Chapter Notes

The History of Classification

From the very beginning of civilization, humans have tried to classify living organisms. Initially, this wasn't for scientific study but for practical reasons—to identify organisms useful for food, shelter, and clothing.

The first person to attempt a more scientific classification was the philosopher Aristotle.

• He classified plants based on their size and structure into trees, shrubs, and herbs.
• He divided animals into two groups: those with red blood and those without.

Later, in the time of Carolus Linnaeus, a Two Kingdom system was developed. This system placed all living things into either Kingdom Plantae (plants) or Kingdom Animalia (animals).

Limitations of the Two Kingdom System

While simple and easy to understand, this system had major drawbacks:

• It didn't distinguish between eukaryotes (cells with a true nucleus) and prokaryotes (cells without a true nucleus).
• It lumped together unicellular (single-celled) and multicellular (many-celled) organisms.
• It grouped photosynthetic organisms like green algae with non-photosynthetic organisms like fungi, just because they both had cell walls.

As our understanding grew, scientists realized that simple appearance (gross morphology) wasn't enough. Other characteristics like cell structure, cell wall composition, mode of nutrition, habitat, and evolutionary relationships were needed for a more accurate classification.

The Five Kingdom Classification

In 1969, R.H. Whittaker proposed the Five Kingdom Classification, which is widely accepted today. This system addresses the shortcomings of the older two-kingdom model.

The five kingdoms are:

1. Monera
2. Protista
3. Fungi
4. Plantae
5. Animalia

Whittaker's classification was based on several key criteria:

• Cell Structure: Prokaryotic or Eukaryotic.
• Body Organisation: Unicellular or Multicellular (tissue, organ, etc.).
• Mode of Nutrition: Autotrophic (makes its own food) or Heterotrophic (gets food from others).
• Reproduction: Methods of creating offspring.
• Phylogenetic Relationships: Evolutionary history and connections between organisms.

Characteristics of the Five Kingdoms

Kingdom Monera

This kingdom is made up entirely of bacteria. They are the most abundant microorganisms on Earth and are found almost everywhere—from soil and water to extreme environments like hot springs, deserts, and deep oceans.

Bacterial Shapes

Bacteria are grouped into four categories based on their shape:

• Coccus (plural: cocci): Spherical
• Bacillus (plural: bacilli): Rod-shaped
• Vibrium (plural: vibrio): Comma-shaped
• Spirillum (plural: spirilla): Spiral

Metabolism and Nutrition

Though structurally simple, bacteria are very complex in their behavior and show the most extensive metabolic diversity of any group of organisms.

• Autotrophic Bacteria: They make their own food.
  • Photosynthetic autotrophs: Use sunlight for energy.
  • Chemosynthetic autotrophs: Get energy by oxidizing inorganic substances like nitrates and ammonia.
• Heterotrophic Bacteria: They depend on other organisms for food. The vast majority of bacteria fall into this category, acting as decomposers or parasites.

Archaebacteria

These are special bacteria that live in some of the most extreme habitats on Earth. Their unique cell wall structure allows them to survive in these harsh conditions.

• Halophiles: Live in extremely salty areas.
• Thermoacidophiles: Live in hot springs.
• Methanogens: Live in marshy areas and the guts of ruminant animals like cows. They are responsible for producing methane (biogas) from animal dung.

Eubacteria

These are the "true bacteria." They are characterized by a rigid cell wall and, if they can move, a flagellum.

• Cyanobacteria (Blue-Green Algae): These are photosynthetic autotrophs that contain chlorophyll a, similar to green plants. They can be unicellular, colonial, or filamentous. They often form "blooms" in polluted water. Some, like Nostoc and Anabaena, can fix atmospheric nitrogen in specialized cells called heterocysts.

• Chemosynthetic Autotrophic Bacteria: These bacteria play a crucial role in recycling nutrients like nitrogen, phosphorus, iron, and sulphur by oxidizing inorganic substances for energy.

• Heterotrophic Bacteria: This is the most abundant group.

  • Decomposers: They break down dead organic matter.
  • Helpful Bacteria: Used in making curd from milk, producing antibiotics, and fixing nitrogen in the roots of legume plants.
  • Pathogens: Cause diseases in humans, animals, and plants, such as cholera, typhoid, tetanus, and citrus canker.

Reproduction in Bacteria

• Bacteria reproduce mainly by fission (splitting in two).
• Under unfavorable conditions, they can produce protective spores.
• They can also engage in a primitive form of sexual reproduction by transferring DNA from one bacterium to another.

Mycoplasma

These are unique organisms that completely lack a cell wall. They are the smallest known living cells and can survive without oxygen. Many are pathogenic in animals and plants.

