Classification, Monera and Viruses

Biodiversity is the heaviest unit of the Botany section — 9 of the 40 questions — and this first chapter of it carries about 2. The questions are built from a short list: who proposed which system and on what basis, the order of the taxonomic ranks, the rules of binomial nomenclature, the parts of a bacterial cell, Gram staining, the modes of bacterial nutrition, the phases of the growth curve, the special features of cyanobacteria (heterocysts, phycocyanin), and the structure and chemistry of viruses (TMV and the T4 phage).

2.1 Classification systems, taxonomic hierarchy and binomial nomenclature

Taxonomy is the science of identifying, naming and classifying organisms (the word was coined by A. P. de Candolle, 1813); systematics adds their evolutionary relationships. A taxon is a group of any rank — a species, a family, a kingdom.

From two kingdoms to three domains

System	Proposed by	Groups	Basis / what it fixed
Two kingdoms	Carolus Linnaeus (1758)	Plantae, Animalia	presence of a cell wall and photosynthesis vs locomotion and ingestion
Three kingdoms	Ernst Haeckel (1866)	+ Protista	unicellular forms separated
Four kingdoms	H. F. Copeland (1956)	Monera, Protista, Plantae, Animalia	prokaryotes separated
Five kingdoms	R. H. Whittaker (1969)	Monera, Protista, Fungi, Plantae, Animalia	cell structure, body organisation, mode of nutrition, reproduction, phylogeny
Six kingdoms	Carl Woese (1977)	Monera split into Archaebacteria and Eubacteria	rRNA differences
Three domains	Carl Woese, O. Kandler and M. Wheelis (1990)	Archaea, Bacteria, Eukarya (above kingdoms)	sequences of 16S/18S ribosomal RNA

Why two kingdoms failed. It put prokaryotes (bacteria, blue-green algae) and eukaryotes in one kingdom; it lumped heterotrophic fungi, which have chitin walls, with green plants; it lumped unicellular and multicellular forms together; and it had no place for Euglena (green, yet wall-less and able to feed like an animal), slime moulds (an animal-like feeding stage and a plant-like spore stage), lichens and viruses.

Feature	Monera	Protista	Fungi	Plantae	Animalia
Cell type	prokaryotic	eukaryotic	eukaryotic	eukaryotic	eukaryotic
Cell wall	non-cellulosic (peptidoglycan)	present in some	present, chitin	present, cellulose	absent
Nuclear membrane	absent	present	present	present	present
Body organisation	cellular	cellular (unicellular)	multicellular or loose tissue	tissue and organ	tissue, organ and organ system
Nutrition	autotrophic (photo- or chemosynthetic) and heterotrophic	photosynthetic and heterotrophic	heterotrophic (absorptive — saprophytic, parasitic)	autotrophic (photosynthetic)	heterotrophic (holozoic)
Examples	bacteria, cyanobacteria, Mycoplasma	diatoms, dinoflagellates, Euglena, slime moulds, Amoeba	yeast, Mucor, Agaricus, Penicillium	algae, mosses, ferns, pines, flowering plants	Hydra, earthworm, frog, humans

Feature	Archaea	Bacteria	Eukarya
Nuclear envelope	absent	absent	present
Peptidoglycan in wall	absent (some have pseudomurein)	present	absent
Membrane lipids	ether-linked, branched chains	ester-linked, unbranched	ester-linked, unbranched
Histones	present in some	absent	present
First amino acid of a protein	methionine	formyl-methionine	methionine
Growth inhibited by streptomycin, chloramphenicol	no	yes	no
Ribosomes	70S	70S	80S (70S in organelles)

Archaea live in extreme habitats: methanogens (Methanobacterium, in marshes and the rumen of cattle — they make the methane of biogas/gobar-gas plants), halophiles (Halobacterium, in salt lakes) and thermoacidophiles (Sulfolobus, Thermoplasma, in hot sulphur springs).

Taxonomic hierarchy

Linnaeus arranged the ranks in a fixed order, the taxonomic hierarchy. Moving up from species to kingdom, each rank contains more organisms that share fewer characters. Species is the basic unit: a group of similar individuals that interbreed in nature to give fertile offspring and are reproductively isolated from other such groups (Ernst Mayr's biological species concept, 1942; the word "species" was first used by John Ray).

