Unit 2: Virology and Bacteriology

1. Viruses: General Characteristics and Distribution

Definition: Viruses are non-cellular, infectious agents consisting of a nucleic acid core (DNA or RNA) enclosed in a protein coat (capsid). They are obligate intracellular parasites, meaning they can only replicate inside a living host cell.

• Non-cellular: They lack cytoplasm, organelles, and a cell membrane. They cannot metabolize or reproduce on their own.
• Living vs. Non-living: They have characteristics of both. They possess genetic material (like living things) but are inert and can be crystallized (like non-living chemicals) outside a host.
• Structure: A complete virus particle is called a virion.
  • Nucleic Acid: Can be DNA or RNA, single-stranded (ss) or double-stranded (ds).
  • Capsid: A protein shell that protects the nucleic acid. Composed of subunits called capsomeres.
  • Envelope (some viruses): A lipid membrane derived from the host cell that surrounds the capsid.
• Distribution: Viruses are ubiquitous. They infect all forms of life, including animals, plants, fungi, and bacteria (viruses that infect bacteria are called bacteriophages).

2. Salient Features: Viroids and Prions

These are "sub-viral" infectious agents, even simpler than viruses.

Viroids

• Structure: They are small, circular, single-stranded RNA molecules.
• Key Feature: They are "naked" RNA—they have no protein capsid.
• Replication: They replicate within the host nucleus or chloroplast, using the host's RNA polymerase.
• Host: They are known to cause diseases only in plants (e.g., Potato spindle tuber viroid - PSTV).

Prions

• Structure: They are infectious protein particles.
• Key Feature: They contain no nucleic acid (no DNA or RNA).
• Mechanism: A prion is a misfolded version (PrP^Sc) of a normal cellular protein (PrP^C). When the prion enters a cell, it causes the normal PrP^C proteins to misfold into the prion form (PrP^Sc), leading to a chain reaction and protein aggregation that damages nerve tissue.
• Host: They cause fatal neurodegenerative diseases called Transmissible Spongiform Encephalopathies (TSEs) in mammals.
  • In humans: Creutzfeldt-Jakob Disease (CJD)
  • In cattle: "Mad Cow Disease" (Bovine Spongiform Encephalopathy - BSE)
  • In sheep: Scrapie

3. Structure and Replication (T-phages and TMV)

T-phages (e.g., T4 Bacteriophage)

• Host: Bacteria (e.g., *E. coli*).
• Structure: A complex symmetry.
  • Head: An icosahedral capsid containing dsDNA.
  • Tail: A hollow sheath (like a syringe) surrounded by a contractile sheath.
  • Base Plate: At the bottom of the tail, with tail fibers and pins that recognize and attach to the host cell.
• Replication (Lytic Cycle):
  1. Attachment (Adsorption): Tail fibers bind to specific receptors on the *E. coli* cell wall.
  2. Penetration (Injection): The sheath contracts, and the tail core injects the viral DNA into the bacterium. The capsid remains outside.
  3. Synthesis: The host cell's machinery (ribosomes, enzymes) is "hijacked" to transcribe and translate viral genes, producing viral proteins and replicating viral DNA.
  4. Assembly (Maturation): New viral heads, tails, and DNA are assembled into new, complete virions.
  5. Lysis (Release): The virus produces an enzyme (lysozyme) that degrades the bacterial cell wall, causing the cell to burst (lyse) and release hundreds of new phages.

Tobacco Mosaic Virus (TMV)

• Host: Plants (e.g., tobacco).
• Structure: A simple helical symmetry.
  • It's a rigid, rod-shaped virus.
  • Consists of a single-stranded RNA (ssRNA) genome.
  • The RNA is coiled in a helix, with protein capsomeres arranged around it, forming a protective tube (the capsid).
• Replication (in plants):
  1. Entry: Enters the plant cell through a wound or damage (e.g., from an insect).
  2. Uncoating: The capsid disassembles, releasing the viral ssRNA into the cytoplasm.
  3. Synthesis: The viral RNA acts as mRNA and is translated by host ribosomes to make viral proteins (including an RNA-dependent RNA polymerase).
  4. Replication: The viral RNA polymerase makes new copies of the viral RNA.
  5. Assembly: New capsomeres and viral RNA self-assemble into new TMV virions.
  6. Spread: The virus moves to adjacent cells through plasmodesmata.

4. Methods of Transmission of Viruses

Transmission in Plants

• Mechanical Transmission: Through wounds caused by wind, handling, or tools.
• Vectors (Biological): This is the most common way.
  • Insects: Aphids, whiteflies, and leafhoppers are common vectors. The virus may be persistent (circulates in the insect's body) or non-persistent (carried on the insect's mouthparts).
  • Nematodes & Fungi: Some soil-borne viruses are transmitted by these organisms.
• Vegetative Propagation: Using infected cuttings, bulbs, or tubers will spread the virus to the new plant.
• Pollen & Seed: Some viruses can be transmitted via infected pollen or seeds.

Transmission in Animals (and Humans)

• Airborne (Respiratory): Inhaling droplets from an infected person's cough or sneeze (e.g., Influenza, COVID-19).
• Water/Food-borne (Fecal-Oral): Ingesting water or food contaminated with feces (e.g., Polio, Hepatitis A).
• Direct Contact: Touching, kissing, or sexual contact (e.g., Herpes, HIV).
• Zoonosis (Animal Vectors): Transmitted from an animal to a human.
  • Bite: Rabies (from mammals).
  • Arthropods: Mosquitoes (Dengue, Zika), Ticks (Tick-borne encephalitis).
• Blood-borne: Through contaminated blood transfusions or shared needles (e.g., HIV, Hepatitis B & C).

