amino acids.
- Occurrence: Happens naturally during digestion, allowing amino acids to be absorbed by the body.
Practise Questions 1
Question 1: State three similarities and three differences between cellulose and collagen.
Answer:
Similarities:
- Structural Role: Both cellulose and collagen serve as structural molecules; cellulose provides rigidity to plant cell walls, while collagen adds strength to animal tissues (e.g., skin, tendons, and bones).
- High Tensile Strength: Both have high tensile strength due to strong bonds within and between their molecular chains.
- Long, Linear Structure: Both are composed of long, repetitive chains that form fibrous structures capable of supporting mechanical stress.
Differences:
- Type of Monomer:
- Cellulose: A polysaccharide made of β-glucose monomers.
- Collagen: A protein composed of amino acids (primarily glycine, proline, and hydroxyproline).
- Bonding Types:
- Cellulose: Chains are held together by hydrogen bonds between glucose monomers.
- Collagen: Chains are stabilized by hydrogen bonds and covalent cross-links between amino acid side chains.
- Location and Function:
- Cellulose: Found in plant cell walls, essential for structural support in plants.
- Collagen: Found in animal tissues, providing tensile strength and elasticity in various connective tissues.
Question 2: Fill in the blanks in the second column of the table using the words below: hydrophilic, haemoglobin, ionic bond, hydrophobic, disaccharide, disulfide bond.
Answer to Table 2.1 (Blanks Filled):
| Statement | Answer |
|---|---|
| A type of molecule containing two monosaccharides | Disaccharide |
| A type of bond formed between two cysteine molecules | Disulfide bond |
| A molecule containing four polypeptide chains, each with a haem group | Haemoglobin |
| Part of a molecule that is attracted to water | Hydrophilic |
| Part of a molecule that repels water | Hydrophobic |
| A bond formed between ionized amino and carboxyl groups | Ionic bond |
Question 3: “The protein-folding problem” box at the beginning of this chapter discussed how scientists are trying to predict the final shapes of proteins from knowledge of their primary structures. What information about amino acids and proteins would be relevant to feed into a computer program trying to make such predictions?
Answer:
To predict the final shape of a protein from its primary structure (sequence of amino acids), the following information about amino acids and protein interactions is essential:
Amino Acid Sequence:
- Exact Sequence: The specific order and types of amino acids in the polypeptide chain determine the folding pathway.
- Properties of R Groups:
- Polarity: Whether the side chains are polar or non-polar influences interactions.
- Charge: Positive, negative, or neutral charges affect bonding and folding.
- Hydrophilicity/Hydrophobicity: Determines the orientation of residues in aqueous environments.
- Size and Structure: Bulky vs. small side chains affect spatial arrangements.
- Types of Bonds and Interactions:
- Hydrogen Bonds: Sites for hydrogen bonding within the backbone and side chains.
- Disulfide Bonds: Potential covalent links between cysteine residues.
- Ionic Bonds: Attractions between charged side chains.
- Hydrophobic Interactions: Clustering of non-polar side chains to avoid water.
- Environmental Influences:
- pH and Temperature: Affect the ionization states and stability of bonds.
- Solvent Presence: Water vs. lipid environments influence residue orientation.
- Potential Secondary Structures:
- Likelihood of α-Helices and β-Sheets: Based on amino acid propensity to form specific secondary structures.
- Known Folding Pathways:
- Patterns from Similar Proteins: Helps predict complex folds and motifs.
Practise Questions 2
Question 1
Describe the basic structure of an amino acid and explain the role of R groups in determining protein properties. (6 marks)
Mark Scheme:
- Each amino acid has a central carbon atom (α-carbon) bonded to four groups. (1 mark)
- These groups include:
- An amino group (–NH₂), which acts as a base. (1 mark)
- A carboxylic acid group (–COOH), which acts as an acid. (1 mark)
- A hydrogen atom (–H). (1 mark)
- An R group (side chain), which varies among amino acids. (1 mark)
- The R group determines the chemical properties of the amino acid, such as polarity, charge, and hydrophobicity, influencing the protein’s structure and function. (1 mark)
Question 2
Compare the structures and functions of globular and fibrous proteins. (6 marks)
Mark Scheme:
| Feature | Globular Proteins | Fibrous Proteins |
|---|---|---|
| Shape | Compact, spherical. | Long, thin, thread-like. |
| Solubility | Soluble in water. | Insoluble in water. |
| Structure | Hydrophilic R groups face outward, hydrophobic R groups cluster inside. | Repetitive amino acid sequences form strong fibers. |
| Functions | Metabolic roles, e.g., enzymes, transport proteins, hormones. | Structural roles, e.g., collagen, keratin. |
| Examples | Haemoglobin, enzymes, antibodies. | Collagen, keratin. |
| Stability | Less stable than fibrous proteins. | Highly stable, providing mechanical strength. |
Question 3
Explain how the structure of haemoglobin enables its function as an oxygen transport molecule. (6 marks)
Mark Scheme:
- Haemoglobin is a globular protein composed of four polypeptide chains: two α-chains and two β-chains. (1 mark)
- Each chain contains a haem group with an iron ion (Fe²⁺) that binds oxygen. (1 mark)
