Biological Classification: NEET notes

1. From Aristotle to two kingdoms

NCERT §2 (introduction)

• People have always sorted living things, at first without scientific criteria, simply by how they could be used for food, clothing and shelter.
• Aristotle made the earliest attempt at a more scientific basis. He split plants by simple form into trees, shrubs and herbs, and split animals into those with red blood and those without.
• In the time of Linnaeus a Two Kingdom system, Plantae and Animalia, took in every plant and every animal.
• The two kingdom system drew no line between prokaryotes and eukaryotes, between unicellular and multicellular organisms, or between photosynthetic green algae and non-photosynthetic fungi.
• Sorting into plants and animals was easy to do and understand, but many organisms fitted neither group, so the scheme was eventually judged inadequate.
• Beyond outward form, biologists wanted classification to use cell structure, the nature of the cell wall, mode of nutrition, habitat, methods of reproduction and evolutionary relationships.
• Plantae and Animalia have remained in every later system, but which organisms belong inside them, and how many other kingdoms exist, has been understood differently by different scientists.

2. The five kingdom classification

NCERT §2 (introduction), Table 2.1

• R.H. Whittaker (1969) proposed the Five Kingdom Classification: Monera, Protista, Fungi, Plantae and Animalia.
• He sorted organisms on five criteria: how the cell is built, how the body is organised, how the organism gets food, how it reproduces, and its phylogenetic (evolutionary) relationships.
• Older schemes put bacteria, blue-green algae, fungi, mosses, ferns, gymnosperms and angiosperms all under 'Plants', because all of them have a cell wall. That one shared feature lumped together groups that differ widely in everything else.
• The old 'Plants' mixed prokaryotic bacteria and cyanobacteria with eukaryotes, mixed unicellular Chlamydomonas with multicellular Spirogyra under algae, and mixed heterotrophic fungi (walls of chitin) with autotrophic green plants (walls of cellulose).
• Whittaker gave fungi their own kingdom, collected every prokaryote into Monera, and placed unicellular eukaryotes in Protista.
• Protista now holds Chlamydomonas and Chlorella, which have walls and were once algae among plants, together with Paramoecium and Amoeba, which lack walls and were once animals. The members moved because the criteria changed.
• Table 2.1 in brief. Monera: prokaryotic, non-cellulosic wall (polysaccharide + amino acid), no nuclear membrane, cellular, autotrophic (chemosynthetic or photosynthetic) or heterotrophic (saprophytic or parasitic). Protista: eukaryotic, wall in some, cellular, autotrophic (photosynthetic) or heterotrophic.
• Table 2.1 continued. Fungi: eukaryotic, wall with chitin, multicellular or loose tissue, heterotrophic (saprophytic or parasitic). Plantae: eukaryotic, cellulose wall, tissue or organ level, autotrophic (photosynthetic). Animalia: eukaryotic, no wall, tissue, organ or organ system level, heterotrophic (holozoic, saprophytic and so on).
• A three-domain system has also been proposed. It splits Monera into two domains and puts all eukaryotic kingdoms in the third, which gives a six kingdom classification.
• Classification keeps being revised as our knowledge of characters and evolutionary relationships improves; the aim is a phylogenetic system, based on evolutionary relationships, not only on form, physiology and reproduction.

3. Kingdom Monera: the bacteria

NCERT §2.1

• Bacteria are the only members of Kingdom Monera, and they are the most abundant micro-organisms.
• They turn up nearly everywhere. A handful of soil holds hundreds of them, and they also survive where little else can, in hot springs, deserts, snow and the deep sea. Many are parasites living in or on other organisms.
• By shape bacteria fall into four groups: spherical coccus (cocci), rod-shaped bacillus (bacilli), comma-shaped vibrium (vibrio) and spiral spirillum (spirilla).
• Their structure is very simple, but their behaviour is complex: as a group bacteria show the widest metabolic diversity of any organisms.
• Some are autotrophs that make their food from inorganic substrates, either by photosynthesis or by chemosynthesis.
• The great majority of bacteria are heterotrophs: they get food from other living organisms or from dead organic matter.

