Microbiology सूक्ष्मजीवशास्त्र

Quick summary

Microbiology (सूक्ष्मजीवशास्त्र) is the study of living things too small to be seen clearly with the naked eye: bacteria, fungi, algae, protozoa and viruses. This topic covers the scientists who built the subject, the famous experiments that ended the idea of spontaneous generation and proved the germ theory, and the many fields where microbiology is used today.

Key points

• Antonie van Leeuwenhoek (Netherlands) made simple single-lens microscopes and was the first to describe bacteria and protozoa, which he called "animalcules" (1670s). He is called the Father of Microbiology (also of bacteriology and protozoology).
• Robert Hooke described "cells" in cork in his book Micrographia (1665).
• Spontaneous generation (abiogenesis) was the old belief that life arises from non-living matter. Francesco Redi (meat and flies), Lazzaro Spallanzani (boiled sealed broth) and finally Louis Pasteur (swan-neck flask experiment, 1860s) disproved it.
• John Tyndall showed that some microbes survive boiling (heat-resistant forms, later known as endospores) and developed tyndallization (intermittent boiling).
• Louis Pasteur (France) also explained fermentation as the work of microbes, developed pasteurization, and made vaccines against chicken cholera, anthrax and rabies (1885). He is called the Father of Modern Microbiology.
• Robert Koch (Germany) proved that a specific microbe causes a specific disease: anthrax (Bacillus anthracis, 1876), and discovered the causes of tuberculosis (Mycobacterium tuberculosis, 1882) and cholera (Vibrio cholerae, 1883). His lab introduced solid media, agar and pure culture methods.
• Edward Jenner (1796) used cowpox material to protect against smallpox — the start of vaccination.
• Joseph Lister used carbolic acid (phenol) in surgery — the start of antiseptic surgery.
• Alexander Fleming discovered penicillin from the mould Penicillium notatum (1928).
• Dmitri Ivanovsky (1892) and Martinus Beijerinck (1898) showed that tobacco mosaic disease is caused by a filterable agent — the start of virology.
• Sergei Winogradsky and Beijerinck founded soil and environmental microbiology (enrichment culture, chemolithotrophy, nitrogen fixation).

Important terms

• Germ theory of disease – infectious diseases are caused by microorganisms.
• Biogenesis – life comes only from pre-existing life.
• Pasteurization – mild heating of milk or juice to kill pathogens without boiling.
• Pure culture – a culture containing only one kind of microorganism.
• Antiseptic – chemical that kills or inhibits microbes on living tissue.
• Vaccine – preparation of a weakened, killed or part of a microbe that produces immunity.

Key facts

Koch's postulates (to prove that a microbe causes a disease):

1. The microbe must be present in every case of the disease and absent in healthy hosts.
2. It must be isolated from the diseased host and grown in pure culture.
3. The pure culture, when put into a healthy susceptible host, must cause the same disease.
4. The same microbe must be re-isolated from the experimentally infected host.

Scope of microbiology (branches): medical, food and dairy, agricultural/soil, industrial, environmental and water, pharmaceutical, genetic engineering and biotechnology, immunology, virology, mycology, phycology.

5 important questions

Q1. Who is called the Father of Microbiology and why?

Antonie van Leeuwenhoek. Using his own simple microscopes he was the first to observe and describe bacteria and protozoa ("animalcules") in the 1670s.

Q2. What is pasteurization?

Heating milk to a set temperature for a fixed time and then cooling it quickly. Example: 63 °C for 30 minutes (holding/LTH method) or 72 °C for 15 seconds (HTST method). It kills pathogens and increases shelf life.

Q3. Describe Pasteur's swan-neck flask experiment.

• Nutrient broth was boiled in flasks whose necks were bent into an S (swan) shape.
• Air could enter, but dust and microbes settled in the bend of the neck.
• The broth stayed clear and free of growth for a long time.
• When the neck was broken or the broth tilted into the bend, microbes grew quickly.
• Conclusion: microbes come from microbes in air and dust, not from the broth itself. This disproved spontaneous generation.

Q4. State Koch's postulates and their limitations.

• Write the four postulates (see Key facts).
• Limitations: some microbes cannot be grown in culture (e.g. Mycobacterium leprae, viruses on ordinary media); healthy carriers exist; some diseases are caused by more than one microbe; no animal model for some human pathogens.

Q5. Explain the scope of microbiology.

• Medicine: diagnosis, vaccines, antibiotics.
• Agriculture: biofertilizers, biopesticides, nitrogen fixation.
• Food and dairy: curd, cheese, bread, fermented foods; food safety.
• Industry: alcohol, organic acids, enzymes, vitamins, antibiotics.
• Environment: sewage treatment, bioremediation, biogas.
• Biotechnology: recombinant insulin, genetic engineering.

Exam tip

Learn scientist – discovery – year as a table. Koch's postulates and the swan-neck experiment are asked almost every year.

Quick summary

All living cells are of two basic types. Prokaryotic cells (bacteria and archaea) have no true nucleus and no membrane-bound organelles. Eukaryotic cells (fungi, algae, protozoa, plants and animals) have a true nucleus enclosed by a nuclear membrane and many organelles. This topic compares the two cell types and explains Woese's three-domain idea, which is asked in almost every first-year exam.

Key points

• The word prokaryote means "before nucleus"; eukaryote means "true nucleus". The terms were made popular by Édouard Chatton and later by Stanier and van Niel.
• Prokaryotes: bacteria (including cyanobacteria, actinomycetes, rickettsiae, chlamydiae, mycoplasmas) and archaea.
• Eukaryotic microbes: fungi (moulds and yeasts), algae and protozoa.
• Prokaryotic DNA lies free in the cytoplasm in a region called the nucleoid; it is usually one circular chromosome, without histones (archaea have histone-like proteins).
• Eukaryotic DNA is linear, packed with histones into chromosomes inside a nucleus; division is by mitosis and meiosis.
• Prokaryotes divide by binary fission; they have no mitosis.
• Prokaryotic ribosomes are 70S (50S + 30S); eukaryotic cytoplasmic ribosomes are 80S (60S + 40S). Mitochondria and chloroplasts have 70S ribosomes, which supports the endosymbiotic theory (Lynn Margulis).
• Most bacteria have a peptidoglycan cell wall. Fungal walls are mainly chitin, plant and many algal walls are cellulose; animal cells and most protozoa have no wall.
• Prokaryotic flagella are simple, made of the protein flagellin, and rotate. Eukaryotic flagella and cilia have the 9 + 2 microtubule arrangement and whip or beat.
• Sterols (cholesterol, ergosterol) are present in eukaryotic membranes; absent in most bacteria (exception: Mycoplasma takes sterols from the host).
• Carl Woese (1977, three domains formally named 1990) used 16S/18S rRNA sequences to divide life into Bacteria, Archaea and Eukarya.
• Prokaryotic cells are small (about 0.2–2 µm wide); eukaryotic cells are usually 10–100 µm.

Important terms

• Nucleoid – irregular region in a prokaryotic cell that holds the chromosome; no membrane around it.
• Organelle – membrane-bound structure with a special function (mitochondrion, chloroplast, Golgi body).
• Svedberg unit (S) – unit of sedimentation rate in an ultracentrifuge; shows size of ribosomes.
• Endosymbiotic theory – idea that mitochondria and chloroplasts came from bacteria that lived inside an early eukaryotic cell.
• Histones – basic proteins around which eukaryotic DNA is wound.

Key facts

5 important questions

Q1. What is a nucleoid?

It is the region in the cytoplasm of a prokaryotic cell where the circular DNA is found. It has no nuclear membrane or nucleolus.

Q2. Name the three domains of life. Who proposed them?

Bacteria, Archaea and Eukarya. They were proposed by Carl Woese on the basis of ribosomal RNA (16S/18S rRNA) sequence comparison.

Q3. Distinguish between prokaryotic and eukaryotic cells.

• Write the comparison table: nucleus, chromosome, organelles, ribosomes, wall, division, flagella, size.
• Give two examples of each.
• Add a labelled outline sketch of a bacterial cell and a eukaryotic cell if time allows.

Q4. Explain the three-domain system of classification.

• Older system: Whittaker's five kingdoms (1969), based on cell type, nutrition and body plan.
• Woese compared rRNA sequences and found archaea as different from bacteria as from eukaryotes.
• Bacteria: peptidoglycan walls, ester-linked membrane lipids.
• Archaea: no peptidoglycan, ether-linked lipids, many live in extreme habitats (methanogens, halophiles, thermophiles).
• Eukarya: true nucleus; includes protists, fungi, plants, animals.

Q5. Give evidence for the endosymbiotic theory.

• Mitochondria and chloroplasts have their own circular DNA.
• They have 70S ribosomes like bacteria.
• They divide by a fission-like process.
• They have a double membrane; the inner one resembles a bacterial membrane.
• Their rRNA sequences are close to those of bacteria (mitochondria to α-proteobacteria, chloroplasts to cyanobacteria).

Exam tip

A neat comparison table with at least 8 points earns full marks in the "distinguish" question. Always write 70S vs 80S and peptidoglycan vs chitin/cellulose.

Quick summary

Actinomycetes and cyanobacteria are two special groups of bacteria. Actinomycetes are Gram-positive bacteria that grow as branched threads like fungi and are famous as antibiotic producers. Cyanobacteria (blue-green algae) are Gram-negative bacteria that carry out plant-like oxygenic photosynthesis and many of them fix nitrogen. Both are prokaryotes, even though they look like fungi or algae.