Rank	Ending in plants	Mango	Wheat	Human
Kingdom	—	Plantae	Plantae	Animalia
Division (plants) / Phylum (animals)	-phyta	Angiospermae	Angiospermae	Chordata
Class	-opsida, -phyceae (algae), -mycetes (fungi)	Dicotyledonae	Monocotyledonae	Mammalia
Order	-ales	Sapindales	Poales	Primata
Family	-aceae	Anacardiaceae	Poaceae	Hominidae
Genus	—	Mangifera	Triticum	Homo
Species	—	indica	aestivum	sapiens

Binomial nomenclature

Every species has a two-word scientific name: the generic name followed by the specific epithet. Gaspard Bauhin used two-word names (1623), but Linnaeus made the system universal in Species Plantarum (1753) for plants and Systema Naturae (10th edition, 1758) for animals. Plant names are governed by the ICN (International Code of Nomenclature for algae, fungi and plants, formerly ICBN), animal names by the ICZN, bacteria by the ICNP and viruses by the ICTV.

1. Names are in Latin or are Latinised, whatever their origin.
2. The generic name starts with a capital letter; the specific epithet is all small letters — Rhododendron arboreum (lali gurans), Azadirachta indica (neem).
3. Printed names are in italics; handwritten names are underlined, each word separately.
4. The author's name may follow in roman type, often abbreviated: Mangifera indica L. (L. = Linnaeus).
5. Priority: the earliest validly published name is the correct one (for plants, counted from 1 May 1753).
6. Tautonyms (genus and species the same word) are not allowed in plants, though zoology allows them — Naja naja (cobra), Rattus rattus.
7. A subspecies or variety gives a trinomial — Homo sapiens sapiens.

2.2 Bacteria and cyanobacteria

Shapes and the bacterial cell

Bacteria were first seen by Antonie van Leeuwenhoek (1676), who called them "animalcules". Most are 0.5–5 μm long; Mycoplasma (0.1–0.3 μm, no cell wall, unaffected by penicillin) is the smallest free-living cell.

Shape	Name	Arrangements and examples
Spherical	coccus	diplococcus (pairs: Streptococcus pneumoniae), streptococcus (chains), staphylococcus (grape-like bunches: Staphylococcus aureus), tetrad (4), sarcina (cube of 8)
Rod	bacillus	single (Bacillus, E. coli), streptobacillus (chain)
Comma	vibrio	Vibrio cholerae
Rigid spiral	spirillum	Spirillum
Flexible spiral	spirochaete	Treponema pallidum (syphilis)

Structure	Facts the paper asks
Glycocalyx	a loose slime layer or a firm capsule; the capsule protects from phagocytes and makes Streptococcus pneumoniae virulent (Griffith's S strain)
Cell wall	rigid peptidoglycan (murein) — chains of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) cross-linked by short peptides; penicillin blocks the cross-linking
Plasma membrane	phospholipid bilayer without sterols; carries the respiratory enzymes (there are no mitochondria)
Mesosome	infolding of the membrane; helps in wall formation, DNA replication and distribution to daughter cells, respiration and secretion
Nucleoid	one circular double-stranded DNA molecule, without a nuclear membrane or true histones
Plasmid	small circular extra-chromosomal DNA that replicates on its own; carries genes such as antibiotic resistance (R plasmid) or fertility (F plasmid); used as a cloning vector
Ribosomes	70S (50S + 30S)
Inclusions	glycogen, poly-β-hydroxybutyrate, volutin (polyphosphate) granules; gas vacuoles in aquatic forms
Flagellum	a single hollow fibril of the protein flagellin, without the 9 + 2 pattern; it rotates
Pili and fimbriae	sex pili (pilin) transfer DNA in conjugation; fimbriae attach cells to surfaces
Endospore	thick-walled resting body of Bacillus and Clostridium, rich in calcium dipicolinate; survives boiling

Flagellar arrangements: atrichous (none), monotrichous (one at one end — Vibrio cholerae), lophotrichous (a tuft at one end — Pseudomonas fluorescens), amphitrichous (at both ends — Spirillum), peritrichous (all over the surface — E. coli, Salmonella typhi).

Gram staining

Hans Christian Gram (1884): stain with crystal violet → fix with iodine (mordant) → wash with alcohol (decolouriser) → counterstain with safranin. Gram-positive cells stay violet; Gram-negative cells lose the violet and take up the pink-red safranin.