- The spherical shape makes haemoglobin soluble in blood plasma. (1 mark)
- Cooperative binding: The binding of one oxygen molecule increases the affinity of haemoglobin for subsequent oxygen molecules. (1 mark)
- This allows efficient oxygen loading in high oxygen environments (e.g., lungs) and unloading in low oxygen areas (e.g., tissues). (1 mark)
- The structure enables haemoglobin to carry up to four oxygen molecules per molecule. (1 mark)
Question 4
Describe the formation of peptide bonds and their role in protein structure. (6 marks)
Mark Scheme:
- Peptide bonds form during a condensation reaction between two amino acids. (1 mark)
- The carboxyl group (–COOH) of one amino acid reacts with the amino group (–NH₂) of another. (1 mark)
- A molecule of water (H₂O) is released. (1 mark)
- The resulting bond is a C–N link called a peptide bond. (1 mark)
- Peptide bonds link amino acids into polypeptides, which fold into functional proteins. (1 mark)
- The sequence of amino acids and peptide bonds determines the primary structure, influencing the overall protein shape and function. (1 mark)
Question 5
Explain the role of hydrogen bonds in maintaining protein structure. (5 marks)
Mark Scheme:
- Hydrogen bonds form between polar groups (e.g., –NH and –C=O) in the polypeptide chain. (1 mark)
- They stabilize the secondary structure, such as α-helices and β-pleated sheets. (1 mark)
- In the tertiary structure, hydrogen bonds form between R groups, contributing to the protein’s three-dimensional shape. (1 mark)
- Hydrogen bonds are weak individually but strong collectively, maintaining structural stability. (1 mark)
- They are essential for protein function, as they help maintain the shape required for activity (e.g., enzyme active sites). (1 mark)
Question 6
What are the key functions of proteins in living organisms? Provide examples. (6 marks)
Mark Scheme:
- Enzymatic Activity: Proteins like amylase and lipase catalyze biochemical reactions. (1 mark)
- Structural Support: Collagen provides strength to connective tissues like tendons and bones. (1 mark)
- Transport: Haemoglobin transports oxygen in the blood. (1 mark)
- Hormonal Regulation: Insulin regulates blood glucose levels. (1 mark)
- Immunity: Antibodies defend against pathogens. (1 mark)
- Movement: Actin and myosin enable muscle contraction. (1 mark)
Question 7
How do the structures of collagen and keratin relate to their functions? (6 marks)
Mark Scheme:
| Feature | Collagen | Keratin |
|---|---|---|
| Function | Provides structural support in tendons, skin, and bones. | Forms protective structures like hair, nails, and skin. |
| Structure | Triple helix of polypeptides, stabilized by hydrogen bonds. | Long polypeptide chains with cross-linking for strength. |
| Strength | High tensile strength due to triple-helix arrangement. | Tough and resilient due to extensive cross-linking. |
| Solubility | Insoluble in water, providing stability. | Insoluble, resistant to environmental damage. |
| Example | Found in connective tissue. | Found in epidermis and appendages. |
| Adaptation | Resists stretching and tearing. | Provides protection against mechanical stress. |
Question 8
What is the importance of hydrolysis in protein digestion? (6 marks)
Mark Scheme:
- Hydrolysis breaks peptide bonds, releasing individual amino acids from proteins. (1 mark)
- Enzymes like pepsin and trypsin catalyze this reaction during digestion. (1 mark)
- The addition of water (H₂O) splits the bond between the carboxyl and amino groups of adjacent amino acids. (1 mark)
- The resulting amino acids are absorbed into the bloodstream for use in protein synthesis. (1 mark)
- Hydrolysis ensures dietary proteins are broken down into forms usable by the body. (1 mark)
- This process is essential for growth, repair, and maintaining cellular functions. (1 mark)
Question 9
Explain the differences between the primary, secondary, and tertiary structures of proteins. (6 marks)
Mark Scheme:
- Primary Structure: Linear sequence of amino acids in a polypeptide chain, determined by peptide bonds. (1 mark)
- Secondary Structure: Local folding into α-helices or β-pleated sheets, stabilized by hydrogen bonds between backbone groups. (1 mark)
- Tertiary Structure: Three-dimensional folding of the polypeptide, stabilized by interactions between R groups (e.g., hydrogen bonds, ionic bonds, disulfide bridges). (1 mark)
- Primary structure determines how the protein folds into secondary and tertiary structures. (1 mark)
- Secondary and tertiary structures give the protein its specific shape and function (e.g., enzyme active sites). (1 mark)
- Changes in any structure level can affect protein function (e.g., in sickle-cell haemoglobin). (1 mark)
Question 10
What is the role of peptide bonds in protein structure, and how are they formed? (6 marks)
Mark Scheme:
- Peptide bonds link amino acids in a polypeptide chain. (1 mark)
- They are formed during condensation reactions, where the carboxyl group of one amino acid reacts with the amino group of another. (1 mark)
- A molecule of water (H₂O) is released in the process. (1 mark)
- Peptide bonds provide structural stability to the primary structure of proteins. (1 mark)
- They allow flexibility for further folding into secondary and tertiary structures. (1 mark)
- The breaking of peptide bonds during hydrolysis releases amino acids for absorption and reuse. (1 mark)