4. Archaebacteria, eubacteria and mycoplasma

NCERT §2.1.1–2.1.2

• Archaebacteria thrive in harsh places: very salty water and soil (halophiles), hot springs (thermoacidophiles) and marshes (methanogens).
• Their cell wall is built differently from that of other bacteria, and this wall is what lets them survive extreme conditions.
• Methanogens live in the gut of ruminants such as cows and buffaloes and produce methane (biogas) from the dung of these animals.
• Eubacteria, the 'true bacteria', come in thousands of kinds. They have a rigid cell wall and, if they move, a flagellum.
• Cyanobacteria (blue-green algae) carry chlorophyll a like green plants and are photosynthetic autotrophs. They may be unicellular, colonial or filamentous, and live in fresh water, the sea or on land; colonies usually have a gelatinous sheath, and they often bloom in polluted water.
• Some cyanobacteria, such as Nostoc and Anabaena, fix atmospheric nitrogen in special cells called heterocysts.
• Chemosynthetic autotrophs get energy by oxidising inorganic compounds such as ammonia, nitrites and nitrates, and use it to make ATP. They matter greatly in recycling nitrogen, phosphorus, iron and sulphur.
• Heterotrophic bacteria are the most abundant in nature, and most are important decomposers. Useful ones help set curd from milk, make antibiotics and fix nitrogen in legume roots; harmful ones cause cholera, typhoid, tetanus and citrus canker.
• Bacteria reproduce mainly by fission; in bad conditions they form spores; and they show a primitive sexual reproduction by passing DNA from one bacterium to another.
• Mycoplasma have no cell wall at all. They are the smallest living cells known, can survive without oxygen, and many cause disease in animals and plants.

5. Kingdom Protista

NCERT §2.2–2.2.4

• Protista holds all single-celled eukaryotes, but its boundaries are fuzzy: one biologist's photosynthetic protist is another's plant. NCERT includes chrysophytes, dinoflagellates, euglenoids, slime moulds and protozoans.
• Protists are mostly aquatic, form a link with plants, animals and fungi, have a well-defined nucleus and membrane-bound organelles, may carry flagella or cilia, and reproduce asexually and sexually through cell fusion and zygote formation.
• Chrysophytes are diatoms and golden algae (desmids), found in fresh and sea water. They are microscopic, drift with water currents as plankton, and most are photosynthetic.
• A diatom's wall is two thin overlapping halves that fit like the lid and base of a soap box. Silica makes the walls practically indestructible, so over billions of years they have piled up as diatomaceous earth, a gritty material used for polishing and for filtering oils and syrups. Diatoms are the chief producers of the oceans.
• Dinoflagellates are mostly marine and photosynthetic, coloured yellow, green, brown, blue or red by their main pigments. The outer wall has stiff cellulose plates, and most have two flagella, one running lengthwise and one crosswise in a groove between the plates.
• Red dinoflagellates such as Gonyaulax can multiply so fast that the sea turns red (red tides); their toxins can kill fish and other marine animals.
• Euglenoids mostly live in stagnant fresh water. They have no cell wall but a protein-rich pellicle that keeps the body flexible, and two flagella, one short and one long.
• Euglenoids photosynthesise in sunlight but, kept in the dark, feed like heterotrophs by preying on smaller organisms. Their pigments are the same as those of higher plants. Example: Euglena.
• Slime moulds are saprophytic protists that creep over rotting twigs and leaves, engulfing organic matter. In good conditions they gather into a plasmodium that can spread over several feet.
• In bad conditions the plasmodium forms fruiting bodies with spores at their tips. The spores have true walls, resist harsh conditions for many years, and are spread by air currents.

6. Protozoans

NCERT §2.2.5

• Every protozoan is a heterotroph, either a predator or a parasite, and the group is considered a primitive relative of animals. NCERT describes four major groups.
• Amoeboid protozoans live in fresh water, the sea or moist soil and move and catch prey with pseudopodia (false feet), as in Amoeba. Marine forms carry silica shells; some, such as Entamoeba, are parasites.
• Flagellated protozoans are free-living or parasitic and move with flagella. Parasitic forms cause diseases such as sleeping sickness. Example: Trypanosoma.
• Ciliated protozoans are aquatic and move actively with thousands of cilia. They have a gullet opening to the outside, and rows of cilia beating together steer food-laden water into it. Example: Paramoecium.
• Sporozoans pass through an infectious, spore-like stage in the life cycle. Plasmodium, the malarial parasite, belongs here; malaria has an enormous effect on human populations.