1Rod-shaped cell (bacillus)2Polar flagella — the whip-like organs of locomotion

Feature	Gram-positive	Gram-negative
Peptidoglycan	thick (20–80 nm), many layers	thin (2–7 nm), one or two layers
Teichoic acids	present	absent
Outer membrane with lipopolysaccharide (endotoxin)	absent	present
Periplasmic space	absent or very small	present
Sensitivity to penicillin	high	lower
Examples	Bacillus, Clostridium, Staphylococcus, Streptococcus, Lactobacillus	E. coli, Salmonella, Vibrio, Pseudomonas, Rhizobium, Azotobacter, cyanobacteria

Nutrition

Mode	Source of energy and carbon	Examples
Photoautotrophic (anoxygenic)	light; H₂S or organic acids as H donor, so no O₂ is released; bacteriochlorophyll	green sulphur (Chlorobium), purple sulphur (Chromatium), purple non-sulphur (Rhodospirillum) bacteria
Photoautotrophic (oxygenic)	light; H₂O is split, O₂ released; chlorophyll a	cyanobacteria
Chemoautotrophic	energy from oxidising inorganic substances; CO₂ fixed	Nitrosomonas (NH₃ → NO₂⁻), Nitrobacter (NO₂⁻ → NO₃⁻), Thiobacillus and Beggiatoa (H₂S → S → SO₄²⁻), iron bacteria (Fe²⁺ → Fe³⁺)
Saprophytic	dead organic matter	Bacillus, Clostridium, Pseudomonas — decomposers
Parasitic	living host, causing disease	Mycobacterium tuberculosis, Vibrio cholerae, Xanthomonas
Symbiotic	living host, mutual benefit	Rhizobium in legume root nodules; E. coli in the colon (makes vitamin K)

Anoxygenic photosynthesis by a green sulphur bacterium: 6CO₂ + 12H₂S → C₆H₁₂O₆ + 6H₂O + 12S. Sulphur, not oxygen, is the by-product.

Reproduction and growth

Bacteria reproduce asexually by binary fission — the DNA replicates, the cell elongates and a septum divides it into two identical cells. It is amitotic: no spindle, no chromosome condensation. Under ideal conditions E. coli divides every 20 minutes. Endospores help survival, not multiplication (one cell → one spore → one cell). There is no true sexual reproduction, but genes are recombined by transformation (uptake of free DNA; Griffith, 1928), conjugation (transfer through a sex pilus; Lederberg and Tatum, 1946) and transduction (transfer by a bacteriophage; Zinder and Lederberg, 1952).

Bacterial growth means an increase in the number of cells. In the log phase the number doubles every generation, so after n generations

where N_0 is the starting number, t the time and g the generation (doubling) time.

Phase	What happens
Lag	cells adapt to the new medium, grow in size and make enzymes; numbers hardly change
Log (exponential)	division at the maximum constant rate; generation time is shortest; cells are most uniform and most sensitive to antibiotics
Stationary	nutrients run out and wastes build up; division rate = death rate; secondary metabolites (antibiotics) and endospores are formed
Decline (death)	deaths exceed divisions; numbers fall exponentially

Cyanobacteria (blue-green algae)

Cyanobacteria are photosynthetic prokaryotes of the kingdom Monera, about 3.5 billion years old (stromatolites); their oxygen built up Earth's atmosphere, and a cyanobacterium engulfed by an early eukaryote became the chloroplast.

• Cell: prokaryotic, with a Gram-negative-type peptidoglycan wall, usually inside a mucilage sheath; no nucleus, no chloroplast, no mitochondria.
• Pigments: chlorophyll a (no chlorophyll b), carotenoids, and the phycobilins — c-phycocyanin (blue) and c-phycoerythrin (red) — held in phycobilisomes on free thylakoids. The blend gives the blue-green colour.
• Photosynthesis is oxygenic, with both photosystems, like green plants.
• Reserve food: cyanophycean starch (glycogen-like) and cyanophycin (protein) granules.
• No flagella at any stage; some filaments glide or oscillate (Oscillatoria).
• Gas vacuoles (pseudovacuoles) keep planktonic forms afloat.
• Heterocysts: large, pale, thick-walled cells of Nostoc and Anabaena that fix nitrogen. They lack photosystem II, so they make no O₂ that would destroy nitrogenase.
• Reproduction: only vegetative and asexual — fission, fragmentation into hormogonia, and thick-walled resting akinetes. No sexual reproduction and no motile cells.
• Forms: unicellular (Chroococcus), colonial (Gloeocapsa, Microcystis), filamentous (Oscillatoria, Nostoc, Anabaena, Spirulina).
• Importance: nitrogen fixation in rice fields (Anabaena, Nostoc, Aulosira); Anabaena azollae inside the water fern Azolla (biofertiliser); Nostoc as the partner of many lichens and in the coralloid roots of Cycas; Spirulina as protein-rich single-cell protein; Microcystis forms toxic water blooms.