Key points

• Actinomycetes are Gram-positive, mostly aerobic, filamentous bacteria with a high G + C content in their DNA.
• They form a branched network of thin threads (about 0.5–1 µm wide) called mycelium: substrate mycelium grows into the medium and aerial mycelium grows into the air.
• Many reproduce by chains of conidia (conidiospores) at the tips of aerial hyphae, or by sporangiospores in sporangia. These spores are not heat-resistant like endospores.
• They are common in soil; the earthy smell of wet soil is due to geosmin made by Streptomyces.
• Streptomyces produce a large share of natural antibiotics: streptomycin (S. griseus; Waksman), tetracyclines (S. aureofaciens), chloramphenicol (S. venezuelae), erythromycin (Saccharopolyspora erythraea, earlier S. erythreus).
• Other genera: Nocardia (partly acid-fast, can cause nocardiosis), Actinomyces (anaerobic, causes actinomycosis), Frankia (nitrogen-fixing nodules on Casuarina and Alnus), Micromonospora (gentamicin).
• Cyanobacteria are Gram-negative, photosynthetic prokaryotes. They have chlorophyll a and phycobiliproteins (phycocyanin – blue, phycoerythrin – red) in phycobilisomes on thylakoids. They release O₂ (oxygenic photosynthesis).
• Forms: unicellular (Synechococcus, Gloeocapsa), colonial (Microcystis), filamentous (Oscillatoria, Nostoc, Anabaena, Spirulina).
• Heterocysts are thick-walled cells in some filaments (Nostoc, Anabaena) where nitrogen fixation takes place; they lack photosystem II, so no O₂ is made inside to damage nitrogenase.
• Akinetes are thick-walled resting cells; hormogonia are short motile pieces of filament used for reproduction.
• Uses: biofertilizer for paddy (blue-green algae, Azolla–Anabaena), Spirulina as protein-rich food supplement. Harm: water blooms (Microcystis) produce toxins and lower oxygen.
• Cyanobacteria are believed to be the ancestors of chloroplasts.

Important terms

• Mycelium – mass of branched threads (hyphae).
• Geosmin – compound giving soil its earthy smell; made by Streptomyces.
• Heterocyst – special nitrogen-fixing cell of filamentous cyanobacteria.
• Phycobilisome – granule on thylakoid carrying light-harvesting pigments phycocyanin and phycoerythrin.
• Water bloom – heavy growth of cyanobacteria on the surface of nutrient-rich water.

Key facts

5 important questions

Q1. Why are actinomycetes placed among bacteria and not fungi?

They are prokaryotic: no nuclear membrane, 70S ribosomes, peptidoglycan wall, and their threads are about 1 µm thick (much thinner than fungal hyphae). They are also sensitive to antibacterial antibiotics.

Q2. What is a heterocyst?

A large, thick-walled, pale cell in filamentous cyanobacteria like Anabaena and Nostoc. It fixes atmospheric nitrogen and protects nitrogenase from oxygen.

Q3. Describe the general characters and economic importance of actinomycetes.

• Gram-positive, filamentous, branched, high G + C.
• Substrate and aerial mycelium; conidia on aerial hyphae.
• Soil decomposers of cellulose, chitin; produce geosmin.
• Antibiotics: streptomycin, tetracycline, chloramphenicol, erythromycin, gentamicin.
• Frankia fixes nitrogen; Nocardia and Actinomyces cause disease.

Q4. Give the characteristics of cyanobacteria.

• Gram-negative prokaryotes; no chloroplasts but thylakoids with chlorophyll a and phycobilins.
• Oxygenic photosynthesis; store cyanophycin and glycogen.
• Forms and examples; gas vacuoles in planktonic forms.
• Reproduction by fission, fragmentation, hormogonia, akinetes.
• Heterocysts for nitrogen fixation.

Q5. Write the importance of cyanobacteria in agriculture and industry.

• Blue-green algae biofertilizer adds nitrogen to paddy fields.
• Azolla–Anabaena symbiosis used as green manure.
• Spirulina as single cell protein, vitamins, food colour (phycocyanin).
• Improve soil structure and reclaim saline soils.
• Negative: toxic blooms in lakes and drinking-water reservoirs.

Exam tip

Remember the pair "actinomycetes = antibiotics, cyanobacteria = nitrogen fixation". Draw a Streptomyces mycelium with spore chains and an Anabaena filament with a heterocyst.

Quick summary

Microbes are too small for the eye, so microscopes are the basic tool of microbiology. This topic covers how a light microscope works, magnification and resolving power, and the main types of microscopes — bright field, dark field, phase contrast, fluorescence and electron microscopes — with their uses.

Key points

• The compound light microscope uses two lens systems: the objective (near the specimen) and the eyepiece/ocular (near the eye).
• Total magnification = magnification of objective × magnification of eyepiece. Example: 100× oil immersion objective with 10× eyepiece = 1000×.
• Resolving power (resolution) is the ability to show two close points as separate. It matters more than magnification.
• The limit of resolution of a good light microscope is about 0.2 µm. Electron microscopes resolve far smaller objects (well below 1 nm in practice for TEM).
• Oil immersion: cedarwood oil or immersion oil has a refractive index (about 1.5) close to glass. It stops light from bending away, increases the numerical aperture and improves resolution with the 100× objective.
• Bright field microscope: dark (stained) object on a bright background; most common, used for stained smears.
• Dark field microscope: a special condenser blocks direct light; only light scattered by the object enters the objective, so the object shines on a dark background. Used for thin, unstained living organisms like Treponema pallidum (syphilis).
• Phase contrast microscope (Frits Zernike, Nobel Prize 1953): converts small differences in refractive index into differences in brightness. Used to see living, unstained cells and internal structures.
• Fluorescence microscope: uses UV or blue light; fluorescent dyes (fluorochromes) or labelled antibodies glow. Used in diagnosis (e.g. auramine staining for TB bacilli, immunofluorescence).
• Electron microscope: uses a beam of electrons and electromagnetic lenses in a vacuum. TEM (transmission) shows internal structure of thin sections; SEM (scanning) shows 3-D surface view. Ernst Ruska and Max Knoll built the first one (1931).

Important terms

• Numerical aperture (NA) – measure of the light-gathering ability of a lens: NA = n sin θ.
• Refractive index – how much a medium bends light.
• Condenser – lens below the stage that focuses light on the specimen.
• Working distance – distance between objective and specimen when in focus; smallest for oil immersion.
• Parfocal – objectives remain nearly in focus when you change from one to another.

Formulas

• Total magnification = M(objective) × M(eyepiece)
• d = smallest distance between two points that can be seen as separate
• λ = wavelength of light used (green light about 550 nm)
• NA = numerical aperture of the objective
• Limit of resolution, d = 0.61 λ / NA (Abbe's formula, often written d = λ / 2NA)
• NA = n sin θ, where n = refractive index of medium between lens and specimen, θ = half the angle of the cone of light entering the objective.
• Shorter wavelength or higher NA → smaller d → better resolution.

5 important questions

Q1. Why is immersion oil used with the 100× objective?

Oil has nearly the same refractive index as glass. Light passing from slide to lens does not bend away, so more light enters the objective, NA increases and the image becomes sharp with better resolution.

Q2. Calculate total magnification with a 45× objective and 10× eyepiece.

Total magnification = 45 × 10 = 450×.

Q3. Calculate the limit of resolution when λ = 550 nm and NA = 1.25 (use d = 0.61 λ/NA).

• d = 0.61 × 550 / 1.25
• 0.61 × 550 = 335.5
• 335.5 / 1.25 = 268.4 nm ≈ 0.27 µm
• So two points closer than about 0.27 µm cannot be seen separately.

Q4. Describe the principle and uses of the dark field microscope.

• A dark field stop (opaque disc) in the condenser blocks central light.
• Only oblique light hits the specimen; scattered light reaches the objective.
• The object appears bright on a black background.
• Uses: living unstained bacteria, spirochaetes like Treponema, motility study.

Q5. Compare light microscope and electron microscope.

Exam tip

Always write the resolution formula with the meaning of each symbol. Draw a labelled compound microscope: eyepiece, body tube, revolving nosepiece, objectives, stage, condenser, iris diaphragm, mirror/light source, coarse and fine adjustment.

Quick summary

Bacteria are prokaryotic cells: they have no true nucleus and no membrane-bound organelles. This topic covers bacterial shapes and arrangements and each part of the cell — from the capsule and flagella outside to the cell wall, membrane, cytoplasm, nucleoid, plasmids and endospores inside.

Key points

• Shapes: coccus (spherical), bacillus (rod), vibrio (comma), spirillum (rigid spiral), spirochaete (flexible spiral).
• Arrangements of cocci: diplococci (pairs, e.g. Streptococcus pneumoniae), streptococci (chains), staphylococci (grape-like clusters), tetrads, sarcinae (cubes of 8).
• Size: most bacteria are about 0.5–5 µm long.
• Capsule / slime layer: outer layer, mostly polysaccharide. It protects from phagocytosis and drying and helps attachment. Capsulated strains are often more virulent.
• Flagella: long, thin protein (flagellin) threads for movement. Parts: filament, hook, basal body. Arrangements: monotrichous (one), lophotrichous (tuft at one end), amphitrichous (at both ends), peritrichous (all over), atrichous (none).
• Pili and fimbriae: short, hair-like protein structures. Fimbriae help attachment; the sex pilus (F pilus) is used in conjugation.
• Cell wall: rigid, gives shape, made of peptidoglycan (murein) — chains of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) cross-linked by short peptides.
• Gram-positive wall: thick peptidoglycan with teichoic acids; no outer membrane.
• Gram-negative wall: thin peptidoglycan, periplasmic space, and an outer membrane containing lipopolysaccharide (LPS). The lipid A part of LPS is the endotoxin.
• Cell membrane: phospholipid bilayer with proteins; controls transport; site of respiration (bacteria have no mitochondria). Mesosomes are infoldings described in older books.
• Cytoplasm: contains 70S ribosomes (50S + 30S), inclusion bodies (glycogen, volutin/polyphosphate granules, PHB, sulphur granules).
• Nucleoid: a single circular, double-stranded DNA chromosome without a nuclear membrane.
• Plasmids: small, circular, extra-chromosomal DNA that replicate on their own; may carry genes for antibiotic resistance (R plasmids) or fertility (F plasmid).
• Endospore: a tough, dormant, resistant body formed by Bacillus and Clostridium. It contains dipicolinic acid and calcium, and survives boiling, drying and chemicals.

Important terms

• Prokaryote – cell without a true nucleus.
• Peptidoglycan – the mesh-like polymer that makes the bacterial wall rigid.
• Periplasm – space between the inner membrane and outer membrane in Gram-negative bacteria.
• Spheroplast / protoplast – cell that has lost part / all of its wall (e.g. by lysozyme or penicillin).
• Sporulation – process of endospore formation; germination – endospore turning back into a vegetative cell.

