Unit 2 Introduction to classification
Key unit competence: Apply the acquired knowledge of classification to group living organisms into the three domains.
Key ideas
- Classification (taxonomy) groups organisms by shared features into a hierarchy of ranks: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species. Organisms in lower ranks share more features. Binomial nomenclature (Linnaeus) gives each species a two-part Latin name: Genus species, e.g. Homo sapiens, Zea mays (written in italics or underlined; genus with a capital letter).
- Three domains (Woese), based on cell structure and ribosomal RNA: Bacteria (prokaryotes, peptidoglycan cell walls), Archaea (prokaryotes, no peptidoglycan, unusual membrane lipids, many live in extreme environments such as hot springs and salt lakes) and Eukarya (eukaryotes: protoctists, fungi, plants, animals).
- Five kingdoms: Prokaryotae/Monera (bacteria), Protoctista (mostly unicellular eukaryotes: Amoeba, Paramecium, algae, Plasmodium), Fungi (eukaryotes, chitin cell walls, heterotrophic by absorption, hyphae forming mycelium, spores: Rhizopus, mushrooms, yeast), Plantae (multicellular, cellulose walls, chlorophyll, photosynthesis) and Animalia (multicellular, no cell wall, heterotrophic by ingestion, nervous coordination).
- Bacteria: prokaryotic, no nucleus (circular DNA in the cytoplasm), plasmids, 70S ribosomes, cell wall of peptidoglycan, sometimes a capsule, flagella and pili. Shapes: cocci (spheres), bacilli (rods), spirilla (spirals), vibrios (commas). Reproduction by binary fission; some form resistant endospores.
- Gram staining separates bacteria: Gram-positive (thick peptidoglycan wall, stain purple, e.g. Staphylococcus) and Gram-negative (thin wall with an outer membrane, stain pink/red, e.g. E. coli). Bacteria may be aerobic or anaerobic, autotrophic or heterotrophic (saprophytic, parasitic, mutualistic).
- Bacterial diseases: humans: tuberculosis, cholera, typhoid, pneumonia, gonorrhoea, syphilis, tetanus; animals: anthrax, brucellosis, bovine TB; plants: bacterial wilt of potatoes and tomatoes, black rot of cabbage.
- Useful bacteria: decomposition and nutrient cycling, nitrogen fixation (Rhizobium), yoghurt and cheese (Lactobacillus), sewage treatment, biogas, production of antibiotics (Streptomyces), insulin by genetically modified E. coli, gut bacteria that make vitamin K and help digestion.
- Viruses are not cells: a nucleic acid core (DNA or RNA) inside a protein coat (capsid), sometimes an envelope. They are obligate parasites: they reproduce only inside living host cells and show no metabolism outside them, so they are on the border of life. Classified by nucleic acid type, shape (helical, polyhedral, complex) and host. Human viral diseases: HIV/AIDS, influenza, measles, polio, hepatitis B, COVID-19, Ebola, rabies.
- Dichotomous keys identify organisms by a series of paired, contrasting statements about clear, fixed features (not size or colour that vary). Animal features: number of legs, body segments, wings, scales, feathers, hair. Plant features: leaf venation, leaf shape and arrangement, flower parts, presence of seeds or spores.
Common misconceptions
- "Archaea are just a type of bacteria." No: Archaea are a separate domain; their membranes, cell walls and rRNA differ from bacteria, and in some ways they are closer to eukaryotes.
- "Fungi are plants because they do not move." No: fungi have chitin walls, no chlorophyll and feed by absorption; they form their own kingdom.
- "Viruses are the smallest bacteria." No: viruses are not cells and have no ribosomes or metabolism.
- "The species name can be written alone, e.g. sapiens." No: a scientific name always has both genus and species.
Worked examples
Example 1. Explain why viruses are placed outside the five kingdoms.
Solution
Viruses have no cells, no cytoplasm, no ribosomes and no metabolism of their own. They consist only of nucleic acid in a protein coat and can reproduce only inside host cells. The kingdoms classify cellular organisms, so viruses are treated separately.
Example 2. Using the Gram stain, explain why E. coli stains pink and Staphylococcus stains purple.
Solution
Staphylococcus is Gram-positive: its thick peptidoglycan wall keeps the crystal violet-iodine complex after alcohol washing, so it stays purple. E. coli is Gram-negative: its thin peptidoglycan layer and outer membrane lose the purple stain, and it takes up the red counterstain (safranin), so it appears pink.
Practice questions
List the taxonomic ranks from domain to species and explain binomial nomenclature.