2.3 Viruses

Discovery and characteristics

Year	Scientist	Discovery
1892	Dmitri Ivanowsky	sap of mosaic-diseased tobacco stays infectious after passing a bacteria-proof filter
1898	M. W. Beijerinck	called the agent "contagium vivum fluidum" (contagious living fluid); named it virus
1898	Loeffler and Frosch	foot-and-mouth disease virus — the first animal virus
1915–17	F. W. Twort, F. d'Hérelle	bacteriophages — viruses of bacteria
1935	W. M. Stanley	crystallised TMV (Nobel Prize 1946)
1936	Bawden and Pirie	TMV is a nucleoprotein (protein + RNA)
1971	T. O. Diener	viroids — potato spindle tuber disease
1982	Stanley Prusiner	prions — infectious proteins (Nobel Prize 1997)

A virus is an acellular, ultramicroscopic (about 20–300 nm), obligate intracellular parasite made of nucleic acid in a protein coat. It has no metabolism of its own and multiplies only inside a living host cell, using the host's ribosomes, enzymes and energy.

Like non-living things	Like living things
no cell, cytoplasm or cell membrane	possess genetic material (DNA or RNA)
no metabolism, respiration or growth outside a host	multiply inside a host and pass on their characters
can be crystallised and stored like chemicals	mutate and evolve
inert outside the host	infect specific hosts and cause disease

Structure and chemical composition

• The complete infectious particle is the virion.
• Capsid — the protein coat, built of identical subunits called capsomeres; it protects the nucleic acid and decides the host by attaching to it. Capsid + nucleic acid = nucleocapsid.
• Nucleic acid — DNA or RNA, never both; single- or double-stranded, linear or circular. It is the infective part.
• Envelope — present in some viruses (HIV, influenza, herpes, SARS-CoV-2): a lipid bilayer taken from the host membrane, studded with viral glycoprotein spikes (peplomers). Viruses without it are naked (TMV, adenovirus, poliovirus, most phages).
• Enzymes in some: reverse transcriptase in retroviruses (HIV); lysozyme in the tail of T4; neuraminidase in influenza.

Chemically, a virus is mostly protein: TMV is about 95 % protein and 5 % RNA.

Feature	Tobacco mosaic virus (TMV)	T4 bacteriophage
Host	tobacco (plant)	Escherichia coli (bacterium)
Shape and symmetry	rigid rod, about 300 × 18 nm; helical	tadpole-like; complex — polyhedral head + helical tail
Nucleic acid	single-stranded RNA, about 6400 nucleotides, coiled helically inside the capsid	double-stranded DNA, linear, packed in the head
Capsid	2130 identical capsomeres, each binding 3 nucleotides	head, collar, contractile tail sheath round a hollow core, base plate with six tail fibres
Envelope	none	none

Types of viruses

Basis	Types and examples
Host	plant viruses — mostly ssRNA (TMV, potato virus X; cauliflower mosaic virus is dsDNA); animal viruses — DNA or RNA (polio, influenza, HIV, herpes, pox); bacteriophages — mostly dsDNA (T2, T4, λ; φX174 has ssDNA); mycophages (fungi) and cyanophages
Nucleic acid	dsDNA (T4, pox, herpes, adenovirus, hepatitis B); ssDNA (φX174, parvovirus); dsRNA (reovirus, rotavirus, wound tumour virus of plants); ssRNA (TMV, polio, influenza, HIV, SARS-CoV-2)
Symmetry	helical (TMV, influenza nucleocapsid); polyhedral / icosahedral — 20 triangular faces (adenovirus, poliovirus, herpes); complex (T4 phage, poxvirus)
Envelope	enveloped (HIV, influenza, herpes) or naked (TMV, adenovirus, polio)
Life cycle (phages)	virulent — lytic cycle only, the host bursts (T4); temperate — can also integrate into the host DNA as a prophage and be copied silently (lysogenic cycle; λ phage)

Sub-viral agents. Viroids are tiny, naked, circular single-stranded RNA molecules (about 250–400 nucleotides) with no protein coat that infect plants (potato spindle tuber, citrus exocortis). Prions are infectious proteins with no nucleic acid that cause scrapie in sheep, mad cow disease (BSE) and Creutzfeldt–Jakob disease in humans.

