describe the principle of the universal genetic code in which different triplets of DNA bases either code for specific amino acids or correspond to start and stop codons

1. Cell Structure (AS)

Learning outcomes

• Identify the main organelles of animal and plant cells and describe their main functions.
• Explain the structural basis for the differences between prokaryotic and eukaryotic cells.
• Describe the role of the cytoskeleton in cell shape, movement and intracellular transport.

Key points

• Plasma membrane – phospholipid bilayer with embedded proteins (fluid‑mosaic model).
• Nucleus – double membrane, nucleolus (ribosome synthesis), chromatin (DNA‑protein complex).
• Endoplasmic reticulum (rough & smooth) – site of protein synthesis and lipid metabolism.
• Golgi apparatus – modification, sorting and packaging of proteins.
• Mitochondria – double‑membrane organelle, site of aerobic respiration (inner membrane folds = cristae).
• Chloroplast (plant cells) – thylakoid stacks (grana) for photosynthesis.
• Vacuoles, lysosomes, peroxisomes – storage, digestion, detoxification.
• Cytoskeleton – microfilaments (actin), intermediate filaments, microtubules (tubulin) – give shape, enable cytokinesis and vesicle transport.

Practical example: Light microscope observation of onion epidermal cells to locate cell wall, vacuole and chloroplasts; comparison with cheek‑cell smear (animal cell).

2. Biological Molecules (AS)

Learning outcomes

• Describe the structure and properties of carbohydrates, lipids, proteins and nucleic acids.
• Explain how the structure of a macromolecule relates to its function in the cell.

Key points

• Carbohydrates: monosaccharides (glucose, fructose), disaccharides, polysaccharides (starch, glycogen, cellulose). Energy storage vs structural roles.
• Lipids: fatty acids, triglycerides, phospholipids, sterols. Hydrophobic nature, membrane formation, energy density.
• Proteins: amino‑acid composition, peptide bonds, levels of structure (primary → quaternary). Enzyme active sites, structural proteins, transport proteins.
• Nucleic acids: DNA (deoxyribose, thymine) vs RNA (ribose, uracil). Polarity (5′→3′), complementary base‑pairing.

Practical example: Iodine test for starch, Biuret test for protein, Thin‑layer chromatography for lipids.

3. Enzymes (AS)

Learning outcomes

• Explain how enzymes act as biological catalysts.
• Describe the factors that affect enzyme activity (temperature, pH, substrate concentration, inhibitors).
• Interpret enzyme kinetic data (V_max, K_m) and draw a Michaelis‑Menten curve.

Key points

• Enzyme–substrate complex; induced‑fit model.
• Active‑site specificity; competitive vs non‑competitive inhibition.
• Temperature optimum – denaturation above optimum; pH optimum – effect on ionisable groups.
• Effect of substrate concentration – hyperbolic relationship (Michaelis‑Menten equation).

Practical example: Catalase activity assay – measuring O₂ evolution from hydrogen peroxide at different temperatures.

4. Membranes & Transport (AS)

Learning outcomes

• Describe the structure of the plasma membrane and the fluid‑mosaic model.
• Explain passive (diffusion, osmosis, facilitated diffusion) and active transport mechanisms.
• Interpret experimental data on transport rates.

Key points

• Selective permeability – role of phospholipid bilayer and membrane proteins (channels, carriers, pumps).
• Diffusion: movement down a concentration gradient; rate affected by size, charge, temperature.
• Osmosis: water movement through a semi‑permeable membrane; tonicity (hypertonic, hypotonic, isotonic).
• Facilitated diffusion – carrier proteins, saturation kinetics.
• Active transport – primary (ATP‑driven pumps, e.g., Na⁺/K⁺‑ATPase) and secondary (co‑transport, anti‑port).

Practical example: Diffusion of starch into agar cubes; measurement of mass change to calculate diffusion rate.

5. Mitotic Cell Cycle (AS)

Learning outcomes

• Identify the phases of mitosis and describe the key events in each phase.
• Explain the purpose of the cell‑cycle checkpoints.
• Describe how errors in the cell cycle can lead to cancer.

Key points

• Interphase (G₁, S, G₂) – growth, DNA replication, preparation for division.
• Prophase – chromatin condenses, spindle forms, nuclear envelope breaks down.
• Metaphase – chromosomes line up at the metaphase plate.
• Anaphase – sister chromatids separate to opposite poles.
• Telophase – nuclear envelopes reform, chromosomes de‑condense.
• Cytokinesis – division of cytoplasm (cleavage furrow in animal cells, cell plate in plant cells).
• Checkpoints: G₁ (size & nutrients), G₂ (DNA integrity), M (spindle attachment).

