Botany Paper I
Microbiology & Plant Pathology
Delve into the world of microorganisms and their profound impact on plant life, agriculture, and beyond. Understand their structure, reproduction, applications, and the intricate dynamics of plant diseases.
Viruses: Acellular, obligate intracellular parasites with DNA/RNA in a protein capsid. Replicate using host machinery.
Viroids: Small, circular, single-stranded RNA molecules lacking a protein coat; infect plants.
Bacteria: Prokaryotic, diverse shapes, peptidoglycan cell wall (most), reproduce by binary fission. Genetic exchange via conjugation, transformation, transduction.
Mycoplasma: Smallest bacteria, lack cell walls, pleomorphic. Cause diseases like Little Leaf of Brinjal.
Structure: Eukaryotic, heterotrophic, chitin cell walls. Body (thallus) typically of hyphae forming a mycelium. Diverse reproductive structures (sporangia, conidiophores).
Reproduction: Asexual (spores like conidia, zoospores) and sexual (e.g., oospores, ascospores, basidiospores).
Key Concepts & Applications
- Agriculture: Biofertilizers (Rhizobium, Azotobacter, Mycorrhizae), biopesticides (Bacillus thuringiensis, Trichoderma), decomposition & nutrient cycling.
- Industry: Fermentation (antibiotics, enzymes, vitamins, organic acids, alcoholic beverages, dairy products), single-cell protein.
- Medicine: Production of vaccines, antibiotics, monoclonal antibodies, probiotics, diagnostics.
- Pollution Control: Bioremediation of soil & water (e.g., oil spills, pesticides, heavy metals), wastewater treatment.
Prions: Infectious proteinaceous particles devoid of nucleic acid. Composed of an abnormally folded isoform (PrPSc) of a normal cellular protein (PrPC).
Prion Hypothesis: PrPSc induces conformational change in PrPC, converting it to PrPSc, leading to aggregation and neurodegenerative diseases (e.g., Scrapie, BSE, CJD). This is a template-directed misfolding process.
Viral: Tobacco Mosaic (TMV), Cucumber Mosaic (CMV), Rice Tungro, Citrus Tristeza.
Bacterial: Citrus Canker (Xanthomonas axonopodis pv. citri), Fire Blight of apple/pear (Erwinia amylovora), Bacterial Blight of Rice (Xanthomonas oryzae pv. oryzae).
Mycoplasmal (Phytoplasmal): Little Leaf of Brinjal, Sandal Spike, Grassy Shoot of Sugarcane.
Fungal: Rusts (Puccinia), Smuts (Ustilago), Powdery Mildews (Erysiphe), Downy Mildews (Peronospora), Late Blight of Potato (Phytophthora infestans), Wilt diseases (Fusarium).
Nematodal: Root-knot (Meloidogyne spp.), Cyst nematodes (Heterodera, Globodera), Lesion nematodes (Pratylenchus). Cause galls, lesions, stunting.
Infection: Direct penetration (fungi, nematodes), through natural openings (stomata, lenticels, hydathodes), through wounds (mechanical, insect-made).
Dissemination: Wind (spores), water (zoospores, bacteria), insects (vectors for viruses, some fungi/bacteria), infected seed/planting material, soil, farm equipment, human activity.
Infection: Pathogen recognition of host, attachment, penetration. Secretion of enzymes (cellulases, pectinases, cutinases) and toxins. Effectors manipulate host cell processes.
Disease Resistance/Defence:
1. Pre-existing/Passive: Physical barriers (cuticle, bark), chemical compounds (phenols, tannins).
2. Induced/Active:
Non-host resistance: Broad-spectrum, effective against most potential pathogens.
PAMP-Triggered Immunity (PTI): Recognition of Pathogen-Associated Molecular Patterns (PAMPs) by host Pattern Recognition Receptors (PRRs).
Effector-Triggered Immunity (ETI): Recognition of pathogen effectors by host Resistance (R) genes. Often leads to Hypersensitive Response (HR) - localized cell death.
Systemic Acquired Resistance (SAR): Broad-spectrum, long-lasting immunity in uninfected parts following localized infection. Salicylic acid (SA) is a key signal.
Induced Systemic Resistance (ISR): Triggered by beneficial microbes, mediated by jasmonic acid (JA) and ethylene (ET).
Focuses on how pathogens interact with and derive nutrients from host plants.
