Biological Classification

Start with the history, because the first NCERT exercise question asks for it. Aristotle made the earliest attempt at a scientific basis for classification. He used simple morphological characters: plants were sorted into trees, shrubs and herbs, and animals into those with red blood and those without.

Much later Linnaeus gave the two-kingdom system, with Kingdom Plantae and Kingdom Animalia. It was used for a long time, but it has clear drawbacks, and the examiner likes you to list them. It did not distinguish (i) eukaryotes from prokaryotes, (ii) unicellular from multicellular organisms, and (iii) photosynthetic organisms (green algae) from non-photosynthetic ones (fungi). Because every organism with a cell wall was called a plant, bacteria, blue-green algae, fungi, mosses, ferns, gymnosperms and angiosperms all sat together under Plants. That lumped together groups that differ in cell wall composition, in nuclear organisation and in the way they obtain food; the fungi, for example, are heterotrophs and have chitin walls, nothing like a green plant.

As more characters were studied, the basis of classification shifted from habitat and simple morphology to cell structure, nutrition and evolutionary relationship. In 1969 R.H. Whittaker proposed the five-kingdom classification: Monera, Protista, Fungi, Plantae and Animalia. His criteria were five, and you should be able to write them from memory: cell structure (prokaryotic or eukaryotic), body organisation (cellular, tissue, organ, organ system), mode of nutrition (autotrophic or heterotrophic), reproduction and phylogenetic relationships.

NCERT's Table 2.1 is the comparison the 5-mark question is built on. In brief: only Monera is prokaryotic and lacks a nuclear membrane. The cell wall is non-cellulosic (polysaccharide plus amino acid) in Monera, present in some Protista, present without cellulose in Fungi, made of cellulose in Plantae, and absent in Animalia. Body organisation is cellular in Monera and Protista, multicellular with loose tissue in Fungi, tissue and organ in Plantae, and tissue, organ and organ system in Animalia. Nutrition is autotrophic (chemosynthetic and photosynthetic) and heterotrophic (saprophytic or parasitic) in Monera; autotrophic (photosynthetic) and heterotrophic in Protista; heterotrophic (saprophytic or parasitic) in Fungi; autotrophic (photosynthetic) in Plantae; heterotrophic (holozoic or saprophytic) in Animalia.

One more line the examiner rewards: a three-domain system has also been proposed. It splits Kingdom Monera into two domains and places the remaining eukaryotic kingdoms in a third domain, so it becomes a six-kingdom classification. NCERT only mentions it and says it is taught in higher classes.

Bacteria are the sole members of Kingdom Monera. They are the most abundant micro-organisms. They live in soil, in hot springs, deserts, snow and deep oceans, in short almost everywhere, and many live as parasites in or on other organisms.

Bacteria are grouped by shape into four types, and the names with their plurals are a standard 1-mark or 2-mark item (NCERT Fig. 2.1): Coccus (plural cocci), spherical; Bacillus (plural bacilli), rod-shaped; Vibrium (plural vibrio), comma-shaped; and Spirillum (plural spirilla), spiral. Draw all four when the question says 'with diagrams'.

The paradox NCERT points out is worth a sentence in any answer: bacteria have a very simple structure but show complex behaviour, and as a group they have more metabolic diversity than any other. Some are autotrophic, making their own food either by photosynthesis (using light) or by chemosynthesis (oxidising inorganic substances). The vast majority, however, are heterotrophs that depend on other organisms or on dead organic matter.

The kingdom is discussed under two headings. Archaebacteria are the ones that live in the harshest habitats and have a distinctive cell wall. Eubacteria, the 'true bacteria', have a rigid cell wall and, when motile, a flagellum; they include the cyanobacteria, the chemosynthetic autotrophs and the huge number of heterotrophic bacteria. Mycoplasma, which lack a wall altogether, are also placed here. Each of these is taken up in the next two sections.

A point of precision for the table question: Monera is the only prokaryotic kingdom. The cells have no true nucleus (no nuclear membrane) and no membrane-bound organelles, the cell wall is non-cellulosic, and the body organisation is cellular. Everything from Protista onwards is eukaryotic.