Practical example: Onion root tip squash – staining with aceto‑orcein to observe mitotic figures.

6. Nucleic Acids & Protein Synthesis (AS & A)

6.1 Structure of Nucleic Acids

• Polymer of nucleotides; each nucleotide = 5‑carbon sugar (deoxyribose in DNA, ribose in RNA) + phosphate + nitrogenous base (A, T, G, C; U replaces T in RNA).
• DNA: double helix, antiparallel strands, complementary base‑pairing (A ↔ T, G ↔ C).
• RNA: single‑stranded, can form secondary structures (hairpins, loops).

6.2 DNA Replication (semi‑conservative)

Learning outcomes

• Describe the overall process of DNA replication and the role of the main enzymes.
• Explain why the replication is semi‑conservative.

Key enzymes (required depth)

• Helicase – unwinds the double helix.
• DNA polymerase – adds nucleotides to the 3′‑OH of the growing strand (5′→3′ synthesis).
• Primase – synthesises short RNA primers for the lagging strand.
• DNA ligase – joins Okazaki fragments.

Process

1. Origin of replication opened → replication fork.
2. Leading strand synthesized continuously toward the fork.
3. Lagging strand synthesised discontinuously (Okazaki fragments) away from the fork.
4. Each daughter DNA molecule contains one parental strand and one newly synthesised strand.

6.3 Transcription – DNA → mRNA

Learning outcomes

• Explain the steps of transcription and the function of promoter and terminator sequences.
• State the differences between transcription in prokaryotes and eukaryotes.

Steps

1. Initiation: RNA polymerase binds the promoter (e.g., TATA box in eukaryotes). DNA unwinds ~10‑12 bp to form an open complex.
2. Elongation: RNA polymerase moves 3′→5′ on the template strand, synthesising mRNA 5′→3′ (A↔U, G↔C).
3. Termination:

   • Prokaryotes – terminator hairpin or rho factor.
   • Eukaryotes – poly‑adenylation signal (AAUAAA); RNA polymerase releases the primary transcript.

6.4 RNA Processing (Eukaryotes)

• 5′‑capping – addition of a modified guanine nucleotide (m⁷G) to protect the mRNA and aid ribosome binding.
• Splicing – removal of introns by the spliceosome; exons ligated to form a continuous coding sequence.
• Poly‑adenylation – addition of a ~200‑A tail at the 3′ end; enhances stability and nuclear export.

6.5 Translation & the Universal Genetic Code

Learning outcomes

• Describe the structure of a ribosome and the roles of the A, P and E sites.
• Explain the three stages of translation (initiation, elongation, termination).
• State the main features of the universal genetic code.

Ribosome structure

• Two subunits (large + small) form three functional sites:

  • A‑site (aminoacyl) – entry point for amino‑acyl‑tRNA.
  • P‑site (peptidyl) – holds tRNA with the growing polypeptide.
  • E‑site (exit) – releases de‑acylated tRNA.

Stages of translation

1. Initiation

   • Small subunit binds the 5′‑cap (or Shine‑Dalgarno sequence in prokaryotes) and scans for the start codon AUG.
   • Initiator tRNA^Met pairs with AUG at the P‑site.
   • Large subunit joins → complete ribosome.

2. Elongation

   • Amino‑acyl‑tRNA matching the next codon enters the A‑site.
   • Peptide bond formation transfers the nascent chain to the A‑site tRNA (catalysed by rRNA).
   • Ribosome translocates one codon; empty tRNA moves to the E‑site and exits; peptidyl‑tRNA shifts to the P‑site.

3. Termination

   • Stop codon (UAA, UAG, UGA) enters the A‑site.
   • Release factors bind → hydrolysis of the peptide‑tRNA bond.
   • Polypeptide released; ribosomal subunits dissociate.

The Universal Genetic Code

• Each codon = three nucleotides → specifies an amino‑acid, a start signal (AUG) or a stop signal (UAA, UAG, UGA).
• Degenerate – most amino‑acids are encoded by more than one codon.
• Nearly universal – the same codons are used by almost all organisms (minor exceptions in mitochondria).

6.6 Mutations

• Point (substitution) mutations

  • Silent – different codon, same amino‑acid (e.g., GAA → GAG = Glu).
  • Missense – codon change → different amino‑acid (e.g., GAA → GAC = Glu → Asp).
  • Nonsense – codon becomes a stop codon (e.g., TGG → TGA).

• Frameshift mutations – insertion or deletion not in multiples of three; shifts the reading frame and alters all downstream codons.

Relevant outcome: 6.2.7 – explain how mutations can affect protein structure and function.

