Biological Classification - Comprehensive University Study Notes

Biological Classification: Overview and History

• Definition: Biological classification is the process of grouping various organisms according to their similarities, dissimilarities, and phylogenetic descent.
• Aristotle's Classification:
  • Proposed the first biological classification of plants and animals based on simple morphological characters.
  • Plants: Classified into three categories: herbs, shrubs, and trees.
  • Animals: Classified into two groups based on the presence or absence of red blood:
    • Enaima: Animals with red blood.
    • Anaima: Animals without red blood.
• Two Kingdom System: Proposed by Linnaeus, dividing living organisms into two kingdoms: Kingdom Plantae and Kingdom Animalia.
• Five Kingdom System: Proposed by R.H. Whittaker, which classified organisms into Monera, Protista, Fungi, Plantae, and Animalia.
  • Main Criteria:
    • Cell structure (Prokaryotic vs. Eukaryotic).
    • Body organization (Complexity of the organism).
    • Mode of nutrition.
    • Reproduction.
    • Phylogenetic relationship.

Comparison of the Five Kingdoms

• Kingdom Monera:

  • Cell Type: Prokaryotic.
  • Cell Wall: Non-cellulosic (composed of Polysaccharide and amino acid).
  • Nuclear Membrane: Absent.
  • Body Organisation: Cellular.
  • Mode of Nutrition: Autotrophic (chemosynthetic and photosynthetic) and Heterotrophic (saprophytic/parasitic).

• Kingdom Protista:

  • Cell Type: Eukaryotic.
  • Cell Wall: Present in some organisms.
  • Nuclear Membrane: Present.
  • Body Organisation: Cellular.
  • Mode of Nutrition: Autotrophic (Photosynthetic) and Heterotrophic.

• Kingdom Fungi:

  • Cell Type: Eukaryotic.
  • Cell Wall: Present (composed of Chitin).
  • Nuclear Membrane: Present.
  • Body Organisation: Multicellular/Loose tissue.
  • Mode of Nutrition: Heterotrophic (Saprophytic/Parasitic).

• Kingdom Plantae:

  • Cell Type: Eukaryotic.
  • Cell Wall: Present (composed of Cellulose).
  • Nuclear Membrane: Present.
  • Body Organisation: Tissue/Organ.
  • Mode of Nutrition: Autotrophic (Photosynthetic).

• Kingdom Animalia:

  • Cell Type: Eukaryotic.
  • Cell Wall: Absent.
  • Nuclear Membrane: Present.
  • Body Organisation: Tissue/Organ/Organ System.
  • Mode of Nutrition: Heterotrophic (Holozoic/Saprophytic, etc.).

Kingdom Monera

• General Characteristics:
  • Includes all kinds of bacteria, which are unicellular prokaryotes.
  • Bacteria are cosmopolitan in distribution and show the most extensive metabolic diversity.
  • The cell does not contain a well-defined nucleus.
  • Reproduce mainly by fission; produce spores under unfavourable conditions; also exhibit a sort of sexual reproduction by a primitive type of DNA transfer.
• Classification by Shape:
  • Coccus (pl.: cocci): Spherical shaped.
  • Bacillus (pl.: bacilli): Rod-shaped.
  • Vibrium (pl.: vibrio): Comma-shaped.
  • Spirillum (pl.: spirilla): Spiral-shaped.
• Groups within Monera:
  • Archaebacteria: Present in the hardest environmental conditions.
    • Halophiles: Survive in salty environments (marine bacteria).
    • Thermoacidophiles: Present in hot water springs.
    • Methanogens: Present in the gut of ruminants; produce biogas.
  • Eubacteria (True Bacteria): Characterized by a rigid cell wall and a flagellum if motile.
    • Cyanobacteria (Blue-green algae): Photosynthetic autotrophs containing chlorophyll similar to green plants. Unicellular, colonial, or filamentous. Often form blooms in polluted water. Some have specialized cells called heterocysts for atmospheric nitrogen fixation (e.g., Nostoc and Anabaena).
    • Chemosynthetic Autotrophic Bacteria: Oxidize inorganic substances (nitrates, nitrites, ammonia) for ATP production. Essential for recycling nutrients (Nitrogen, Phosphorous, Iron, and Sulphur).
    • Heterotrophic Bacteria: Most abundant in nature; important decomposers. Used in making curd, producing antibiotics, and fixing nitrogen in legumes.
    • Pathogenic Bacteria: Cause diseases such as Cholera, typhoid, tetanus, and citrus canker.
  • Mycoplasma: Organisms that completely lack a cell wall. Smallest living cells known. Can survive without oxygen ($O_2$). Many are pathogenic to animals and plants.