Formula and fact sheet

Item	Fact
Two kingdoms	Linnaeus, Systema Naturae (1758): Plantae, Animalia
Protista / Monera	Haeckel 1866 / Copeland 1956
Five kingdoms	Whittaker 1969 — Monera, Protista, Fungi, Plantae, Animalia; main criteria cell structure, body organisation, nutrition
Three domains	Woese, Kandler and Wheelis 1990 — Archaea, Bacteria, Eukarya; based on rRNA sequences
Hierarchy	kingdom → division (phylum) → class → order (-ales) → family (-aceae) → genus → species
Binomial nomenclature	Linnaeus, Species Plantarum 1753; genus capital, epithet small, italics or separate underlines; no tautonyms in plants
Codes	ICN (plants, algae, fungi), ICZN (animals), ICNP (bacteria), ICTV (viruses)
Archaea	ether-linked lipids, no peptidoglycan; methanogens, halophiles, thermoacidophiles
Bacterial cell	peptidoglycan wall, 70S ribosomes, nucleoid, plasmid, mesosome, flagellin flagella
Smallest cell	Mycoplasma (PPLO), 0.1–0.3 μm, no wall, penicillin-resistant
Flagella	monotrichous Vibrio; lophotrichous Pseudomonas; peritrichous E. coli, Salmonella
Gram stain	crystal violet → iodine → alcohol → safranin; + violet (thick wall), − pink (thin wall + outer membrane)
Chemoautotrophs	Nitrosomonas NH₃ → NO₂⁻; Nitrobacter NO₂⁻ → NO₃⁻; Thiobacillus, Beggiatoa sulphur; iron bacteria
Anoxygenic photosynthesis	green and purple sulphur bacteria, H₂S donor, bacteriochlorophyll, no O₂
Growth	N = N_0 \times 2^n, n = t/g; E. coli g ≈ 20 min; lag → log → stationary → decline
Recombination	transformation (Griffith 1928), conjugation (Lederberg and Tatum 1946), transduction (Zinder and Lederberg 1952)
Cyanobacteria	chlorophyll a + phycocyanin + phycoerythrin; cyanophycean starch; heterocysts (N₂ fixation, no PS II); akinetes; hormogonia; no flagella, no sex
N-fixing cyanobacteria	Nostoc, Anabaena, Aulosira; Anabaena azollae in Azolla
Virus history	Ivanowsky 1892; Beijerinck 1898 (contagium vivum fluidum); Stanley 1935 (crystallised TMV); Diener 1971 (viroids); Prusiner 1982 (prions)
TMV	rod 300 × 18 nm, helical, ssRNA ≈ 6400 nt, 2130 capsomeres, 95 % protein
T4 phage	complex symmetry, dsDNA, head + collar + contractile tail + base plate + 6 tail fibres; host E. coli
Viroid / prion	naked circular ssRNA / protein without nucleic acid

Chapter summary

• Linnaeus (1758) gave two kingdoms; Whittaker (1969) gave five — Monera, Protista, Fungi, Plantae, Animalia — chiefly on cell structure, body organisation and mode of nutrition; Woese (1990) placed three domains — Archaea, Bacteria, Eukarya — above them, on rRNA sequences.
• The hierarchy runs kingdom, division, class, order (-ales), family (-aceae), genus, species; species is the basic unit.
• Binomial names (Linnaeus, 1753): Latin, genus capitalised, epithet small, italicised or underlined separately; tautonyms are not allowed in plants.
• Bacteria have a peptidoglycan wall, 70S ribosomes, a nucleoid and often plasmids; they are cocci, bacilli, vibrios or spirilla.
• Gram-positive walls have thick peptidoglycan and stay violet; Gram-negative walls are thin with an outer lipopolysaccharide membrane and stain pink.
• Bacteria are photoautotrophic (anoxygenic, except cyanobacteria), chemoautotrophic (Nitrosomonas, Nitrobacter), saprophytic, parasitic or symbiotic.
• Binary fission doubles the population each generation (N = N_0 \times 2^n); the growth curve has lag, log, stationary and decline phases.
• Cyanobacteria are oxygenic prokaryotes with chlorophyll a and phycobilins, cyanophycean starch, heterocysts for N₂ fixation, and no flagella or sexual reproduction.
• Viruses are acellular obligate parasites with DNA or RNA (never both) in a protein capsid; TMV is a helical ssRNA rod, T4 a complex dsDNA phage.
• Viroids are naked RNA; prions are infectious proteins.

