1.2 Biological Classification

Biological classification is the scientific process of arranging organisms into groups based on similarities and differences. This helps in understanding the diversity of life and its evolutionary relationships. The primary goals of classification are to:

• Identify and name organisms: Providing a universal name for each organism.
• Group organisms: Placing organisms into hierarchical categories based on shared characteristics.
• Understand evolutionary relationships: Reflecting the evolutionary history and common ancestry among different groups.

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Three Domains of Life

The Three-Domain system, proposed by Carl Woese in 1977, is a biological classification that divides cellular life forms into three domains: Archaea, Bacteria, and Eukarya. This system is based on differences in ribosomal RNA (rRNA) structure, which reflects fundamental evolutionary divergences.

1. Domain Bacteria (Eubacteria)

• Distinguishing Features:
  • Cell Type: Prokaryotic (no true nucleus or membrane-bound organelles).
  • Cell Wall: Contains peptidoglycan (murein).
  • Ribosomal RNA: Unique rRNA sequences.
  • Membrane Lipids: Ester-linked fatty acids.
  • Initiator tRNA: Formylmethionine.
  • RNA Polymerase: Simple, one type.
  • Habitat: Ubiquitous, found in diverse environments.
• Examples: Escherichia coli, Cyanobacteria (blue-green algae), Staphylococcus aureus.

2. Domain Archaea (Archaebacteria)

• Distinguishing Features:
  • Cell Type: Prokaryotic (no true nucleus or membrane-bound organelles).
  • Cell Wall: Lacks peptidoglycan; composed of pseudomurein, glycoproteins, or polysaccharides.
  • Ribosomal RNA: Unique rRNA sequences, more similar to Eukarya than Bacteria.
  • Membrane Lipids: Ether-linked branched hydrocarbons (isoprenoids), forming monolayers or bilayers.
  • Initiator tRNA: Methionine (like Eukarya).
  • RNA Polymerase: Complex, multiple types (like Eukarya).
  • Habitat: Often found in extreme environments (extremophiles) like hot springs, highly saline lakes, or anaerobic sediments.
• Examples: Methanogens (produce methane), Halophiles (live in high salt concentrations), Thermophiles (live in high temperatures), Acidophiles (live in acidic conditions).

3. Domain Eukarya

• Distinguishing Features:
  • Cell Type: Eukaryotic (possess a true nucleus and membrane-bound organelles like mitochondria, endoplasmic reticulum, Golgi apparatus, etc.).
  • Cell Wall: Present in plants (cellulose) and fungi (chitin); absent in animals and some protists.
  • Ribosomal RNA: Unique rRNA sequences.
  • Membrane Lipids: Ester-linked fatty acids.
  • Initiator tRNA: Methionine.
  • RNA Polymerase: Complex, multiple types.
  • Habitat: Diverse, includes all multicellular organisms and many unicellular ones.
• Examples: Animals, Plants, Fungi, Protists.

The Three-Domain system emphasizes that Archaea are more closely related to Eukarya than to Bacteria, despite both Archaea and Bacteria being prokaryotic.

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Five-Kingdom System of Classification

The Five-Kingdom Classification, proposed by R.H. Whittaker in 1969, categorizes organisms based on cell structure (prokaryotic vs. eukaryotic), body organization (unicellular vs. multicellular), and mode of nutrition (autotrophic, heterotrophic, absorptive, ingestive).

1. Kingdom Monera

• Characteristics:
  • Cell Type: Prokaryotic (lack true nucleus, membrane-bound organelles).
  • Body Organization: Unicellular, colonial, or filamentous.
  • Cell Wall: Present, made of peptidoglycan (in bacteria) or pseudomurein (in archaea).
  • Mode of Nutrition: Autotrophic (photosynthetic or chemosynthetic) or Heterotrophic (saprophytic or parasitic).
  • Reproduction: Primarily asexual (binary fission); sexual reproduction (conjugation, transduction, transformation) is primitive.
• Examples: Bacteria, Cyanobacteria (blue-green algae), Archaebacteria.

2. Kingdom Protista

• Characteristics:
  • Cell Type: Eukaryotic (possess true nucleus and membrane-bound organelles).
  • Body Organization: Mostly unicellular, some colonial or simple multicellular forms.
  • Cell Wall: Present in some (e.g., diatoms, dinoflagellates), absent in others (e.g., protozoans).
  • Mode of Nutrition: Autotrophic (photosynthetic), Heterotrophic (ingestive or absorptive), or Mixotrophic (both).
  • Reproduction: Asexual (binary fission, budding) and sexual (fusion of gametes).
• Examples: Amoeba, Paramecium, Euglena, Diatoms, Slime moulds.