6.7 Post‑Translational Modifications & Folding

• Signal‑peptide cleavage – directs proteins to the secretory pathway.
• Phosphorylation, glycosylation, acetylation – regulate activity, localisation, stability.
• Disulphide‑bond formation – stabilises extracellular proteins.
• Folding assisted by chaperones; mis‑folding can lead to aggregation diseases.

7. Transport in Plants & Mammals (AS)

Learning outcomes

• Describe the mechanisms of water and mineral transport in plants (xylem, phloem).
• Explain the principles of gas exchange and nutrient transport in mammals (respiratory surface, capillaries).

Key points

• Plant water movement – cohesion‑tension theory, transpiration pull, root pressure.
• Phloem transport – pressure‑flow hypothesis (source → sink).
• Animal gas exchange – diffusion across alveolar membrane; role of partial pressures.
• Bulk transport in mammals – filtration (glomerulus), reabsorption, active transport in intestinal epithelium.

Practical example: Measuring transpiration rate of a leaf using a potometer; observing diffusion of a dye across a chicken‑skin membrane.

8. Gas Exchange (AS)

Learning outcomes

• Explain how the structure of respiratory surfaces maximises diffusion.
• Describe the factors affecting the rate of gas exchange in plants and animals.

Key points

• Large surface area, thin moist membrane, short diffusion distance, maintained partial‑pressure gradient.
• Plants – stomatal opening, intercellular air spaces.
• Animals – alveoli (type I pneumocytes), surfactant reduces surface tension.

Practical example: Measuring the rate of O₂ consumption in Daphnia using a sealed chamber and a dissolved‑oxygen probe.

9. Infectious Disease (AS)

Learning outcomes

• Identify the main types of pathogens (bacteria, viruses, fungi, protozoa) and their modes of transmission.
• Explain the concepts of pathogenicity, virulence and host defence.

Key points

• Bacterial infections – Gram‑positive vs Gram‑negative cell walls; antibiotics target cell wall synthesis or protein synthesis.
• Viral infections – attachment, entry, replication strategy (DNA vs RNA viruses); vaccines stimulate adaptive immunity.
• Protozoan malaria – life cycle in Anopheles mosquito and human host.
• Antimicrobial resistance – mechanisms (enzyme degradation, efflux pumps).

Practical example: Observing bacterial growth on agar plates with different antibiotics (zone of inhibition assay).

10. Immunity (AS)

Learning outcomes

• Describe the innate and adaptive immune responses.
• Explain how antibodies are produced and how vaccines work.

Key points

• Innate immunity – physical barriers, phagocytes, inflammation, complement.
• Adaptive immunity – B‑cell (humoral) and T‑cell (cell‑mediated) responses; memory cells.
• Antibody structure (IgG, IgM, IgA) and antigen‑binding specificity.
• Vaccination – introduction of attenuated/killed pathogen or subunit to generate memory without disease.

Practical example: ELISA test to detect specific antibodies in serum.

11. Summary of AS Topics (1‑11)

This section provides a quick‑reference checklist for revision. Each bullet corresponds to a required outcome in the Cambridge International AS & A Level Biology (9700) syllabus.

• Cell structure – organelles, cytoskeleton, prokaryote vs eukaryote.
• Biological molecules – structure–function relationships.
• Enzymes – catalytic mechanism, factors affecting activity, Michaelis‑Menten kinetics.
• Membranes & transport – fluid‑mosaic model, diffusion, osmosis, active transport.
• Mitotic cell cycle – phases, checkpoints, errors → cancer.
• Nucleic acids & protein synthesis – replication, transcription, RNA processing, translation, genetic code, mutations, post‑translational modification.
• Transport in plants & mammals – xylem/phloem, alveolar diffusion, capillary exchange.
• Gas exchange – structural adaptations, factors influencing rate.
• Infectious disease – pathogen types, mechanisms of disease, antibiotic resistance.
• Immunity – innate vs adaptive, antibodies, vaccines.

12. Energy & Respiration (A‑Level)

Learning outcomes

• Write the overall equation for aerobic respiration and calculate the ATP yield.
• Explain the role of glycolysis, the Krebs cycle and oxidative phosphorylation.
• Interpret experimental data on respiration rates (e.g., respirometer).

Key equations

• Aerobic respiration: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ~30‑38 ATP
• Respiratory Quotient (RQ) = CO₂ produced / O₂ consumed (≈1.0 for carbohydrate).

Practical example: Measuring O₂ consumption of germinating beans using a sealed respirometer and a water‑displacement system.

13. Photosynthesis (A‑Level)

Learning outcomes

• Write the overall equation for photosynthesis and identify the light‑dependent and light‑independent reactions.
• Explain the role of chlorophyll, photosystems I & II, and the electron transport chain.
• Analyse data from a photosynthesis rate experiment (e.g., effect of light intensity, CO₂ concentration).

