Biological Classification: A Definitive Study Guide

Introduction to Biological Classification

• Historical Context:

  • Since the dawn of civilization, humans have attempted to classify living organisms.
  • Initial classifications were instinctive and based on utility (food, shelter, and clothing) rather than scientific criteria.

• Aristotle's Scientific Basis:

  • Aristotle was the first to attempt a more scientific basis for classification.
  • Plants: Classified into three groups based on simple morphological characters: Trees, Shrubs, and Herbs.
  • Animals: Divided into two groups: those possessing red blood and those that did not.

• The Two Kingdom System (Linnaeus):

  • Developed during Linnaeus' time, this system divided organisms into Kingdom Plantae and Kingdom Animalia.
  • Limitations:
    • Did not distinguish between eukaryotes and prokaryotes.
    • Did not distinguish between unicellular and multicellular organisms.
    • Grouped photosynthetic organisms (green algae) with non-photosynthetic organisms (fungi).
    • Inadequacy arose because many organisms did not fit strictly into either category, and gross morphology was insufficient.

• Expansion of Criteria:

  • A need was felt to include characteristics such as cell structure, nature of the cell wall, mode of nutrition, habitat, methods of reproduction, and evolutionary (phylogenetic) relationships.

The Five Kingdom Classification System

• Proponent: R.H. Whittaker (1969).

• Kingdoms: Monera, Protista, Fungi, Plantae, and Animalia.

• Main Criteria for Classification:

  1. Cell structure.
  2. Body organization.
  3. Mode of nutrition.
  4. Reproduction.
  5. Phylogenetic relationships.

• Comparative Characteristics of the Five Kingdoms:

  • Monera:
    • Cell type: Prokaryotic.
    • Cell wall: Non-cellulosic (Polysaccharide + amino acid).
    • Nuclear membrane: Absent.
    • Body organization: Cellular.
    • Mode of nutrition: Autotrophic (chemosynthetic and photosynthetic) and Heterotrophic (saprophytic/parasitic).
  • Protista:
    • Cell type: Eukaryotic.
    • Cell wall: Present in some.
    • Nuclear membrane: Present.
    • Body organization: Cellular.
    • Mode of nutrition: Autotrophic (photosynthetic) and Heterotrophic.
  • Fungi:
    • Cell type: Eukaryotic.
    • Cell wall: Present (contains chitin).
    • Nuclear membrane: Present.
    • Body organization: Multicellular/loose tissue.
    • Mode of nutrition: Heterotrophic (saprophytic/parasitic).
  • Plantae:
    • Cell type: Eukaryotic.
    • Cell wall: Present (cellulose).
    • Nuclear membrane: Present.
    • Body organization: Tissue/organ.
    • Mode of nutrition: Autotrophic (photosynthetic).
  • Animalia:
    • Cell type: Eukaryotic.
    • Cell wall: Absent.
    • Nuclear membrane: Present.
    • Body organization: Tissue/organ/organ system.
    • Mode of nutrition: Heterotrophic (holozoic/saprophytic, etc.).

• Evolution of Content within Kingdoms:

  • Earlier systems placed bacteria, blue-green algae, fungi, mosses, ferns, gymnosperms, and angiosperms under 'Plants' solely because they possessed a cell wall.
  • This grouped prokaryotic bacteria/cyanobacteria with eukaryotic organisms.
  • It grouped unicellular Chlamydomonas with multicellular Spirogyra under algae.
  • Whittaker's system moved fungi (chitinous walls) and all prokaryotes (Monera) into separate kingdoms.
  • Chlamydomonas and Chlorella (formerly in Plantae) and Amoeba and Paramoecium (formerly in Animalia) were brought together in Kingdom Protista based on being unicellular eukaryotes.

• The Three-Domain System:

  • Proposed to divide Kingdom Monera into two domains, with the remaining eukaryotic kingdoms in a third domain, resulting in a six-kingdom classification.

Kingdom Monera

• General Features:

  • Bacteria are the sole members.
  • Most abundant microorganisms; cosmopolitan distribution (found everywhere, including extreme habitats like hot springs, deserts, snow, and deep oceans).
  • Can exist as parasites.

• Classification by Shape (Morphology):

  1. Coccus (pl. cocci): Spherical.
  2. Bacillus (pl. bacilli): Rod-shaped.
  3. Vibrium (pl. vibrio): Comma-shaped.
  4. Spirillum (pl. spirilla): Spiral.

• Metabolic Diversity:

  • Bacteria show the most extensive metabolic diversity as a group.
  • Autotrophic: Synthesize food from inorganic substrates. Subdivided into:
    • Photosynthetic autotrophic.
    • Chemosynthetic autotrophic (oxidize inorganic substances like nitrates, nitrites, and ammonia for energy to produce ATP).
  • Heterotrophic: The vast majority. Depend on other organisms or dead organic matter.