Archaebacteria are special because they live in some of the most harsh habitats on Earth. NCERT names three groups, each defined by its habitat, and the 3-mark question is simply these three with their habitats:

• Halophiles, in extremely salty areas (salt pans, salt lakes).
• Thermoacidophiles, in hot springs (hot and acidic water).
• Methanogens, in marshy areas.

What lets them survive where other cells die? They differ from other bacteria in having a different cell wall structure, and NCERT attributes their survival in extreme conditions to this feature. That single sentence is the most common 1-mark and Assertion–Reason item from this section, so state it exactly.

The methanogens have a direct economic link that you already know from the Class 12 chapter on biogas. They are present in the gut of several ruminant animals such as cows and buffaloes and are responsible for the production of methane (biogas) from the dung of these animals. When exercise question 2 asks for two economically important uses of archaebacteria, the safe answers are: (i) methanogens produce methane, the main component of biogas, from cattle dung and other organic waste; and (ii) methanogens in the rumen help ruminants digest cellulose-rich food (and, from wider reading, halophiles and thermoacidophiles are used in bioleaching and in industrial enzyme work; NCERT itself only mentions biogas).

Do not confuse the three groups with the shapes of bacteria; the groups are ecological, the shapes are morphological. And note that the three-domain system mentioned in the introduction separates the archaebacteria from the eubacteria as two distinct domains, which is exactly why NCERT stresses that their cell wall is different.

Eubacteria, the 'true bacteria', are characterised by a rigid cell wall and, if motile, a flagellum. NCERT describes four sets of organisms under this heading.

Cyanobacteria (blue-green algae). They have chlorophyll a similar to green plants and are photosynthetic autotrophs. They may be unicellular, colonial or filamentous, living in fresh water, in the sea or on land. Colonies are generally surrounded by a gelatinous sheath. They often form blooms in polluted water bodies. Some of them, such as Nostoc and Anabaena, can fix atmospheric nitrogen in specialised cells called heterocysts. The filament of Nostoc with a heterocyst is NCERT Fig. 2.2 and is a favourite diagram question. Note that they are called algae only by an old habit; they are prokaryotes and belong in Monera, not Plantae.

Chemosynthetic autotrophic bacteria. These oxidise various inorganic substances such as nitrates, nitrites and ammonia and use the released energy for their ATP production. They play a great role in recycling nutrients like nitrogen, phosphorus, iron and sulphur.

Heterotrophic bacteria. These are the most abundant in nature. The majority are important decomposers. Many have a significant impact on human affairs: they help in making curd from milk, in the production of antibiotics, and in fixing nitrogen in legume roots. Some are pathogens, causing damage to humans, crops, farm animals and pets: cholera, typhoid, tetanus and citrus canker are the NCERT examples.

Reproduction. Bacteria reproduce mainly by fission. Under unfavourable conditions they produce spores. They also reproduce by a sort of sexual reproduction, adopting a primitive type of DNA transfer from one bacterium to another.

Mycoplasma. These organisms completely lack a cell wall. They are the smallest living cells known and can survive without oxygen. Many are pathogenic in animals and plants. Three facts, three possible 1-mark questions.

All single-celled eukaryotes are placed under Protista, but NCERT is honest that the boundaries of this kingdom are not well defined; what one biologist calls a photosynthetic protist another may treat as a plant. Members are primarily aquatic. Because it contains photosynthetic, fungus-like and animal-like forms, Protista forms a link with the kingdoms of plants, animals and fungi. Being eukaryotic, protistan cells have a well-defined nucleus and membrane-bound organelles. Some have flagella or cilia. They reproduce asexually and also sexually, by a process involving cell fusion and zygote formation.

The kingdom is discussed in five groups: chrysophytes, dinoflagellates, euglenoids, slime moulds and protozoans. Each group has three or four signature facts and an example; learn them as a table.

2.2.1 Chrysophytes. This group includes the diatoms and the golden algae (desmids). They are found in fresh water as well as marine environments. They are microscopic and float passively in water currents (plankton). Most of them are photosynthetic.

