Chapter 3.2: Biomolecules

1. Carbohydrates

Definition: Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield these on hydrolysis. They are the most important source of energy for living organisms. They are also known as saccharides.
Classification:
- Monosaccharides (Simple Sugars): Cannot be hydrolyzed further. General formula is (CHâ‚‚O)n.
  - Glucose: A six-carbon sugar (hexose) that is the primary source of energy for most living organisms. It is an aldohexose, meaning it has an aldehyde group at position 1.
  - Ribose: A five-carbon sugar (pentose) that is a component of ribonucleic acid (RNA). It is an aldopentose.
  - Deoxyribose: A modified five-carbon sugar that is a component of deoxyribonucleic acid (DNA). It is derived from ribose by the removal of an oxygen atom from the second carbon.
- Disaccharides: Formed by the condensation of two monosaccharide units, joined by a glycosidic bond.
Sweet Test The ability of a sugar to reduce Benedict's solution depends on its free aldehyde or ketone group. Sucrose is a non-reducing sugar because these groups are locked in the glycosidic bond, whereas Maltose and Lactose are reducing sugars.
- Maltose (Malt Sugar): Composed of two glucose units. It is a reducing sugar.
- Lactose (Milk Sugar): Composed of glucose and galactose. It is a reducing sugar and is found in milk.
- Sucrose (Cane Sugar): Composed of glucose and fructose. It is a non-reducing sugar and is the common table sugar.
- Polysaccharides (Complex Carbohydrates): Long chains of monosaccharides linked by glycosidic bonds.
  - Glycogen: The main storage polysaccharide in animals, stored primarily in the liver and muscles. It is a branched polymer of glucose.
  - Starch: The main storage polysaccharide in plants. It is a mixture of two polymers: amylose (a linear polymer of glucose) and amylopectin (a branched polymer of glucose).
  - Cellulose: A structural polysaccharide that forms the cell wall of plants. It is a linear polymer of glucose with beta-1,4-glycosidic bonds, which makes it indigestible by most animals.
  - Inulin: A polymer of fructose, found in many plants, such as chicory. It is used as a prebiotic and a fat substitute.
  - Chitin: A structural polysaccharide found in the exoskeletons of arthropods and the cell walls of fungi. It is a polymer of N-acetylglucosamine.

2. Proteins

Definition: Proteins are polymers of amino acids, linked by peptide bonds. They are the most abundant organic molecules in living systems and have a wide range of functions.
Amino Acids:
- Structure: An amino acid is a substituted methane, with four substituent groups occupying the four valency positions: a carboxyl group, an amino group, a hydrogen atom, and a variable group designated as R group.
  - Glycine: The simplest amino acid, with hydrogen as its R group.
  - Alanine: Has a methyl group as its R group.
  - Serine: Has a hydroxymethyl group as its R group.
- Zwitter-ion: An amino acid can exist as a zwitter-ion, which is a molecule with both a positive and a negative charge. The amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).
- Types:
  - Acidic: Have an acidic R group (e.g., Aspartic acid, Glutamic acid).
  - Basic: Have a basic R group (e.g., Lysine, Arginine).
  - Neutral: Have a neutral R group (e.g., Glycine, Alanine, Valine).
  - Sulphur-containing: Contain a sulphur atom in the R group (e.g., Cysteine, Methionine).
- Essential and Non-essential Amino Acids:
  - Essential: Cannot be synthesized by the body and must be obtained from the diet (e.g., Lysine, Leucine, Isoleucine).
  - Non-essential: Can be synthesized by the body (e.g., Glycine, Alanine, Serine).
Levels of Protein Structure:
- Primary Structure: The linear sequence of amino acids in a polypeptide chain.
- Secondary Structure: The polypeptide chain is folded into regular structures like the Î±-helix and the Î²-pleated sheet. These structures are stabilized by hydrogen bonds.
- Tertiary Structure: The overall three-dimensional shape of a polypeptide chain. It is stabilized by various types of bonds, including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
- Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) in a protein. e.g., Haemoglobin.
Functions of Proteins:
- Enzymes: Catalyze biochemical reactions.
- Structural proteins: Provide support and shape to cells and tissues (e.g., collagen, keratin).
- Transport proteins: Carry substances across cell membranes or in the blood (e.g., hemoglobin).
- Hormones: Regulate physiological processes (e.g., insulin).
- Antibodies: Defend the body against pathogens.