Kingdom Protista

• General Characteristics:
  • Includes all unicellular eukaryotes.
  • Link between plants and animals.
  • Contain a well-defined nucleus and membrane-bound organelles.
• Major Groups:
  • Chrysophytes: Includes Diatoms and golden algae (desmids). Found in freshwater and marine environments. Microscopic plankton. Diatom cell walls form two thin overlapping shells (like a soap box) embedded with silica, making them indestructible. Accumulation of cell wall deposits over billions of years is called diatomaceous earth, used in polishing and filtration. Diatoms are the chief ‘producers’ in the oceans.
  • Dinoflagellates: Mostly marine and photosynthetic. Appear in various colors based on pigments. Cell walls have stiff cellulose plates. Usually have two flagella (one longitudinal, one transverse in a furrow). Example: Gonyaulax, which causes ‘red tides’ due to rapid multiplication.
  • Euglenoids: Mostly freshwater organisms found in stagnant water. Lack a cell wall; have a protein-rich layer called a pellicle for flexibility. Have two flagella (one short, one long). Example: Euglena. They are mixotrophic: photosynthetic in sunlight, heterotrophic/predators when deprived of sunlight.
  • Slime Moulds: Saprophytic protists. Form aggregations called plasmodium under suitable conditions. Under unfavourable conditions, they form fruiting bodies with spores possessing true walls (extremely resistant, dispersed by air currents).
  • Protozoans: All are heterotrophs (parasites or predators). Divided into four groups:
    1. Amoeboid protozoans: Live in freshwater, seawater, or moist soil. Use pseudopodia (false feet) to move and capture prey (e.g., Amoeba). Marine forms have silica shells. Example: Entamoeba.
    2. Flagellated protozoans: Free-living or parasitic. Have flagella. Example: Trypanosoma (causes sleeping sickness).
    3. Ciliated protozoans: Aquatic and actively moving via thousands of cilia. Have a cavity called a gullet. Example: Paramecium.
    4. Sporozoans: Have an infectious spore-like stage in their life cycle. Example: Plasmodium (the malarial parasite).

Kingdom Fungi

• General Characteristics:
  • Cosmopolitan organisms found everywhere.
  • Cell wall made of chitin or fungal cellulose.
  • Main food reserve is glycogen.
  • Can be unicellular (e.g., yeast used in bread/beer) or multicellular.
  • Bodies consist of thread-like hyphae; a network of hyphae is a mycelium.
  • Coenocytic hyphae: Continuous tubes filled with multinucleated cytoplasm.
  • Can be saprophytes, parasites, or symbionts (Lichens with algae; mycorrhiza with higher plant roots).
• Reproduction:
  • Vegetative: Fragmentation, budding, fission.
  • Sexual Cycle:
    1. Plasmogamy: Fusion of protoplasms.
    2. Karyogamy: Fusion of two nuclei.
    3. Meiosis: Occurs in the zygote resulting in haploid spores.
  • Dikaryophase: A stage in Ascomycetes and Basidiomycetes where plasmogamy is not immediately followed by karyogamy, resulting in a dikaryon ($n+n$) cell.
• Classes of Fungi:
  1. Phycomycetes: Aquatic or on decaying wood. Aseptate and coenocytic mycelium. Asexual: zoospores (motile) or aplanospores (non-motile). Sexual: zygospore. Examples: Mucor, Rhizopus (bread mould), Albugo.
  2. Ascomycetes (Sac-fungi): Mostly multicellular (Penicillium), rarely unicellular (Yeast/Saccharomyces). Mycelium is branched and septate. Asexual spores: conidia produced exogenously on conidiophores. Sexual spores: ascospores produced endogenously in sac-like asci arranged in ascocarps. Examples: Aspergillus, Claviceps, Neurospora (used in genetics).
  3. Basidiomycetes: Mushrooms, bracket fungi, puffballs. Mycelium is branched and septate. Sex organs absent; plasmogamy via fusion of somatic cells results in a dikaryotic basidium. Karyogamy and meiosis in basidium produce four basidiospores exogenously. Fruiting bodies: basidiocarps. Examples: Agaricus (mushroom), Ustilago (smut), Puccinia (rust fungus).
  4. Deuteromycetes (Imperfect Fungi): Only asexual or vegetative phases are known. Reproduce only by conidia. Mycelium is septate and branched. Important for mineral cycling. Examples: Alternaria, Colletotrichum, Trichoderma.