The diatoms carry the exam facts. In diatoms the cell walls form two thin overlapping shells which fit together as in a soap box. The walls are embedded with silica, and so the walls are indestructible. Because of this, diatoms have left behind a large amount of cell wall deposits in their habitat, and this accumulation over billions of years is called diatomaceous earth. Being gritty, this soil is used in polishing and in the filtration of oils and syrups. Diatoms are the chief 'producers' in the oceans, which is why they matter beyond this chapter.

Exercise question 3 asks for the nature of the diatom cell wall; the two marking points are the two overlapping halves (like a soap box) and the silica impregnation that makes them indestructible.

Dinoflagellates are mostly marine and photosynthetic. They appear yellow, green, brown, blue or red depending on the main pigments present in their cells. The cell wall has stiff cellulose plates on the outer surface. Most of them have two flagella: one lies longitudinally and the other transversely in a furrow between the wall plates. This arrangement (NCERT Fig. 2.3) is what gives them their spinning motion and is a diagram worth practising.

The application fact: very often, red dinoflagellates (for example Gonyaulax) undergo such rapid multiplication that they make the sea appear red, the so-called red tides. The toxins released by such large numbers may even kill other marine animals such as fishes. Exercise question 4 asks what 'algal bloom' and 'red tide' signify: an algal bloom is the rapid, excessive growth of algae (often cyanobacteria) in a water body rich in nutrients, which discolours the water, depletes oxygen and may release toxins; a red tide is a bloom of red dinoflagellates such as Gonyaulax in the sea.

Euglenoids. The majority are 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. They are photosynthetic in the presence of sunlight, but when deprived of sunlight they behave like heterotrophs by predating on other smaller organisms; this dual mode is why exam papers call them a connecting link between plants and animals (that phrase is not in NCERT, but the two modes of nutrition are). Interestingly, the pigments of euglenoids are identical to those present in higher plants. Example: Euglena (NCERT Fig. 2.4, showing the pellicle, the two flagella, the eye spot, chloroplasts and the nucleus).

Exercise question 10 is the euglenoid list; write habitat, pellicle, two unequal flagella, mixotrophic nutrition, plant-like pigments, and the example, and you have full marks.

Slime moulds are saprophytic protists. The body moves along decaying twigs and leaves, engulfing organic material. Under suitable conditions they form an aggregation called plasmodium which may grow and spread over several feet. During unfavourable conditions the plasmodium differentiates and forms fruiting bodies bearing spores at their tips. The spores possess true walls, are extremely resistant and survive for many years, even under adverse conditions. The spores are dispersed by air currents. Four facts (saprophytic, plasmodium, fruiting bodies, resistant walled spores dispersed by air) make the 3-mark answer.

Protozoans. All protozoans are heterotrophs and live as predators or parasites. They are believed to be primitive relatives of animals. NCERT gives four major groups, and exercise question 6 asks for exactly these:

1. Amoeboid protozoans. Live in fresh water, sea water or moist soil. They move and capture prey by putting out pseudopodia (false feet), as in Amoeba. Marine forms have silica shells on their surface. Some are parasites: Entamoeba.
2. Flagellated protozoans. Either free-living or parasitic. They have flagella. The parasitic forms cause diseases such as sleeping sickness. Example: Trypanosoma.
3. Ciliated protozoans. Aquatic, actively moving organisms because of the presence of thousands of cilia. They have a cavity (gullet) that opens to the outside of the cell surface. The coordinated movement of rows of cilia causes the water laden with food to be steered into the gullet. Example: Paramoecium.
4. Sporozoans. A diverse group that has an infectious spore-like stage in the life cycle. The most notorious is Plasmodium (malarial parasite), which causes malaria, a disease with a staggering effect on the human population.

Match the locomotory organ to the group and the example, because that is how the MCQ is set: pseudopodia to Amoeba, flagella to Trypanosoma, cilia to Paramoecium, and no locomotory organ but a spore stage to Plasmodium.

Fungi are a unique kingdom of heterotrophic organisms with great diversity in morphology and habitat. NCERT's opening examples are the ones the examiner recognises: the mushroom; the white spots on mustard leaves caused by a parasitic fungus (Albugo); the unicellular yeast used to make bread and beer; Puccinia, which causes wheat rust; and Penicillium, a source of antibiotics. Fungi are cosmopolitan, occurring in air, water, soil and on animals and plants, and they prefer warm and humid places (which is why bread and pickles get mouldy in the rainy season).

