Unit 2: Bacteria and Viruses — Interactive Notes
Over the years many schemes have been proposed for classifying organisms into kingdoms. The five-kingdom classification system, proposed by Robert H. Whittaker in 1969, is recommended in biology. This system classified the organisms in a comprehensive way that reflects evolutionary history of organisms. According to this classification system, all prokaryotes are included in a separate kingdom i.e., the kingdom Monera.
In the last decade, molecular studies have highlighted serious flaws in the five-kingdom classification system. In 1990, American microbiologist Carl Woese suggested that there are two separate groups of prokaryotes i.e., Archaea and Bacteria. He classified living organisms into three domains i.e., domain Archaea, domain Bacteria and domain Eukarya. According to three-domain system, domain Archaea and domain Bacteria contain prokaryotes but they differ in a number of features e.g. cell membrane lipids, cell wall composition, metabolic differences. Molecular evidence suggests that archaea are more closely related to eukaryotes than to bacteria.
Most biologists favour replacing it with a new system, called three-domain system. It is more aligned with the data gained from molecular studies. Bacteria are the prokaryotes classified in the domain of their own, i.e., the domain Bacteria.
Cell wall composition: It is a rigid wall around the plasma membrane of bacterial cell. The major component of bacterial cell wall is a unique macromolecule, called peptidoglycan or murein. It is composed of long glycan (polysaccharide) chain, cross-linked with short peptide fragments. Its amount differs in different bacteria. Cell wall also contains lipids, which are linked to peptidoglycan.
★ Sir Hans Christian Gram devised the technique of Gram's staining. Gram-positive bacteria stain purple because they retain violet dye (CV-I complex) in their cell walls. Gram-negative bacteria do not retain violet dye (they retain safranin) and so they appear in original (pink) colour.
Gram-Positive Bacteria: The cell wall contains thick layer of peptidoglycan and has less lipid content.
Gram-Negative Bacteria: The cell wall has a thin layer of peptidoglycan and more lipid content. They have an outer membrane made of lipopolysaccharides and lipoproteins (makes them resistant to many antibiotics), containing a protein called porin (pore for specific molecules). Has more periplasmic space than Gram-positive.
| Characteristics | Gram-Positive | Gram-Negative |
|---|---|---|
| Number of major layers | One | Two |
| Chemical make up | Peptidoglycan (50% of dry weight), Teichoic & lipoteichoic acid, Lipids (1-4%) | Peptidoglycan (10%), Lipopolysaccharides & Lipoproteins, Lipids (11-12%) |
| Overall thickness | 20-80nm | 8-11nm |
| Outer membrane | No | Yes |
| Periplasmic space | Present in some | Present in all |
| Permeability | More permeable | Less permeable |
Location: Present just beneath cell wall. It lies at the outermost in bacteria that lack cell wall (e.g., Mycoplasmas and Spiroplasmas).
Lack Sterols: The cell membrane of bacteria does not have sterols (e.g., cholesterol) in its chemical makeup.
Mesosomes: At some points, cell membrane invaginates and forms vesicles, tubules or lamellae in cytoplasm. These structures are involved in DNA replication, cell division and also serve as respiratory centres.
Composition: Contains dissolved substances and large structures such as nucleoid, ribosomes, and mesosomes.
Organelles: Lacks cytoskeleton and membrane-bounded organelles. Ribosomes are smaller than eukaryotic (80S); bacterial ribosomes sediment at 70S (larger subunit 50S, smaller 30S).
Nucleoid and Genetic Material: Near the centre of cytoplasm, an irregular-shaped dense area i.e., nucleoid contains DNA. A bacterium possesses a single, circular, double stranded DNA without attached histones — sometimes called the chromosome of bacterium.
Plasmids: Circular, double-stranded extra chromosomal DNA molecules, self-replicating, containing genes for resistance against unfavourable conditions (e.g., antibiotics).
Definition: Endospores are thick-walled, metabolically inactive (dormant) specialized "resting" cells, which enable bacteria to survive extended periods of harsh conditions.
Sporulation: The process by which bacteria make endospores.
Examples: Endospore formation is common in Gram-positive bacteria like Bacillus and Clostridium.