Practice questions

Set A — Recall (20 questions)

1. The five-kingdom system of classification was proposed byaCarl WoesebR. H. WhittakercErnst HaeckeldCarolus Linnaeus
2. The three-domain system is based chiefly on the comparison ofacell-wall chemistrybmode of nutritioncbody organisationdribosomal RNA sequences
3. Which taxonomic category lies between order and genus?afamilybclasscdivisiondspecies
4. Which of the following is correctly written in print?aMangifera Indicabmangifera indicacMangifera indicadMangifera Indica
5. The botanical code of nomenclature does NOT permitatautonymsbLatinised namescauthor citationsditalicised names
6. Peptidoglycan is absent from the cell walls ofaGram-positive bacteriabarchaeacGram-negative bacteriadcyanobacteria
7. Methanogens such as Methanobacterium belong toaEubacteriabCyanobacteriacProtistadArchaea
8. Comma-shaped bacteria are calledacoccibbacillicvibriosdspirilla
9. Bacteria that bear flagella all over the cell surface are described asamonotrichousbperitrichousclophotrichousdamphitrichous
10. The ribosomes of bacteria are of the typea70Sb80Sc60Sd90S
11. Plasmids areaprotein granules in the cytoplasmbinfoldings of the cell membranecsmall circular DNA molecules outside the nucleoiddstorage granules of polyphosphate
12. In Gram staining, the counterstain isacrystal violetbiodinecalcoholdsafranin
13. Nitrosomonas obtains its energy by oxidisingaammonia to nitritebnitrite to nitratechydrogen sulphide to sulphurdferrous to ferric ions
14. The phase of the bacterial growth curve in which cells divide at a constant, maximum rate is thealag phasebstationary phasecdecline phasedlog phase
15. The thick-walled, nitrogen-fixing cells of Nostoc and Anabaena are calledaakinetesbheterocystschormogoniadendospores
16. The blue pigment characteristic of cyanobacteria isachlorophyll bbfucoxanthincc-phycocyanindbacteriochlorophyll
17. The term "contagium vivum fluidum" for the agent of tobacco mosaic was used byaD. IvanowskybW. M. StanleycF. d'HérelledM. W. Beijerinck
18. The genetic material of a virus isaeither DNA or RNAbboth DNA and RNA togethercalways DNAdalways RNA
19. The protein coat of a virus is called theaenvelopebnucleoidccapsiddpeplomer
20. Tobacco mosaic virus hasadouble-stranded DNA and polyhedral symmetrybsingle-stranded RNA and helical symmetrycdouble-stranded RNA and complex symmetrydsingle-stranded DNA and helical symmetry

Answers and explanations — Set A

1. (b) — Whittaker (1969) added Fungi as a kingdom beside Monera, Protista, Plantae and Animalia. Woese gave the three domains; Linnaeus two kingdoms; Haeckel added Protista.

2. (d) — Woese compared 16S/18S rRNA sequences and found archaea as different from bacteria as from eukaryotes.

3. (a) — The order is kingdom, division, class, order, family, genus, species.

4. (c) — Genus with a capital, specific epithet in small letters, both in italics when printed.

5. (a) — Tautonyms (genus and species the same word) are forbidden by the ICN but allowed in zoology (Naja naja).

6. (b) — Archaeal walls lack peptidoglycan (some have pseudomurein). Cyanobacteria have a Gram-negative-type peptidoglycan wall.

7. (d) — Methanogens are archaea with ether-linked membrane lipids; they produce methane in marshes, the rumen and biogas plants.

8. (c) — Vibrios are comma-shaped, e.g. Vibrio cholerae. Spirilla are rigid spirals.

9. (b) — Peritrichous (E. coli, Salmonella); monotrichous is one flagellum at one end, lophotrichous a tuft at one end.

10. (a) — Prokaryotic ribosomes are 70S (50S + 30S); 80S ribosomes are in the eukaryotic cytoplasm.

11. (c) — Plasmids are extra-chromosomal, self-replicating circular DNA. Option (b) is the mesosome; option (d) volutin.