Kingdom Protista

This kingdom includes all single-celled eukaryotes. Its members are primarily aquatic and form a link between the other kingdoms of plants, animals, and fungi.

General Characteristics

• The cell body contains a well-defined nucleus and other membrane-bound organelles.
• Some have flagella or cilia for movement.
• They reproduce both asexually and sexually (through cell fusion and zygote formation).

Chrysophytes

This group includes diatoms and golden algae (desmids).

• They are found in both freshwater and marine environments.
• They are microscopic and float passively in water currents (plankton).
• Most are photosynthetic.
• Diatoms have cell walls that form two thin, overlapping shells that fit together like a soapbox. These walls are embedded with silica, making them indestructible.
• Over billions of years, these deposits have formed diatomaceous earth, a gritty soil used in polishing and filtering oils and syrups.
• Diatoms are the chief "producers" in the oceans.

Dinoflagellates

• These organisms are mostly marine and photosynthetic.
• They appear yellow, green, brown, blue, or red depending on their main pigments.
• The cell wall has stiff cellulose plates.
• Most have two flagella.
• Some, like Gonyaulax, can multiply rapidly and cause red tides, which can release toxins that kill fish and other marine animals.

Euglenoids

• Majority live in freshwater stagnant water.
• Instead of a cell wall, they have a protein-rich layer called a pellicle, which makes their body flexible.
• They have two flagella: a short one and a long one.
• They are mixotrophic: photosynthetic in sunlight, but they act as heterotrophs (preying on smaller organisms) when deprived of light.
• Their photosynthetic pigments are identical to those in higher plants. Example: Euglena.

Slime Moulds

• These are saprophytic protists, meaning they feed on decaying organic matter.
• Under suitable conditions, they form an aggregation called a plasmodium, which can grow and spread over several feet.
• During unfavorable conditions, the plasmodium forms fruiting bodies that bear spores. These spores have true walls, are extremely resistant, and can survive for many years.

Protozoans

All protozoans are heterotrophs and live as predators or parasites. They are considered primitive relatives of animals.

• Amoeboid protozoans: Found in freshwater, seawater, or moist soil. They move and capture prey using pseudopodia (false feet). Some are parasites, like Entamoeba.

• Flagellated protozoans: They have flagella for movement. They can be free-living or parasitic. The parasite Trypanosoma causes sleeping sickness.

• Ciliated protozoans: These are aquatic and actively move using thousands of cilia. They have a cavity called a gullet where food is ingested. The coordinated movement of cilia steers food into the gullet. Example: Paramoecium.

• Sporozoans: These organisms have an infectious spore-like stage in their life cycle. The most notorious is Plasmodium, the parasite that causes malaria.

Kingdom Fungi

Fungi are a unique kingdom of heterotrophic organisms. They are found everywhere (cosmopolitan) and prefer to grow in warm, humid places. This group includes everything from mushrooms and toadstools to yeast and mould.

Structure

• With the exception of unicellular yeasts, fungi are filamentous.
• Their bodies are made of long, slender, thread-like structures called hyphae.
• A network of hyphae is called a mycelium.
• Coenocytic hyphae: Continuous tubes filled with multinucleated cytoplasm.
• Septate hyphae: Have cross-walls or septa.
• The cell walls of fungi are composed of chitin and polysaccharides.

Nutrition

• Saprophytes: Absorb nutrients from dead organic matter (like bread mould).
• Parasites: Live on or in living plants and animals (like Puccinia, which causes wheat rust).
• Symbionts: Live in mutually beneficial relationships.
  • Lichens: A symbiotic association between fungi and algae.
  • Mycorrhiza: A symbiotic association between fungi and the roots of higher plants.

Reproduction

Fungi reproduce through vegetative, asexual, and sexual means.

• Asexual reproduction is by spores like conidia, sporangiospores, or zoospores.
• Sexual reproduction involves three steps:
  1. Plasmogamy: Fusion of the protoplasm of two gametes.
  2. Karyogamy: Fusion of the two nuclei.
  3. Meiosis: The zygote undergoes meiosis to produce haploid spores.

In some fungi (ascomycetes and basidiomycetes), after plasmogamy, the two nuclei don't fuse immediately. This creates an intermediate stage where a cell has two nuclei ($n+n$), known as a dikaryon.

Classes of Fungi

Phycomycetes

• Found in aquatic habitats and on decaying wood.
• The mycelium is aseptate and coenocytic.
• Asexual spores (zoospores or aplanospores) are produced inside a sporangium.
• Examples: Mucor, Rhizopus (the bread mould), Albugo (a parasite on mustard).