- Enzyme Production: Pathogens secrete enzymes like cellulases, pectinases, lignases to degrade host cell walls and tissues for penetration and nutrient release.
- Toxin Production: Host-specific toxins (e.g., Victorin by Cochliobolus victoriae) and non-host-specific toxins (e.g., Tabtoxin by Pseudomonas syringae) disrupt host metabolism or structure.
- Growth Regulators: Pathogens can alter host hormone balance, leading to symptoms like galls, stunting, or "green islands".
- Nutrient Acquisition: Formation of haustoria (fungi, oomycetes) for direct nutrient uptake from living host cells. Creation of metabolic sinks to divert host nutrients.
- Suppression of Host Defenses: Pathogen effectors can interfere with host recognition, signaling pathways, or defense compound production.
Cultural: Crop rotation, sanitation, proper irrigation/fertilization, resistant varieties, certified disease-free seed.
Chemical: Fungicides, bactericides, nematicides. Proper application and management to avoid resistance.
Biological: Use of antagonistic microorganisms (e.g., Trichoderma, Bacillus subtilis).
Physical: Heat treatment, soil solarization.
Genetic Engineering: Developing transgenic plants with enhanced resistance.
Integrated Pest Management (IPM): Combines multiple strategies for sustainable disease control.
Secondary metabolites produced by fungi, toxic to humans and animals when contaminated food/feed is ingested.
- Aflatoxins: Produced by Aspergillus flavus/parasiticus. Carcinogenic. Found in maize, peanuts, cottonseed.
- Ochratoxins: Produced by Aspergillus and Penicillium. Nephrotoxic. Found in cereals, coffee, wine.
- Fumonisins: Produced by Fusarium verticillioides. Carcinogenic, affect horses/pigs. Found in maize.
- Trichothecenes (e.g., Deoxynivalenol/DON): Produced by Fusarium. Cause vomiting, feed refusal. Found in wheat, barley.
- Zearalenone: Produced by Fusarium. Estrogenic effects. Found in maize, other cereals.
Modelling & Disease Forecasting: Uses weather data, crop phenology, and pathogen biology to predict disease outbreaks. Helps in timely application of control measures (e.g., BLITECAST for potato late blight).
Plant Quarantine: Legal enforcement of measures to prevent introduction or spread of plant pests (including pathogens and weeds) into new areas.
Aims: Protect agriculture, forestry, and ecosystems.
Methods: Inspection at ports of entry, import permits, phytosanitary certificates, post-entry quarantine, treatment of infested material, restrictions on movement of plants/plant products. International (IPPC) and national regulations.
Cryptogams: The Hidden Reproduction
Explore non-seed bearing plants: Algae, Fungi (in this context, as traditionally studied with cryptogams), Lichens, Bryophytes, and Pteridophytes. Focus on their structure, reproduction from an evolutionary viewpoint, distribution, and importance.
Structure: Simple, thalloid, aquatic (mostly) autotrophs. Unicellular to complex multicellular forms (e.g., Chlamydomonas, Volvox, Ulva, Sargassum). Varied pigments (chlorophylls, carotenoids, phycobilins).
Reproduction: Vegetative (fragmentation), asexual (zoospores, aplanospores), sexual (isogamy, anisogamy, oogamy). Alternation of generations in many.
Evolutionary Viewpoint: From simple prokaryotic cyanobacteria-like ancestors to complex forms showing differentiation. Ancestors of land plants.
Distribution in India: Abundant in marine, freshwater, and terrestrial habitats across India.
Importance: Primary producers, food (Spirulina, Chlorella, Porphyra), fodder, agar, alginates, carrageenan, biofuels, biofertilizers (BGA).
Structure: Eukaryotic, achlorophyllous, heterotrophic. Thallus typically mycelial (hyphae). Cell wall of chitin. Storage product: glycogen.
Reproduction: Vegetative (fragmentation, budding, fission), asexual (spores like sporangiospores, conidia), sexual (plasmogamy, karyogamy, meiosis leading to oospores, zygospores, ascospores, basidiospores). Complex life cycles.
Evolutionary Viewpoint: Evolved from flagellated protistan ancestors. Show progression in thallus organization and reproductive complexity (e.g., Phycomycetes to Ascomycetes/Basidiomycetes).
Distribution in India: Ubiquitous, diverse across various ecosystems.
Importance: Decomposers, symbiotic (mycorrhizae, lichens), pathogens, food (mushrooms), industrial (antibiotics, enzymes), research tools.