12. (d) — Safranin stains the decolourised Gram-negative cells pink. Crystal violet is the primary stain, iodine the mordant, alcohol the decolouriser.

13. (a) — Nitrosomonas oxidises NH₃ (NH₄⁺) to NO₂⁻; Nitrobacter then oxidises NO₂⁻ to NO₃⁻.

14. (d) — In the log (exponential) phase the generation time is shortest and constant. In the lag phase cells adapt; in the stationary phase division equals death.

15. (b) — Heterocysts lack photosystem II and have thick walls, so nitrogenase is protected from O₂. Akinetes are resting spores; hormogonia are fragments for propagation.

16. (c) — c-Phycocyanin is the blue phycobilin. Cyanobacteria lack chlorophyll b; fucoxanthin is the pigment of brown algae.

17. (d) — Beijerinck (1898) called it a contagious living fluid. Ivanowsky (1892) first showed it passes bacteria-proof filters; Stanley crystallised TMV in 1935.

18. (a) — A virus has a genome of DNA or of RNA, not both. Many are DNA viruses (T4, pox) and many RNA viruses (TMV, HIV).

19. (c) — The capsid is made of capsomeres. The envelope is the extra lipid layer of some viruses; peplomers are its spikes.

20. (b) — TMV is a rigid rod of 2130 capsomeres wound helically round single-stranded RNA.

Set B — Understanding (12 questions)

1. Euglena was a problem for the two-kingdom system mainly because itais prokaryoticbhas a cell wall of chitincreproduces sexuallydhas chlorophyll yet lacks a cell wall and can feed heterotrophically
2. Whittaker placed fungi in a kingdom of their own chiefly because theyaare prokaryoticbare absorptive heterotrophs with chitin wallsclack a nucleusdare all unicellular
3. Archaea resemble eukaryotes more than they resemble bacteria in that archaeaabegin protein synthesis with methionine, not formyl-methioninebhave peptidoglycan wallschave 80S ribosomesdhave a nuclear membrane
4. Gram-negative bacteria lose the crystal violet during decolourisation because their wall hasaa thick peptidoglycan layer with teichoic acidsbno peptidoglycan at allca thin peptidoglycan layer beneath a lipid-rich outer membranedchitin instead of peptidoglycan
5. Mycoplasma is not affected by penicillin because itahas a very thick cell wallbhas no cell wallclives only inside host nucleidhas 80S ribosomes
6. The endospore of Bacillus is not regarded as a means of reproduction becauseait forms only in Gram-negative bacteriabit can never germinatecit forms by the fusion of two cellsdone cell forms one spore, which gives back one cell
7. Cyanobacteria differ from green and purple sulphur bacteria in that cyanobacteriaalack chlorophyllbuse H₂S as the hydrogen donorcsplit water and release oxygendhave a nuclear membrane
8. Heterocysts can fix nitrogen inside an oxygen-producing filament because theyahave thick walls and lack photosystem II, so no O₂ is made insidebcontain chlorophyll bcare dead cells filled with airdcontain haemoglobin like root nodules
9. Viruses are regarded as living because theyacan be crystallisedblack enzymes of metabolismcare acellulardmultiply and mutate inside a host cell
10. Penicillin and other antibacterial antibiotics are useless against viral infections because virusesahave no cell wall, ribosomes or metabolism of their ownbare too small to absorb the drugcalways have a lipid envelopedcontain both DNA and RNA
11. A newly found virus contains uracil but no thymine and has a lipid envelope. It is most likelyaT4 bacteriophagebadenoviruscinfluenza virusdcauliflower mosaic virus
12. Viroids differ from viruses in that viroidsacontain DNA and proteinbare small circular RNA molecules without a protein coatcare infectious proteins without nucleic aciddinfect only bacteria

Answers and explanations — Set B

1. (d) — Euglena photosynthesises like a plant but has no wall and can absorb food like an animal, so it fits neither kingdom. It is eukaryotic and has no chitin.

2. (b) — Fungi lack chlorophyll, absorb food from outside, and have chitin walls — nutrition was a key criterion for Whittaker. They are eukaryotic, and most are multicellular.

3. (a) — Archaea, like eukaryotes, start proteins with methionine and have histones; bacteria use formyl-methionine. Archaea still have 70S ribosomes and no nucleus.

