Diversity of Living World: Attributes, Organization, and Virology

Foundation of the Living World

• Earth's Formation and Environment: Earth was formed approximately $4.6 \times 10^9$ years ago. It is a life-supporting planet featuring diverse landforms including mountains, plateaus, and glaciers.
• The Biosphere: Life exists within a complex structure known as the biosphere, which encompasses both living (biotic) and non-living (abiotic) components.
• Wonders of the Living World: The living world exhibits various visible and subtle activities:
  • The response of sunflowers to sunlight.
  • The twinkling of fireflies in dark forests.
  • Water droplets rolling on the surface of lotus leaves.
  • The closure of Venus flytrap leaves upon being touched by an insect.
  • A squid squeezing ink to escape a predator.
• Molecular Basis of Life: DNA (Deoxyribonucleic acid) molecules are essential for the regulation of life. DNA is composed of chemical elements including Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), Nitrogen ($N$), and Phosphorus ($P$).
• Species Diversity: According to a 2011 survey by Mora et al., the estimated number of species on Earth is approximately $8.7 \times 10^6$. This includes microbes, plants, animals, and human beings, each possessing unique characteristic features.

Attributes of Living Organisms

Growth

• Definition: Growth is an intrinsic property of all living organisms, characterized by an increase in cell number and mass.
• Mechanism: Both unicellular and multicellular organisms grow via cell division.
• Plant Growth: Indefinite and occurs throughout the entire lifespan of the plant.
• Animal Growth: Definite and occurs only for a specific period.
• Intrinsic vs. Extrinsic Growth:
  • Intrinsic: Living cells grow by the addition of new protoplasm from within the cells.
  • Extrinsic: Non-living objects like mountains, boulders, and sand mounds grow by the simple aggregation of material on their external surface.
• Unicellular Organisms: In organisms like Bacteria and Amoeba, growth and reproduction are mutually inclusive events because cell division leads to population growth.

Cellular Structure

• Universal Composition: All living organisms are composed of cells, which are categorized as either prokaryotic or eukaryotic.
• Prokaryotes: Unicellular organisms that lack a membrane-bound nucleus and organelles such as mitochondria, endoplasmic reticulum, and Golgi bodies (e.g., Bacteria and Blue-green algae).
• Eukaryotes: Organisms with a definite nucleus and membrane-bound organelles. They can be unicellular (e.g., Amoeba) or multicellular (e.g., Oedogonium).

Response to Stimuli and Homeostasis

• Consciousness: The ability of animals to sense their surroundings through sense organs.
• Irritability: The response of plants to stimuli, such as bending toward sunlight or the closure of leaves in the touch-me-not plant (Mimosa pudica) upon contact.
• Homeostasis: The property of self-regulation and the tendency to maintain a steady internal state within an external environment that is liable to change. This is essential for survival.

Detailed Study of Reproduction and Metabolism

Reproduction

• Purpose: A fundamental feature of living organisms used to perpetuate their own species.
• Sexual Reproduction: Involves recombination, which brings about genetic variation in the progeny.
• Asexual Reproduction: Produces progeny with features more or less similar to the parents. Specific methods include:
  • Conidia Formation: Observed in Aspergillus and Penicillium.
  • Budding: Observed in Hydra and Yeast.
  • Binary Fission: Observed in Bacteria and Amoeba.
  • Fragmentation: Observed in Spirogyra.
  • Protonema: Observed in Mosses.
  • Regeneration: Observed in Planaria.
• Exceptions: Certain organisms like sterile worker bees and mules do not reproduce.

Metabolism

• Definition: The sum total of all chemical reactions taking place within the cells of a living organism.
• Anabolism (Building up process):
  • Smaller molecules combine to form larger molecules.
  • Chemical energy is formed and stored.
  • Example: Synthesis of proteins from amino acids.
• Catabolism (Breaking down process):
  • Larger molecules are broken down into smaller units.
  • Stored chemical energy is released and used.
  • Example: Breaking down of glucose to $CO_2$ and water.

The Levels of Biological Organization and Integration

• Hierarchy of Organization: Living organisms are organized in a hierarchy that begins at the atomic level and culminates in the biosphere:
  • Non-Living Levels: Atoms $\rightarrow$ Molecules & Compounds $\rightarrow$ Mixture $\rightarrow$ Crystals $\rightarrow$ Colloids $\rightarrow$ Organelles.
  • Living Levels: Living cells $\rightarrow$ Tissues $\rightarrow$ Organs $\rightarrow$ Organ systems $\rightarrow$ Individual organism $\rightarrow$ Population $\rightarrow$ Community $\rightarrow$ Ecosystem $\rightarrow$ Biosphere.
• Integration: These levels do not exist in isolation but form integrated systems.
• Cytoplasmic Streaming: Also known as cyclosis, this is the movement of cytoplasm within cells (e.g., observable in the internodal regions of Chara or leaves of Vallisneria).

Viruses: The Biological Puzzle

• Definition: The word virus is derived from the Latin for "Poison." They are described as sub-microscopic, obligate intracellular parasites.
• Composition: They consist of a nucleic acid core (either DNA or RNA) surrounded by a protein coat (capsid).
• Virology: The specialized study of viruses.
• W.M. Stanley (1904-1971): In 1935, Stanley obtained the tobacco mosaic virus in crystallized form from infected tobacco juice. He was jointly awarded the Nobel Prize for Chemistry in 1946.