3. Kingdom Fungi

• Characteristics:
  • Cell Type: Eukaryotic.
  • Body Organization: Mostly multicellular (filamentous, forming hyphae), some unicellular (yeasts).
  • Cell Wall: Present, made of chitin.
  • Mode of Nutrition: Heterotrophic (primarily saprophytic, obtaining nutrients by absorption from dead organic matter; some are parasitic).
  • Reproduction: Asexual (spore formation, budding, fragmentation) and sexual (spore formation).
• Examples: Mushrooms, molds, yeasts, puffballs.

4. Kingdom Plantae

• Characteristics:
  • Cell Type: Eukaryotic.
  • Body Organization: Multicellular.
  • Cell Wall: Present, made of cellulose.
  • Mode of Nutrition: Autotrophic (photosynthesis).
  • Reproduction: Asexual (vegetative propagation) and sexual (alternation of generations).
• Examples: Algae (some forms), mosses, ferns, conifers, flowering plants.

5. Kingdom Animalia

• Characteristics:
  • Cell Type: Eukaryotic.
  • Body Organization: Multicellular.
  • Cell Wall: Absent.
  • Mode of Nutrition: Heterotrophic (ingestive).
  • Reproduction: Primarily sexual.
  • Locomotion: Most are motile.
• Examples: Insects, fish, amphibians, reptiles, birds, mammals.

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Kingdom Monera: Bacteria

General Structure of a Typical Bacterial Cell

A typical bacterial cell is prokaryotic, meaning it lacks a membrane-bound nucleus and other membrane-bound organelles.

• Cell Wall: A rigid outer layer, primarily composed of peptidoglycan, providing structural support and protection.
• Cell Membrane: Located just inside the cell wall, controls the passage of substances.
• Cytoplasm: The jelly-like substance filling the cell, containing ribosomes and genetic material.
• Nucleoid: The region where the single, circular chromosome (DNA) is located; not enclosed by a membrane.
• Ribosomes: Sites of protein synthesis.
• Flagella (optional): Long, whip-like appendages for locomotion.
• Pili/Fimbriae (optional): Hair-like appendages for attachment to surfaces or other cells.
• Capsule/Slime Layer (optional): An outer protective layer, often made of polysaccharides.
• Plasmids (optional): Small, circular, extra-chromosomal DNA molecules that carry additional genes (e.g., antibiotic resistance).

Classification of Bacteria

According to Shape:

• Coccus (plural: Cocci): Spherical or oval-shaped.
  • Examples: Staphylococcus (grape-like clusters), Streptococcus (chains), Diplococcus (pairs).
• Bacillus (plural: Bacilli): Rod-shaped.
  • Examples: Escherichia coli, Bacillus subtilis.
• Spirillum (plural: Spirilla): Spiral or helical-shaped, often rigid with external flagella.
  • Examples: Spirillum minus.
• Vibrio (plural: Vibrios): Comma-shaped.
  • Examples: Vibrio cholerae.

According to Nutrition:

• Autotrophic: Synthesize their own food.
  • Photosynthetic Autotrophs: Use light energy (e.g., Cyanobacteria).
  • Chemosynthetic Autotrophs: Use chemical energy from oxidation of inorganic substances (e.g., nitrifying bacteria, sulfur bacteria).
• Heterotrophic: Obtain food from external sources.
  • Saprophytic: Decompose dead organic matter.
  • Parasitic: Live on or in other organisms, causing disease.
  • Symbiotic: Live in mutually beneficial relationships with other organisms.

According to Mode of Respiration:

• Aerobic: Require oxygen for respiration.
  • Obligate Aerobes: Absolutely require oxygen.
  • Facultative Aerobes: Can grow without oxygen but prefer oxygen.
• Anaerobic: Do not require oxygen for respiration.
  • Obligate Anaerobes: Cannot survive in the presence of oxygen.
  • Facultative Anaerobes: Can grow in the presence or absence of oxygen.

Differences between Gram-Positive (+ve) and Gram-Negative (-ve) Bacteria:

The Gram stain is a differential staining technique used to classify bacteria into two large groups based on their cell wall composition.

