describe the classification of organisms into three domains: Archaea, Bacteria and Eukarya

Classification of Organisms – Cambridge International AS & A Level Biology (9700)

Learning Objectives

• Explain why the three‑domain system (Archaea, Bacteria, Eukarya) replaced the five‑kingdom system.
• Describe the structural, biochemical and genetic differences that separate the three domains.
• Apply the taxonomic hierarchy and binomial nomenclature to name organisms correctly.
• Analyse phylogenetic trees and construct simple dichotomous keys (AO2).
• Relate classification to biodiversity indices, conservation status and biotechnological applications (AO3).
• Integrate knowledge of cell structure, metabolism, transport, genetics, division, energy carriers, respiration, photosynthesis, nutrition, homeostasis and reproduction across the three domains.

How This Note Meets the Cambridge Syllabus

1. Historical Development of Classification

• Five‑kingdom system (1970s) – based on morphology & nutrition (Monera, Protista, Fungi, Plantae, Animalia).
• Limitations: All prokaryotes were grouped in Monera despite profound biochemical differences; system relied solely on observable traits.
• Molecular revolution (late 1970s–1980s): Carl Woese sequenced the small sub‑unit ribosomal RNA (16S rRNA) from many organisms.
• Key discovery: Two distinct prokaryotic lineages emerged – one with “bacterial” signatures, another with unique “archaeal” signatures.
• Three‑Domain System (1990): Archaea, Bacteria, Eukarya – reflects deep evolutionary splits revealed by rRNA phylogeny and later whole‑genome analyses.

2. Taxonomic Hierarchy & Binomial Nomenclature

Ranks from most specific to most inclusive:

1. Species
2. Genus
3. Family
4. Order
5. Class
6. Phylum (or Division for plants)
7. Kingdom
8. Domain

Binomial nomenclature rules (Linnaean system):

• Two‑part name: Genus species (e.g., Escherichia coli).
• Genus capitalised, species lowercase; both italicised (or underlined when handwritten).
• Authority may follow (e.g., Homo sapiens Linnaeus, 1758).
• Subspecies/varieties add a third epithet (e.g., Canis lupus familiaris).

3. The Three‑Domain System – Comparative Overview

Domain‑Specific Summaries

Archaea

• Cell biology: Prokaryotic; S‑layer or pseudo‑peptidoglycan; ether‑linked lipids give resistance to heat, acidity and salinity.
• Genetic organisation: Circular chromosome; histone‑like proteins (e.g., HMf) compact DNA; multiple replication origins.
• Enzymes & metabolism: DNA polymerase B (high‑fidelity, thermostable), methyl‑CoM reductase (methanogenesis), sulphide:quinone oxidoreductase.
• Ecological role: Major contributors to global carbon (methane) and sulfur cycles; thrive in extreme niches exploited for industrial enzymes (e.g., Taq‑like polymerases).

Bacteria

• Cell biology: Prokaryotic; peptidoglycan cell wall; diverse shapes (cocci, bacilli, spirilla); often possess flagella, pili, capsules.
• Genetic organisation: Circular chromosome; plasmids; histone‑like HU protein; transcription & translation coupled.
• Enzymes & metabolism: RNA polymerase σ‑factor (promoter specificity), RuBisCO (cyanobacterial CBB cycle), nitrogenase (N₂ fixation).
• Biotechnological relevance: Pathogens (Mycobacterium tuberculosis), antibiotic producers (Streptomyces), recombinant DNA host (E. coli).

Eukarya

• Cell biology: Nucleus with linear chromosomes; membrane‑bound organelles (mitochondria, chloroplasts, ER, Golgi, lysosome, peroxisome, vacuole).
• Genetic organisation: DNA wrapped around histones (nucleosomes); multiple origins of replication; introns & RNA processing.
• Energy production: Mitochondrial oxidative phosphorylation; chloroplast photosynthesis; cytosolic glycolysis.
• Reproduction: Asexual (binary fission, budding, fragmentation) and sexual (meiosis → fertilisation).
• Diversity: Unicellular protists to complex multicellular plants, animals and fungi.