Milestones in Virology

• 1796: Edward Jenner used vaccination for smallpox.
• 1886: Adolf Mayer demonstrated the infectious nature of Tobacco Mosaic Virus (TMV) using the sap of mosaic leaves.
• 1892: Dimitry Ivanowsky proved that viruses are smaller than bacteria.
• 1898: M.W. Beijierink defined the infectious agent in tobacco leaves as Contagium vivum fluidum (contagious living fluid).
• 1915: F.W. Twort identified viral infections in bacteria.
• 1917: d'Herelle coined the term "Bacteriophage."
• 1984: Luc Montagnier and Robert Gallo discovered HIV (Human Immunodeficiency Virus).

Physical and Structural Properties of Viruses

• Size: Viruses are ultramicroscopic. Their diameter typically ranges from $20$ to $300\,nm$ ($1\,nm = 10^{-9}\text{ metres}$). Bacteriophages measure approximately $10$ to $100\,nm$. TMV measures $300 \times 20\,nm$.
• Symmetry and Shapes:
  1. Cuboid Symmetry: Examples include Adenovirus and Herpes virus.
  2. Helical Symmetry: Examples include Influenza virus and Tobacco Mosaic Virus (TMV).
  3. Complex or Atypical Symmetry: Examples include Bacteriophage and Vaccinia virus.
• Living Characters of Viruses:
  • Presence of protein and nucleic acid.
  • Capable of mutation (sudden change).
  • Ability to multiply within living cells.
  • Ability to infect and cause disease.
  • Show irritability.
  • Host-specific nature.
• Non-Living Characters of Viruses:
  • Can be crystallized.
  • Absence of cellular metabolism.
  • Inactive outside the host organism.
  • Lack of functional autonomy.
  • Absence of an energy-producing enzyme system.

Classification of Viruses

Baltimore Classification (1971)

Proposed by David Baltimore, this system classifies viruses into seven classes based on the mechanism of RNA production, genome nature ($ss$—single stranded or $ds$—double stranded), presence of DNA or RNA, and use of reverse transcriptase (RT).

• Class 1: Viruses with $dsDNA$ (e.g., Adenoviruses).
• Class 2: Viruses with $(+)$ sense $ssDNA$ (e.g., Parvoviruses).
• Class 3: Viruses with $dsRNA$ (e.g., Reoviruses).
• Class 4: Viruses with $(+)$ sense $ssRNA$ (e.g., Togaviruses).
• Class 5: Viruses with $(-)$ sense $ssRNA$ (e.g., Rhabdoviruses).
• Class 6: Viruses with $(+)$ sense $ssRNA$-RT (Replicate with DNA intermediate; e.g., Retroviruses).
• Class 7: Viruses with $dsDNA$-RT (Replicate with RNA intermediate; e.g., Hepadna viruses).

Viral Genome Types

• Deoxyviruses: Viruses containing DNA. Most animal and bacterial viruses belong here.
• Riboviruses: Viruses containing RNA. Most plant viruses belong here.
• Exceptions: HIV is an animal virus with RNA. Cauliflower Mosaic virus is a plant virus with DNA.
• Strand Variations:
  • $ssDNA$: Parvoviruses.
  • $dsDNA$: Bacteriophages.
  • $ssRNA$: TMV.
  • $dsRNA$: Wound Tumour Virus.

Case Study: Tobacco Mosaic Virus (TMV)

• Discovery: Discovered in 1892 by Dimitry Ivanowsky.
• Transmission: Infects plants via vectors like aphids and locusts.
• Symptoms: Discoloration along leaf veins, yellow and green mottling (mosaic pattern), downward curling and distortion of young apical leaves, stunted growth, and reduced yield.
• Structure:
  • Rod-shaped helical virus measuring $300 \times 20\,nm$.
  • Molecular weight is approximately $39 \times 10^6\,Daltons$.
  • Capsid: A protein coat made of approximately $2130$ identical protein subunits called capsomeres.
  • Nucleic Acid: A central single-stranded RNA ($ssRNA$) molecule consisting of $6500$ nucleotides.

Case Study: Bacteriophage

• Definition: Viruses that infect bacteria; the name literally means "eaters of bacteria" (from Greek Phagein to eat).
• Habitats: Found abundantly in soil, sewage water, fruits, vegetables, and milk.
• Structure of $T_4$ Bacteriophage:
  • Tadpole Shape: Consists of a head, collar, tail, base plate, and fibres.
  • Head: Hexagonal, composed of about $2000$ identical protein subunits.
  • Tail: Long and helical with an inner tubular core, connected to the head via a collar.
  • Base Plate: Attached to the end of the tail, containing six spikes and tail fibres for host cell attachment.
  • Genome: A $dsDNA$ molecule of about $50\,\mu m$ is tightly packed inside the head. This DNA is approximately $1000$ times longer than the phage itself.
• Life Cycles: Phages multiply via two distinct cycles:
  1. Lytic or Virulent Cycle: Leads to the disintegration of the host bacterial cell and the release of progeny virions.
  2. Lysogenic or Avirulent Cycle: Alternative multiplication path.