7. Kingdom Fungi: body, nutrition and reproduction

NCERT §2.3

• Fungi are a distinct kingdom of heterotrophs with great variety in form and habitat: mould on moist bread and rotting fruit, mushrooms and toadstools, and the white spots on mustard leaves caused by a parasitic fungus.
• Yeast, a unicellular fungus, is used to make bread and beer; Puccinia causes wheat rust; Penicillium is a source of antibiotics.
• Fungi occur in air, water, soil and on plants and animals, and prefer warm, humid places; this is why food is kept in the refrigerator, to slow bacterial and fungal spoilage.
• Except for unicellular yeasts, fungi are filamentous. Their bodies are made of long thread-like hyphae, and the network of hyphae is the mycelium.
• Some hyphae are continuous tubes with many nuclei in the cytoplasm (coenocytic hyphae); others are divided by cross walls called septae. Fungal cell walls are made of chitin and polysaccharides.
• Most fungi are saprophytes, absorbing soluble organic matter from dead substrates; some are parasites on living plants and animals; some are symbionts, with algae as lichens and with plant roots as mycorrhiza.
• Vegetative reproduction is by fragmentation, fission and budding. Asexual spores are conidia, sporangiospores or zoospores; sexual spores are oospores, ascospores or basidiospores, all formed in fruiting bodies.
• The sexual cycle has three steps: plasmogamy (fusion of protoplasms of two gametes, motile or not), karyogamy (fusion of two nuclei) and meiosis in the zygote, which gives haploid spores.
• In sexual reproduction two haploid hyphae of compatible mating types fuse. In some fungi this gives diploid (2n) cells at once; in ascomycetes and basidiomycetes a dikaryotic stage (n + n, two nuclei per cell) comes in between, called the dikaryon, in the dikaryophase.
• The parental nuclei later fuse to make the cells diploid, and meiosis in the fruiting bodies produces haploid spores. Fungi are split into classes by the form of the mycelium, how spores are formed, and the fruiting bodies.

8. The four classes of fungi

NCERT §2.3.1–2.3.4

• Phycomycetes grow in water, on rotting wood in damp spots, or as obligate parasites of plants. Their mycelium has no septa and is coenocytic.
• Phycomycetes reproduce asexually by motile zoospores or non-motile aplanospores formed inside a sporangium (endogenous). A zygospore forms when two gametes fuse; the gametes may be alike (isogamous) or unlike (anisogamous or oogamous). Examples: Mucor, Rhizopus (bread mould) and Albugo (parasite on mustard).
• Ascomycetes, the sac fungi, are mostly multicellular (Penicillium) and rarely unicellular (yeast, Saccharomyces). They are saprophytes, decomposers, parasites or coprophilous (growing on dung), with branched, septate mycelium.
• Ascomycete asexual spores are conidia, formed outside (exogenously) on special hyphae called conidiophores. Sexual spores are ascospores formed inside sac-like asci, which sit in fruiting bodies called ascocarps.
• Examples of ascomycetes are Aspergillus, Claviceps and Neurospora; Neurospora is widely used in biochemical and genetic work, and morels and truffles are prized edible members.
• Basidiomycetes include mushrooms, bracket fungi and puffballs, growing in soil, on logs and stumps, or as parasites in living plants (rusts and smuts). Mycelium is branched and septate.
• Basidiomycetes usually lack asexual spores but often fragment. They have no sex organs; plasmogamy is by fusion of two somatic cells of different strains, giving a dikaryotic structure that forms the basidium.
• Karyogamy and meiosis happen in the basidium, producing four basidiospores on its outside (exogenous). Basidia sit in fruiting bodies called basidiocarps. Examples: Agaricus (mushroom), Ustilago (smut) and Puccinia (rust).
• Deuteromycetes are the imperfect fungi, so called because only their asexual or vegetative phases are known. When a member's sexual stage is found, it is moved to its proper class, often ascomycetes or basidiomycetes.
• Deuteromycetes reproduce only by conidia and have septate, branched mycelium. Some are saprophytes or parasites, and many decompose litter and help mineral cycling. Examples: Alternaria, Colletotrichum and Trichoderma.