3. Lipids

Definition: A diverse group of organic compounds that are insoluble in water but soluble in nonpolar organic solvents.
Classification, Structure, and Functions of Fats and Oils:
- Fats and Oils (Triglycerides): Composed of three fatty acid molecules esterified to a glycerol molecule.
  - Fats: Solid at room temperature and are generally of animal origin. They are rich in saturated fatty acids.
  - Oils: Liquid at room temperature and are generally of plant origin. They are rich in unsaturated fatty acids.
- Functions:
  - Energy storage: They are the main form of energy storage in animals.
  - Insulation: They provide thermal insulation.
  - Protection: They protect vital organs from shock.
  - Source of fat-soluble vitamins: They are a source of vitamins A, D, E, and K.

4. Enzymes

Definition: Biological catalysts that speed up the rate of biochemical reactions without being consumed in the reaction.
General Properties:
- Almost all enzymes are proteins.
- They are highly specific for their substrates.
- They work best at a specific temperature and pH (optimum temperature and pH).
- They are required in small amounts.
Nomenclature and Classification:
- Nomenclature: Enzymes are usually named by adding the suffix "-ase" to the name of the substrate they act on (e.g., sucrase, lactase).
- Classification: Classified into 6 classes based on the type of reaction they catalyze:
  1. Oxidoreductases: Catalyze oxidation-reduction reactions.
  2. Transferases: Catalyze the transfer of a functional group from one molecule to another.
  3. Hydrolases: Catalyze the hydrolysis of a bond.
  4. Lyases: Catalyze the removal of a group from a substrate to form a double bond.
  5. Isomerases: Catalyze the interconversion of isomers.
  6. Ligases: Catalyze the joining of two molecules.
Co-factors: Non-protein constituents bound to the enzyme to make it catalytically active.
- Prosthetic groups: Tightly bound to the enzyme (e.g., heme in hemoglobin).
- Co-enzymes: Loosely bound to the enzyme (e.g., NAD, FAD).
- Metal ions: Act as a bridge between the enzyme and the substrate (e.g., Zn2+, Mg2+).
Factors Affecting Enzyme Activity:
- Temperature: Enzymes show a bell-shaped activity curve. At low temperatures, the enzyme is temporarily inactive. As temperature rises, kinetic energy increases, speeding up the reaction. Above the optimum temperature (typically $37^\circ\text{C}$ for human enzymes), high thermal energy breaks the weak hydrogen and ionic bonds, causing denaturation (loss of tertiary structure and catalytic activity).
- pH: Each enzyme operates maximally at a specific optimum pH. Deviations in pH alter the ionization state of acidic and basic amino acid side chains at the active site, disrupting substrate binding and enzyme structure.
- Substrate Concentration & Michaelis-Menten Kinetics:
  - As substrate concentration $[S]$ increases, the velocity of the reaction rises.
  - $V_{max}$ (Maximum Velocity): The rate reaches a plateau ( $V_{max}$ ) when all enzyme active sites are fully saturated with substrate.
  - $K_m$ (Michaelis Constant): The substrate concentration at which the reaction velocity is half of its maximum ( $\frac{1}{2}V_{max}$ ). It is an inverse measure of enzyme-substrate affinity; a low $K_m$ indicates high affinity.