Body. With the exception of yeast, which is unicellular, fungi are filamentous. The body consists of long, slender thread-like structures called hyphae; the network of hyphae is the mycelium. Some hyphae are continuous tubes filled with multinucleated cytoplasm; these are coenocytic hyphae. Others have septae (cross walls). The cell wall is composed of chitin and polysaccharides. This is the feature that separates Fungi from Plantae in the five-kingdom table.

Nutrition. Most fungi are heterotrophic and absorb soluble organic matter from dead substrates; such fungi are saprophytes. Those that depend on living plants and animals are parasites. Fungi also live as symbionts: in association with algae as lichens, and with the roots of higher plants as mycorrhiza.

Reproduction. Vegetative reproduction is by fragmentation, fission and budding. Asexual reproduction is by spores called conidia, sporangiospores or zoospores. Sexual reproduction is by oospores, ascospores and basidiospores. The various spores are produced in distinct structures called fruiting bodies. The sexual cycle involves three steps, and this is a guaranteed 3-mark question:

1. Plasmogamy: fusion of the protoplasms between two motile or non-motile gametes.
2. Karyogamy: fusion of the two nuclei.
3. Meiosis in the zygote, resulting in haploid spores.

When a fungus reproduces sexually, two haploid hyphae of compatible mating types come together and fuse. In some fungi the fusion of two haploid cells immediately gives diploid cells (2n). In others (ascomycetes and basidiomycetes) an intervening dikaryotic stage (n + n, two nuclei per cell) occurs; the condition is called a dikaryon and the phase the dikaryophase. Later the parental nuclei fuse and the cell becomes diploid. The fungi then form fruiting bodies in which reduction division occurs, leading to haploid spores.

The morphology of the mycelium, the mode of spore formation and the fruiting bodies are the basis on which the kingdom is divided into its classes.

Phycomycetes. Members are found in aquatic habitats, on decaying wood in moist and damp places, or as obligate parasites on plants. The mycelium is aseptate and coenocytic. Asexual reproduction takes place by zoospores (motile) or by aplanospores (non-motile); these spores are endogenously produced in a sporangium. A zygospore is formed by the fusion of two gametes, and the gametes may be similar in morphology (isogamous) or dissimilar (anisogamous or oogamous). Examples: Mucor, Rhizopus (the bread mould) and Albugo (the parasitic fungus on mustard). Fig. 2.5(a) is Mucor, with sporangia on sporangiophores rising from the mycelium.

Ascomycetes. Commonly known as sac-fungi. Mostly multicellular (for example Penicillium) or rarely unicellular (yeast, Saccharomyces). They are saprophytic, decomposers, parasitic or coprophilous (growing on dung). The mycelium is branched and septate. The asexual spores are conidia, produced exogenously on special mycelium called conidiophores; conidia on germination produce mycelium. The sexual spores are ascospores, produced endogenously in sac-like asci (singular ascus). The asci are arranged in fruiting bodies called ascocarps. Examples: Aspergillus (Fig. 2.5(b), with its conidiophore, vesicle and chains of conidia), Claviceps and Neurospora. Neurospora is used extensively in biochemical and genetic work, and many members such as morels and truffles are edible and considered delicacies.

Keep the two classes apart by three contrasts: Phycomycetes have aseptate coenocytic hyphae, Ascomycetes have septate hyphae; Phycomycetes form asexual spores inside a sporangium (endogenous), Ascomycetes form conidia on conidiophores (exogenous); Phycomycetes end sexual reproduction in a zygospore, Ascomycetes in ascospores inside asci packed in ascocarps.