Key facts

5 important questions

Q1. What is peptidoglycan?

A polymer of alternating NAG and NAM sugars linked into chains, with short peptides on NAM cross-linking the chains. It forms the rigid bacterial cell wall.

Q2. Name the types of flagellar arrangement with examples.

Monotrichous (Vibrio cholerae), lophotrichous (Pseudomonas fluorescens is often cited), amphitrichous (Spirillum), peritrichous (E. coli, Salmonella typhi).

Q3. Compare the cell walls of Gram-positive and Gram-negative bacteria.

• Thickness of peptidoglycan.
• Teichoic acids only in Gram-positive.
• Outer membrane with LPS, porins and lipoproteins only in Gram-negative.
• Periplasmic space in Gram-negative.
• Effect: Gram-positive more sensitive to penicillin and lysozyme; Gram-negative LPS acts as endotoxin.
• Draw both wall diagrams.

Q4. Describe the structure of a bacterial endospore.

• Layers from inside out: core (DNA, ribosomes, dipicolinic acid + Ca²⁺), inner membrane, cortex (special peptidoglycan), spore coat (protein), exosporium (outer thin layer).
• Formed when nutrients run out.
• Very low water, highly resistant to heat, radiation, chemicals.
• Position: central, subterminal, terminal (e.g. drumstick in Clostridium tetani).

Q5. Draw and label a typical bacterial cell.

• Labels: capsule, cell wall, cell membrane, cytoplasm, ribosomes, nucleoid, plasmid, inclusion bodies, pili, flagellum.
• Add one line on the function of each part.

Exam tip

A neat labelled diagram of the bacterial cell and of the two cell walls earns full marks. Learn the 70S ribosome and endospore layers.

Quick summary

The cell wall is the rigid layer outside the cell membrane that gives a bacterium its shape and protects it from bursting. Its main material is peptidoglycan (murein). Differences in wall structure divide bacteria into Gram-positive and Gram-negative groups, explain the Gram stain result, and decide which antibiotics work. Acid-fast walls and wall-less forms are also part of this topic.

Key points

• Functions: gives shape, prevents osmotic lysis (the inside of the cell has high osmotic pressure), acts as a sieve, anchors flagella, carries antigens, and is a target of antibiotics.
• Peptidoglycan = long glycan chains of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) joined by β-1,4 bonds, cross-linked by short peptides attached to NAM.
• The tetrapeptide often contains L-alanine, D-glutamic acid, a diamino acid (L-lysine in many Gram-positives, meso-diaminopimelic acid (DAP) in Gram-negatives) and D-alanine. D-amino acids are unusual and protect against ordinary proteases.
• In Staphylococcus aureus the cross-link is a pentaglycine bridge; in E. coli the link is direct (DAP to D-alanine).
• Gram-positive wall: thick (about 20–80 nm), many layers of peptidoglycan, with teichoic acids (wall teichoic acid and lipoteichoic acid). No outer membrane.
• Gram-negative wall: thin peptidoglycan (about 2–7 nm) in the periplasmic space, covered by an outer membrane made of phospholipid, lipopolysaccharide (LPS), porins and Braun's lipoprotein (which anchors the outer membrane to peptidoglycan).
• LPS has three parts: lipid A (the toxic endotoxin part), core polysaccharide, and O-antigen (O-specific side chain).
• Lysozyme (tears, saliva, egg white) breaks the β-1,4 bond between NAM and NAG. Penicillin blocks the transpeptidation (cross-linking) step.
• In hypertonic medium, lysozyme gives a protoplast from Gram-positive cells (wall fully removed) and a spheroplast from Gram-negative cells (outer membrane remains).
• Acid-fast wall (Mycobacterium): peptidoglycan linked to arabinogalactan and long mycolic acids, making it waxy; stained by Ziehl–Neelsen method.
• Mycoplasma have no wall at all; they are pleomorphic and resistant to penicillin. L-forms are wall-deficient variants of normal bacteria.
• Archaea have no peptidoglycan; some have pseudomurein (NAM replaced by N-acetyltalosaminuronic acid, β-1,3 bonds) and are lysozyme-resistant.

Important terms

• Peptidoglycan (murein) – mesh-like polymer of sugars and peptides in bacterial walls.
• Teichoic acid – polymer of glycerol or ribitol phosphate found in Gram-positive walls.
• Periplasmic space – gap between cell membrane and outer membrane in Gram-negatives; holds enzymes and binding proteins.
• Porins – protein channels in the outer membrane that allow small molecules to pass.
• Endotoxin – lipid A of LPS; causes fever and shock when released.

Key facts

5 important questions

Q1. What is lipid A?

It is the lipid part of lipopolysaccharide in the outer membrane of Gram-negative bacteria. It is the endotoxin; when released after cell death it causes fever, inflammation and septic shock.

Q2. Differentiate protoplast and spheroplast.

A protoplast is a Gram-positive cell whose wall is fully removed by lysozyme; a spheroplast is a Gram-negative cell that keeps part of its wall and outer membrane. Both are round and burst unless kept in hypertonic solution.

Q3. Describe the chemical structure of peptidoglycan.

• Backbone of NAG–NAM repeating units joined by β-1,4 bonds.
• Tetrapeptide on each NAM: L-Ala, D-Glu, L-Lys or DAP, D-Ala.
• Cross-linking directly (Gram-negative) or through pentaglycine bridges (S. aureus).
• Forms a bag-like sacculus around the cell.
• Lysozyme and penicillin act on this structure (draw a simple diagram).

Q4. Compare the cell walls of Gram-positive and Gram-negative bacteria with diagrams.

• Diagrams of both walls with labels.
• Comparison table (thickness, teichoic acid, outer membrane, LPS, porins, periplasm).
• Explain how these differences cause different Gram stain results.

Q5. Write a note on the acid-fast cell wall and on wall-less bacteria.

• Mycobacterium: mycolic acid, arabinogalactan, waxy, slow growth, resistant to drying and many disinfectants; ZN stain.
• Mycoplasma: no wall, sterols in membrane, smallest free-living cells, fried-egg colonies, not affected by penicillin.
• L-forms: arise when wall synthesis is blocked.

Exam tip

Always draw the two wall diagrams side by side and label LPS, porins, periplasm and teichoic acid. The NAG–NAM β-1,4 link is a favourite one-mark question.

Quick summary

An endospore is a tough, dormant body formed inside some Gram-positive bacteria when conditions become poor. It can survive boiling, drying, radiation and many chemicals for years, and can grow back into a normal cell (germination) when conditions improve. Endospores matter in sterilization, food canning and diseases like tetanus, botulism and anthrax.

Key points

• Endospores are made mainly by Bacillus (aerobic) and Clostridium (anaerobic); also Sporosarcina, Desulfotomaculum.
• One vegetative cell forms one endospore, and one spore gives one cell on germination, so sporulation is a survival method, not reproduction.
• Sporulation is triggered by nutrient starvation (lack of carbon or nitrogen); it takes about 6–8 hours in Bacillus subtilis.
• Position of the spore helps identification: central (Bacillus anthracis), subterminal (Clostridium botulinum), terminal (Clostridium tetani – "drumstick" or tennis-racket appearance).
• Structure from outside in: exosporium (thin outer layer, not in all species) → spore coat (protein layers) → cortex (special loosely cross-linked peptidoglycan) → core wall → core (DNA, ribosomes, enzymes, very little water).
• Very low water in the core (dehydration).
• Calcium dipicolinate (about 10% of spore dry weight) stabilizes DNA and proteins.
• Small acid-soluble spore proteins (SASPs) bind and protect DNA from heat, UV and chemicals.
• Thick, impermeable spore coat.
• Almost no metabolic activity.
• Reasons for resistance:
• Stages of sporulation (seven stages): axial filament of DNA → asymmetric septum forms the forespore → engulfment by mother cell → cortex formation → coat formation → maturation (resistance develops) → lysis of mother cell releases the spore.
• Germination has three steps: activation (e.g. mild heat), germination proper (spore swells, loses calcium dipicolinate and resistance, takes up water) and outgrowth (new vegetative cell emerges).
• Endospores are killed by autoclaving (121 °C, 15 psi, 15–20 min) or by tyndallization; boiling alone does not kill them.
• Geobacillus stearothermophilus spores are used as biological indicators to check autoclave efficiency.
• They are stained by the Schaeffer–Fulton method (malachite green with steaming; spores green, cells pink).

Important terms

• Sporulation (sporogenesis) – process of endospore formation.
• Forespore – the smaller compartment that becomes the spore after the asymmetric division.
• Cortex – thick peptidoglycan layer that helps keep the core dehydrated.
• Dipicolinic acid – chemical found only in endospores; with calcium it forms calcium dipicolinate.
• Germination – return of a spore to an active vegetative cell.

Key facts

5 important questions

Q1. Why is sporulation not a method of reproduction?

Because one bacterial cell forms only one endospore, and one endospore germinates into only one cell. The number of cells does not increase; the spore only helps the cell survive.

Q2. Name two spore-forming bacteria and the disease each causes.

Clostridium tetani – tetanus; Bacillus anthracis – anthrax. (Also C. botulinum – botulism, C. perfringens – gas gangrene.)

Q3. Describe the structure of a bacterial endospore with a labelled diagram.

• Diagram showing exosporium, coat, cortex, core wall and core.
• Role of each layer in resistance.
• Core contents: DNA with SASPs, ribosomes, calcium dipicolinate.

Q4. Explain the stages of sporulation.

• Starvation signal; DNA forms axial filament.
• Asymmetric septum; forespore and mother cell.
• Engulfment; forespore surrounded by two membranes.
• Cortex laid between the membranes; coat proteins added.
• Maturation and release by lysis of mother cell.
• Add a simple flow diagram.

Q5. Why are endospores highly resistant? What is their practical importance?

• Low water, calcium dipicolinate, SASPs, impermeable coat, dormancy.
• Importance: sterilization standards (autoclave, biological indicators), food canning (C. botulinum is the target), hospital infections, soil survival and dust-borne spread, possible bioterrorism (anthrax).

Exam tip

Learn the three spore positions with one example each and the five reasons for resistance. A neat labelled diagram of the spore layers is expected in every long answer.

