Unit 1: Microbes

1. Viruses

Characteristics

Definition: Viruses are non-cellular, sub-microscopic infectious agents that are obligate intracellular parasites. They can only replicate inside the living cells of a host.

• Living Characteristics:
  • They possess genetic material (either DNA or RNA).
  • They can replicate (inside a host) and produce new viruses.
  • They can undergo mutations.
• Non-living Characteristics:
  • They are non-cellular (acellular). They lack cytoplasm, a cell membrane, and organelles.
  • They are metabolically inert outside a host cell. They cannot respire, grow, or perform any biosynthesis on their own.
  • They can be crystallized, like a chemical.
• Structure: A complete virus particle is called a virion.
  • Core: The central genetic material, which can be ssDNA, dsDNA, ssRNA, or dsRNA.
  • Capsid: A protective protein coat surrounding the core. It is made of repeating subunits called capsomeres.
  • Envelope (some viruses): A lipid membrane derived from the host cell that surrounds the capsid (e.g., Influenza virus, HIV).
• Symmetry: The arrangement of capsomeres gives the virus its shape.
  • Helical: Rod-shaped (e.g., TMV).
  • Icosahedral (Polyhedral): Roughly spherical (e.g., Adenovirus).
  • Complex: A combination of shapes (e.g., T-phage).

Economic importance

Negative Importance (Harmful)

• Human Diseases: Cause numerous diseases, from mild (common cold - Rhinovirus) to fatal (AIDS - HIV, COVID-19 - SARS-CoV-2, Rabies, Ebola).
• Plant Diseases: Cause major crop losses. Examples include Tobacco Mosaic Virus (TMV), Tomato Yellow Leaf Curl Virus, and Citrus Tristeza Virus, leading to reduced yield and quality.
• Animal Diseases: Cause diseases in livestock (e.g., Foot-and-Mouth disease, Avian influenza), leading to economic losses in agriculture.

Positive Importance (Beneficial)

• Bacteriophages (Phages): Viruses that infect and kill bacteria.
  • Phage Therapy: Used as an alternative to antibiotics to treat bacterial infections, especially antibiotic-resistant ones.
  • Phage Display: A lab technique using phages to study protein-protein interactions.
• Genetic Engineering: Viruses are used as vectors to deliver desired genes into cells for gene therapy and biotechnology.
• Biological Control: Some viruses are used as natural pesticides to control insect pests (e.g., Baculoviruses).
• Vaccines: Viruses (either weakened, killed, or just parts of them) are the basis for vaccines, which train the immune system (e.g., Measles, Mumps, Polio vaccines).

T-phage virus (e.g., T4 Bacteriophage)

• Host: Infects *Escherichia coli* (E. coli) bacteria.
• Structure (Complex Symmetry):
  • Head: An icosahedral (polyhedral) head containing the genetic material, which is double-stranded DNA (dsDNA).
  • Tail: A cylindrical, contractile sheath surrounding a hollow core.
  • Base Plate: A hexagonal plate at the bottom of the tail.
  • Tail Fibers and Tail Pins: Attached to the base plate. The fibers recognize and attach to specific receptors on the bacterial cell wall.

TMV (Tobacco Mosaic Virus)

• Host: Infects plants, especially tobacco, causing mosaic (mottled) patterns on leaves.
• Structure (Helical Symmetry):
  • A long, rigid rod.
  • Core: A single-stranded RNA (ssRNA) molecule.
  • Capsid: The ssRNA is coiled in a helix, with thousands of identical capsomere protein subunits arranged around it, forming a tube.

Lytic and Lysogenic cycles

These are the two main replication cycles of bacteriophages.

Lytic Cycle (Virulent)

This is a rapid cycle that ends in the death (lysis) of the host cell.

1. Attachment (Adsorption): The phage uses its tail fibers to attach to the host bacterium.
2. Penetration (Injection): The phage sheath contracts, injecting its DNA into the bacterial cytoplasm. The phage capsid remains outside.
3. Synthesis: The phage DNA "hijacks" the host cell. It shuts down host DNA replication and uses the host's ribosomes and enzymes to make copies of the viral DNA and viral proteins (capsids, tails, etc.).
4. Assembly (Maturation): The new viral components are assembled into hundreds of new, complete virions.
5. Lysis (Release): The phage produces an enzyme (lysozyme) that degrades the bacterial cell wall, causing the cell to burst and release the new phages.

Lysogenic Cycle (Temperate)

In this cycle, the phage DNA integrates into the host's chromosome and remains dormant.

1. Attachment and Penetration: Same as the lytic cycle.
2. Integration: The phage DNA does *not* take over the cell. Instead, it integrates itself into the bacterial chromosome. The integrated phage DNA is now called a prophage.
3. Replication: The host cell is unharmed and continues to live and reproduce normally. Every time the bacterium divides, it copies its *own* chromosome *and* the prophage, passing it to its daughter cells.
4. Induction: The prophage can remain dormant for many generations. However, if the host cell is stressed (e.g., by UV light or chemicals), the prophage can "excise" (cut) itself out of the host chromosome and enter the lytic cycle, leading to synthesis, assembly, and lysis.

