Biological Molecules

Overview

• Summary of AQA A-level Biology Topic 1: biological molecules, enzymes, DNA, ATP, water, and inorganic ions.

• Focus on monomers/polymers, reactions (condensation/hydrolysis), and how structure links to function.

• Emphasis on exam-style definitions and keywords required by the specification.

Monomers and Polymers

• Monomer: a small unit from which larger molecules are made.

• Polymer: molecule made from many monomers joined together.

• Key monomers: monosaccharides, amino acids, nucleotides.

• Key polymers: carbohydrates (starch, cellulose, glycogen), proteins, DNA/RNA.

• Reactions:

  • Condensation: joins two molecules, forms a bond, eliminates one water molecule.

  • Hydrolysis: breaks a bond using one water molecule.

• Applied examples: name molecules and bond (e.g., two amino acids form peptide bond; glucose + glucose → maltose via glycosidic bond).

Carbohydrates

• Classes:

  • Monosaccharides: glucose, fructose, galactose.

  • Disaccharides: maltose (glucose + glucose), lactose (glucose + galactose), sucrose (glucose + fructose).

  • Polysaccharides: starch, cellulose, glycogen.

• Bond: glycosidic bond formed by condensation between hydroxyl groups.

• Glucose:

  • Formula C6H12O6.

  • Two isomers: alpha and beta glucose (different orientation at carbon-1).

• Disaccharide formation: water released from two hydroxyl groups; can be 1→4 glycosidic bond (between C1 and C4).

• Hydrolysis: water added, glycosidic bond broken to yield monosaccharides.

Polysaccharides: Starch, Glycogen, Cellulose

• Common notes:

  • Starch and glycogen use alpha glucose; cellulose uses beta glucose.

  • Glycosidic bonds: 1→4 and 1→6 (branching when 1→6 present).

• Starch:

  • Components: amylose (unbranched 1→4, coils into helix), amylopectin (1→4 and 1→6, branched).

  • Function: plant glucose storage in chloroplasts.

  • Structure-function: coils compact storage; branches increase exposed ends for rapid hydrolysis.

  • Insoluble: does not affect water potential.

• Glycogen:

  • Highly branched (more 1→6 bonds than starch).

  • Function: animal glucose storage (muscle, liver).

  • Structure-function: greater branching allows faster hydrolysis for rapid ATP generation.

  • Insoluble, mostly uncoiled.

• Cellulose:

  • Straight, long chains of beta glucose with 1→4 bonds; alternate glucose flipped 180°.

  • Chains held in parallel by many hydrogen bonds forming microfibrils (fibres).

  • Function: structural strength in plant cell walls.

  • Insoluble.

Tests for Carbohydrates

• Starch test: iodine solution; positive turns brown/orange → blue/black.

• Reducing sugars test: Benedict’s reagent and heat; positive: blue → green/yellow/orange/brick red (more red = higher concentration).

• Non-reducing sugar (sucrose) test: negative Benedict first; hydrolyse with acid and boil, neutralize with alkali, then Benedict’s and heat again to show positive result.

Lipids

• Two main types: triglycerides and phospholipids.

• Triglycerides:

  • Made by condensation: glycerol + three fatty acids → three ester bonds + three water molecules.

  • Function: energy storage (lots of C–H bonds), metabolic water source, insoluble (hydrophobic), low density (good for storage without mass).

• Phospholipids:

  • Glycerol + two fatty acids + phosphate group (two ester bonds).

  • Amphipathic: hydrophilic (polar) head with phosphate, hydrophobic (nonpolar) tails.

  • Function: form phospholipid bilayer of cell membranes; heads face water, tails face inward.

• Fatty acids R group:

  • Saturated: only single C–C bonds, maximum H atoms.

  • Unsaturated: at least one C=C double bond, fewer H atoms.

• Lipid test: mix sample with ethanol then add distilled water; positive emulsion is white/cloudy.

Proteins

• Amino acids:

  • Central carbon with four groups: amine (NH2) on left, carboxyl (COOH) on right, H and variable R group.

  • 20 different amino acids distinguished by R group.

• Peptide formation:

  • Condensation between carboxyl of one and amine of another forms a peptide bond and water.

  • Dipeptide = two amino acids; polypeptide = many.

• Protein structure levels:

  • Primary: sequence of amino acids held by peptide bonds (order determines later folding).

  • Secondary: alpha helix or beta pleated sheet formed by hydrogen bonds between backbone (C=O and N–H).

  • Tertiary: further folding into unique 3D shape; held by ionic bonds, hydrogen bonds, disulfide bonds (if R groups contain sulfur).

  • Quaternary: multiple polypeptide chains assembled (e.g., haemoglobin).

• Importance: one amino acid change can alter tertiary folding, changing protein function (relevance to mutations).

• Protein test: Biuret reagent (blue → purple) — heat not required. Correct spelling: Biuret.

Enzymes

• Enzymes are proteins with a specific tertiary structure and active site.

• Role: catalyze reactions by lowering activation energy; form enzyme-substrate complex.

