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Biological Molecules Overview

Sep 14, 2025

Overview

This lecture covers AQA A-Level Biology Topic 1, focusing on the structure and function of biological molecules: monomers, polymers, carbohydrates, lipids, proteins, enzymes, nucleic acids, ATP, water, and inorganic ions. It includes definitions, key reactions, structural details, biochemical tests, and the relationship between structure and function.

Monomers and Polymers

  • Monomer: A small unit from which larger molecules (polymers) are made. "Mono" means one.
  • Polymer: A molecule made from many monomers joined together. "Poly" means many.
  • Key biological monomers: monosaccharides (e.g., glucose), amino acids, nucleotides.
  • Key biological polymers: starch, cellulose, glycogen (carbohydrates); proteins; DNA and RNA (nucleic acids).
  • Condensation reaction: Joins two molecules together, forms a chemical bond, and eliminates a water molecule. Essential for building polymers from monomers.
  • Hydrolysis reaction: Breaks a chemical bond between two molecules using water, splitting polymers into monomers.
  • In exam questions, always specify the molecules and bonds involved in applied examples (e.g., peptide bond in proteins, glycosidic bond in carbohydrates).

Carbohydrates

  • Monosaccharides: Single sugar units; examples include glucose, fructose, and galactose. These are the monomers of carbohydrates.
  • Disaccharides: Formed by condensation of two monosaccharides, joined by a glycosidic bond. Examples:
    • Glucose + Glucose → Maltose + Water
    • Glucose + Galactose → Lactose + Water
    • Glucose + Fructose → Sucrose + Water
    • All disaccharide formation produces water due to condensation.
  • Polysaccharides: Polymers made from many monosaccharides joined by glycosidic bonds. Examples: starch, glycogen, cellulose.
  • Glucose Isomers: Alpha (α) and beta (β) glucose differ in the arrangement of the H and OH groups on carbon 1. This affects the structure and function of the resulting polysaccharides.
  • Starch: Polymer of α-glucose, found in plants. Contains amylose (unbranched, helical, 1-4 glycosidic bonds) and amylopectin (branched, 1-4 and 1-6 glycosidic bonds). Coiled and branched structure allows compact storage and rapid hydrolysis for energy.
  • Glycogen: Polymer of α-glucose, found in animals (mainly liver and muscle). Highly branched (more 1-6 bonds than starch), allowing even faster hydrolysis to glucose for respiration.
  • Cellulose: Polymer of β-glucose, found in plant cell walls. Long, straight, unbranched chains with every other β-glucose inverted. Chains held together by hydrogen bonds to form strong fibres (fibrils), providing structural strength.
  • Biochemical Tests:
    • Starch: Add iodine solution; positive result is blue-black.
    • Reducing sugars: Add Benedict’s reagent and heat; positive result is green/yellow/orange/brick red (depending on concentration).
    • Non-reducing sugars (e.g., sucrose): First test with Benedict’s (should be negative/blue), then boil with acid, neutralize, add Benedict’s and heat again; positive result is orange/brick red.

Lipids

  • Triglycerides: Formed by condensation of one glycerol and three fatty acids, creating three ester bonds and releasing three water molecules. Used for energy storage.
  • Phospholipids: Similar to triglycerides, but one fatty acid is replaced by a phosphate group. Structure: glycerol, two fatty acids, one phosphate group.
  • Fatty Acids:
    • Saturated: Only single bonds between carbon atoms; maximum number of hydrogens.
    • Unsaturated: At least one double bond between carbon atoms; fewer hydrogens.
  • Properties and Functions:
    • Triglycerides: High energy storage (many C-H bonds), insoluble (do not affect water potential), hydrophobic, can provide metabolic water when oxidized, low mass for efficient storage.
    • Phospholipids: Form cell membranes (phospholipid bilayer). Hydrophilic (water-attracting) head (phosphate group), hydrophobic (water-repelling) tails (fatty acids). Heads face outwards towards water, tails inwards, creating a barrier.
  • Biochemical Test for Lipids: Mix sample with ethanol, then add water. A positive result is a white, cloudy emulsion.

Proteins and Enzymes

  • Amino Acids: Monomers of proteins. Structure: central carbon, amine group (NH₂, left), carboxyl group (COOH, right), hydrogen, and variable R group (side chain).
  • Dipeptide: Two amino acids joined by a peptide bond (condensation reaction).
  • Polypeptide: Many amino acids joined by peptide bonds; folds into a protein.
  • Protein Structure:
    • Primary: Sequence/order of amino acids, held by peptide bonds.
    • Secondary: Alpha helix or beta pleated sheet, held by hydrogen bonds between amino acids.
    • Tertiary: Further folding into a unique 3D shape, held by ionic, hydrogen, and disulfide (sulfur-sulfur) bonds between R groups.
    • Quaternary: More than one polypeptide chain joined (e.g., hemoglobin has four).
    • The sequence of amino acids determines the folding and final shape, which determines function.
  • Biochemical Test for Proteins: Add Biuret reagent; positive result is purple (no heat needed).
  • Enzymes: Proteins with a specific tertiary structure and active site. Catalyze reactions by lowering activation energy. The active site is specific to the substrate due to the protein’s unique folding.
  • Enzyme Models:
    • Lock-and-key: Active site is a fixed shape, perfectly complementary to substrate.
    • Induced fit: Active site molds around substrate upon binding, becoming fully complementary and putting strain on bonds to lower activation energy.