Quick summary

Most bacteria are colourless and transparent, so we stain them to see their shape, size and arrangement. This topic covers dyes, smear preparation, simple staining, negative staining, and differential stains like the Gram stain and acid-fast (Ziehl–Neelsen) stain, plus special stains for capsules, spores and flagella.

Key points

• Basic dyes have a positively charged coloured ion (e.g. methylene blue, crystal violet, safranin, basic fuchsin). Bacterial surfaces are negatively charged, so basic dyes stain them well.
• Acidic dyes have a negatively charged coloured ion (e.g. nigrosin, eosin, India ink). They are repelled by the cell and colour the background — used in negative staining.
• Smear preparation: a thin film of culture on a clean slide → air dry → heat fix (pass through flame 2–3 times). Heat fixing kills cells and sticks them to the slide.
• Simple staining: one dye only (e.g. methylene blue 1 min). Shows shape and arrangement.
• Negative staining: background is coloured, cells stay clear. No heat fixing, so shape is not distorted. Used to see capsules.
• Gram stain (Hans Christian Gram, 1884) divides bacteria into Gram-positive (violet) and Gram-negative (pink/red).
• Acid-fast stain (Ziehl–Neelsen): for Mycobacterium whose walls are rich in mycolic acid (waxy). Acid-fast bacteria stay red; others take the blue counterstain.
• Endospore stain (Schaeffer–Fulton): malachite green with heat stains spores green; safranin stains vegetative cells red.
• Capsule stain: negative stain with India ink or nigrosin — clear halo around cells (e.g. Anthony's method uses crystal violet and copper sulphate).
• Flagella stain: flagella are too thin for light microscopy; a mordant coats them and makes them thick enough to see (e.g. Leifson's method).
• Metachromatic granules (volutin) are seen with Albert's stain in Corynebacterium diphtheriae.

Important terms

• Mordant – substance that fixes the dye more firmly (e.g. Gram's iodine).
• Decolourizer – removes dye from some cells (alcohol or acetone; acid-alcohol in ZN stain).
• Counterstain – second dye of contrasting colour (safranin in Gram stain; methylene blue in ZN stain).
• Differential stain – a stain that separates bacteria into groups (Gram, acid-fast).
• Chromophore – the coloured part of a dye molecule.

Key facts

Gram staining steps:

Ziehl–Neelsen steps: carbol fuchsin with heating (steaming) → decolourize with acid-alcohol (or 20% H₂SO₄) → counterstain with methylene blue. Acid-fast = red; non-acid-fast = blue.

5 important questions

Q1. Why is heat fixing done before staining?

It kills the bacteria, makes them stick to the slide so they are not washed away, and helps the dye penetrate. It is not done for negative staining.

Q2. What is negative staining? Give its advantage.

An acidic dye like nigrosin or India ink colours the background, leaving cells clear. Since no heat is used, the true size and shape are seen; capsules appear as clear zones.

Q3. Explain the principle and procedure of Gram staining.

• Steps: crystal violet → iodine → alcohol → safranin (see table).
• Crystal violet and iodine form a large CV–I complex inside the cell.
• Gram-positive: thick peptidoglycan dehydrates and shrinks with alcohol, pores close and the complex is trapped → violet.
• Gram-negative: alcohol dissolves the outer membrane lipid, the thin peptidoglycan cannot hold the complex → colourless, then pink with safranin.
• Importance: identification, choice of antibiotic.

Q4. Describe the Ziehl–Neelsen stain.

• Used for Mycobacterium tuberculosis and M. leprae.
• Mycolic acid makes the wall waxy and hard to stain; heat helps carbol fuchsin enter.
• Once stained, the cells resist decolourization by acid-alcohol (acid-fast).
• Methylene blue counterstains other cells and background.
• Result: red rods on blue background. Used in sputum examination for TB.

Q5. How are endospores stained?

• Schaeffer–Fulton method: smear flooded with malachite green, steamed for about 5 min.
• Wash with water (decolourizes vegetative cells).
• Counterstain with safranin.
• Spores green, vegetative cells pink/red. Example: Bacillus, Clostridium.

Exam tip

Learn the four Gram reagents in order with their roles (primary stain, mordant, decolourizer, counterstain). Write the result table in every staining answer.

Quick summary

Sterilization (निर्जंतुकीकरण) means killing or removing all microbes, including spores. Disinfection kills most harmful microbes but not always spores. This topic covers physical methods (heat, filtration, radiation) and chemical methods (disinfectants and antiseptics), how they act, and how they are checked.

Key points

• Moist heat kills by coagulating (denaturing) proteins; it is more effective than dry heat at the same temperature.
• Autoclave: steam under pressure. Standard cycle: 121 °C at 15 lb/in² (psi) for 15–20 minutes. Kills spores. Used for media, glassware, surgical cloth.
• Boiling (100 °C) kills vegetative cells but not all spores.
• Tyndallization: steaming at 100 °C for about 30 min on three successive days. Spores germinate between heatings and are then killed. Used for media that cannot stand autoclaving.
• Pasteurization: 63 °C for 30 min (holding method) or 72 °C for 15 s (HTST). It is not sterilization.
• Dry heat kills by oxidation. Hot air oven: 160 °C for 2 hours (or 170 °C for 1 hour; 180 °C for 30 min). Used for glassware, metal instruments, oils and powders.
• Incineration burns waste; flaming/red heat sterilizes inoculating loops.
• Filtration removes microbes from heat-sensitive liquids (serum, antibiotics, vitamins). Membrane filters of 0.22 µm pore size hold back bacteria. HEPA filters clean air in laminar air flow hoods.
• Radiation: UV light (about 260 nm is most germicidal) damages DNA by forming thymine dimers; poor penetration, used for surfaces and air. Ionizing radiation (gamma rays from cobalt-60) penetrates deeply; used for disposable syringes and plasticware.
• Chemical agents: alcohols (70% ethanol), phenol and its derivatives, halogens (chlorine, iodine), heavy metals (mercury, silver), aldehydes (formaldehyde, glutaraldehyde), gases (ethylene oxide), quaternary ammonium compounds (detergents), hydrogen peroxide.
• 70% alcohol works better than absolute alcohol because water is needed to denature proteins.

Important terms

• Sterilization – removal or killing of all forms of life, including spores.
• Disinfection – killing pathogens on non-living objects.
• Antiseptic – chemical safe on living tissue (e.g. iodine tincture, Dettol).
• Sanitization – lowering microbes to safe public-health levels.
• -cidal / -static – kills (bactericidal) / stops growth (bacteriostatic).
• Thermal death time (TDT) – shortest time to kill all cells at a given temperature.
• D-value (decimal reduction time) – time at a fixed temperature to kill 90% of the population.

Formulas

• Phenol coefficient = (highest dilution of test disinfectant that kills the test organism in 10 min but not 5 min) ÷ (the same dilution of phenol). A value above 1 means the disinfectant is stronger than phenol.
• D-value: after each D minutes, the number of survivors falls to one tenth (90% killed).

5 important questions

Q1. Why is moist heat better than dry heat?

Water helps proteins coagulate at lower temperatures, and steam carries more heat (latent heat) and penetrates better. So moist heat sterilizes at 121 °C in 15 min, while dry heat needs 160 °C for 2 hours.

Q2. What is tyndallization?

Intermittent sterilization: steaming at 100 °C for about 30 minutes on three successive days, with incubation in between so that spores germinate and are killed on the next heating.

Q3. Describe the principle, working and uses of the autoclave.

• Principle: water boils at a higher temperature under higher pressure; steam at 15 psi reaches 121 °C.
• Working: water heated in a closed chamber, air removed through the vent, steam pressure built to 15 psi, held for 15–20 min, then pressure released slowly.
• Kills all microbes including spores by denaturing proteins.
• Uses: culture media, glassware, surgical items, lab waste.
• Checked by biological indicator spores of Geobacillus stearothermophilus and chemical indicator tape.

Q4. Explain sterilization by radiation.

• Non-ionizing (UV): forms thymine dimers in DNA; used in lab hoods, operation theatres, water; low penetration.
• Ionizing (gamma, X-rays, electron beams): form free radicals that break DNA; high penetration.
• Uses: cold sterilization of syringes, catheters, gloves, some foods and spices.

Q5. Write about chemical disinfectants and their mode of action.

• Alcohols: denature proteins, dissolve lipids.
• Phenols: damage membranes, denature proteins.
• Halogens: oxidize cell components (chlorine for water, iodine for skin).
• Heavy metals: bind –SH groups of proteins.
• Aldehydes and ethylene oxide: alkylate proteins and nucleic acids; ethylene oxide gas sterilizes heat-sensitive items.
• Detergents (QACs): disrupt cell membranes.

Exam tip

Remember the three standard numbers: autoclave 121 °C/15 psi/15 min, hot air oven 160 °C/2 h, membrane filter 0.22 µm.

Quick summary

A microbiology laboratory handles living organisms, some of which can cause disease. Biosafety means the rules, equipment and lab design that protect the worker, other people and the environment from these organisms. This topic covers good laboratory practices, the four biosafety levels (BSL-1 to BSL-4), biosafety cabinets and the safe disposal of biomedical waste.

Key points

• Risk groups: microorganisms are grouped (WHO) from Risk Group 1 (unlikely to cause disease, e.g. Bacillus subtilis) to Risk Group 4 (cause severe, easily spread disease with no cure, e.g. Ebola virus).
• Routes of lab infection: inhalation of aerosols, ingestion (mouth pipetting, eating in lab), accidental injection (needles, broken glass), and contact with eyes or broken skin.
• Wear a lab coat, closed shoes and gloves; tie long hair.
• Never mouth-pipette; use a pipette bulb or pipette aid.
• No eating, drinking, applying cosmetics or storing food in the lab.
• Disinfect the work bench before and after work (e.g. 70% ethanol, 1% sodium hypochlorite).
• Flame loops to red-hot; cool before touching cultures.
• Label all cultures; report every spill and injury.
• Wash hands with soap before leaving.
• Good laboratory practices (GLP / basic rules):
• Biosafety levels describe increasing containment (see table).
• Biosafety cabinets (BSC) use HEPA filters (High Efficiency Particulate Air; remove at least 99.97% of particles of 0.3 µm). Class I protects worker and environment, Class II (most common) protects worker, environment and the sample, Class III is a fully sealed glove box for BSL-4 work.
• A laminar air flow (LAF) bench protects only the sample (sterile work, media pouring), not the worker; it is not a biosafety cabinet.
• Spill handling: cover with paper towels, pour disinfectant from the edges inward, wait about 20–30 minutes, then clean and autoclave the waste.
• Biomedical waste in India is handled under the Bio-Medical Waste Management Rules, 2016 with colour-coded bags: yellow (infectious anatomical/soiled waste, incineration), red (contaminated recyclable plastics like tubing and gloves, autoclave then recycle), white translucent puncture-proof container (sharps), blue (glassware). Check your university syllabus for the exact list.
• Used cultures and media are autoclaved before disposal.

