Biological Classification

🎯 Key Points

• 5 kingdoms (Whittaker, 1969): Monera, Protista, Fungi, Plantae, Animalia — viruses/viroids/lichens are NOT included in any kingdom
• Monera = all prokaryotes (bacteria, cyanobacteria, archaebacteria); cell wall present, NO nucleus/organelles
• Fungi: cell wall of CHITIN (not cellulose); body = hyphae forming mycelium; mostly saprophytic
• Viruses: DNA OR RNA (never both); non-cellular, show no signs of life outside a host; Viroids: RNA only, NO protein coat (smaller than viruses)
• Lichens = alga (phycobiont, photosynthesis) + fungus (mycobiont, shelter/water) in symbiosis; used as pollution indicators (don't grow in polluted air)
• Protozoan groups by locomotion: Amoeboid (pseudopodia), Flagellated (flagella), Ciliated (cilia), Sporozoan (no locomotory structure, infectious spores)

Whittaker's Five Kingdom Classification

• R.H. Whittaker (1969) proposed the five kingdom system: Monera, Protista, Fungi, Plantae, Animalia
• Classification criteria used: cell structure, body organization, mode of nutrition, reproduction, and phylogenetic relationships
• Earlier two-kingdom system (Plantae and Animalia) was inadequate because it did not distinguish between prokaryotes and eukaryotes, unicellular and multicellular organisms, or photosynthetic and non-photosynthetic organisms
• Viruses, viroids, and lichens are not included in any of the five kingdoms

Kingdom Monera

• Includes all prokaryotes: bacteria, cyanobacteria (blue-green algae), mycoplasma, and archaebacteria
• Cell wall present (made of peptidoglycan/murein in eubacteria), no membrane-bound nucleus or organelles
• Archaebacteria: distinct cell wall structure, survive in extreme habitats; halophiles (high salt), thermoacidophiles (hot springs), methanogens (marshy areas, gut of ruminants, produce biogas)
• Eubacteria (true bacteria): rigid cell wall, may or may not have flagella; classified by shape as coccus, bacillus, vibrium, and spirillum
• Cyanobacteria: photosynthetic, unicellular, colonial, or filamentous; have chlorophyll a; some fix atmospheric nitrogen in specialized cells called heterocysts, e.g., Nostoc, Anabaena
• Modes of nutrition: autotrophic (photosynthetic or chemosynthetic) and heterotrophic (saprophytic or parasitic)
• Reproduction: asexual by fission, sometimes by budding; genetic material is transferred via conjugation, transduction, or transformation
• Mycoplasma (PPLO) lack a cell wall and are the smallest living cells; can survive without oxygen

Kingdom Protista

• Includes all single-celled (unicellular) eukaryotes; acts as a link between Monera, Fungi, Plantae, and Animalia
• Mode of reproduction is by sexual and asexual means, both involving cell fusion and zygote formation
• Chrysophytes: includes diatoms and golden algae (desmids); found in fresh water and marine environments; cell wall forms two thin overlapping shells (frustule); diatoms are chief producers in oceans
• Dinoflagellates: mostly marine and photosynthetic; have two flagella, one lateral and one longitudinal; cell wall has stiff cellulose plates; some cause red tides, e.g., Gonyaulax
• Slime moulds: saprophytic protists that move and feed on decaying organic matter; under suitable conditions form an aggregation called plasmodium
• Protozoans: heterotrophic, live as predators or parasites; four major groups:
• Amoeboid protozoans: pseudopodia for movement and capturing prey, e.g., Amoeba, Entamoeba
• Flagellated protozoans: free-living or parasitic, with flagella, e.g., Trypanosoma (causes sleeping sickness)
• Ciliated protozoans: aquatic, have numerous cilia for locomotion and feeding, e.g., Paramecium
• Sporozoans: have an infectious spore-like stage, e.g., Plasmodium (causes malaria)

Kingdom Fungi

• Eukaryotic, heterotrophic (mostly saprophytic); cell wall made of chitin and polysaccharides (not cellulose)
• Body is a network of filaments called hyphae; the mesh of hyphae is called mycelium; hyphae may be septate or aseptate (coenocytic)
• Modes of nutrition: saprophytic (decaying organic matter), parasitic (depend on living organisms), or symbiotic (lichen with algae, mycorrhiza with plant roots)
• Reproduction: vegetative (fragmentation, fission, budding), asexual (conidia, sporangiospores, zoospores), sexual (oospores, ascospores, basidiospores); sexual cycle has plasmogamy, karyogamy, and meiosis
• Phycomycetes: aquatic or in decaying wood, damp/moist places, or as obligate parasites on plants; coenocytic mycelium; asexual spores are zoospores or aplanospores; e.g., Mucor, Rhizopus (bread mould), Albugo
• Ascomycetes (sac fungi): mostly multicellular, some unicellular (Saccharomyces); septate mycelium; produce sexual spores called ascospores inside an ascus; e.g., Penicillium, Aspergillus, Neurospora, yeast
• Basidiomycetes: mushrooms, bracket fungi, puffballs; mycelium is septate and branched; sex organs absent, but plasmogamy occurs by fusion of two vegetative cells; basidiospores produced on basidium; e.g., Agaricus (mushroom), Ustilago (smut), Puccinia (rust)
• Deuteromycetes (imperfect fungi): only asexual and vegetative reproductive stages known; once a sexual stage is discovered, the fungus gets moved to its proper class; e.g., Alternaria, Trichoderma, Colletotrichum

Lichens

• Lichens are a symbiotic/mutualistic association between algae (autotrophic partner, phycobiont) and fungi (heterotrophic partner, mycobiont)
• Algae provide food via photosynthesis; fungi provide shelter, absorb water and nutrients for the algal partner
• Lichens are good pollution indicators as they do not grow in polluted areas