Types of Reproduction (Details not required, only definitions):

• Fission (Binary Fission): The most common asexual reproduction, where a single bacterial cell divides into two identical daughter cells.
• Conjugation: A process of genetic exchange where genetic material (usually a plasmid) is transferred directly from one bacterium to another through a pilus.
• Transduction: The transfer of bacterial DNA from one bacterium to another via a bacteriophage (virus that infects bacteria).
• Transformation: The uptake of naked DNA from the environment by a bacterial cell, leading to genetic alteration of the recipient cell.

Archaebacteria: Role in Extreme Environments

Archaebacteria are a group of ancient prokaryotes that thrive in harsh conditions.

• Methanogens:
  • Habitat: Anaerobic environments like marshes, swamps, ruminant guts (cattle, sheep), and sewage treatment plants.
  • Role: Produce methane (CH4) as a metabolic byproduct by reducing carbon dioxide. They are important in the carbon cycle and contribute to biogas production.
• Halophiles:
  • Habitat: Extremely saline environments like salt lakes, salt marshes, and highly salty soils.
  • Role: Tolerate and often require high salt concentrations for growth. They have specialized adaptations to prevent water loss and maintain osmotic balance.
• Thermoacidophiles:
  • Habitat: Hot and acidic environments like hot springs, volcanic vents, and sulfurous solfataras.
  • Role: Thrive at high temperatures (up to 100°C or more) and low pH (acidic conditions). They often obtain energy by oxidizing sulfur.

Mycoplasma

Mycoplasma are the smallest known living organisms and are unique among bacteria.

• Three Distinctive Features:
  1. Lack a Cell Wall: They are pleomorphic (can change shape) due to the absence of a rigid cell wall.
  2. Smallest Living Cells: Their size ranges from 0.1 to 0.3 micrometers.
  3. Resistant to Cell Wall-Targeting Antibiotics: Due to the lack of a cell wall, they are naturally resistant to antibiotics like penicillin.

Economic Importance of Bacteria

• Sewage Treatment: Bacteria play a crucial role in breaking down organic matter in wastewater treatment plants, purifying water before discharge.
• Antibiotics: Many antibiotics (e.g., streptomycin, tetracycline) are produced by bacteria (e.g., Streptomyces species), used to treat bacterial infections.
• Energy Production: Methanogenic bacteria are used in anaerobic digesters to produce biogas (methane), a renewable energy source.
• Household Products:
  • Curd: Lactobacillus bacteria convert lactose in milk into lactic acid, causing milk to coagulate into curd.
  • Cheese: Specific bacteria (and fungi) are used in the ripening process of cheese, contributing to its flavor and texture.

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Kingdom Protista

General Characteristics

1. Eukaryotic: Possess a true nucleus and membrane-bound organelles.
2. Mostly Unicellular: Though some are colonial or simple multicellular.
3. Diverse Modes of Nutrition: Can be photosynthetic (plant-like), heterotrophic (animal-like or fungus-like), or mixotrophic.
4. Diverse Modes of Locomotion: Use flagella, cilia, pseudopodia, or are non-motile.

Subgroups of Protista

(i) Chrysophytes

• Characteristics: Golden-algae and diatoms. Photosynthetic. Have silica shells (diatoms) that form diatomaceous earth.
• Examples: Diatoms, Desmids.

(ii) Dinoflagellates

• Characteristics: Mostly marine, photosynthetic. Have two flagella (one longitudinal, one transverse) and often a stiff cellulose plate cell wall. Can cause "red tides."
• Examples: Gonyaulax, Noctiluca.

(iii) Euglenoids

• Characteristics: Unicellular flagellates, mostly freshwater. Have a protein-rich pellicle instead of a cell wall. Mixotrophic (photosynthetic in light, heterotrophic in dark).
• Examples: Euglena.

(iv) Slime Moulds

• Characteristics: Saprophytic protists. Form a plasmodium (acellular slime moulds) or aggregate (cellular slime moulds) during their life cycle.
• Examples: Physarum (acellular), Dictyostelium (cellular).