• Models of action:

  • Lock-and-key: active site rigid and complementary to substrate.

  • Induced fit: active site molds around substrate when binding; accepted model.

• Factors affecting enzyme activity:

  • Temperature: increasing temp increases rate up to optimum; above optimum tertiary bonds break (denaturation) and rate falls.

  • pH: deviations break ionic interactions, denature enzyme; each enzyme has its own optimum pH.

  • Substrate concentration: rate rises with substrate until enzymes saturated (plateau).

  • Enzyme concentration: rate rises with enzyme until substrate becomes limiting.

  • Inhibitors:

    • Competitive inhibitors: similar shape to substrate, compete for active site; effect can be overcome by excess substrate.

    • Non-competitive inhibitors: bind elsewhere (allosteric site), change active site shape; cannot be overcome by more substrate.

Nucleic Acids

• DNA and RNA are polymers of nucleotides.

• Nucleotide components: phosphate group, pentose sugar, nitrogenous base.

• Differences:

  • DNA: deoxyribose sugar; bases A, G, C, T.

  • RNA: ribose sugar; bases A, G, C, U (uracil replaces thymine).

• Bonding: phosphodiester bonds between sugar and phosphate via condensation; strong covalent linkage.

• DNA structure:

  • Two polynucleotide strands joined by hydrogen bonds between complementary bases (A–T with two H bonds; G–C with three H bonds).

  • Double helix; complementary base pairing ensures accurate replication and mRNA transcription.

  • RNA is single-stranded and shorter.

• Roles:

  • DNA stores genetic information; both strands can act as templates.

  • RNA transfers genetic information; ribosomes contain RNA and proteins.

• DNA replication:

  • Semi-conservative: each daughter DNA has one parental and one new strand.

  • Enzymes: DNA helicase unwinds and separates strands; free nucleotides align by complementary pairing; DNA polymerase catalyzes phosphodiester bond formation.

• Historical note: Watson and Crick model aided by Rosalind Franklin; Meselson and Stahl provided evidence for semi-conservative replication.

ATP

• ATP = adenosine triphosphate; nucleotide derivative with adenine base, ribose sugar, three phosphates.

• Function: immediate energy source for metabolic reactions; constant supply needed.

• Hydrolysis of ATP: ATP + H2O → ADP + Pi + energy; catalyzed by ATPase (ATP hydrolase).

• Released Pi can be added to molecules (phosphorylation) to make them more reactive.

• Re-synthesis: ADP + Pi → ATP via condensation catalyzed by ATP synthase (occurs in respiration and photosynthesis).

Water

• Water is polar (oxygen slightly negative; hydrogens slightly positive), enabling hydrogen bonding.

• Five important properties and functional implications:

  • Metabolite: used in many reactions (condensation and hydrolysis).

  • Solvent: dissolves solutes so metabolic reactions occur in solution.

  • High heat capacity: buffers temperature changes, stable internal temperatures.

  • Large latent heat of vaporization: evaporation absorbs lots of energy, provides cooling (e.g., sweating).

  • Strong cohesion: water molecules stick together, forming continuous columns in xylem and surface tension habitats.

Inorganic Ions

• Inorganic ions occur in cytoplasm and body fluids at varying concentrations; each has specific roles.

• Examples:

  • H+ (hydrogen ions): determine pH and affect enzyme activity.

  • Fe2+ (iron ions): component of haemoglobin; binds oxygen in transport.

  • Na+ (sodium ions): involved in co-transport (e.g., absorption of glucose/amino acids in ileum).

  • PO4^3- (phosphate ions): components of DNA, RNA, and ATP.

Key Terms and Definitions

• Monomer / Polymer

• Condensation reaction / Hydrolysis

• Glycosidic bond / Ester bond / Phosphodiester bond / Peptide bond

• Alpha glucose / Beta glucose / Isomer

• Hydrophobic / Hydrophilic / Polar / Nonpolar

• Primary, Secondary, Tertiary, Quaternary protein structures

• Enzyme-substrate complex / Induced fit

• Competitive / Non-competitive inhibitor

• Complementary base pairing

• Semi-conservative replication

• ATP hydrolysis / Phosphorylation

Action Items (Study & Exam Tips)

• Memorize exact exam definitions: condensation reaction and hydrolysis (include water elimination/use).

• Learn word equations for disaccharides and know that water is always a product of condensation.

• Practice drawing alpha-glucose ring and indicate C1 and C4 positions for glycosidic bonds.

• Memorize tests and required steps: iodine for starch; Benedict’s reagent and heat (and acid hydrolysis for non-reducing sugar); ethanol then water for lipids; Biuret for proteins (correct spelling: Biuret).

• Remember structures → functions: starch/glycogen branching; cellulose parallel chains; phospholipid bilayer arrangement.

• Be able to explain enzyme activity graphs (temperature, pH, substrate/enzyme concentration, inhibitors) with correct terminology (optimum, denaturation, saturation).

• Recall enzymes in DNA replication: helicase (unwinds/separates), polymerase (joins nucleotides).

• Practice short, precise exam answers using the specification wording for full marks.