Viruses, Viroids and Prions

• Viruses are obligate intracellular parasites, non-cellular (acellular), made of nucleoprotein (genetic material plus protein coat called capsid)
• Viruses contain either DNA or RNA, never both; outside a living host cell they show no signs of life, so they are not placed in any of the five kingdoms
• The term "virus" was coined by Pasteur; D.J. Ivanowsky (1892) first noted viruses as smaller than bacteria (in tobacco mosaic disease); M.W. Beijerinck described the contagious nature and called the fluid Contagium vivum fluidum; W.M. Stanley (1935) showed viruses could be crystallized and that they are largely protein
• Viruses infecting plants have single-stranded RNA; those infecting animals have either single or double-stranded RNA or double-stranded DNA; bacteriophages are usually double-stranded DNA viruses
• Capsid is made of small subunits called capsomeres, which can be arranged helically or polyhedrally
• Viroids: discovered by T.O. Diener (1971); smaller than viruses; consist of free RNA only, lacking the protein coat found in viruses; caused potato spindle tuber disease
• Prions: abnormally folded infectious proteins responsible for diseases like mad cow disease (linked to Creutzfeldt-Jakob disease in humans)

Kingdom Protista: Euglenoids

• Euglenoids: mostly fresh-water organisms found in stagnant water; instead of a cell wall they have a protein-rich layer called the pellicle which makes their body flexible
• They have two flagella, a short and a long one; though they are photosynthetic in the presence of sunlight, when deprived of sunlight they behave like heterotrophs by predating on other smaller organisms — hence they are considered a connecting link between plants and animals (mixotrophic)
• The pigments of euglenoids are identical to those present in higher plants; example: Euglena

Kingdom Plantae

• Includes all eukaryotic, chlorophyll-containing organisms commonly called plants; they are autotrophic (photosynthetic), though a few are partially heterotrophic (insectivorous plants like Venus flytrap/bladderwort, or parasites like Cuscuta)
• Cells have a cell wall made mainly of cellulose; the group includes algae, bryophytes, pteridophytes, gymnosperms, and angiosperms
• Plants show a clear alternation of generations — the diploid sporophytic and haploid gametophytic phases alternate in the life cycle

Kingdom Animalia

• Includes multicellular, eukaryotic, heterotrophic organisms that lack a cell wall; they directly or indirectly depend on plants for food (holozoic nutrition — food is ingested and digested in an internal cavity)
• Most are capable of locomotion; they store food reserve as glycogen or fat; their growth to adult form is definite (reaches a certain size and shape)
• Sexual reproduction is by copulation of male and female followed by embryological development

Five Kingdoms at a Glance

Gram-Positive vs Gram-Negative Bacteria

• Bacteria are also classified by their response to Gram's staining (developed by Christian Gram), which depends on the structure of the bacterial cell wall
• Gram-positive bacteria: retain the crystal violet stain and appear purple/violet under the microscope; they have a thick peptidoglycan (murein) cell wall; e.g. Bacillus, Clostridium, Staphylococcus
• Gram-negative bacteria: do NOT retain crystal violet and instead take up the counterstain (safranin), appearing pink/red; they have a thin peptidoglycan layer plus an outer lipopolysaccharide membrane; e.g. Escherichia coli, Salmonella, Pseudomonas
• This distinction is important not only for identification but also because the two groups often differ in their sensitivity to particular antibiotics

Mycorrhiza: Fungus–Root Symbiosis

• A mycorrhiza is a symbiotic association between a fungus and the roots of a higher plant — a second major symbiotic association of fungi besides lichens
• The fungus absorbs mineral nutrients (especially phosphorus) and water from the soil and passes them to the plant; in return the plant supplies the fungus with sugars and other organic food
• Ectomycorrhiza: fungal hyphae form a sheath around the root and grow between cortical cells without penetrating them; endomycorrhiza (vesicular–arbuscular type): hyphae penetrate into the cortical cells of the root
• Benefits to the plant include enhanced phosphorus and mineral uptake, greater drought resistance, and protection against root pathogens; many plants (e.g. Pinus) fail to establish without their mycorrhizal fungal partner

Diatoms and Diatomaceous Earth

• Diatoms are photosynthetic chrysophytes found in both fresh water and the sea; they are among the chief producers in the oceans, forming the base of aquatic food chains
• The cell wall (frustule) fits together as two thin overlapping shells, like a soap box; the walls are embedded with silica and are therefore practically indestructible
• Over billions of years the indestructible silica walls of dead diatoms have piled up as large deposits called diatomaceous earth (kieselguhr)
• Being gritty, this diatomaceous earth is used in polishing, and as a fine filtration medium in the filtration of oils and syrups

🚀 NEET Advanced Edge

Viruses vs viroids vs prions — what each lacks: Virus = nucleic acid (DNA or RNA) + protein capsid. Viroid = RNA only, NO capsid (smaller, simpler than a virus). Prion = protein ONLY, no nucleic acid at all — the most stripped-down infectious agent, which is exactly why exam questions test "which infectious agent has no genetic material."

Archaebacteria vs Eubacteria cell wall distinction: Archaebacteria have a DIFFERENT, non-peptidoglycan cell wall chemistry (unlike eubacteria's peptidoglycan/murein) — this fundamental biochemical difference, not just habitat, is why archaebacteria are classified separately even though both groups are prokaryotic Monera.

Plasmogamy vs karyogamy timing in fungi: Plasmogamy (fusion of cytoplasm of two cells) happens BEFORE karyogamy (fusion of nuclei) in the fungal sexual cycle, creating a transient dikaryotic (n+n) stage unique to fungi — this delay between the two fusion events is a distinctly fungal feature not seen in animal/plant fertilisation, where both happen together.