4. (c) — Alcohol dissolves the outer lipid membrane and the thin peptidoglycan cannot hold the dye–iodine complex. Option (a) describes Gram-positive walls, which keep the stain.

5. (b) — Penicillin blocks the cross-linking of peptidoglycan in a growing wall; Mycoplasma has no wall to attack.

6. (d) — Reproduction must increase the number of individuals; an endospore is only a survival stage. It germinates readily under good conditions.

7. (c) — Cyanobacteria have both photosystems and split H₂O, releasing O₂ (oxygenic). Sulphur bacteria use H₂S and release sulphur instead (anoxygenic).

8. (a) — Nitrogenase is destroyed by O₂. Heterocysts lack PS II (no water splitting) and have thick walls that slow O₂ entry. Leghaemoglobin protects nitrogenase in legume nodules, not in heterocysts.

9. (d) — Reproduction with inheritance and mutation are properties of life. Crystallisation and lack of metabolism are non-living features.

10. (a) — Antibacterial drugs attack walls, 70S ribosomes or bacterial enzymes; a virus uses the host's machinery, so there is no target. Many viruses are naked, so (c) is false.

11. (c) — Uracil without thymine means RNA; influenza is an enveloped ssRNA virus. T4, adenovirus and cauliflower mosaic virus are all naked DNA viruses.

12. (b) — Viroids (Diener, 1971) are naked circular ssRNA. Option (c) describes prions.

Set C — Application (8 questions)

1. A bacterium divides every 20 minutes. Starting with 100 cells in the log phase, how many cells are present after 2 hours?a600b1200c6400d12 800
2. In the log phase, a culture grows from 1000 cells to 1 024 000 cells in 5 hours. The generation time isa30 minutesb20 minutesc50 minutesd60 minutes
3. A student hand-writes the scientific name of lali gurans, Nepal's national flower. The correct form isaRhododendron Arboreum, underlined as one unitbrhododendron arboreum, not underlinedcRHODODENDRON ARBOREUM, underlineddRhododendron arboreum, each word underlined separately
4. A rod-shaped bacterium from a typhoid patient's blood stains pink in Gram's method and bears flagella all over its surface. It is aaGram-positive peritrichous bacillusbGram-negative peritrichous bacilluscGram-negative monotrichous coccusdGram-positive lophotrichous vibrio
5. An organism is prokaryotic, has chlorophyll a, releases O₂ in light and has a peptidoglycan wall. In Whittaker's system it belongs toaMonerabProtistacPlantaedFungi
6. Particles from a diseased potato pass bacteria-proof filters, are destroyed by ribonuclease but not by protease, and show no protein coat under the electron microscope. They are most likelyabacteriophagesbprionscviroidsdmycoplasmas
7. A bacterium grows in the dark in a medium containing only mineral salts, NH₄⁺ and CO₂, and the medium becomes rich in nitrite. Its mode of nutrition isaphotoautotrophicbsaprophyticcparasiticdchemoautotrophic
8. The RNA of TMV has about 6400 nucleotides and its capsid has 2130 identical capsomeres. About how many nucleotides does each capsomere cover?a1b3c6d30

Answers and explanations — Set C

1. (c) — n = 120 min ÷ 20 min = 6 generations; N = 100 × 2⁶ = 100 × 64 = 6400. Option (a) adds instead of doubling; (d) counts seven generations.

2. (a) — 1 024 000 ÷ 1000 = 1024 = 2¹⁰, so 10 generations in 300 minutes: g = 300 ÷ 10 = 30 minutes.

3. (d) — Handwritten binomials are underlined, each word separately, with the genus capitalised and the epithet in small letters.

4. (b) — Pink after Gram's stain means Gram-negative; rod-shaped is a bacillus; flagella all over is peritrichous — Salmonella typhi.

5. (a) — Prokaryotic with a peptidoglycan wall means Monera; chlorophyll a with O₂ release marks a cyanobacterium. Algae with chloroplasts would be eukaryotes.

6. (c) — Destroyed by RNase (so RNA), unharmed by protease and without a coat: a viroid, as in potato spindle tuber disease. Prions are protein and would be destroyed by protease.

7. (d) — Energy comes from oxidising NH₄⁺ to NO₂⁻ without light, and carbon from CO₂: a chemoautotroph such as Nitrosomonas.

8. (b) — 6400 ÷ 2130 ≈ 3. Each TMV coat-protein subunit binds three nucleotides of the RNA helix.