Important terms

• Biosafety – protecting people and the environment from biological agents in the lab.
• Biosecurity – preventing theft or misuse of dangerous microorganisms.
• Aerosol – tiny liquid droplets in air that can carry microbes.
• HEPA filter – high-efficiency filter that traps microbes from air.
• Containment – safe methods and equipment used to keep infectious agents within the lab.

Key facts

5 important questions

Q1. Why is mouth pipetting prohibited in a microbiology lab?

Because the culture or chemical may be sucked into the mouth by accident and cause infection or poisoning. Pipette bulbs or automatic pipettes are used instead.

Q2. What is a HEPA filter?

A High Efficiency Particulate Air filter that removes at least 99.97% of particles 0.3 µm in size from air. It is used in biosafety cabinets and laminar air flow benches.

Q3. Describe the four biosafety levels with examples.

• Write the table: agents, practices, equipment and facility for each level.
• Mention that each level includes all practices of the level below.
• Give one Indian example of a high-containment lab, e.g. the BSL-4 facility at ICMR–National Institute of Virology, Pune.

Q4. List the general safety rules in a microbiology laboratory.

• Personal protection, no eating/drinking, no mouth pipetting.
• Bench disinfection, proper flaming, labelling.
• Handling spills and injuries; reporting.
• Autoclaving of waste and hand washing.

Q5. Differentiate between a biosafety cabinet and a laminar air flow bench.

• LAF: HEPA-filtered air blows towards the worker; protects only the sample.
• BSC Class II: inward air curtain at front and HEPA-filtered downflow; protects worker, sample and environment.
• LAF must not be used for pathogens.

Exam tip

Memorise one example organism for each BSL and the colour code of biomedical waste bags. Short notes on "HEPA filter" and "biosafety cabinet" are common.

Quick summary

Every microbial cell is built from a few kinds of large molecules: carbohydrates, proteins, lipids and nucleic acids. Water and minerals make up the rest. Knowing the basic chemistry of these molecules — their units, bonds and roles — helps in understanding cell structure, metabolism and genetics later. This is the "chemical basis of microbiology" unit.

Key points

• A bacterial cell is about 70% water. Of its dry weight, protein is the largest part (roughly half), followed by nucleic acids (RNA more than DNA), lipids and polysaccharides.
• Main elements: C, H, O, N, P, S (CHONPS), plus K, Mg, Ca, Fe and trace elements.
• Chemical bonds: covalent bonds hold atoms within molecules; weak bonds — hydrogen bonds, ionic bonds, hydrophobic and van der Waals interactions — shape proteins and hold the DNA double helix together.
• Water is a polar solvent, has a high specific heat and takes part in hydrolysis and condensation reactions.
• Monosaccharides: glucose, fructose (hexoses); ribose, deoxyribose (pentoses).
• Disaccharides: sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose + glucose), joined by glycosidic bonds.
• Polysaccharides: starch, glycogen (storage), cellulose (β-1,4 glucose), chitin (fungal walls), peptidoglycan (bacterial walls), dextran (capsules).
• Carbohydrates (CH₂O)n:
• Proteins: polymers of 20 standard amino acids joined by peptide bonds. Structure levels: primary (sequence), secondary (α-helix, β-sheet), tertiary (3-D folding), quaternary (several chains). Roles: enzymes, transport, flagellin, pili, toxins.
• Amino acids (except glycine) are optically active; proteins use L-amino acids, but bacterial walls also have D-alanine and D-glutamic acid.
• Lipids: fats (glycerol + 3 fatty acids, ester bonds), phospholipids (amphipathic; form the membrane bilayer), sterols (in eukaryotes), waxes such as mycolic acid in Mycobacterium, and poly-β-hydroxybutyrate (PHB) as a storage material in bacteria.
• Nucleic acids: polymers of nucleotides (phosphate + pentose sugar + nitrogen base) joined by phosphodiester bonds. DNA has A, G, C, T and deoxyribose; RNA has A, G, C, U and ribose.
• ATP (adenosine triphosphate) is a nucleotide that carries energy in its high-energy phosphate bonds.
• Denaturation by heat, pH or chemicals destroys protein shape and function — the basis of sterilization by heat and of many disinfectants.

Important terms

• Monomer / polymer – small unit / large chain made of many units.
• Glycosidic bond – link between two sugar units.
• Peptide bond – link between the –COOH of one amino acid and –NH₂ of the next.
• Phosphodiester bond – link between nucleotides in DNA and RNA.
• Amphipathic – having both water-loving and water-fearing parts (e.g. phospholipid).

Key facts

5 important questions

Q1. What is a peptide bond?

A covalent C–N bond formed between the carboxyl group of one amino acid and the amino group of the next, with the loss of one water molecule (condensation).

Q2. Name two storage polymers found in bacteria.

Glycogen (polysaccharide) and poly-β-hydroxybutyrate (lipid-like). Volutin (polyphosphate) is a third.

Q3. Describe the classification and microbial importance of carbohydrates.

• Mono-, di-, oligo- and polysaccharides with examples.
• Energy source (glucose), structural (peptidoglycan, chitin, cellulose), capsule (dextran), storage (glycogen).
• Sugars in culture media and in biochemical tests (fermentation of glucose, lactose).

Q4. Explain the levels of protein structure.

• Primary to quaternary, with the bonds that stabilize each (peptide, hydrogen, disulfide, ionic, hydrophobic).
• Example: haemoglobin for quaternary; enzymes for tertiary.
• Denaturation and its use in sterilization.

Q5. Give the structure and functions of lipids in microorganisms.

• Fats, phospholipids, sterols, waxes.
• Phospholipid bilayer of the cell membrane.
• Lipid A of LPS (endotoxin), mycolic acid of acid-fast walls.
• PHB as reserve food; archaeal ether-linked lipids.

Exam tip

Make a four-row table of unit, bond and example for each biomolecule; it answers many short questions. Remember: DNA has thymine and deoxyribose, RNA has uracil and ribose.

Quick summary

A culture medium is a nutrient preparation used to grow microbes in the lab. This topic covers the ingredients of media, their classification (by consistency, composition and use), and the methods used to get a pure culture — streak plate, pour plate and spread plate — and to preserve it.

Key points

• Basic needs of microbes: water, carbon source, nitrogen source, minerals, growth factors (vitamins), and right pH, temperature and oxygen.
• Common ingredients: peptone (nitrogen), beef extract and yeast extract (vitamins, minerals), NaCl (osmotic balance), sugars (carbon and energy), agar (solidifying agent), water.
• Agar comes from red algae (seaweeds like Gelidium). It melts at about 100 °C and sets at about 40–45 °C; most bacteria cannot digest it. Fanny Hesse suggested its use in Koch's lab. Usual concentration about 1.5–2%.
• By consistency: liquid (broth), semi-solid (about 0.5% agar, for motility), solid (about 1.5–2% agar).
• By composition: synthetic/defined (exact chemical composition known) and complex/non-synthetic (contains extracts, e.g. nutrient broth).
• Selective media allow some microbes and inhibit others (e.g. MacConkey agar with bile salts and crystal violet selects Gram-negative enteric bacteria).
• Differential media show differences between colonies (MacConkey: lactose fermenters pink, non-fermenters colourless).
• Enriched media have extra nutrients like blood or serum for fastidious organisms (blood agar, chocolate agar).
• Enrichment media (liquid) favour growth of one organism over others (e.g. selenite F broth for Salmonella).
• Other types: transport media, anaerobic media (e.g. Robertson's cooked meat medium, thioglycollate broth), assay media.
• Pure culture contains only one kind of microbe. Methods: streak plate, pour plate, spread plate, serial dilution, and micromanipulation (single cell).
• Preservation: periodic subculturing, refrigeration (4 °C), covering with mineral oil, freezing with glycerol, lyophilization (freeze-drying — best long-term).

Important terms

• Colony – visible mass of cells grown from one cell (or a few) on solid medium.
• Inoculation – putting microbes into a medium.
• Aseptic technique – working so that no unwanted microbes enter.
• Fastidious organism – one with complex nutrient needs.
• CFU (colony forming unit) – a viable cell or group that forms one colony.

Formulas

• Viable count (CFU/mL) = number of colonies ÷ (volume plated in mL × dilution).
• Example: 150 colonies from 0.1 mL of a 10⁻⁵ dilution → 150 ÷ (0.1 × 10⁻⁵) = 1.5 × 10⁸ CFU/mL.
• Countable plates usually have 30–300 colonies.

5 important questions

Q1. Why is agar preferred as a solidifying agent?

It is not digested by most bacteria, it stays solid at incubation temperatures (melts near 100 °C), it sets only at about 40–45 °C so heat-sensitive nutrients can be added, and it is transparent.

Q2. Differentiate selective and differential media.

Selective medium inhibits unwanted organisms and allows the desired one to grow (e.g. bile salts in MacConkey). Differential medium allows several organisms to grow but shows them in different ways (e.g. pink vs colourless colonies on MacConkey).

Q3. Describe the streak plate method.

• Sterilize the loop by flaming and cool it.
• Take a loopful of mixed culture and streak on one area of the agar plate.
• Flame the loop, rotate the plate, streak again from the end of the first lines; repeat for 3–4 sectors (quadrant streak).
• The cells are thinned out; in the last sector, single cells grow into separate colonies.
• Incubate, pick an isolated colony and subculture to get a pure culture.