4. Cell Structure (Syllabus Topic 1)

• Prokaryotic cells (Archaea & Bacteria)

  • Plasma membrane – site of ATP generation (e.g., archaeal archaeal ATP synthase, bacterial electron transport chain).
  • Cell wall – peptidoglycan (Bacteria) or pseudo‑peptidoglycan/S‑layer (Archaea).
  • Ribosomes – 70 S (30 S + 50 S); no compartmentalisation of transcription/translation.
  • Extracellular structures – flagella (different basal body proteins in Archaea vs Bacteria), pili, capsules.

• Eukaryotic cells (Eukarya)

  • Plasma membrane – phospholipid bilayer with cholesterol (animals) or sterols (plants).
  • Nucleus – double membrane, nuclear pores, nucleolus (rRNA synthesis).
  • Organelles – mitochondria (ATP via chemiosmosis), chloroplasts (photosynthesis), ER (protein/lipid synthesis), Golgi (modification & sorting), lysosome (hydrolytic enzymes), peroxisome (oxidative reactions).
  • Cytoskeleton – microtubules, actin filaments, intermediate filaments (cell shape, transport, division).

5. Enzymes & Metabolism (Syllabus Topic 2)

Key Concepts

• Enzyme specificity – active‑site complementarity; examples: DNA polymerase (template‑directed synthesis), RuBisCO (CO₂ fixation), nitrogenase (N₂ reduction).
• Kinetic factors – Vmax, Km; temperature & pH optima differ markedly between domains (thermostable archaeal enzymes vs mesophilic bacterial enzymes).
• Regulation – feedback inhibition (e.g., ATP inhibition of phosphofructokinase), allosteric activation, covalent modification.

Domain‑Specific Metabolic Pathways

6. Transport Across Membranes (Syllabus Topic 3)

• Simple diffusion – movement of gases (O₂, CO₂) down concentration gradient; rate proportional to surface area, inversely to membrane thickness.
• Osmosis – water movement through a semi‑permeable membrane; importance in bacterial turgor and plant cell turgidity.
• Facilitated diffusion – carrier proteins (e.g., GLUT transporters) allow polar molecules (glucose, amino acids) to cross without energy input.
• Active transport – primary (ATP‑driven pumps such as Na⁺/K⁺‑ATPase) and secondary (symport/antiport using ion gradients, e.g., bacterial lactose permease).
• Endocytosis & exocytosis – exclusive to eukaryotes; receptor‑mediated uptake of macromolecules, secretion of hormones, neurotransmitters.
• Quantitative investigation tip: Use a diffusion chamber to measure rate of glucose uptake; plot rate vs concentration to determine Km (Michaelis‑Menten).

7. Genetic Material & Protein Synthesis (Syllabus Topic 4)

DNA Organisation

• Archaea: Circular chromosome + histone‑like proteins (e.g., HMf); multiple replication origins.
• Bacteria: Single circular chromosome, plasmids; nucleoid‑associated proteins (HU, IHF).
• Eukarya: Linear chromosomes with telomeres; DNA wrapped around histone octamers (nucleosomes); chromatin remodeling.

Replication

• Key enzymes – DNA helicase, primase, DNA polymerase (III in Bacteria, B in Archaea, δ/ε in Eukarya), DNA ligase.
• Bidirectional replication forks; origin of replication (OriC in Bacteria, multiple origins in Archaea & Eukarya).

Transcription & Translation

• Prokaryotes (Archaea & Bacteria): Coupled transcription‑translation; σ‑factor directs RNA polymerase to promoters; mRNA often polycistronic.
• Eukaryotes: Transcription in nucleus (RNA polymerases I, II, III); 5’ cap, poly‑A tail, splicing of introns; export to cytoplasm; translation on free ribosomes or rough ER.
• Universal genetic code with few exceptions (e.g., pyrrolysine in some Archaea).

8. Cell Division (Syllabus Topic 5)

Binary Fission (Archaea & Bacteria)

1. DNA replication (bidirectional) → segregation.
2. Cell elongation; septum formation by FtsZ ring.
3. Septum closure → two daughter cells.