Bacteria use different motility patterns to navigate and explore natural habitats.
a. Flagellar movements: Locomotion powered by flagella — swimming (individual bacteria in liquid, most bacilli/spirilla) or swarming (coordinated movement of a group/population in liquid media). Counter clockwise rotation of flagellum pushes the cell forward with flagellum trailing behind.
b. Twitching or crawling: Used to move over surfaces; mediated by pili, which bind to surrounding solid surface and retract, pulling the cell forward.
c. Gliding: Bacteria secrete slimy substance for smooth gliding over solid surfaces — similar to twitching.
d. Sliding: Movement due to expansion created by the pushing force of dividing cells.
e. Brownian movement: Some bacteria (e.g., Streptococcus) without flagella or pili move due to random, uncontrolled movements of particles in fluid.
f. Movement by axial filament: Some bacteria (e.g., spirochaetes) have a modified flagellum called axial filament — anchored at one end, running length-wise in periplasmic space (between cell membrane and outer membrane); two sets of flagella-like fibrils anchored at the two poles; helps flexing, swimming, creeping and spinning movements.
Bacterial flagella are entirely different from eukaryotic flagella. They are not built on the 9+2 pattern of microtubules, but are composed of flagellin protein.
The bacterial flagellum consists of a basal body, a hook and a filament.
i. Basal Body: Present just beneath cell membrane; consists of rotating rings (one pair in Gram-positive, two pairs in Gram-negative bacteria); anchors flagellum in cell membrane and cell wall.
ii. Hook: A curved structure connecting basal body with filament.
iii. Filament: Elongated thread-like structure composed of flagellin protein subunits in helical fashion.
1. Atrichous — no flagella. 2. Monotrichous — single polar flagellum. 3. Lophotrichous — tuft of flagella at one pole. 4. Amphitrichous — tuft of flagella at each of two poles. 5. Peritrichous — flagella surrounding the whole cell.
Margulis and Schwartz proposed a useful classification system for all prokaryotes, classifying bacteria into 16 phyla.
1. Omnibacteria — rigid, rod-shaped, heterotrophic, Gram-negative; many pathogens; most have flagella; do not produce spores; usually aerobic. E.g. Escherichia coli, vibrios.
2. Cyanobacteria — photosynthetic; increased free oxygen in Earth's atmosphere; contain chlorophyll-a + carotenoids + blue/red phycobilins; fix atmospheric N in heterocysts; common as mats in soil/sea sediments; found in lichens on rocks. ★ Bulk of modern petroleum deposits formed by decayed cyanobacteria; colourful algal blooms in polluted water from their photosynthetic pigments.
3. Mycoplasmas and Spiroplasmas — lack cell walls (smallest bacteria), resistant to penicillin; mycoplasmas cause pneumonia; spiroplasmas cause lethal yellowing disease of coconuts.
4. Spirochaetes — long spirilla, Gram-negative, 2 to >100 flagella; Treponema causes syphilis.
5. Pseudomonas — straight/curved Gram-negative rods, one or many flagella at one end; found in soil/water; break down organic compounds; many plant pathogens; role in denitrification; Pseudomonas aeruginosa causes infections in weak immunity.
6. Actinomycetes — filamentous growth, produce resistant spores; some are N-fixers in root nodules; some cause dental plaque; Mycobacterium leprae (leprosy), M. tuberculosis (tuberculosis); source of antibiotics (tetracycline, chloramphenicol, erythromycin, neomycin).
7. Nitrogen-fixing aerobic bacteria — economically important, Gram-negative, mostly flagellated; Azotobacter converts atmospheric N into nitrates.
8. Chemosynthetic bacteria (chemoautotrophs) — derive energy from oxidation of inorganic N, S, Fe compounds; Nitrosomonas and Nitrobacter oxidize NH₃ → nitrite → nitrate, vital in the nitrogen cycle.
1. Recyclers of Nature: Involved in biogeochemical cycles. Nitrifying bacteria (Nitrosomonas, Nitrobacter, Azotobacter) and denitrifying bacteria (Pseudomonas) complete the nitrogen cycle. Decomposer bacteria play a key role in the carbon-hydrogen-oxygen cycle; photosynthetic bacteria (cyanobacteria) increase free atmospheric oxygen.
2. Environmental Cleaners: Degrade organic compounds (bioremediation) — decompose city sewage, digest petroleum hydrocarbons (oil spill cleanup), bioremediate industrial toxic wastes.
1. Makers of useful products: Fermented foods (cheese, pickles, soy sauce, vinegar, wine, yogurt via Lactobacillus + yeasts/molds); pharmaceutical/agrochemical production; antibiotics; leather goods processing.