(v) Protozoans

• Characteristics: Heterotrophic (predators or parasites). Lack a cell wall. Classified based on their mode of locomotion.
  • Rhizopods (Amoeboid Protozoans):
    • Characteristics: Move and capture food using pseudopodia (false feet).
    • Examples: Amoeba proteus, Entamoeba histolytica (causes amoebic dysentery).
  • Flagellates:
    • Characteristics: Possess flagella for locomotion. Some are parasitic.
    • Examples: Trypanosoma (causes sleeping sickness), Leishmania (causes kala-azar).
  • Ciliates:
    • Characteristics: Possess numerous cilia for locomotion and feeding. Have a gullet.
    • Examples: Paramecium, Vorticella.
  • Sporozoans:
    • Characteristics: Non-motile. All are endoparasites, having an infectious spore-like stage in their life cycle.
    • Examples: Plasmodium (causes malaria), Toxoplasma.

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Kingdom Fungi

General Characteristics

• Eukaryotic: Possess a true nucleus and membrane-bound organelles.
• Heterotrophic: Obtain nutrients by absorption (saprophytic or parasitic).
• Cell Wall: Composed of chitin.
• Body Structure: Most are filamentous, forming hyphae (thread-like structures) that collectively form a mycelium. Yeasts are unicellular.
• Storage Food: Glycogen.

Mode of Reproduction

Fungi reproduce both asexually and sexually.

Asexual Reproduction:

• Fragmentation: Mycelium breaks into pieces, each growing into a new mycelium.
• Fission: Unicellular fungi (like yeasts) divide into two daughter cells.
• Budding: A small outgrowth (bud) forms on the parent cell and eventually detaches.
• Spore Formation: The most common method. Spores are asexual reproductive units.
  • Conidia: Non-motile, exogenous spores produced on specialized hyphae (conidiophores).
  • Sporangiospores: Non-motile, endogenous spores produced inside a sporangium.
  • Zoospores: Motile, flagellated spores (found in some lower fungi).

Sexual Reproduction:

Involves the fusion of two compatible nuclei. It typically occurs in three steps:

1. Plasmogamy: Fusion of protoplasts (cytoplasm) of two motile or non-motile gametes. This brings the two haploid nuclei together in the same cell.
2. Karyogamy: Fusion of the two haploid nuclei (from plasmogamy) to form a diploid zygote nucleus.
3. Meiosis: The diploid zygote nucleus undergoes meiosis to produce haploid spores.

• Isogamy: Fusion of two gametes that are morphologically similar but may be physiologically different.
• Anisogamy: Fusion of two gametes that are morphologically dissimilar (e.g., one larger, one smaller).
• Oogamy: Fusion of a large, non-motile female gamete (egg) and a smaller, motile male gamete (sperm).
• Dikaryophase (n+n): In some fungi (Ascomycetes and Basidiomycetes), plasmogamy is not immediately followed by karyogamy. Instead, a dikaryotic stage (n+n) occurs where each cell contains two haploid nuclei (one from each parent). This dikaryophase can be prolonged, and the dikaryotic cells divide to form a dikaryotic mycelium before karyogamy occurs.

Classes of Fungi

1. Zygomycetes (e.g., Bread Moulds)

• Characteristics: Aseptate (coenocytic) hyphae. Asexual reproduction by sporangiospores. Sexual reproduction by fusion of two gametangia to form a zygospore (thick-walled, resistant spore).
• Examples: Rhizopus (bread mould), Mucor.

2. Ascomycetes (Sac Fungi)

• Characteristics: Septate hyphae. Asexual reproduction by conidia. Sexual reproduction involves the formation of ascospores (endogenous spores) inside sac-like asci. Asci are often grouped into fruiting bodies called ascocarps. Exhibit dikaryophase.
• Examples: Saccharomyces cerevisiae (yeast), Penicillium, Aspergillus, Neurospora (used in genetic studies), Morels, Truffles.

3. Basidiomycetes (Club Fungi)

• Characteristics: Septate hyphae. Asexual spores are generally absent, but vegetative reproduction by fragmentation is common. Sexual reproduction involves the formation of basidiospores (exogenous spores) on club-shaped structures called basidia. Basidia are arranged in fruiting bodies called basidiocarps (e.g., mushrooms). Exhibit dikaryophase.
• Examples: Mushrooms (Agaricus), Bracket fungi, Puffballs, Rusts, Smuts.

4. Deuteromycetes (Fungi Imperfecti)

• Characteristics: Known as imperfect fungi because only their asexual or vegetative phases are known. Sexual reproduction is either absent or not yet discovered. Once their sexual forms are discovered, they are moved to Ascomycetes or Basidiomycetes. Many are decomposers and some are parasitic.
• Examples: Alternaria, Colletotrichum, Trichoderma.