Mitosis (Eukarya)

1. Prophase: Chromosome condensation, spindle formation.
2. Metaphase: Alignment at metaphase plate.
3. Anaphase: Sister chromatids separate to opposite poles.
4. Telophase & Cytokinesis: Nuclear envelopes reform, cell plate (plants) or cleavage furrow (animals) divides cytoplasm.

Meiosis (Eukarya – sexual reproduction)

1. Meiosis I (reductional): homologous chromosomes pair, cross‑over, separate.
2. Meiosis II (equational): sister chromatids separate – analogous to mitosis.
3. Result: four haploid gametes, each genetically distinct.

Telomeres & Ageing

• Telomeric repeats (TTAGGG) protect chromosome ends.
• Telomerase (reverse transcriptase) adds repeats in germ cells, stem cells, many cancers.

9. Energy Carriers – ATP & NAD(P)H (Syllabus Topic 6)

• Substrate‑level phosphorylation: Direct transfer of a phosphate group to ADP (e.g., phosphoglycerate kinase in glycolysis).
• Oxidative phosphorylation (chemiosmosis): Electron transport chain creates a proton motive force; ATP synthase (F₁F₀) synthesises ATP as protons flow back.
• NAD⁺/NADH and NADP⁺/NADPH: Electron carriers; NADH feeds respiratory chain; NADPH supplies reducing power for biosynthesis (e.g., fatty‑acid synthesis, Calvin cycle).
• Domain differences – archaeal ATP synthase is V‑type (often reversible); bacterial ATP synthase is F‑type; eukaryotic mitochondrial ATP synthase is also F‑type.

10. Respiration (Syllabus Topic 7)

Step‑by‑Step Pathway (Aerobic)

1. Glycolysis (cytosol): Glucose → 2 pyruvate + 2 ATP + 2 NADH.
2. Link reaction (mitochondrial matrix / archaeal cytoplasm): Pyruvate → acetyl‑CoA + CO₂ + NADH.
3. Krebs (TCA) cycle: Acetyl‑CoA → 3 NADH + FADH₂ + GTP (≈ ATP) + 2 CO₂.
4. Electron transport chain (ETC): NADH/FADH₂ donate electrons → O₂ (terminal electron acceptor) → water; proton gradient drives ATP synthase (≈ 34 ATP).

Anaerobic Pathways

• Fermentation (Bacteria & Eukaryotes): Pyruvate reduced to lactate (lactic acid fermentation) or ethanol + CO₂ (alcoholic fermentation); regenerates NAD⁺.
• Methanogenesis (Archaea): CO₂ + 4 H₂ → CH₄ + 2 H₂O; uses unique co‑enzymes (coenzyme M, F₄₂₀).
• Sulphate reduction (Archaea & some Bacteria): SO₄²⁻ → H₂S; energy yield lower than aerobic respiration.

11. Photosynthesis (Syllabus Topic 8)

Light‑Dependent Reactions

• Location: thylakoid membranes (chloroplasts) or thylakoid‑like membranes in cyanobacteria.
• Photosystems II & I absorb photons (λ≈680 nm & 700 nm); water split → O₂, electrons, H⁺.
• Electron transport creates a proton gradient; ATP synthase produces ATP (photophosphorylation).
• Final electron acceptor NADP⁺ → NADPH.

Calvin‑Benson (C₃) Cycle – Light‑Independent

1. Carbon fixation – Rubisco adds CO₂ to ribulose‑1,5‑bisphosphate (RuBP) → 3‑phosphoglycerate (3‑PGA).
2. Reduction – ATP + NADPH convert 3‑PGA to glyceraldehyde‑3‑phosphate (G3P).
3. Regeneration – G3P used to regenerate RuBP.

Variations

• C₄ plants: CO₂ first fixed into oxaloacetate in mesophyll cells, transported to bundle‑sheath cells where Calvin cycle occurs – reduces photorespiration.
• CAM plants: Temporal separation – CO₂ fixed at night, stored as malate, released for Calvin cycle during daylight.
• Cyanobacteria: Perform oxygenic photosynthesis; possess phycobilisomes (light‑harvesting pigments).