Enzyme Inhibition:
- Competitive Inhibition:
  - A competitive inhibitor has a structural resemblance to the substrate and competes for binding at the active site.
  - Effect: It decreases the affinity of the enzyme for the substrate, meaning it increases $K_m$ . However, at high substrate concentrations, the substrate outcompetes the inhibitor, so $V_{max}$ remains unchanged.
  - Classic Example: Inhibition of succinate dehydrogenase by malonate (which competes with succinate).
- Non-Competitive Inhibition:
  - A non-competitive inhibitor binds to an allosteric site (a site other than the active site), altering the 3D conformation of the enzyme so it can no longer catalyze the reaction.
  - Effect: It reduces the number of functional enzymes, meaning it decreases $V_{max}$ . Since it does not interfere with substrate binding, the affinity remains the same, so $K_m$ remains unchanged.

Competitive Edge: The Vmax and Km Trap Memorize this rule for exams:

Competitive Inhibitor: $V_{max}$ is Unchanged, $K_m$ Increases. (You can overcome it by flooding the system with more substrate).
Non-Competitive Inhibitor: $V_{max}$ Decreases, $K_m$ is Unchanged. (Adding more substrate won't fix the broken allosteric enzymes).

5. Secondary Metabolites

Definition: Organic compounds that are not directly involved in the normal growth, development, or reproduction of an organism. They are often produced as by-products of metabolism and have important ecological functions.
Examples:
- Alkaloids: Morphine, Codeine (pain relievers)
- Terpenoids: Monoterpenes (e.g., menthol), Diterpenes (e.g., gibberellins)
- Essential oils: Lemon grass oil (used in aromatherapy and as an insect repellent)
- Toxins: Abrin, Ricin (highly toxic proteins)
- Lectins: Concanavalin A (a protein that binds to carbohydrates)
- Drugs: Vinblastin (an anticancer drug), Curcumin (an anti-inflammatory agent)
- Polymeric substances: Rubber, Gums, Cellulose

1. Carbohydrates

Definition: Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield these on hydrolysis. They are the most important source of energy for living organisms. They are also known as saccharides.

Classification:

Monosaccharides (Simple Sugars): Cannot be hydrolyzed further. General formula is (CHâ‚‚O)n.
- Glucose: A six-carbon sugar (hexose) that is the primary source of energy for most living organisms. It is an aldohexose, meaning it has an aldehyde group at position 1.
- Ribose: A five-carbon sugar (pentose) that is a component of ribonucleic acid (RNA). It is an aldopentose.
- Deoxyribose: A modified five-carbon sugar that is a component of deoxyribonucleic acid (DNA). It is derived from ribose by the removal of an oxygen atom from the second carbon.
Disaccharides: Formed by the condensation of two monosaccharide units, joined by a glycosidic bond.

Sweet Test The ability of a sugar to reduce Benedict's solution depends on its free aldehyde or ketone group. Sucrose is a non-reducing sugar because these groups are locked in the glycosidic bond, whereas Maltose and Lactose are reducing sugars.

Maltose (Malt Sugar): Composed of two glucose units. It is a reducing sugar.
Lactose (Milk Sugar): Composed of glucose and galactose. It is a reducing sugar and is found in milk.
Sucrose (Cane Sugar): Composed of glucose and fructose. It is a non-reducing sugar and is the common table sugar.
Polysaccharides (Complex Carbohydrates): Long chains of monosaccharides linked by glycosidic bonds.
- Glycogen: The main storage polysaccharide in animals, stored primarily in the liver and muscles. It is a branched polymer of glucose.
- Starch: The main storage polysaccharide in plants. It is a mixture of two polymers: amylose (a linear polymer of glucose) and amylopectin (a branched polymer of glucose).
- Cellulose: A structural polysaccharide that forms the cell wall of plants. It is a linear polymer of glucose with beta-1,4-glycosidic bonds, which makes it indigestible by most animals.
- Inulin: A polymer of fructose, found in many plants, such as chicory. It is used as a prebiotic and a fat substitute.
- Chitin: A structural polysaccharide found in the exoskeletons of arthropods and the cell walls of fungi. It is a polymer of N-acetylglucosamine.