Key equation

C₆H₁₂O₆ + 6O₂  ←→  6CO₂ + 6H₂O + light energy

Practical example: Using a leaf disc assay to investigate the effect of different wavelengths of light on the rate of oxygen evolution.

14. Homeostasis (A‑Level)

Learning outcomes

• Describe the feedback mechanisms that maintain blood glucose, temperature and water balance.
• Explain the roles of hormones (insulin, glucagon, ADH) and the nervous system in regulation.

Key points

• Negative feedback – deviation from set‑point → corrective response.
• Glucose regulation – pancreas β‑cells release insulin (lowers blood glucose); α‑cells release glucagon (raises blood glucose).
• Thermoregulation – hypothalamic control, vasodilation/vasoconstriction, sweating, shivering.
• Water balance – ADH increases water reabsorption in the collecting ducts.

Practical example: Measuring blood glucose before and after ingestion of a glucose solution using a glucometer.

15. Control & Coordination (A‑Level)

Learning outcomes

• Explain the structure and function of neurons and synaptic transmission.
• Describe the hormonal control of the menstrual cycle and the role of the hypothalamic‑pituitary axis.

Key points

• Neuron – dendrite, soma, axon, myelin sheath; action potential propagation (depolarisation, repolarisation, refractory period).
• Synapse – neurotransmitter release, receptor binding, termination (re‑uptake, enzymatic breakdown).
• Endocrine control – feedback loops (e.g., LH/FSH surge triggering ovulation).

Practical example: Measuring reflex time with a ruler drop test to illustrate neuronal response speed.

16. Inheritance (A‑Level)

Learning outcomes

• Apply Mendelian genetics to predict offspring phenotypes and genotypes.
• Explain the basis of linked genes, crossing‑over and genetic maps.
• Interpret pedigree charts and calculate probabilities of inheritance of traits.

Key concepts

• Monohybrid & dihybrid crosses – law of segregation, law of independent assortment.
• Linkage – genes on the same chromosome; recombination frequency (RF) = (cross‑overs / total meioses) × 100 %.
• Pedigree analysis – dominant, recessive, autosomal, sex‑linked patterns.

Practical example: Drosophila eye‑colour crosses to map linked genes and calculate map distances.

17. Evolution (A‑Level)

Learning outcomes

• Describe the mechanisms of natural selection, genetic drift and gene flow.
• Explain how fossil evidence, comparative anatomy and molecular data support evolution.

Key points

• Hardy–Weinberg equilibrium – conditions for no evolution; use to calculate allele frequencies.
• Speciation – allopatric vs sympatric mechanisms.
• Evidence – transitional fossils, homologous structures, DNA sequence similarity.

Practical example: Simulating genetic drift with a small population of coloured beads representing alleles.

18. Biodiversity & Conservation (A‑Level)

Learning outcomes

• Explain the importance of biodiversity and the threats it faces.
• Describe strategies for conservation (protected areas, captive breeding, legislation).

Key points

• Levels of biodiversity – genetic, species, ecosystem.
• Threats – habitat loss, invasive species, over‑exploitation, climate change.
• Conservation tools – IUCN Red List, CITES, biodiversity hotspots.

Practical example: Surveying local pond biodiversity and calculating a Simpson’s diversity index.

19. Genetic Technology (A‑Level)

Learning outcomes

• Describe the principles and applications of DNA cloning, PCR, gel electrophoresis and DNA sequencing.
• Explain how genetically modified organisms (GMOs) are produced and discuss ethical considerations.

Key techniques

• Restriction enzymes – cut DNA at specific palindromic sequences.
• Polymerase Chain Reaction (PCR) – denaturation, annealing, extension; exponential amplification.
• Gel electrophoresis – separation of DNA fragments by size; visualised with ethidium bromide or SYBR‑Safe.
• DNA sequencing – Sanger method (chain‑termination) or next‑generation sequencing.
• Recombinant DNA – insertion of a gene of interest into a plasmid vector; transformation of host cells.

Practical example: Amplifying a segment of the human β‑globin gene by PCR and confirming size on an agarose gel.

20. Integrated Overview – From Gene to Phenotype

A flow diagram (textual) summarises the whole pathway:

DNA (gene) → replication → transcription → RNA processing → mRNA → translation (ribosome, tRNA) → polypeptide → folding & post‑translational modifications → functional protein → phenotype (structure, metabolism, behaviour)

Mutations at any stage can alter the final phenotype, linking the molecular details covered in sections 6‑6.7 to the organism‑level topics in sections 12‑19.