Basidiomycetes. The commonly known forms are mushrooms, bracket fungi and puffballs. They grow in soil, on logs and tree stumps, and in living plant bodies as parasites, for example the rusts and smuts. The mycelium is branched and septate. Asexual spores are generally not found, but vegetative reproduction by fragmentation is common. Sex organs are absent; plasmogamy is brought about by the fusion of two vegetative or somatic cells of different strains or genotypes. The resultant structure is dikaryotic and ultimately gives rise to the basidium. Karyogamy and meiosis take place in the basidium, producing four basidiospores. The basidiospores are exogenously produced on the basidium. The basidia are arranged in fruiting bodies called basidiocarps. Examples: Agaricus (mushroom), Ustilago (smut) and Puccinia (rust fungus). Fig. 2.5(c) is Agaricus: the basidiocarp with cap (pileus), gills and stalk (stipe), and the underground mycelium.

Deuteromycetes. Commonly called imperfect fungi because only the asexual or vegetative phases of these fungi are known. When the sexual forms of these fungi were discovered, they were moved into the classes they rightly belong to. It is also true that the deuteromycetes reproduce only by asexual spores known as conidia. The mycelium is septate and branched. Some are saprophytes or parasites, while a large number are decomposers of litter and help in mineral cycling. Examples: Alternaria, Colletotrichum and Trichoderma.

The 5-mark 'comparative account of the classes of Kingdom Fungi' (exercise question 9) is best written as a table with rows for habitat, mycelium, asexual spores, sexual spores, fruiting body and examples. The model answer in the NCERT-questions section below gives that table.

Kingdom Plantae includes all eukaryotic, chlorophyll-containing organisms commonly called plants. A few members are partially heterotrophic, such as the insectivorous plants or the parasites. NCERT's examples, and the answer to exercise question 7, are the bladderwort and the Venus fly trap (insectivorous) and Cuscuta (a parasite). Insectivorous plants remain photosynthetic; they trap insects mainly to supplement nitrogen in poor soils, so they are 'partially' heterotrophic. Cuscuta, the dodder, has no chlorophyll worth the name and draws food from its host.

Plant cells have a eukaryotic structure with prominent chloroplasts and a cell wall mainly made of cellulose. This is the cell wall entry for Plantae in the five-kingdom table, in contrast with chitin in Fungi and the non-cellulosic wall of Monera.

The kingdom includes algae, bryophytes, pteridophytes, gymnosperms and angiosperms, each of which is a section of the next chapter (Plant Kingdom).

Life cycle. The life cycle of plants has two distinct phases: the diploid sporophytic phase and the haploid gametophytic phase, and these alternate with each other. The lengths of the haploid and diploid phases, and whether these phases are free-living or dependent on others, vary among the different groups. This phenomenon is called alternation of generations. Chapter 3 builds the haplontic, diplontic and haplo-diplontic patterns on this one paragraph, so learn the definition exactly: the alternation of a diploid spore-producing generation with a haploid gamete-producing generation.

A short-answer question on this section is usually 'Why are some plants called partially heterotrophic? Give examples' or 'Define alternation of generations'. Both are answered from the lines above; nothing more is needed at this stage.

Kingdom Animalia is characterised by heterotrophic eukaryotic organisms that are multicellular and whose cells lack cell walls. Animals depend directly or indirectly on plants for food. They digest their food in an internal cavity and store food reserves as glycogen or fat. Their mode of nutrition is holozoic, that is, by ingestion of food. This is the nutrition entry for Animalia in Table 2.1.

Animals follow a definite growth pattern and grow into adults that have a definite shape and size, unlike plants, which keep growing from meristems throughout life. Higher forms show an elaborate sensory and neuromotor mechanism. Most of them are capable of locomotion. Sexual reproduction is by copulation of male and female followed by embryological development.

For the five-kingdom table, Animalia is the kingdom with cell wall absent, nuclear membrane present, body organisation reaching tissue, organ and organ system level, and heterotrophic (holozoic or saprophytic) nutrition. In exam answers on 'Distinguish between Plantae and Animalia', the reliable points are: cell wall (cellulose versus absent), chloroplasts (present versus absent), mode of nutrition (autotrophic versus holozoic), food reserve (starch versus glycogen or fat), growth (indefinite versus definite shape and size), and locomotion (absent versus present in most).

NCERT keeps this section short because the whole of Chapter 4 (Animal Kingdom) expands it. What the examiner wants from this chapter is the set of defining features, stated in NCERT's words, and the contrast with plants.