5. Bacteria: General Characteristics and Cell Wall

General Characteristics

• Prokaryotic: Lack a membrane-bound nucleus and organelles.
• Unicellular: Most are single-celled.
• Genetic Material: A single, circular chromosome located in a region called the nucleoid. May also have small, extra-chromosomal DNA circles called plasmids.
• Ribosomes: Have 70S ribosomes (different from eukaryotic 80S).
• Reproduction: Primarily asexual (binary fission).
• Cell Wall: Most bacteria have a rigid cell wall containing peptidoglycan.

Bacterial Cell Wall (Gram +ve vs. Gram -ve)

The Gram Stain (developed by Hans Christian Gram) is a critical differential stain that separates bacteria into two large groups based on their cell wall structure.

6. Bacteria: Reproduction

Bacteria reproduce asexually but can exchange genetic material horizontally.

Asexual: Binary Fission

This is the main method of bacterial reproduction. It is a process of cell division.

1. The bacterial cell elongates.
2. The single circular chromosome replicates, creating two identical copies.
3. The chromosomes move to opposite ends of the cell.
4. A septum (new cell wall) forms down the middle, dividing the cell.
5. The result is two genetically identical daughter cells.

Genetic Recombination (Horizontal Gene Transfer)

This is *not* reproduction, but a way to create genetic diversity.

Conjugation

• Mechanism: Direct, cell-to-cell transfer of genetic material (usually a plasmid).
• Process: A donor cell (F+) contains a fertility plasmid (F-plasmid). It forms a sex pilus that connects to a recipient cell (F-). The F-plasmid replicates, and a copy is transferred to the F- cell, converting it to an F+ cell.
• Hfr: In some cases, the F-plasmid integrates into the main bacterial chromosome. This is called an Hfr (High-frequency recombination) cell. When an Hfr cell conjugates, it can transfer parts of its chromosome, leading to high-level recombination.

Transformation

• Mechanism: Uptake of "naked" DNA (fragments or plasmids) from the environment.
• Process: Some bacteria are naturally "competent," meaning they can take up external DNA. This DNA can then be integrated into the bacterium's own chromosome.
• Significance: First demonstrated by Griffith's experiment (1928) with *Streptococcus pneumoniae* (transforming non-virulent "R" strain to virulent "S" strain).

Transduction

• Mechanism: Transfer of bacterial DNA from one bacterium to another via a bacteriophage (virus).
• Process (Generalized): During phage assembly, a piece of the *host* bacterial DNA is accidentally packaged into a new phage head instead of viral DNA. When this "transducing phage" infects a new bacterium, it injects the *bacterial* DNA, which can then be incorporated by the recipient.

7. Bacteria: Economic Significance (General)

Bacteria are a "double-edged sword" with immense economic and ecological impact.

• Beneficial (Positive):
  • Decomposition: As decomposers, they recycle nutrients (C, N, S) in ecosystems.
  • Nitrogen Fixation: Convert atmospheric N2 into ammonia (e.g., *Rhizobium*).
  • Food Industry: Fermentation to produce yogurt, cheese, pickles (*Lactobacillus*).
  • Industrial: Production of antibiotics (*Streptomyces*), enzymes, organic acids.
  • Biotechnology: Used as 'factories' to produce insulin, hormones (*E. coli*).
  • Digestion: Gut microbiome (e.g., *E. coli*) helps digest food and produces vitamins (K, B12).
• Harmful (Negative):
  • Disease (Pathogens): Cause diseases in humans (cholera, typhoid), animals, and plants (blights, wilts).
  • Food Spoilage: Cause food to rot, resulting in economic loss.
  • Denitrification: Some bacteria convert useful nitrates back to N2 gas, reducing soil fertility.

8. Special Groups of Bacteria

Mycoplasmas and Spiroplasmas

• Key Feature: They are bacteria that lack a cell wall.
• Mycoplasma: Because they lack a rigid wall, they are pleomorphic (have variable shapes). Their cell membrane contains sterols (unusual for bacteria). They are the smallest free-living organisms. Cause diseases like "walking pneumonia" in humans and "Little leaf" in plants.
• Spiroplasma: They also lack a cell wall but have a distinct helical/spiral shape and are motile (corkscrew-like motion). Often found in plants and insects.

Actinomycetes

• Characteristics: Gram-positive bacteria that grow as branching, thread-like filaments, similar to fungi (hence their old name, "ray fungi").
• Habitat: Abundant in soil, where they contribute to the "earthy" smell (geosmin).
• Economic Importance: They are a major source of antibiotics. The genus Streptomyces alone produces over two-thirds of all clinically useful antibiotics (e.g., Streptomycin, Tetracycline, Chloramphenicol).

Archaebacteria (Domain Archaea)

• Characteristics: Although prokaryotic, they are a separate domain from Bacteria.
• Cell Wall: They lack peptidoglycan. Their cell wall is made of other substances (like pseudopeptidoglycan).
• Cell Membrane: Their membrane lipids have ether linkages (not ester linkages like Bacteria and Eukarya) and branched fatty acid chains.
• Habitat: Many are extremophiles (live in extreme environments):
  • Methanogens: Strict anaerobes, produce methane. Found in swamps, sewage, cow stomachs.
  • Halophiles: Require high salt concentrations (e.g., Great Salt Lake).
  • Thermophiles/Hyperthermophiles: Thrive at very high temperatures (e.g., hot springs, deep-sea hydrothermal vents).

9. Economic Importance of Specific Genera