Show answer
Domain, kingdom, phylum, class, order, family, genus, species. Binomial nomenclature gives each species a two-part Latin name, genus (capital letter) then species (small letter), in italics or underlined, e.g. Zea mays.
Common mistake: Writing the species name with a capital letter.
Give four differences between Bacteria and Eukarya.
Show answer
Bacteria: no nucleus, no membrane-bound organelles, 70S ribosomes, circular DNA, peptidoglycan wall. Eukarya: true nucleus, membrane-bound organelles, 80S ribosomes, linear chromosomes, walls of cellulose or chitin or none.
Common mistake: Saying bacteria have no DNA.
State the main features of kingdom Fungi.
Show answer
Eukaryotic; cell walls of chitin; no chlorophyll; heterotrophic, feed by absorption (saprophytic or parasitic); body of hyphae forming mycelium (except yeast); reproduce by spores.
Common mistake: Saying fungi photosynthesise.
Draw and label (in words) the structure of a bacterial cell.
Show answer
Capsule; cell wall (peptidoglycan); cell membrane; cytoplasm; circular DNA (nucleoid); plasmids; 70S ribosomes; flagellum; pili.
Common mistake: Including a nucleus.
Give three harmful and three useful roles of bacteria.
Show answer
Harmful: diseases (TB, cholera, typhoid), food spoilage, plant diseases (bacterial wilt). Useful: decomposition and nutrient cycling, nitrogen fixation, yoghurt/cheese, biogas, sewage treatment, antibiotics and insulin production.
Common mistake: Listing only harmful roles.
Explain why viruses are considered to be on the borderline between living and non-living.
Show answer
Living features: contain genetic material, reproduce and mutate inside host cells. Non-living features: not cells, no metabolism, no growth, can be crystallised, inactive outside hosts.
Common mistake: Saying viruses respire.
Describe the Gram staining procedure.
Show answer
Fix a smear; stain with crystal violet; add iodine; wash with alcohol (decolouriser); counterstain with safranin. Gram-positive stay purple; Gram-negative become pink.
Common mistake: Leaving out the alcohol wash.
Construct a dichotomous key for: housefly, spider, millipede, earthworm.
Show answer
1a Has legs → 2; 1b No legs → earthworm. 2a Six legs and wings → housefly; 2b No wings → 3. 3a Eight legs → spider; 3b Many legs (two pairs per segment) → millipede.
Common mistake: Using colour as a feature.
Matching and drag-and-drop
Matching
Match each item in column A with the correct answer in column B. Write the letter next to each number.
Column A Column B 1. Small circular DNA molecules in bacteria are: a. genus 2. A bacterial disease of animals that can spread to humans is: b. plasmids 3. In the name Homo sapiens, Homo is the: c. anthrax 4. Bacteria that fix nitrogen in legume nodules are: d. Rhizobium Show answer
1 → b (plasmids) · 2 → c (anthrax) · 3 → a (genus) · 4 → d (Rhizobium)
- They often carry resistance genes.
- Caused by Bacillus anthracis.
- The genus starts with a capital letter.
- They are mutualistic.
Drag and drop
Choose the correct word or phrase from the box for each gap. One word in the box is not needed.
nucleus · bacteria, Archaea and Eukarya · chitin · capsid- The protein coat of a virus is the .
- The three domains are .
- Fungal cell walls are made of .
Show answer
1: capsid · 2: bacteria, Archaea and Eukarya · 3: chitin
- It surrounds the nucleic acid.
- Proposed by Carl Woese.
- Insects' exoskeletons also contain chitin.
Matching
Match each item in column A with the correct answer in column B. Write the letter next to each number.
Column A Column B 1. HIV is a virus whose genetic material is: a. binary fission 2. A useful bacterium used to make yoghurt is: b. RNA 3. The highest rank in the modern classification system is the: c. domain 4. Bacteria reproduce asexually by: d. Lactobacillus Show answer
1 → b (RNA) · 2 → d (Lactobacillus) · 3 → c (domain) · 4 → a (binary fission)
- It is a retrovirus.
- It produces lactic acid.
- There are three domains.
- One cell divides into two.
Drag and drop
Choose the correct word or phrase from the box for each gap. One word in the box is not needed.
two contrasting statements · inside living host cells · three choices · peptidoglycan- Viruses can reproduce only .
- Bacterial cell walls contain .
- In a dichotomous key, each step has .
Show answer
1: inside living host cells · 2: peptidoglycan · 3: two contrasting statements
- They are obligate parasites.
- Gram staining depends on it.
- Dichotomous means dividing in two.