2. Bacteria

General characteristics

• Prokaryotic: They are single-celled organisms that lack a true, membrane-bound nucleus and other membrane-bound organelles (like mitochondria, chloroplasts).
• Genetic Material: A single, circular chromosome of dsDNA, located in a region of the cytoplasm called the nucleoid.
• Plasmids: Many bacteria also contain small, circular, extra-chromosomal DNA molecules called plasmids, which often carry genes for antibiotic resistance.
• Ribosomes: Have 70S ribosomes (composed of 30S and 50S subunits), which are smaller than eukaryotic 80S ribosomes.
• Cell Wall: Most bacteria have a rigid cell wall (outside the plasma membrane) made of peptidoglycan, which provides shape and protection.
• Nutrition: Extremely diverse. Can be autotrophic (photosynthetic or chemosynthetic) or heterotrophic (saprophytic or parasitic).
• Shapes:
  • Coccus (plural: cocci): Spherical.
  • Bacillus (plural: bacilli): Rod-shaped.
  • Spirillum (plural: spirilla): Spiral-shaped.

Cell structure

• Outermost Layers:
  • Capsule/Slime Layer (Glycocalyx): A gelatinous layer outside the cell wall. Protects against dehydration and the host's immune system.
  • Cell Wall: Rigid layer of peptidoglycan. (See Gram + vs. Gram - below).
  • Plasma Membrane: Selectively permeable lipid bilayer inside the cell wall. Site of respiration (it has folds called mesosomes).
• Cytoplasm: The internal contents, containing:
  • Nucleoid: The region with the single circular chromosome.
  • Ribosomes (70S): Sites of protein synthesis.
  • Inclusion Bodies: Granules for storing nutrients (e.g., glycogen, sulfur).
• Appendages:
  • Flagellum (plural: flagella): A long, whip-like tail used for motility (movement).
  • Pili (singular: pilus): Short, hair-like projections.
    • Attachment Pili (Fimbriae): Used to stick to surfaces.
    • Sex Pilus (F-pilus): A special, long pilus used for conjugation (transferring DNA).

Reproduction

1. Vegetative Reproduction

This is the most common method, a form of asexual reproduction.

• Binary Fission: The primary method. The bacterial cell grows to twice its size, replicates its single chromosome, and then a cross-wall (septum) forms in the middle, dividing the cell into two genetically identical daughter cells.

2. Asexual Reproduction (Spore Formation)

• Endospores: This is a survival mechanism, not reproduction. When conditions become harsh (no food, drought), some bacteria (like *Bacillus*) form a highly resistant, dormant structure called an endospore *inside* the cell. The rest of the cell dies, but the endospore can survive for centuries. When conditions are good, it germinates back into a single vegetative cell.

3. Genetic Recombination

This is *not* reproduction (no new cells are made), but it is a way to create genetic diversity by transferring DNA from one bacterium to another. This is also called Horizontal Gene Transfer.

• Conjugation:
  • Mechanism: Direct, cell-to-cell transfer of DNA.
  • Process: A donor cell (F+) with an F-plasmid forms a sex pilus and connects to a recipient cell (F-). A copy of the F-plasmid is transferred, turning the F- cell into an F+ cell.
• Transformation:
  • Mechanism: Uptake of "naked" DNA fragments from the environment.
  • Process: When a bacterium dies, its chromosome breaks apart. A living, "competent" bacterium can absorb these DNA fragments and incorporate them into its own chromosome.
• Transduction:
  • Mechanism: Transfer of bacterial DNA via a bacteriophage (virus).
  • Process: During the lytic cycle, the phage accidentally packages a piece of the *host* bacterial DNA into a new virus particle. When this phage infects a *new* bacterium, it injects the *old* bacterium's DNA, which can then be integrated.

3. Mycoplasma

General account

• Key Feature: Mycoplasmas are the smallest free-living organisms. They are a type of bacteria that naturally lack a cell wall.
• Cell Structure:
  • Because they have no cell wall, they are pleomorphic (have no fixed shape; can be spherical, filamentous, etc.).
  • Their plasma membrane is unique among prokaryotes because it contains sterols (like cholesterol), which they acquire from their host. This makes the membrane more stable.
• Growth: They are very difficult to grow in the lab, requiring a rich medium (including sterols). On agar, they form tiny "fried egg" shaped colonies.

Economic importance

Mycoplasmas are primarily known as pathogens.

• Human Diseases:
  • Mycoplasma pneumoniae is a major cause of "walking pneumonia" (atypical pneumonia) in humans.
• Animal Diseases:
  • Mycoplasma bovis causes mastitis and pneumonia in cattle.
  • They cause various respiratory and joint diseases in poultry, swine, and other livestock, leading to significant economic losses.
• Plant Diseases:
  • Known as phytoplasmas, these organisms cause numerous plant diseases, often transmitted by insects.
  • Examples: Little leaf of brinjal (eggplant), sandal spike, and aster yellows. These diseases cause symptoms like stunting, yellowing, and the growth of sterile, leaf-like flowers (phyllody).