Enzyme Activity

  • Factors Affecting Enzyme Activity:
    • Temperature: Low temp = low kinetic energy, fewer collisions. Rate increases with temp until optimum, then decreases as bonds break and enzyme denatures.
    • pH: Each enzyme has an optimum pH. Too high or too low disrupts ionic/hydrogen bonds, denatures enzyme, changes active site shape.
    • Substrate concentration: Low substrate = low rate. Rate increases with more substrate until all active sites are occupied (saturation), then plateaus.
    • Enzyme concentration: Low enzyme = low rate. Rate increases with more enzyme until substrate becomes limiting, then plateaus.
  • Inhibitors:
    • Competitive inhibitor: Similar shape to substrate, binds active site, prevents substrate binding. Can be overcome by increasing substrate concentration.
    • Non-competitive inhibitor: Binds elsewhere (not active site), changes enzyme’s tertiary structure and active site shape, substrate can’t bind. Adding more substrate does not overcome inhibition.
  • Enzyme-Substrate Complex: Temporary complex formed when enzyme binds substrate; essential for catalysis.

Nucleic Acids

  • DNA (Deoxyribonucleic Acid): Double-stranded polymer of nucleotides. Each nucleotide: deoxyribose sugar, phosphate group, nitrogenous base (adenine, thymine, cytosine, guanine).
  • RNA (Ribonucleic Acid): Single-stranded polymer of nucleotides. Each nucleotide: ribose sugar, phosphate group, nitrogenous base (adenine, uracil, cytosine, guanine).
  • Nucleotide Structure: Phosphate group, pentose sugar, nitrogenous base.
  • Phosphodiester Bonds: Join nucleotides via condensation between sugar and phosphate.
  • DNA Structure: Two polynucleotide strands joined by hydrogen bonds between complementary bases (A-T, C-G), forming a double helix. A-T pairs have two hydrogen bonds; C-G pairs have three.
  • RNA Structure: Single, shorter polynucleotide chain.
  • Function: DNA stores genetic information; RNA transfers genetic information and forms part of ribosomes (with proteins).
  • DNA Replication: Semi-conservative. Each new DNA molecule has one original (parental) strand and one new strand.
    • Process: DNA helicase breaks hydrogen bonds, separating strands. Free nucleotides align by complementary base pairing. DNA polymerase catalyzes condensation reactions, forming new phosphodiester bonds.
    • Evidence: Meselson and Stahl’s experiment confirmed semi-conservative replication.
  • Key Enzymes: DNA helicase (unwinds and separates strands), DNA polymerase (joins nucleotides).

ATP

  • Structure: Adenosine triphosphate (ATP) is a nucleotide derivative: adenine base, ribose sugar, three phosphate groups.
  • Function: Immediate energy source for metabolic processes; all cells require a constant supply.
  • ATP Hydrolysis: ATP + water → ADP + Pi + energy (catalyzed by ATP hydrolase). Releases energy for cellular reactions; inorganic phosphate can phosphorylate other molecules, making them more reactive.
  • ATP Synthesis: ADP + Pi → ATP (condensation reaction, catalyzed by ATP synthase). Occurs in respiration and photosynthesis.

Water

  • Structure: Polar molecule (H₂O) with uneven charge distribution (oxygen slightly negative, hydrogens slightly positive). Forms hydrogen bonds between molecules.
  • Key Properties:
    • Metabolite: Involved in condensation and hydrolysis reactions.
    • Solvent: Dissolves solutes, allowing metabolic reactions in solution.
    • High heat capacity: Buffers temperature changes; takes a lot of energy to raise temperature due to hydrogen bonds.
    • Large latent heat of vaporization: Requires much energy to evaporate, providing cooling (e.g., sweating).
    • Strong cohesion: Water molecules stick together (hydrogen bonds), supporting continuous columns in xylem and creating surface tension (habitat for some organisms).

Inorganic Ions

  • Location: Found in solution in cytoplasm and body fluids; concentration and role depend on the specific ion.
  • Key Ions and Functions:
    • H⁺ (hydrogen ions): Affect pH; more H⁺ = lower pH (acidic).
    • Fe²⁺ (iron ions): Part of hemoglobin; binds oxygen for transport in blood.
    • Na⁺ (sodium ions): Involved in co-transport of glucose and amino acids (e.g., absorption in the ileum).
    • PO₄³⁻ (phosphate ions): Component of DNA, RNA, and ATP.

Key Terms & Definitions

  • Monomer: Small molecule that can join to form a polymer.
  • Polymer: Large molecule made from repeated monomer units.
  • Condensation reaction: Joins molecules, releases water.
  • Hydrolysis reaction: Splits molecules, uses water.
  • Glycosidic bond: Bond between carbohydrate monomers.
  • Ester bond: Bond in lipids between glycerol and fatty acids.
  • Peptide bond: Bond between amino acids in proteins.
  • Phosphodiester bond: Bond between nucleotides in nucleic acids.
  • Active site: Specific region of enzyme where substrate binds.
  • Enzyme-substrate complex: Intermediate formed when enzyme binds substrate.
  • Competitive inhibitor: Competes with substrate for enzyme active site.
  • Non-competitive inhibitor: Binds enzyme away from active site, alters active site shape.

Action Items / Next Steps

  • Review definitions and bond types for each biological molecule.
  • Practice drawing and labelling diagrams of glucose, amino acids, and nucleotides.
  • Memorize biochemical test procedures and expected observations for carbohydrates, proteins, and lipids.
  • Complete workbook exercises or summaries as prompted in the lecture.
  • Highlight key points about structure-function relationships, especially for polysaccharides, lipids, proteins, and nucleic acids.
  • Ensure understanding of enzyme models and factors affecting enzyme activity, including the effects of inhibitors.

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