• 2.1.1 Archaebacteria:

  • Inhabit harsh environments: Halophiles (salty areas), Thermoacidophiles (hot springs), and Methanogens (marshy areas).
  • Different cell wall structure compared to other bacteria, enabling survival in extremes.
  • Methanogens: Found in the gut of ruminants (cows, buffaloes) and produce methane (biogas) from dung.

• 2.1.2 Eubacteria ("True Bacteria"):

  • Characterized by a rigid cell wall and a flagellum if motile.
  • Cyanobacteria (Blue-green algae): Unicellular, colonial, or filamentous; have chlorophyll $a$ (like plants). Often surrounded by a gelatinous sheath and form blooms in polluted water. Some have specialized cells called heterocysts (e.g., Nostoc and Anabaena) to fix atmospheric nitrogen.
  • Chemosynthetic Autotrophs: Recycle nutrients like Nitrogen, Phosphorus, Iron, and Sulphur.
  • Heterotrophic Bacteria: Most abundant and important decomposers.
    • Helpful in making curd, antibiotics, and fixing nitrogen in legumes.
    • Pathogenic ones cause diseases: Cholera, typhoid, tetanus, and citrus canker.
  • Reproduction: Primarily by fission. Under unfavorable conditions, they produce spores. Sexual reproduction involves a primitive type of DNA transfer.
  • Mycoplasma: Smallest known living cells; completely lack a cell wall. Can survive without oxygen ($O_2$) and are often pathogenic.

Kingdom Protista

• Overview:

  • Includes all single-celled eukaryotes.
  • Boundaries are not well-defined (some may appear as plants/animals).
  • Primarily aquatic; forms a link between plants, animals, and fungi.
  • Features: Well-defined nucleus, membrane-bound organelles, some have flagella or cilia.
  • Reproduction: Asexual and sexual (cell fusion and zygote formation).

• 2.2.1 Chrysophytes:

  • Includes diatoms and golden algae (desmids).
  • Microscopic, passive floaters (plankton) in fresh and marine water.
  • Diatoms: Cell walls form two thin overlapping shells (like a soap box) embedded with silica, making them indestructible. Large deposits of walls form diatomaceous earth. Used in polishing and filtration of oils/syrups. Diatoms are the chief producers in oceans.

• 2.2.2 Dinoflagellates:

  • Mostly marine and photosynthetic; pigments range from yellow, green, brown, blue, to red.
  • Cell wall has stiff cellulose plates.
  • Two flagella: one longitudinal, one transverse (in a furrow).
  • Red tides: Caused by rapid multiplication of Gonyaulax. Toxins released can kill marine animals like fish.

• 2.2.3 Euglenoids:

  • Freshwater, stagnant water organisms.
  • Lack a cell wall; have a protein-rich pellicle for body flexibility.
  • Two flagella: one short, one long.
  • Mixotrophic: Photosynthetic in sunlight; heterotrophic (predatory) when light is absent.
  • Pigments are identical to higher plants (e.g., Euglena).

• 2.2.4 Slime Moulds:

  • Saprophytic protists.
  • Form an aggregation called plasmodium under suitable conditions, which can spread for feet.
  • Under unfavorable conditions, they form fruiting bodies with spores at tips.
  • Spores have true walls, are highly resistant, and are dispersed by air currents.

• 2.2.5 Protozoans (Heterotrophs, primitive relatives of animals):

  1. Amoeboid: Live in fresh/sea water or moist soil; use pseudopodia ("false feet"). Marine forms have silica shells. Example: Entamoeba (parasitic).
  2. Flagellated: Free-living or parasitic with flagella. Example: Trypanosoma (causes sleeping sickness).
  3. Ciliated: Aquatic, use thousands of cilia for movement and steering food into the gullet. Example: Paramoecium.
  4. Sporozoans: Diverse infectious organisms with a spore-like stage. Example: Plasmodium (malarial parasite).

Kingdom Fungi

• Characteristics:

  • Heterotrophic, cosmopolitan (air, water, soil, animals, plants).
  • Prefer warm and humid places. Refrigeration prevents fungal/bacterial spoilage.
  • Structure: Except for unicellular yeast, fungi are filamentous.
  • Hyphae: Long thread-like structures. A network of hyphae is a mycelium.
  • Coenocytic hyphae: Continuous tubes with multinucleated cytoplasm; others have septae/cross-walls.
  • Cell walls: Composed of chitin and polysaccharides.