2. Proteins

Definition: Proteins are polymers of amino acids, linked by peptide bonds. They are the most abundant organic molecules in living systems and have a wide range of functions.

Amino Acids:

Structure: An amino acid is a substituted methane, with four substituent groups occupying the four valency positions: a carboxyl group, an amino group, a hydrogen atom, and a variable group designated as R group.
- Glycine: The simplest amino acid, with hydrogen as its R group.
- Alanine: Has a methyl group as its R group.
- Serine: Has a hydroxymethyl group as its R group.
Zwitter-ion: An amino acid can exist as a zwitter-ion, which is a molecule with both a positive and a negative charge. The amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).
Types:
- Acidic: Have an acidic R group (e.g., Aspartic acid, Glutamic acid).
- Basic: Have a basic R group (e.g., Lysine, Arginine).
- Neutral: Have a neutral R group (e.g., Glycine, Alanine, Valine).
- Sulphur-containing: Contain a sulphur atom in the R group (e.g., Cysteine, Methionine).
Essential and Non-essential Amino Acids:
- Essential: Cannot be synthesized by the body and must be obtained from the diet (e.g., Lysine, Leucine, Isoleucine).
- Non-essential: Can be synthesized by the body (e.g., Glycine, Alanine, Serine).

Levels of Protein Structure:

Primary Structure: The linear sequence of amino acids in a polypeptide chain.
Secondary Structure: The polypeptide chain is folded into regular structures like the Î±-helix and the Î²-pleated sheet. These structures are stabilized by hydrogen bonds.
Tertiary Structure: The overall three-dimensional shape of a polypeptide chain. It is stabilized by various types of bonds, including hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.
Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) in a protein. e.g., Haemoglobin.

Functions of Proteins:

Enzymes: Catalyze biochemical reactions.
Structural proteins: Provide support and shape to cells and tissues (e.g., collagen, keratin).
Transport proteins: Carry substances across cell membranes or in the blood (e.g., hemoglobin).
Hormones: Regulate physiological processes (e.g., insulin).
Antibodies: Defend the body against pathogens.

3. Lipids

Definition: A diverse group of organic compounds that are insoluble in water but soluble in nonpolar organic solvents.

Classification, Structure, and Functions of Fats and Oils:

Fats and Oils (Triglycerides): Composed of three fatty acid molecules esterified to a glycerol molecule.
- Fats: Solid at room temperature and are generally of animal origin. They are rich in saturated fatty acids.
- Oils: Liquid at room temperature and are generally of plant origin. They are rich in unsaturated fatty acids.
Functions:
- Energy storage: They are the main form of energy storage in animals.
- Insulation: They provide thermal insulation.
- Protection: They protect vital organs from shock.
- Source of fat-soluble vitamins: They are a source of vitamins A, D, E, and K.

4. Enzymes

Definition: Biological catalysts that speed up the rate of biochemical reactions without being consumed in the reaction.

General Properties:

Almost all enzymes are proteins.
They are highly specific for their substrates.
They work best at a specific temperature and pH (optimum temperature and pH).
They are required in small amounts.

Nomenclature and Classification:

Nomenclature: Enzymes are usually named by adding the suffix "-ase" to the name of the substrate they act on (e.g., sucrase, lactase).
Classification: Classified into 6 classes based on the type of reaction they catalyze:
1. Oxidoreductases: Catalyze oxidation-reduction reactions.
2. Transferases: Catalyze the transfer of a functional group from one molecule to another.
3. Hydrolases: Catalyze the hydrolysis of a bond.
4. Lyases: Catalyze the removal of a group from a substrate to form a double bond.
5. Isomerases: Catalyze the interconversion of isomers.
6. Ligases: Catalyze the joining of two molecules.