Viruses, viroids, prions and lichens are not mentioned in the five-kingdom classification. Viruses did not find a place because they are not truly 'living', if living means having a cell structure: they are non-cellular. Outside their specific host cell they are inert, and NCERT even says they are inert crystalline structures outside the host. Once they infect a cell they take over the machinery of the host cell to replicate themselves, killing the host. So viruses are obligate parasites.

Discovery. The name virus, meaning venom or poisonous fluid, was given by Pasteur. D.J. Ivanowsky (1892) recognised certain microbes as the causal organism of the mosaic disease of tobacco; they were found to be smaller than bacteria because they passed through bacteria-proof filters. M.W. Beijerinek (1898) demonstrated that the extract of infected tobacco plants could cause infection in healthy plants and called the fluid Contagium vivum fluidum (infectious living fluid). W.M. Stanley (1935) showed that viruses could be crystallised and that the crystals consist largely of proteins. Four names, three years: they appear as MCQ, fill-in-the-blank and case-based questions.

Structure and genetic material. Viruses are nucleoproteins, and the genetic material is infectious. A virus contains either RNA or DNA, never both. In general, viruses that infect plants have single-stranded RNA; viruses that infect animals have either single- or double-stranded RNA or double-stranded DNA; bacteriophages (bacterial viruses) are usually double-stranded DNA viruses. The protein coat, the capsid, is made of small subunits called capsomeres and protects the nucleic acid. Capsomeres are arranged in helical or polyhedral geometric forms. NCERT Fig. 2.6 shows the two standard diagrams: the Tobacco Mosaic Virus (TMV), a rod with a helical capsid around a coiled RNA, and the bacteriophage, with a polyhedral head containing DNA, a collar, a sheath (tail) and tail fibres.

Diseases. Viruses cause mumps, small pox, herpes and influenza. AIDS in humans is also caused by a virus. In plants the symptoms are mosaic formation, leaf rolling and curling, yellowing and vein clearing, dwarfing and stunted growth. Exercise question 11 asks for four common viral diseases; any four of the list above are accepted.

Living or non-living? (exercise question 12). Living features: they have genetic material (DNA or RNA), they multiply inside a host, they mutate and evolve, they are host-specific. Non-living features: no cellular structure, no metabolism of their own, inert outside the host, and they can be crystallised and stored like chemicals. The balanced conclusion is that viruses lie at the boundary between living and non-living.

Viroids. In 1971 T.O. Diener discovered a new infectious agent that was smaller than viruses and caused potato spindle tuber disease. It was found to be a free RNA; it lacked the protein coat that is found in viruses, hence the name viroid. The RNA of the viroid was of low molecular weight. Exercise question 5 asks how viroids differ from viruses, and the answer is a three-row table: size (viroid smaller), protein coat (absent in viroids, present as capsid in viruses), genetic material (only low-molecular-weight RNA in viroids; DNA or RNA in viruses). Viroids are known to infect only plants.

Prions. In modern medicine certain infectious neurological diseases were found to be transmitted by an agent consisting of abnormally folded protein. The agent was similar in size to viruses. These agents are called prions. The most notable diseases are bovine spongiform encephalopathy (BSE), commonly called mad cow disease, in cattle, and its analogous variant Creutzfeldt–Jacob disease (CJD) in humans. Three words to remember: protein, abnormally folded, neurological.

Lichens. Lichens are symbiotic associations, that is, mutually useful associations between algae and fungi. The algal component is the phycobiont and the fungal component the mycobiont; the alga is autotrophic and the fungus heterotrophic. The algae prepare food for the fungi, and the fungi provide shelter and absorb mineral nutrients and water for their partner. The association is so close that if one saw a lichen on a tree, one would never imagine that it is made of two different organisms. Lichens are very good pollution indicators: they do not grow in polluted areas, especially where sulphur dioxide is high. Exercise question 8 (phycobiont and mycobiont) and the lichen case study both come from this paragraph.

Do not mix lichen and mycorrhiza. Both are fungal symbioses, but the lichen partner is an alga (or cyanobacterium) and the mycorrhiza partner is the root of a higher plant. A 2-mark 'distinguish' question on this pair is common.