Role of Fungi

• Medicine: Source of antibiotics (e.g., Penicillin from Penicillium notatum), immunosuppressants (e.g., cyclosporin A from Tolypocladium inflatum).
• Bakery: Yeast (Saccharomyces cerevisiae) is used in baking bread (fermentation produces CO2, causing dough to rise) and brewing alcohol.
• Environmental Decomposition: Fungi are primary decomposers, breaking down dead organic matter and recycling nutrients in ecosystems.

Definitions

• Lichens: A symbiotic association between a fungus (mycobiont) and a photosynthetic organism (photobiont), which can be an alga or cyanobacterium. The fungus provides protection, moisture, and minerals, while the photobiont provides food through photosynthesis.
• Mycorrhiza: A symbiotic association between a fungus and the roots of vascular plants.
  • Ectomycorrhiza: The fungal hyphae form a dense sheath around the root surface and grow into the intercellular spaces of the root cortex.
  • Endomycorrhiza: The fungal hyphae penetrate the root cells and form structures like vesicles and arbuscules within the cells.

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Viruses, Viroids, and Prions

Viruses

• Characteristic Features:

  • Link between Living and Non-living:
    • Living Characteristics: Possess genetic material (DNA or RNA), can replicate (only inside host cells), can mutate, and evolve.
    • Non-living Characteristics: Are acellular (not made of cells), cannot carry out metabolic activities independently, can be crystallized, and lack cellular organelles.
  • Obligate Intracellular Parasites: They can only replicate inside living host cells, using the host's cellular machinery for their own reproduction.
  • Structure: Consist of genetic material (DNA or RNA, never both) enclosed in a protein coat called a capsid. The capsid is made of smaller protein subunits called capsomeres. Some viruses also have an outer lipid envelope derived from the host cell membrane.

• Structure of TMV (Tobacco Mosaic Virus):

  • Shape: Rod-shaped.
  • Genetic Material: Single-stranded RNA (ssRNA).
  • Capsid: Helical capsid composed of approximately 2130 identical protein subunits (capsomeres) arranged helically around the RNA.

• Structure of Bacteriophage (e.g., T4 Phage):

  • Shape: Tadpole-like structure with a distinct head and tail.
  • Genetic Material: Double-stranded DNA (dsDNA) located in the head.
  • Head: Polyhedral (icosahedral) protein capsid.
  • Tail: Consists of a helical sheath, a central core, a base plate, and tail fibers (for attachment to bacterial cells).

• Contribution of Scientists:

  • D.J. Ivanowsky (1892): Discovered viruses. He observed that the causative agent of tobacco mosaic disease could pass through bacteria-proof filters, suggesting it was smaller than bacteria.
  • M.W. Beijerinck (1898): Coined the term "virus" (meaning venom or poisonous fluid). He demonstrated that the extract from infected tobacco plants could cause infection in healthy plants and called the infectious agent "contagium vivum fluidum" (contagious living fluid).
  • W.M. Stanley (1935): Successfully crystallized TMV, showing that viruses are largely composed of protein and can be crystallized, yet retain their infectivity. This discovery further blurred the line between living and non-living.

Viroids

• Definition: Infectious RNA molecules that are even smaller than viruses and lack a protein coat (capsid).
• Structure: Small, circular, single-stranded RNA molecules.
• Diseases Caused: Primarily cause diseases in plants (e.g., Potato Spindle Tuber Disease, Chrysanthemum Stunt Disease).

Prions

• Definition: Abnormally folded proteins that can induce normal forms of the same protein to misfold. They are infectious agents composed solely of protein, lacking nucleic acids.
• Diseases Caused by Prions:
  • BSE (Bovine Spongiform Encephalopathy) / Mad Cow Disease: A neurodegenerative disease in cattle.
  • CJD (Creutzfeldt-Jakob Disease): A rare, fatal neurodegenerative disease in humans.
  • Scrapie: A fatal, degenerative disease affecting the nervous systems of sheep and goats.
  • Kuru: A rare, incurable, and fatal neurodegenerative disorder endemic to the Fore people of Papua New Guinea, transmitted through ritualistic cannibalism.

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This detailed classification helps us organize the immense diversity of life on Earth, understand their evolutionary relationships, and study their unique characteristics and ecological roles.