• Nutrition:

  • Saprophytes: Absorb soluble organic matter from dead substrates.
  • Parasites: Depend on living plants/animals.
  • Symbionts: Lichens (with algae) and mycorrhiza (with roots of higher plants).

• Reproduction:

  • Vegetative: Fragmentation, fission, and budding.
  • Asexual: Spores (conidia, sporangiospores, or zoospores).
  • Sexual: Oospores, ascospores, and basidiospores.

• Sexual Cycle Steps:

  1. Plasmogamy: Fusion of protoplasms.
  2. Karyogamy: Fusion of two nuclei.
  3. Meiosis: Occurs in the zygote resulting in haploid spores ($n$).

• Dikaryon phase: In ascomycetes and basidiomycetes, fusion does not immediately lead to diploidy; instead, a phase with two nuclei per cell ($n + n$) occurs.

• Classes of Fungi:

  1. Phycomycetes: Aquatic/moist wood/parasites. Aseptate, coenocytic mycelium. Asexual spores (zoospores/aplanospores) produced endogenously. Isogamous or anisogamous/oogamous gametes form a zygospore. Examples: Mucor, Rhizopus (bread mould), Albugo.
  2. Ascomycetes (Sac-fungi): Mostly multicellular (Penicillium) or unicellular (Yeast). Branched/septate. Asexual spores: Conidia (produced exogenously). Sexual spores: Ascospores (produced endogenously in sac-like asci). Asci are in ascocarps. Examples: Aspergillus, Claviceps, Neurospora, morels, truffles.
  3. Basidiomycetes: Mushrooms, bracket fungi, puffballs. Branched/septate. Asexual spores absent; vegetative fragmentation is common. Plasmogamy by fusion of somatic cells, resulting in a dikaryotic structure that becomes a basidium. Karyogamy and meiosis in basidium produce four exogenous basidiospores. Basidia are in basidiocarps. Examples: Agaricus (mushroom), Ustilago (smut), Puccinia (rust).
  4. Deuteromycetes (Imperfect Fungi): Only asexual/vegetative phases known. Once the sexual ("perfect") stage is found, they are moved to Ascomycetes or Basidiomycetes. Reproduce by conidia. Septate/branched. Often decomposers of litter. Examples: Alternaria, Colletotrichum, Trichoderma.

Kingdom Plantae and Kingdom Animalia

• Kingdom Plantae:

  • Eukaryotic, chlorophyll-containing organisms with cellulose cell walls.
  • Partial heterotrophs: Insectivorous plants (Bladderwort, Venus fly trap) and parasites (Cuscuta).
  • Groups: Algae, bryophytes, pteridophytes, gymnosperms, angiosperms.
  • Alternation of Generations: Lifecycle has a diploid ($2n$) sporophytic phase and a haploid ($n$) gametophytic phase.

• Kingdom Animalia:

  • Multicellular, eukaryotic heterotrophs lacking cell walls.
  • Nutrition: Holozoic (ingestion). Store food as glycogen or fat.
  • Characteristics: Definite growth pattern, sensory and neuromotor mechanisms, locomotion in most, sexual reproduction by copulation.

Viruses, Viroids, Prions, and Lichens

• Viruses:

  • Acellular; not considered truly "living" because they lack a cell structure.
  • Inert crystalline structure outside a host; take over host machinery inside.
  • Discovery:
    • Ivanowsky (1892): Identified Tobacco Mosaic Virus (TMV); smaller than bacteria.
    • Beijerinck (1898): Named them "virus" and coined Contagium vivum fluidum (infectious living fluid).
    • Stanley (1935): Showed viruses could be crystallized (consist largely of proteins).
  • Genetic Material: Either RNA or DNA (never both). Plant viruses usually have $ssRNA$; animal viruses have $ssRNA$, $dsRNA$, or $dsDNA$; bacteriophages have $dsDNA$.
  • Structure: Protein coat called capsid made of capsomeres.
  • Diseases: Mumps, small pox, herpes, influenza, AIDS. TMV symptoms include leaf rolling, yellowing, and stunted growth.

• Viroids:

  • Discovered by T.O. Diener (1971).
  • Smaller than viruses; free low molecular weight RNA without a protein coat.
  • Causes Potato spindle tuber disease.

• Prions:

  • Infectious agents consisting of abnormally folded protein.
  • Similar in size to viruses.
  • Diseases: Bovine Spongiform Encephalopathy (BSE/mad cow disease) and Creutzfeldt-Jakob Disease (CJD).

• Lichens:

  • Symbiotic association between algae (phycobiont - autotrophic) and fungi (mycobiont - heterotrophic).
  • Algae provide food; fungi provide shelter and absorb minerals/water.
  • Pollution Indicators: Do not grow in polluted areas (very sensitive to ${SO}_2$).