9. Kingdom Plantae and Kingdom Animalia

NCERT §2.4–2.5

• Plantae includes all eukaryotic organisms with chlorophyll, commonly called plants. A few are partly heterotrophic: insectivorous plants such as bladderwort and Venus fly trap, and the parasite Cuscuta.
• Plant cells are eukaryotic, with prominent chloroplasts and a cell wall made mainly of cellulose. Plantae includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms.
• A plant life cycle has two phases that alternate, the diploid sporophyte and the haploid gametophyte. This is alternation of generations; how long each phase lasts, and whether it is free-living or dependent, varies between plant groups.
• Animalia contains heterotrophic, multicellular eukaryotes whose cells have no cell walls. They depend directly or indirectly on plants for food.
• Animals digest food in an internal cavity, store reserves as glycogen or fat, and feed holozoically, by ingesting food.
• Animals follow a definite growth pattern into adults of definite shape and size; higher forms have elaborate sensory and neuromotor systems, and most can move from place to place.
• Animals reproduce sexually by the mating (copulation) of a male and a female, and the embryo then develops.

10. Viruses

NCERT §2.6

• Whittaker's five kingdoms make no mention of lichens or of acellular agents such as viruses, viroids and prions.
• Viruses were left out because they are not truly 'living' if living means having a cell. They are non-cellular, and outside a living cell they exist as an inert crystalline structure.
• Once inside a cell, a virus takes over the host's machinery to copy itself, killing the host. The word virus means venom or poisonous fluid.
• Dmitri Ivanowsky (1892) found that the agent of tobacco mosaic disease was smaller than bacteria, since it passed through bacteria-proof filters.
• M.W. Beijerinck (1898) showed that extract of infected tobacco plants infected healthy ones; he named the agent 'virus' and called the fluid Contagium vivum fluidum (infectious living fluid).
• W.M. Stanley (1935) showed that viruses can be crystallised and that the crystals are mostly protein. Viruses are inert outside their specific host and are obligate parasites.
• Besides protein, a virus contains genetic material, either RNA or DNA, never both. A virus is a nucleoprotein, and its genetic material is infectious.
• Plant viruses generally have single-stranded RNA; animal viruses have single- or double-stranded RNA or double-stranded DNA; bacteriophages (viruses of bacteria) usually have double-stranded DNA.
• A protein coat, the capsid, built of subunits called capsomeres, protects the nucleic acid. Capsomeres are arranged in helical or polyhedral forms.
• Viruses cause mumps, smallpox, herpes, influenza and AIDS in humans. In plants, symptoms include mosaic patterns, leaf rolling and curling, yellowing and vein clearing, dwarfing and stunted growth.

11. Viroids, prions and lichens

NCERT §2.6

• T.O. Diener (1971) discovered the viroid, an infectious agent smaller than a virus that causes potato spindle tuber disease.
• A viroid is free RNA with no protein coat, which is what separates it from a virus; its RNA is of low molecular weight.
• Prions are infectious agents made of abnormally folded protein, about the size of viruses, that transmit certain neurological diseases.
• Prion diseases include bovine spongiform encephalopathy (BSE, mad cow disease) in cattle and its human counterpart, Creutzfeldt-Jakob disease (CJD).
• Lichens are symbiotic, mutually useful associations between algae and fungi. The algal partner is the phycobiont (autotrophic) and the fungal partner is the mycobiont (heterotrophic).
• In a lichen the alga makes food for the fungus, while the fungus gives shelter and absorbs water and mineral nutrients for the alga. The two are so closely joined that a lichen looks like a single organism.
• Lichens are very good indicators of pollution because they do not grow in polluted areas.