Q4. Explain the pour plate and spread plate methods.

• Pour plate: sample serially diluted; 1 mL mixed with molten cooled agar (45 °C) in a Petri plate; colonies grow inside and on the surface. Used for counting.
• Spread plate: 0.1 mL diluted sample spread on the surface of solid agar with a sterile L-shaped glass spreader; only surface colonies.
• Both give isolated colonies and viable counts.
• Worked example: 150 colonies from 0.1 mL of 10⁻⁵ dilution = 1.5 × 10⁸ CFU/mL.

Q5. Classify culture media with examples.

• Consistency: liquid, semi-solid, solid.
• Composition: synthetic, complex.
• Purpose: basal/general (nutrient agar), enriched (blood agar), selective (MacConkey), differential (MacConkey, blood agar for haemolysis), enrichment (selenite F), transport, anaerobic (Robertson's cooked meat).

Exam tip

Draw the quadrant streak pattern. Always give one example medium for each type.

Quick summary

In microbiology, "growth" means an increase in the number of cells, not the size of one cell. Bacteria divide by binary fission, so their number doubles every generation. This topic covers the growth curve, generation time, ways to measure growth, and how temperature, pH, oxygen and other factors affect growth.

Key points

• Binary fission: the cell copies its DNA, grows longer, forms a septum (cross wall) in the middle and splits into two equal daughter cells.
• Exponential growth: 1 → 2 → 4 → 8 … ; after n generations, N = N₀ × 2ⁿ.
• Generation time (doubling time): time for the population to double. E. coli in rich medium at 37 °C: about 20 minutes. Mycobacterium tuberculosis: about 18–24 hours (much slower).
• Lag phase – no increase in number; cells adapt, make enzymes, grow in size.
• Log (exponential) phase – steady, fastest division; cells most uniform and most sensitive to antibiotics.
• Stationary phase – nutrients run out and wastes collect; new cells = dying cells; secondary metabolites (e.g. antibiotics) and endospores often formed.
• Death (decline) phase – cells die exponentially.
• Growth curve (batch culture) has four phases:
• Continuous culture: fresh medium added and used medium removed at the same rate, keeping cells in log phase. Devices: chemostat (growth controlled by a limiting nutrient) and turbidostat (controlled by turbidity).
• Synchronous culture: all cells divide at the same time (by filtration or temperature shift methods).
• Measuring growth: direct microscopic count (Petroff–Hausser counting chamber), viable plate count (CFU), turbidity (spectrophotometer, optical density), dry weight, and chemical measures (protein, DNA).
• Temperature groups: psychrophiles (optimum below about 15 °C), mesophiles (about 20–45 °C; most pathogens, optimum 37 °C), thermophiles (about 45–80 °C), hyperthermophiles (above 80 °C).
• Oxygen groups: obligate aerobes, obligate anaerobes, facultative anaerobes (e.g. E. coli), microaerophiles, aerotolerant anaerobes.
• pH groups: acidophiles, neutrophiles (most bacteria), alkaliphiles.
• Salt: halophiles need high salt (e.g. Halobacterium); halotolerant bacteria like Staphylococcus aureus survive it.

Important terms

• Generation time (g) – time per doubling.
• Growth rate (k) – number of generations per hour.
• Batch culture – closed system with fixed nutrients.
• Turbidity – cloudiness of a broth due to cells.
• Cardinal temperatures – minimum, optimum and maximum growth temperatures.

Formulas

• N = N₀ × 2ⁿ (N = final number, N₀ = initial number, n = number of generations)
• n = (log N − log N₀) / log 2 = (log N − log N₀) / 0.301
• Generation time g = t / n (t = time of growth)
• Growth rate k = n / t = 1 / g (generations per unit time)

5 important questions

Q1. Define generation time.

The time needed for a bacterial population (or one cell) to double in number. It is calculated as g = t / n.

Q2. A culture starts with 100 cells and grows for 3 generations. How many cells are there?

N = N₀ × 2ⁿ = 100 × 2³ = 100 × 8 = 800 cells.

Q3. A culture grows from 10³ cells to 10⁹ cells in 10 hours. Find n and g.

• log N − log N₀ = 9 − 3 = 6
• n = 6 / 0.301 = 19.93 ≈ 20 generations
• g = t / n = 10 h / 20 = 0.5 h = 30 minutes
• So the generation time is about 30 minutes.

Q4. Describe the bacterial growth curve with a diagram.

• Graph: log of cell number (y-axis) against time (x-axis).
• Lag phase: flat line; adaptation, enzyme synthesis.
• Log phase: straight rising line; constant doubling.
• Stationary phase: flat top; nutrients exhausted, toxic waste, growth = death.
• Death phase: falling line; exponential loss of viable cells.
• Importance: industrial harvesting, antibiotic action, vaccine production.

Q5. Explain the effect of temperature and oxygen on bacterial growth.

• Temperature controls enzyme activity; too high denatures proteins, too low makes membranes rigid.
• Groups: psychrophiles, mesophiles, thermophiles, hyperthermophiles, with one example each (e.g. Thermus aquaticus is a thermophile).
• Oxygen: aerobes need O₂; obligate anaerobes are killed by it (e.g. Clostridium) as they lack catalase/superoxide dismutase; facultative anaerobes grow both ways; microaerophiles need low O₂ (e.g. Campylobacter).
• Growth in thioglycollate broth shows these patterns (top, bottom, throughout).

Exam tip

Practise generation time numericals: always write the formula, then log values, then the answer with units. Draw the growth curve with all four phases labelled.

Quick summary

Classification (वर्गीकरण) arranges living things into groups based on similarities. This topic covers the main systems — Haeckel's three kingdoms, Whittaker's five kingdoms and Woese's three domains — the place of microbes in them, binomial nomenclature, and the basis of bacterial classification as in Bergey's Manual.

Key points

• Taxonomy has three parts: classification (grouping), nomenclature (naming) and identification.
• Taxonomic ranks: Domain → Kingdom → Phylum (Division) → Class → Order → Family → Genus → Species.
• Binomial nomenclature (Carl Linnaeus): every species has two names — genus (capital first letter) and species (small letter), printed in italics or underlined when hand-written. Example: Escherichia coli, short form E. coli.
• Ernst Haeckel (1866) proposed a third kingdom, Protista, for microorganisms, beside plants and animals.
• R. H. Whittaker (1969) proposed five kingdoms: Monera (prokaryotes — bacteria, cyanobacteria), Protista (unicellular eukaryotes — protozoa, some algae), Fungi, Plantae, Animalia. Based on cell type, body organization and mode of nutrition.
• Carl Woese (1977, formalised 1990) used 16S rRNA sequences and proposed three domains: Bacteria, Archaea and Eukarya.
• Archaea are prokaryotes but differ from bacteria: no peptidoglycan in walls, ether-linked membrane lipids, and some features of gene expression close to eukaryotes. Many live in extreme places (methanogens, extreme halophiles, thermoacidophiles).
• Viruses are not placed in any kingdom because they are not cells.
• Bergey's Manual is the standard reference for bacterial classification. Bergey's Manual of Determinative Bacteriology helps identification; Bergey's Manual of Systematic Bacteriology (2nd edition) arranges bacteria mainly by 16S rRNA phylogeny.
• Basis of bacterial classification: morphology (shape, Gram reaction, spores, flagella), cultural characters, biochemical tests (sugar fermentation, IMViC, catalase, oxidase), serology, G + C content of DNA, DNA–DNA hybridization, rRNA sequencing.
• Numerical taxonomy (Adansonian) gives equal weight to many characters and calculates similarity coefficients.
• A bacterial species is often defined by over 70% DNA–DNA reassociation, or over about 97% 16S rRNA similarity as a working guide.

Important terms

• Taxon – any group at any rank (e.g. a genus).
• Strain – a population descended from a single isolate within a species.
• Phylogeny – evolutionary history of organisms.
• Type strain – the reference strain that the species name is attached to.
• Phenetic classification – based on overall similarity of characters.

Key facts

Similarity coefficient (numerical taxonomy): S_J = a / (a + b + c), where a = characters positive in both, b and c = characters positive in only one of the two strains.

5 important questions

Q1. What is binomial nomenclature? Give an example.

A system of giving each species a two-part Latin name — genus and species — introduced by Linnaeus. Example: Bacillus subtilis.

Q2. Name Whittaker's five kingdoms.

Monera, Protista, Fungi, Plantae and Animalia.

Q3. Explain Woese's three-domain classification.

• Based on comparison of 16S (small subunit) rRNA sequences.
• Domains: Bacteria, Archaea, Eukarya.
• Showed that archaea are a separate line, not just odd bacteria.
• Write differences (table above).
• Importance: modern classification is phylogenetic.

Q4. What characters are used to classify bacteria?

• Morphological: shape, size, arrangement, Gram stain, capsule, spores, flagella.
• Cultural: colony type, growth in broth, pigment.
• Biochemical: sugar fermentation, enzymes (catalase, oxidase, urease), IMViC.
• Physiological: temperature, oxygen, pH needs.
• Serological: antigen–antibody reactions.
• Molecular: G + C content, DNA hybridization, 16S rRNA sequencing.

Q5. Compare Whittaker's and Woese's systems.

• Whittaker: five kingdoms, based on cell structure, body form, nutrition; all prokaryotes in Monera.
• Woese: three domains above kingdoms, based on rRNA; prokaryotes split into Bacteria and Archaea.
• Woese's system reflects evolution better.

Exam tip

Write scientific names correctly: genus capitalised, species small, in italics (underline in handwritten answers).

Quick summary

Rickettsiae, chlamydiae and mycoplasmas are small, unusual bacteria that were once thought to lie between bacteria and viruses. Rickettsiae and chlamydiae are obligate intracellular parasites, while mycoplasmas can grow on cell-free media but have no cell wall. They are true bacteria (prokaryotes with both DNA and RNA, 70S ribosomes and sensitivity to some antibiotics), and they cause important human, animal and plant diseases.