Ascomycetes (Sac-fungi)

• Mostly multicellular (e.g., Penicillium) but can be unicellular (e.g., yeast).
• Mycelium is branched and septate.
• Asexual spores are conidia, which are produced externally on structures called conidiophores.
• Sexual spores are ascospores, produced internally in a sac-like structure called an ascus. Asci are arranged in fruiting bodies called ascocarps.
• Examples: Aspergillus, Neurospora (used in genetic research), and edible morels and truffles.

Basidiomycetes (Club-fungi)

• Includes mushrooms, bracket fungi, and puffballs.
• Mycelium is branched and septate.
• Asexual spores are generally not found.
• Sex organs are absent. Sexual reproduction occurs by the fusion of two vegetative cells, forming a dikaryotic structure that gives rise to a basidium.
• Karyogamy and meiosis occur in the basidium, producing four basidiospores externally.
• Examples: Agaricus (mushroom), Ustilago (smut), and Puccinia (rust fungus).

Deuteromycetes (Imperfect Fungi)

• This is a temporary group for fungi where only the asexual or vegetative phases are known.
• If a sexual stage is discovered, the fungus is moved to the class it belongs to (usually Ascomycetes or Basidiomycetes).
• They reproduce only by asexual spores known as conidia.
• Mycelium is septate and branched.
• Many are decomposers that help in mineral cycling.
• Examples: Alternaria, Colletotrichum, Trichoderma.

Kingdom Plantae

This kingdom includes all eukaryotic, chlorophyll-containing organisms, commonly called plants.

Key Features

• Their cells have a eukaryotic structure with chloroplasts and a cell wall made mainly of cellulose.
• Most are autotrophic, but a few are partially heterotrophic.
  • Insectivorous plants: Bladderwort and Venus fly trap.
  • Parasites: Cuscuta.
• The kingdom includes algae, bryophytes, pteridophytes, gymnosperms, and angiosperms.
• The life cycle of plants shows an alternation of generations, where a diploid sporophytic phase alternates with a haploid gametophytic phase.

Kingdom Animalia

This kingdom consists of heterotrophic, eukaryotic, multicellular organisms whose cells lack cell walls.

Key Features

• They depend directly or indirectly on plants for food.
• Their mode of nutrition is holozoic—by ingestion of food.
• They store food reserves as glycogen or fat.
• They follow a definite growth pattern into adults with a definite shape and size.
• Higher forms show elaborate sensory and neuromotor mechanisms.
• Most are capable of locomotion (movement).
• Sexual reproduction is by copulation of male and female, followed by embryological development.

Viruses, Viroids, Prions, and Lichens

These are acellular organisms (or symbiotic associations) that are not included in Whittaker’s five-kingdom classification.

Viruses

Viruses are not considered truly "living" because they are non-cellular. They have an inert, crystalline structure outside of a living cell but become active once they infect a host.

• Nature: They are obligate parasites, meaning they can only replicate by taking over the machinery of a host cell, eventually killing it.
• Structure: A virus is a nucleoprotein.
  • Genetic Material: It contains either DNA or RNA, but never both. Plant viruses typically have single-stranded RNA, while animal viruses can have single or double-stranded RNA or double-stranded DNA. Bacteriophages (viruses that infect bacteria) usually have double-stranded DNA.
  • Capsid: A protein coat that protects the nucleic acid. It is made of small subunits called capsomeres.
• Diseases: Viruses cause many diseases, including the common cold, flu, mumps, smallpox, herpes, and AIDS in humans. In plants, they cause symptoms like mosaic formation, leaf rolling, and stunted growth.

Viroids

Discovered in 1971 by T.O. Diener, viroids are infectious agents even smaller than viruses.

• They consist of a free, low molecular weight RNA.
• They lack the protein coat (capsid) found in viruses.
• They cause diseases like potato spindle tuber disease.

Prions

Prions are infectious agents consisting of abnormally folded proteins.

• They are similar in size to viruses.
• They cause fatal neurological diseases like bovine spongiform encephalopathy (BSE), or "mad cow disease," in cattle and its human variant, Creutzfeldt-Jakob disease (CJD).

Lichens

Lichens are symbiotic associations between algae and fungi. This means the two organisms live together in a mutually beneficial relationship.

• The algal component is the phycobiont. It is autotrophic and prepares food for the fungus.
• The fungal component is the mycobiont. It is heterotrophic and provides shelter, water, and mineral nutrients for the alga.
• The association is so close that a lichen appears to be a single organism.
• Lichens are very good pollution indicators because they do not grow in polluted areas.