2. As biopesticides: Bacillus thuringiensis (Gram-positive, soil-dwelling) used in biological pest control — environmentally friendly, little effect on humans/wildlife/pollinators.
Determine the Function of Genes and Enzymes: Bacteria grow quickly and are easily manipulated (e.g., E. coli) — used in molecular biology, genetics, biochemistry. Scientists mutate bacterial DNA, examine changes, and determine gene/enzyme function — knowledge then applied to more complex organisms.
Human Genes in Bacteria: Scientists insert human genes in bacterial plasmids to produce therapeutic proteins e.g., insulin, growth hormones, antibodies.
Definition: The mixture of organisms regularly found at any anatomical site.
Description: Internal tissues (blood, brain, muscle) are normally free of microorganisms; surface tissues (skin, mucous membranes) are constantly colonized. Normal flora of humans consists of bacteria, a few fungi and protists, and some methanogenic archaea — bacteria are the most numerous.
Benefits to normal flora: Mutualistic association — normal flora gets nutrients, stable environment, constant temperature, protection, and transport.
Benefits to Humans:
i. Synthesis of vitamins: enteric bacteria secrete Vitamin K and B₁₂; lactic acid bacteria produce B-vitamins.
ii. Prevent colonization by pathogens: compete for attachment sites and nutrients.
iii. Inhibit or kill pathogens: intestinal bacteria produce inhibitory substances.
iv. Stimulates production of cross-reactive antibodies: normal flora behaves as antigens, low antibody levels cross-react with pathogens preventing infection.
Structure of Virus: Extremely small infectious agents, seen only under electron microscope.
Size: Range from 20 nm (parvovirus) to 250 nm (pox viruses) — 10 to 1000 times smaller than most bacteria; can pass through filter paper pores.
Genome: Central core is the genome, made of nucleic acid (DNA or RNA).
Capsid and Capsomeres: Core surrounded by a protein coat (capsid), giving definite shape; made of protein subunits (capsomeres) — number/kind characteristic of a particular virus. Herpes virus: 162 capsomeres; Adenovirus: 252 capsomeres. Central core + capsid = nucleocapsid.
Envelope: Lipid-rich membrane derived from host cell, covering nucleocapsid in enveloped viruses. Non-enveloped viruses = naked viruses.
General appearance: Animal/plant viruses may be polyhedron or helical. Bacterial viruses (bacteriophages) may be cubical, icosahedral (20 faces), helical, or complex (polyhedral head + rod-shaped tail).
Bacteriophages are a diverse group of viruses that attack bacteria — among the most complex viruses. Best known phages of Escherichia coli are T-phages.
Consists of a head and a tail.
i. Head: Elongated pyramidal (two triangles with common base), hexagonal, prism-shaped. Capsid made of proteins; core contains long double-stranded DNA. A straight tail is attached with head.
ii. Tail: Made of inner core and outer sheath (different proteins). A neck attaches sheath with head; an end plate is on the other side of sheath. Six tail fibres attached with end plate.
Function: Tail fibres help the phage attach to the bacterial wall.
Human Immunodeficiency Virus (HIV) belongs to the group called retroviruses — a special group of animal viruses. Retroviruses contain RNA and capsids.
Envelope: Surrounded by lipid-rich envelope comprising glycoprotein spikes, which help the virus identify and bind to its target. Spherical, about 100 nm in diameter.
Reverse transcriptase: The most distinguishing character of retroviruses — catalyses reverse transcription, where single-stranded RNA is reversely transcribed into a strand of DNA; the enzyme then uses this DNA strand to complete a double helix of DNA.
★ Possible Origin of HIV: Experts concluded HIV originated in the jungles of Africa among wild chimps. Evidence suggests a form of this virus entered the human species and became HIV via monkey bites or ingesting monkey meat and brains.
AIDS: HIV is responsible for Acquired Immunodeficiency Syndrome — weakens the immune system; fatal because the body cannot defend against other viral/bacterial (opportunistic) infections without an immune system.
Discovery: First reported in 1981, patients found homosexual. Later discovered in non-homosexual patients who received blood/blood products from AIDS patients. In 1984, the causative agent was found to be a virus. In 1986, it was named Human Immunodeficiency Virus (HIV) — a host-specific virus that can multiply in monkeys but does not cause AIDS in them, because HIV attaches to human cells using the specific binding factor CD4 receptor, which is not present in monkeys.
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