Key points

• Small Gram-negative rods or coccobacilli (about 0.3 × 1–2 µm); stain well with Giemsa or Gimenez stain.
• Obligate intracellular; grow in the cytoplasm (and sometimes nucleus) of host cells; cultured in yolk sac of embryonated eggs, cell cultures or animals.
• Spread by arthropod vectors: lice, fleas, ticks, mites.
• Diseases: epidemic typhus (Rickettsia prowazekii, body louse), endemic/murine typhus (R. typhi, rat flea), Rocky Mountain spotted fever (R. rickettsii, tick), scrub typhus (Orientia tsutsugamushi, mite larva – common in India).
• Weil–Felix test: patient serum agglutinates certain Proteus strains (OX-19, OX-2, OX-K) because of shared antigens.
• Treated with doxycycline (tetracyclines) or chloramphenicol.
• Rickettsiae
• Very small Gram-negative bacteria that cannot make enough of their own ATP ("energy parasites").
• Unique developmental cycle with two forms: elementary body (EB) – small, infectious, non-dividing; reticulate body (RB) – larger, non-infectious, divides inside a vacuole called an inclusion. Cycle takes about 48–72 hours.
• Their wall lacks a typical peptidoglycan layer (only traces detected).
• Diseases: trachoma (a leading infectious cause of blindness) and genital infections by Chlamydia trachomatis; pneumonia by Chlamydia pneumoniae; psittacosis by Chlamydia psittaci (from birds).
• Treated with azithromycin or doxycycline.
• Chlamydiae
• Smallest free-living organisms (about 0.2–0.3 µm); no cell wall, so they are pleomorphic and resistant to penicillin; pass through bacterial filters.
• Membrane contains sterols; most need cholesterol in the medium.
• Colonies look like "fried eggs" (dense centre growing into agar, lighter edge).
• Diseases: primary atypical ("walking") pneumonia (Mycoplasma pneumoniae), urogenital infections (Ureaplasma, M. genitalium); bovine pleuropneumonia (M. mycoides, the first discovered – hence "PPLO").
• Plant pathogens of this type are called phytoplasmas (e.g. little leaf of brinjal, sandal spike, grassy shoot of sugarcane).
• Common contaminants of cell cultures.
• Mycoplasmas

Important terms

• Obligate intracellular parasite – organism that can grow only inside living host cells.
• Elementary body – infectious, spore-like form of chlamydiae.
• Reticulate body – dividing intracellular form of chlamydiae.
• PPLO – pleuropneumonia-like organisms; old name for mycoplasmas.
• Pleomorphism – having many shapes.

Key facts

5 important questions

Q1. Why are mycoplasmas resistant to penicillin?

Penicillin acts by blocking cell wall (peptidoglycan) synthesis. Mycoplasmas have no cell wall, so penicillin has no target in them.

Q2. What is the Weil–Felix reaction?

An agglutination test for rickettsial infections. The patient's serum agglutinates non-motile Proteus strains OX-19, OX-2 or OX-K because they share antigens with rickettsiae.

Q3. Describe the developmental cycle of Chlamydia.

• EB attaches and enters the host cell by endocytosis.
• Inside a vacuole (inclusion) EB changes to RB.
• RB divides by binary fission.
• RBs reorganize into new EBs.
• Host cell bursts and EBs are released (draw the cycle).

Q4. Give the general characters and diseases of rickettsiae.

• Size, shape, staining, obligate intracellular growth, cultivation.
• Arthropod transmission.
• Table of diseases, agents and vectors.
• Diagnosis (Weil–Felix, serology, PCR) and treatment.

Q5. Compare rickettsiae, chlamydiae, mycoplasmas and viruses.

• Use the table above and add viruses: no cell structure, one type of nucleic acid, no ribosomes, not killed by antibiotics.
• Conclude that the first three are true bacteria.

Exam tip

For comparison questions always include viruses as a fourth column. Remember "fried egg colony = Mycoplasma" and "EB and RB = Chlamydia".

Quick summary

Fungi are eukaryotic, non-photosynthetic organisms that absorb food from their surroundings. They include moulds (filamentous) and yeasts (single-celled). Fungi are the main decomposers of plant matter, they give us bread, alcohol, antibiotics and enzymes, and some cause diseases of humans and crops. The branch that studies them is mycology.

Key points

• Fungi are eukaryotic, heterotrophic (saprophytic, parasitic or symbiotic) and absorptive in nutrition; they have no chlorophyll.
• Cell wall is mainly chitin with glucans; the membrane sterol is ergosterol (target of antifungal drugs like amphotericin B and azoles).
• Reserve food is glycogen and lipids (not starch).
• Moulds grow as hyphae (thread-like, 2–10 µm wide); a mass of hyphae is a mycelium. Hyphae are septate (with cross walls, e.g. Aspergillus, Penicillium) or aseptate/coenocytic (no cross walls, e.g. Rhizopus, Mucor).
• Yeasts are unicellular, oval cells (about 3–5 µm) that usually reproduce by budding (Saccharomyces cerevisiae) or fission (Schizosaccharomyces). Some form pseudohyphae (chains of elongated buds, e.g. Candida albicans).
• Dimorphic fungi grow as mould at 25 °C (environment) and yeast at 37 °C (in the body), e.g. Histoplasma, Blastomyces.
• Asexual spores: sporangiospores (inside a sporangium, Rhizopus), conidia (free at hyphal tips, Aspergillus, Penicillium), arthrospores, chlamydospores, blastospores (buds).
• Sexual spores decide the main groups: zygospores, ascospores (in an ascus), basidiospores (on a basidium).
• Main groups (traditional): Zygomycetes, Ascomycetes, Basidiomycetes and Deuteromycetes (fungi imperfecti, no known sexual stage).
• Fungi prefer acidic pH (about 5–6), moist conditions and 20–30 °C; Sabouraud dextrose agar (pH about 5.6) is the common medium.
• Useful: baker's and brewer's yeast, penicillin (Penicillium chrysogenum), citric acid (Aspergillus niger), cheese ripening (P. roqueforti, P. camemberti), edible mushrooms, mycorrhiza.
• Harmful: food spoilage, aflatoxin (Aspergillus flavus), plant diseases (rusts, smuts, blights), human mycoses (ringworm, candidiasis).

Important terms

• Hypha – single filament of a mould.
• Mycelium – network of hyphae forming the body of a mould.
• Budding – asexual reproduction where a small outgrowth forms and separates from a yeast cell.
• Conidium – asexual spore formed at the tip of a hypha, not enclosed in a sac.
• Dimorphism – ability to exist in two forms (mould and yeast).

Key facts

5 important questions

Q1. What is ergosterol? Why is it important?

Ergosterol is the main sterol of fungal cell membranes (humans have cholesterol instead). Antifungal drugs such as amphotericin B (binds it) and azoles (block its synthesis) act on it, so they harm fungi more than human cells.

Q2. Differentiate septate and aseptate hyphae.

Septate hyphae have cross walls (septa) dividing them into cells, e.g. Aspergillus. Aseptate (coenocytic) hyphae have no cross walls and many nuclei in a common cytoplasm, e.g. Rhizopus.

Q3. Give the general characteristics of fungi.

• Eukaryotic, heterotrophic, absorptive nutrition.
• Chitin wall, ergosterol, glycogen reserve.
• Thallus: yeast or mycelium; dimorphism.
• Asexual and sexual spores.
• Habitat and growth conditions; Sabouraud agar.

Q4. Describe the structure and reproduction of yeast.

• Oval cell with wall, nucleus, vacuole, mitochondria (draw diagram).
• Budding: nucleus divides, bud enlarges and separates; bud scar left.
• Sexual: two haploid cells fuse; diploid cell forms an ascus with 4 ascospores.
• Uses of Saccharomyces cerevisiae in bread, beer, wine and ethanol.

Q5. Write the economic importance of fungi.

• Industry: alcohol, antibiotics, organic acids, enzymes (amylase, cellulase).
• Food: mushrooms, cheese, fermented foods; single cell protein.
• Agriculture: mycorrhiza, biocontrol (Trichoderma).
• Harmful: spoilage, mycotoxins, plant and human diseases.

Exam tip

Draw a Rhizopus sporangium, an Aspergillus conidial head and a budding yeast cell — these three diagrams cover most fungal questions.

Quick summary

Algae and protozoa are eukaryotic microorganisms usually placed in the kingdom Protista (Protoctista). Algae are photosynthetic, mostly aquatic, and produce a large part of the earth's oxygen. Protozoa are animal-like, heterotrophic, usually motile single cells; most are free-living, but some cause serious diseases such as malaria and amoebiasis. The study of algae is phycology and of protozoa is protozoology.

Key points

• Eukaryotic, photoautotrophic, with chlorophyll a plus accessory pigments; have chloroplasts.
• Body (thallus) is not divided into root, stem and leaf; forms are unicellular (Chlamydomonas, Chlorella), colonial (Volvox), filamentous (Spirogyra) or large seaweeds (Sargassum).
• Cell wall mostly cellulose; diatoms have a silica wall (frustule).
• Reproduce vegetatively, asexually (zoospores) and sexually (isogamy, anisogamy, oogamy).
• General characters of algae:
• Main algal groups by pigment and stored food (see table).
• Importance of algae: primary producers in water; oxygen release; food and supplements (Chlorella); agar and carrageenan from red algae, alginates from brown algae; diatomaceous earth used in filters; biofuel research. Harm: toxic blooms, red tides (dinoflagellates), clogging of filters.
• Eukaryotic, unicellular, no cell wall (a flexible pellicle in some), heterotrophic (holozoic or saprozoic).
• Usually 10–200 µm; have contractile vacuoles (osmoregulation) and food vacuoles.
• Many form cysts (resistant, infective stage) and trophozoites (active feeding stage).
• Reproduce asexually by binary fission, multiple fission (schizogony) or budding; sexually by conjugation (ciliates) or gamete fusion (Plasmodium in mosquito).
• General characters of protozoa:
• Sarcodina – pseudopodia: Amoeba, Entamoeba histolytica (amoebic dysentery).
• Mastigophora – flagella: Euglena, Giardia lamblia (giardiasis), Trypanosoma (sleeping sickness), Leishmania donovani (kala-azar).
• Ciliophora – cilia: Paramecium, Balantidium coli.
• Sporozoa (Apicomplexa) – no locomotory organs in adults: Plasmodium (malaria), Toxoplasma.
• Classification of protozoa by locomotion (traditional):
• Protozoa feed on bacteria and help in sewage treatment (activated sludge); termite gut flagellates digest wood.