Co-factors: Non-protein constituents bound to the enzyme to make it catalytically active.

Prosthetic groups: Tightly bound to the enzyme (e.g., heme in hemoglobin).
Co-enzymes: Loosely bound to the enzyme (e.g., NAD, FAD).
Metal ions: Act as a bridge between the enzyme and the substrate (e.g., Zn2+, Mg2+).

Factors Affecting Enzyme Activity:

Temperature: Enzymes show a bell-shaped activity curve. At low temperatures, the enzyme is temporarily inactive. As temperature rises, kinetic energy increases, speeding up the reaction. Above the optimum temperature (typically $37^\circ\text{C}$ for human enzymes), high thermal energy breaks the weak hydrogen and ionic bonds, causing denaturation (loss of tertiary structure and catalytic activity).
pH: Each enzyme operates maximally at a specific optimum pH. Deviations in pH alter the ionization state of acidic and basic amino acid side chains at the active site, disrupting substrate binding and enzyme structure.
Substrate Concentration & Michaelis-Menten Kinetics:
- As substrate concentration $[S]$ increases, the velocity of the reaction rises.
- $V_{max}$ (Maximum Velocity): The rate reaches a plateau ( $V_{max}$ ) when all enzyme active sites are fully saturated with substrate.
- $K_m$ (Michaelis Constant): The substrate concentration at which the reaction velocity is half of its maximum ( $\frac{1}{2}V_{max}$ ). It is an inverse measure of enzyme-substrate affinity; a low $K_m$ indicates high affinity.

Enzyme Inhibition:

Competitive Inhibition:
- A competitive inhibitor has a structural resemblance to the substrate and competes for binding at the active site.
- Effect: It decreases the affinity of the enzyme for the substrate, meaning it increases $K_m$ . However, at high substrate concentrations, the substrate outcompetes the inhibitor, so $V_{max}$ remains unchanged.
- Classic Example: Inhibition of succinate dehydrogenase by malonate (which competes with succinate).
Non-Competitive Inhibition:
- A non-competitive inhibitor binds to an allosteric site (a site other than the active site), altering the 3D conformation of the enzyme so it can no longer catalyze the reaction.
- Effect: It reduces the number of functional enzymes, meaning it decreases $V_{max}$ . Since it does not interfere with substrate binding, the affinity remains the same, so $K_m$ remains unchanged.

Competitive Edge: The Vmax and Km Trap Memorize this rule for exams:

Competitive Inhibitor: $V_{max}$ is Unchanged, $K_m$ Increases. (You can overcome it by flooding the system with more substrate).
Non-Competitive Inhibitor: $V_{max}$ Decreases, $K_m$ is Unchanged. (Adding more substrate won't fix the broken allosteric enzymes).

5. Secondary Metabolites

Definition: Organic compounds that are not directly involved in the normal growth, development, or reproduction of an organism. They are often produced as by-products of metabolism and have important ecological functions.

Examples:

Alkaloids: Morphine, Codeine (pain relievers)
Terpenoids: Monoterpenes (e.g., menthol), Diterpenes (e.g., gibberellins)
Essential oils: Lemon grass oil (used in aromatherapy and as an insect repellent)
Toxins: Abrin, Ricin (highly toxic proteins)
Lectins: Concanavalin A (a protein that binds to carbohydrates)
Drugs: Vinblastin (an anticancer drug), Curcumin (an anti-inflammatory agent)
Polymeric substances: Rubber, Gums, Cellulose

Biomolecules

Chapter 3.2: Biomolecules

1. Carbohydrates

2. Proteins

3. Lipids

4. Enzymes

5. Secondary Metabolites

On this page

BioBot

Biomolecules

Chapter 3.2: Biomolecules

1. Carbohydrates

2. Proteins

3. Lipids

4. Enzymes

5. Secondary Metabolites

On this page