Must-know facts

1. Aristotle: plants as trees, shrubs and herbs; animals with and without red blood.
2. Linnaeus: two kingdoms, Plantae and Animalia.
3. R.H. Whittaker (1969): five kingdoms Monera, Protista, Fungi, Plantae, Animalia.
4. Whittaker's criteria: cell structure, body organisation, mode of nutrition, reproduction, phylogenetic relationships.
5. Monera wall: non-cellulosic (polysaccharide + amino acid); Fungi wall: chitin; Plantae wall: cellulose; Animalia: no wall.
6. Three-domain system splits Monera into two domains, giving six kingdoms.
7. Bacterial shapes: coccus, bacillus, vibrium (comma), spirillum (spiral).
8. Archaebacteria: halophiles, thermoacidophiles, methanogens; different wall structure; methanogens make biogas in ruminant gut.
9. Nostoc and Anabaena fix nitrogen in heterocysts.
10. Mycoplasma: no wall, smallest living cells, can live without oxygen.
11. Diatoms: soap-box silica walls, diatomaceous earth, chief producers of the oceans.
12. Gonyaulax causes red tides; dinoflagellates have cellulose plates and two flagella.
13. Euglena: pellicle instead of wall, two flagella, pigments same as higher plants.
14. Slime mould spores have true walls and are dispersed by air.
15. Protozoan examples: Amoeba and Entamoeba (amoeboid), Trypanosoma (flagellated, sleeping sickness), Paramoecium (ciliated), Plasmodium (sporozoan, malaria).
16. Fungal walls: chitin and polysaccharides; coenocytic hyphae have no septa.
17. Sexual cycle of fungi: plasmogamy, karyogamy, meiosis; dikaryon (n + n) in ascomycetes and basidiomycetes.
18. Phycomycetes: aseptate coenocytic mycelium, zygospore; Mucor, Rhizopus, Albugo.
19. Ascomycetes: conidia exogenous, ascospores endogenous in asci; Penicillium, yeast, Aspergillus, Claviceps, Neurospora.
20. Basidiomycetes: four exogenous basidiospores on the basidium; Agaricus, Ustilago, Puccinia.
21. Deuteromycetes: only asexual stage known; Alternaria, Colletotrichum, Trichoderma.
22. Partly heterotrophic plants: bladderwort, Venus fly trap (insectivorous), Cuscuta (parasite).
23. Ivanowsky 1892, Beijerinck 1898 (Contagium vivum fluidum), Stanley 1935 (crystallised virus).
24. A virus has RNA or DNA, never both; bacteriophages usually double-stranded DNA; plant viruses usually single-stranded RNA.
25. Viroid: free low-molecular-weight RNA, no protein coat, potato spindle tuber, Diener 1971. Prions: misfolded protein, BSE and CJD. Lichen: phycobiont + mycobiont, pollution indicator.

Common traps

Key terms

Five kingdom classification

Whittaker's 1969 system: Monera, Protista, Fungi, Plantae and Animalia.

Three-domain system

A proposed system that splits Monera into two domains and places all eukaryotes in a third, giving six kingdoms.

Archaebacteria

Bacteria of extreme habitats (halophiles, thermoacidophiles, methanogens) with a distinctive cell wall structure.

Heterocyst

A specialised cell in some cyanobacteria, such as Nostoc and Anabaena, where atmospheric nitrogen is fixed.

Mycoplasma

Wall-less prokaryotes; the smallest living cells known, able to survive without oxygen.

Diatomaceous earth

Gritty deposits of silica-rich diatom walls, used for polishing and for filtering oils and syrups.

Red tide

Reddening of the sea by rapid multiplication of red dinoflagellates such as Gonyaulax, whose toxins can kill fish.

Pellicle

The protein-rich flexible layer that euglenoids have in place of a cell wall.

Plasmodium (slime mould)

The spreading aggregation formed by a slime mould in favourable conditions.

Pseudopodia

Temporary projections ('false feet') used by amoeboid protozoans to move and capture prey.

Hypha and mycelium

A hypha is a single thread of a fungal body; the network of hyphae is the mycelium.

Coenocytic hypha

A hypha without cross walls, a continuous tube of cytoplasm with many nuclei.

Plasmogamy

Fusion of the protoplasms of two gametes or cells, the first step of the fungal sexual cycle.

Karyogamy

Fusion of two nuclei, the second step of the fungal sexual cycle.

Dikaryon

A cell with two separate haploid nuclei (n + n), found between plasmogamy and karyogamy in ascomycetes and basidiomycetes.

Ascus and ascocarp

The ascus is the sac in which ascospores form; ascocarps are the fruiting bodies that hold the asci.

Basidium and basidiocarp

The basidium bears four basidiospores on its outside; basidiocarps are the fruiting bodies that hold the basidia.

Deuteromycetes

The imperfect fungi, whose sexual stage is unknown; they reproduce only by conidia.

Alternation of generations

The alternation of a diploid sporophytic phase and a haploid gametophytic phase in plant life cycles.

Capsid and capsomeres

The capsid is the protein coat of a virus; capsomeres are the small subunits that build it.

Bacteriophage

A virus that infects bacteria, usually with double-stranded DNA.

Viroid

An infectious agent of free, low-molecular-weight RNA without a protein coat, e.g. the cause of potato spindle tuber disease.

Prion

An infectious agent made of abnormally folded protein that causes neurological diseases such as BSE and CJD.

Phycobiont and mycobiont

The algal (autotrophic) and fungal (heterotrophic) partners of a lichen.