Kingdom Plantae and Kingdom Animalia

• Kingdom Plantae:

  • Eukaryotic, chlorophyll-containing, autotrophic organisms.
  • Cell walls made of cellulose.
  • Partial heterotrophs: Insectivorous plants (Venus flytrap, bladderwort) and parasites (Cuscuta).
  • Groups: Algae, Bryophytes, Pteridophytes, Gymnosperms, and Angiosperms.
  • Alternation of Generation: Life cycle has a diploid sporophytic phase and a haploid gametophytic phase.

• Kingdom Animalia:

  • Multicellular, heterotrophic eukaryotes without cell walls.
  • Mode of Nutrition: Holozoic (ingestion).
  • Digest food in an internal cavity; store food as glycogen or fat.
  • Follow a definite growth pattern to reach adult stage.
  • Reproduce mostly by sexual mode.

Acellular Organisms and Symbiotic Associations

• Viruses:
  • Acellular, non-living outside the host cell. Remain in inert crystalline form outside the host.
  • Contain either DNA or RNA (never both) surrounded by a protein coat called a capsid.
  • Establishment: Dmitri Ivanowsky named "Virus" (Tobacco Mosaic Disease); Beijerinck called the fluid "Contagium Vivum Fluidum"; W.M. Stanley crystallised TMV.
  • Plant viruses usually have single-stranded RNA; Bacteriophages (infecting bacteria) usually have double-stranded DNA.
  • Diseases: common cold, AIDS, mumps, measles, smallpox (animals); leaf curling, yellowing (plants).
• Viroids:
  • Discovered by T.O. Diener as agents of potato spindle tuber disease.
  • Smaller than viruses; lack a protein coat.
  • Consist of single-stranded RNA of low molecular weight.
• Prions:
  • Smaller than viruses; consist of abnormally folded protein.
  • Cause Bovine Spongiform Encephalopathy (BSE/Mad Cow) and Cr-Jacob disease (CJD).
• Lichens:
  • Symbiotic association between Algae (Phycobiont - autotrophic) and Fungi (Mycobiont - heterotrophic).
  • Algae prepare food; Fungi provide shelter and absorb minerals/water.
  • Very good pollution indicators; do not grow in polluted areas.

Practice Worksheet: Questions & Discussion

• Multiple Choice Questions:
  • Q: In which kingdom are Archaea and Nitrogen-fixing organisms classified? A: Monera.
  • Q: Main basis of the five-kingdom system? A: Mode of Nutrition.
  • Q: False statement about fungi? A: They possess a purely cellulosic cell wall (False, it is Chitin).
  • Q: Genes of Tobacco Mosaic Virus? A: Single-stranded RNA.
  • Q: T.O. Diener discovered? A: Free infectious RNA.
• Assertion and Reason:
  • Q: Assertion: Viruses are readily killed by antibiotics. Reason: Antibiotics are the medicines used to kill bacteria. A: Assertion is false but Reason is correct.
  • Q: Assertion: Gram-negative bacteria do not retain the stain when washed with alcohol. Reason: The outer face of the outer membrane… contain lipopolysaccharides… A: Both Assertion and Reason are true and the Reason is the correct explanation.
• Short Answer Explanations:
  • Neurospora usage: Used in genetics because it is easily grown in minimal media, has a short life cycle, and mutations are easy to introduce using X-rays.
  • Eubacteria classification: Autotrophic cyanobacteria and heterotrophic bacteria are both placed in Monera because they lack a true nucleus, have DNA without a protein coat, contain $70S$ ribosomes, and lack membranous organelles.
  • Pearls of the ocean: Diatoms are so-called due to unique cell wall ornamentations (frustules). They form diatomaceous earth used in industries.
  • Case Study Comparison: Sample A (Archaebacteria) vs Sample D (Eubacteria) - separated due to differences in cell membrane structure and habitat, despite both being prokaryotic.