12. Nutrition (Syllabus Topic 9)

• Autotrophs: Photoautotrophs (cyanobacteria, plants, algae) – use light energy; chemoautotrophs (nitrifying bacteria, sulfur oxidisers) – use inorganic electron donors.
• Heterotrophs: Obligate heterotrophs (most animals, fungi, many bacteria) – obtain organic carbon from other organisms.
• Digestive strategies:

  • Extracellular digestion – enzymes secreted into environment (e.g., bacterial cellulases, fungal secreted proteases).
  • Intracellular digestion – phagocytosis in amoebae, engulfment by macrophages.
  • Specialised organs – animal stomach, intestinal brush border enzymes.

• Absorption & transport: Membrane transporters (SGLT1, GLUT2) for glucose; amino acid carriers; passive diffusion of fatty acids.

13. Homeostasis (Syllabus Topic 10)

• Temperature regulation:

  • Archaea – protein and membrane adaptations (e.g., increased ionic bonds, ether lipids) allow survival at > 100 °C.
  • Eukaryotes – endothermy (birds, mammals) via metabolic heat production; ectothermy (reptiles, plants) via behavioural thermoregulation.

• Water balance:

  • Bacterial osmoregulation – accumulation of compatible solutes (e.g., proline, betaine).
  • Plant stomatal control; animal kidney filtration; archaeal compatible solutes in hypersaline environments.

• Gas exchange:

  • Diffusion of O₂ and CO₂ across membranes; respiratory pigments (haemoglobin, cytochrome c oxidase) increase efficiency.
  • Archaea – some use alternative electron acceptors (e.g., nitrate, sulphate) when O₂ limited.

• Feedback mechanisms: Negative feedback loops (e.g., blood glucose regulation via insulin/glucagon); hormonal control in plants (abscisic acid for drought response).

14. Reproduction & Development (Syllabus Topic 11)

Asexual Reproduction

• Binary fission (Archaea & Bacteria).
• Budding (yeast, some algae).
• Fragmentation (planarians, some fungi).
• Vegetative propagation (plant cuttings, tubers).

Sexual Reproduction (Eukarya)

• Gamete formation – meiosis produces haploid gametes (sperm, egg, spores).
• Fertilisation – fusion of gametes restores diploid chromosome number.
• Development – cleavage (holoblastic or meroblastic), gastrulation, organogenesis; regulated by gene expression (Hox genes).
• Alternation of generations – seen in plants and many algae (haploid gametophyte ↔ diploid sporophyte).

15. Biodiversity Metrics & Conservation (Syllabus Topic 12)

15.1 Biodiversity Indices

• Species richness (S): Simple count of species in a defined area.
• Evenness (E): E = – Σ(pᵢ ln pᵢ) / ln S; values 0–1, 1 = perfectly even.
• Simpson’s Diversity Index (D): D = Σ nᵢ (nᵢ – 1) / N(N – 1); probability that two randomly selected individuals belong to different species.
• Shannon–Wiener Index (H′): H′ = – Σ pᵢ ln pᵢ; higher values indicate greater diversity.

15.2 Conservation Frameworks

• IUCN Red List: Categories – Extinct (EX), Extinct in the Wild (EW), Critically Endangered (CR), Endangered (EN), Vulnerable (VU), Near Threatened (NT), Least Concern (LC).
• CITES: Appendices I‑III regulate international trade of threatened species.
• Convention on Biological Diversity (CBD): Three objectives – conservation of biodiversity, sustainable use of its components, fair and equitable sharing of benefits arising from genetic resources.

15.3 Threats & Mitigation

• Habitat loss & fragmentation – protected areas, habitat corridors.
• Invasive species – biosecurity, eradication programmes.
• Over‑exploitation – quotas, sustainable harvesting, aquaculture.
• Pollution & climate change – emission reductions, restoration of polluted sites, assisted migration for vulnerable taxa.

16. Practical Skills – Classification & Phylogeny (AO2)

17. Links to Remaining Syllabus Topics (Place‑holders for Future Expansion)