Important terms

• Thallus – simple plant-like body without true roots, stem and leaves.
• Frustule – glass-like silica wall of a diatom.
• Pellicle – firm outer covering of some protozoa.
• Trophozoite / cyst – active feeding form / dormant resistant form of a protozoan.
• Pseudopodium – temporary "false foot" used for movement and feeding.

Key facts

5 important questions

Q1. Why are cyanobacteria not called true algae?

They are prokaryotes: no nucleus, no chloroplasts, 70S ribosomes and a peptidoglycan wall. True algae are eukaryotes with chloroplasts.

Q2. Name the source of agar and its use in microbiology.

Agar comes from red algae such as Gelidium and Gracilaria. It is used to solidify culture media because most bacteria cannot digest it and it melts at about 85–100 °C but sets at about 32–40 °C.

Q3. Give the general characters and economic importance of algae.

• Characters: eukaryotic, photosynthetic, thallus forms, pigments, walls, reproduction.
• Table of groups.
• Uses: food, agar, alginate, carrageenan, diatomite, oxygen, biofuel.
• Harm: blooms and toxins.

Q4. Describe the classification of protozoa with examples.

• Four groups based on locomotion with organelle and examples.
• Mention disease-causing members of each.
• Add a simple sketch of Amoeba, Euglena, Paramecium.

Q5. Explain the general characters of protozoa.

• Size, shape, pellicle, organelles (nucleus, contractile vacuole, food vacuole).
• Nutrition types; habitat.
• Encystment and excystment.
• Asexual and sexual reproduction.
• Ecological and medical importance.

Exam tip

Learn one pathogen per protozoan group and the pigment + stored food of each algal group. "Agar from red algae" is a favourite one-mark question.

Quick summary

Viruses (विषाणू) are very small, non-cellular infectious particles that can multiply only inside living host cells. This topic covers their general properties, structure, symmetry, classification, the lytic and lysogenic cycles, and how viruses are grown in the lab.

Key points

• Viruses are obligate intracellular parasites: outside a host they are inert particles; inside they use the host's machinery.
• They contain only one type of nucleic acid — DNA or RNA, never both.
• Size: roughly 20–300 nm; most pass through bacterial filters and are seen only with an electron microscope.
• They have no ribosomes and no energy-producing system, so they do not grow or divide by binary fission.
• Virion: a complete infectious virus particle.
• Structure: nucleic acid core + protein coat called capsid, made of subunits called capsomeres. Nucleic acid + capsid = nucleocapsid. Some viruses have an outer lipid envelope with glycoprotein spikes (e.g. influenza, HIV).
• Symmetry of capsid: helical (e.g. tobacco mosaic virus), icosahedral (20 triangular faces, e.g. adenovirus, poliovirus), complex (e.g. T4 bacteriophage, poxvirus).
• Baltimore classification puts viruses in seven groups based on genome type and how mRNA is made (dsDNA, ssDNA, dsRNA, +ssRNA, −ssRNA, ssRNA with reverse transcriptase, dsDNA with reverse transcriptase).
• Classification is also based on host: animal, plant and bacterial viruses (bacteriophages).
• Lytic cycle: attachment → penetration → synthesis of viral parts → assembly → release by lysis of host cell. Example: T4 phage.
• Lysogenic cycle: viral DNA joins the host chromosome as a prophage and is copied with it; it may later switch to the lytic cycle (induction). Example: lambda (λ) phage.
• Cultivation of viruses: (1) in animals (e.g. mice), (2) in embryonated chicken eggs (influenza vaccine production), (3) in cell/tissue culture (most common). Bacteriophages are grown on bacterial lawns; they form clear zones called plaques.
• Viroids are small naked circular RNA molecules that infect plants (e.g. potato spindle tuber viroid). Prions are infectious proteins without nucleic acid (e.g. mad cow disease, Creutzfeldt–Jakob disease).
• Discovery: Ivanovsky (1892) and Beijerinck (1898) with tobacco mosaic disease; W. M. Stanley crystallized TMV (1935).

Important terms

• Capsid / capsomere – protein coat / its subunits.
• Envelope – lipid membrane taken from the host, with viral proteins.
• Prophage – phage DNA integrated in a bacterial chromosome.
• Plaque – clear area on a bacterial lawn where phages have lysed cells.
• Cytopathic effect (CPE) – visible damage to cultured cells caused by a virus.

Key facts

5 important questions

Q1. Why are viruses called obligate intracellular parasites?

Because they have no metabolic machinery or ribosomes of their own and can multiply only by using a living host cell.

Q2. What are viroids and prions?

Viroids are small, naked, circular RNA molecules without a protein coat that cause plant diseases. Prions are infectious protein particles without nucleic acid that cause brain diseases such as mad cow disease.

Q3. Describe the general structure of a virus with a diagram.

• Nucleic acid core (DNA or RNA).
• Capsid made of capsomeres; nucleocapsid.
• Envelope with spikes in some viruses.
• Symmetry types: helical, icosahedral, complex, each with example.
• Draw: icosahedral virus or T4 phage (head, collar, tail sheath, base plate, tail fibres).

Q4. Explain the lytic and lysogenic cycles.

• Lytic: adsorption, penetration (DNA injection), early proteins, replication, late proteins, assembly, lysis and release.
• Lysogenic: DNA integrates as prophage, replicates with host, host survives; induction (e.g. by UV) starts lytic cycle.
• Examples: T4 (lytic), lambda (temperate).
• Lysogenic conversion: e.g. diphtheria toxin gene carried by a phage.

Q5. How are viruses cultivated?

• Animal inoculation (mice, guinea pigs).
• Embryonated egg: sites — chorioallantoic membrane, amniotic cavity, allantoic cavity, yolk sac.
• Cell culture: primary, diploid and continuous cell lines (e.g. HeLa); detect by CPE.
• Phages: plaque assay on a bacterial lawn.

Exam tip

Always state that viruses have only DNA or RNA. A labelled T4 phage diagram is a common 5-mark question.

Quick summary

Only a small fraction of microorganisms cause disease; most are harmless or useful. Microbes recycle nutrients, make soil fertile, give us food, medicines and industrial chemicals, clean wastewater and live in our gut. Others spoil food, cause diseases of humans, animals and plants, and damage materials. This topic gives an overview of both sides, with Indian examples, as asked in first-year exams.

Key points

• Decomposition of dead matter and recycling of C, N, S and P (biogeochemical cycles).
• Nitrogen fixation by Rhizobium, Azotobacter, cyanobacteria; biofertilizers.
• Biopesticides: Bacillus thuringiensis (Bt toxin), Trichoderma against soil fungi.
• Sewage treatment and bioremediation (oil-eating Pseudomonas).
• Biogas (methane) from cow dung by methanogenic archaea.
• Beneficial — environment and agriculture
• Curd and cheese (Lactobacillus, Lactococcus, Streptococcus thermophilus), bread and alcohol (Saccharomyces cerevisiae), idli–dosa batter fermentation (lactic acid bacteria and yeasts), vinegar (Acetobacter).
• Antibiotics: penicillin (Penicillium), streptomycin (Streptomyces).
• Organic acids (citric acid by Aspergillus niger), enzymes (amylase, protease), vitamins (B₁₂), amino acids (glutamic acid by Corynebacterium glutamicum).
• Vaccines and recombinant products: insulin made in E. coli or yeast.
• Beneficial — food and industry
• Beneficial — health: normal flora of gut makes vitamin K and B vitamins and blocks pathogens; probiotics.
• Harmful — human diseases: bacteria (tuberculosis, typhoid, cholera), viruses (polio, measles, COVID-19), fungi (ringworm, candidiasis), protozoa (malaria, amoebiasis).
• Harmful — animal diseases: anthrax, foot-and-mouth disease, bird flu.
• Harmful — plant diseases: citrus canker (Xanthomonas), bacterial blight of rice, late blight of potato (Phytophthora infestans), rust of wheat (Puccinia), tobacco mosaic (TMV).
• Harmful — food: spoilage (souring of milk, mould on bread) and food poisoning (Staphylococcus aureus toxin, Clostridium botulinum toxin, Salmonella).
• Harmful — materials: biodeterioration of wood, paper, leather, paints; corrosion of iron pipes by sulphate-reducing bacteria (Desulfovibrio).
• Harm and benefit often depend on place: E. coli is normal in the gut but causes urinary tract infection in the bladder.

Important terms

• Pathogen – microbe that causes disease.
• Normal flora – microbes that normally live on or in a healthy body without harm.
• Biofertilizer – living microbial preparation that adds nutrients to soil.
• Biodeterioration – damage to useful materials by microbes.
• Probiotic – live microbes that give a health benefit when taken in enough amount.

Key facts

5 important questions

Q1. Give two examples of microorganisms used as biopesticides.

Bacillus thuringiensis (its crystal protein kills caterpillars) and the fungus Trichoderma (controls soil-borne plant pathogens). Nuclear polyhedrosis viruses are another example.

Q2. What is biodeterioration? Give an example.

The damage of useful materials by microbial activity. Example: fungi rotting wood and paper, or sulphate-reducing bacteria corroding iron pipes.

Q3. Describe the beneficial activities of microorganisms.

• Agriculture: nitrogen fixation, decomposition, biopesticides.
• Food: fermented foods and beverages.
• Industry: antibiotics, acids, enzymes, vitamins, alcohol.
• Environment: sewage treatment, biogas, bioremediation.
• Health: normal flora, vaccines, probiotics, recombinant drugs.

Q4. Explain the harmful effects of microorganisms.

• Diseases of humans, animals and plants with one example each.
• Food spoilage and food poisoning.
• Biodeterioration and corrosion.
• Toxins and allergies (fungal spores).

Q5. "Microorganisms are friends as well as foes." Justify.

• Write a balanced answer using the table.
• Give at least four useful and four harmful examples.
• Conclude that useful roles far outnumber harmful ones.

Exam tip

In "friend and foe" answers, a two-column table with Indian examples (idli, curd, biogas, Bt crops, rice blight) scores well.