Structure: Dual organisms - symbiotic association of a fungus (mycobiont, mostly Ascomycetes) and an alga or cyanobacterium (phycobiont). Thallus forms: crustose, foliose, fruticose. Internal structure shows distinct layers.
Reproduction: Primarily by fragmentation, soredia, isidia (containing both partners). Mycobiont can reproduce sexually (apothecia, perithecia).
Evolutionary Viewpoint: Highly successful symbiotic strategy allowing colonization of harsh environments.
Distribution in India: Widely distributed, especially in unpolluted hilly areas, Himalayas.
Importance: Pioneer colonizers, bioindicators of air pollution, food for animals (reindeer moss), dyes (litmus), perfumes, traditional medicines.
Structure: "Amphibians of plant kingdom". Small, non-vascular, require moist, shady places. Dominant gametophyte generation; sporophyte dependent on gametophyte. Thalloid (liverworts, hornworts) or foliose (mosses with stem-like, leaf-like structures, rhizoids).
Reproduction: Vegetative (fragmentation, gemmae). Sexual via antheridia and archegonia. Distinct alternation of heteromorphic generations.
Evolutionary Viewpoint: Transition from aquatic algae to terrestrial life. Show adaptations like cuticle, stomata (in sporophyte), protected embryos.
Distribution in India: Common in Himalayas, Western Ghats, moist plains.
Importance: Soil formation, prevent soil erosion, peat (Sphagnum) as fuel and horticultural substrate, indicator species.
Structure: First true vascular land plants ("vascular cryptogams"). Dominant sporophyte generation, differentiated into true root, stem, and leaves (microphylls or megaphylls/fronds). Vascular tissues (xylem, phloem).
Reproduction: Asexual by spores (homosporous or heterosporous) produced in sporangia (often in sori or strobili). Gametophyte (prothallus) is small, independent (usually). Water essential for fertilization.
Evolutionary Viewpoint: Show key advancements for terrestrial life: vascular system, dominant sporophyte. Heterospory is a precursor to seed habit.
Distribution in India: Abundant in moist, shady places, especially in Eastern Himalayas and Western Ghats.
Importance: Ornamental plants, soil binders, some medicinal, biofertilizers (Azolla), food (fern fiddleheads), indicators of mineral deposits.
Phanerogams: The Seed Bearers
Discover Gymnosperms (naked seeds) and Angiosperms (flowering plants). Covers evolution, classification, structure, reproduction, anatomy, and embryology.
Gymnosperms: Ancient Seed Plants
Concept of Progymnosperms (e.g., Archaeopteris) as transitional fossils linking pteridophytes to gymnosperms. Gymnosperms are characterized by naked ovules/seeds borne on sporophylls, often forming cones. Xylem lacks vessels (except Gnetales), phloem lacks companion cells (has albuminous cells).
Classification & Distribution: Primarily classified into Cycadales, Ginkgoales, Coniferales, and Gnetales. Distributed globally, often dominant in temperate and alpine regions.
Cycadales (e.g., Cycas, Zamia): Palm-like, dioecious, unbranched stems (mostly), large pinnately compound leaves. Large male and female cones (megasporophylls may be loose in Cycas). Motile sperm. Coralloid roots with N2-fixing cyanobacteria.
Ginkgoales (Ginkgo biloba): "Living fossil", dioecious deciduous tree. Fan-shaped leaves with dichotomous venation. Male strobili, ovules in pairs on peduncles. Motile sperm.
Coniferales (e.g., Pinus, Cedrus, Abies): Largest group. Mostly evergreen trees/shrubs with woody cones. Needle or scale-like leaves. Non-motile sperm. Resin canals common. Economically vital for timber, paper, resin.
Gnetales (Gnetum, Ephedra, Welwitschia): Unique features, some angiosperm-like (vessels in xylem, aspects of fertilization).
Gnetum: Trees/climbers, broad leaves.
Ephedra: Shrubby, scale-leaves, source of ephedrine.
Welwitschia mirabilis: Peculiar desert plant with two massive leaves.
Fossil Gymnosperms:
Cycadofilicales (Seed Ferns, e.g., Lyginopteris): Fern-like foliage, but bore seeds. Paleozoic.
Bennettitales (Cycadeoids, e.g., Williamsonia, Cycadeoidea): Cycad-like habit, but with flower-like reproductive structures. Mesozoic.
Cordaitales (e.g., Cordaites): Tall trees with strap-shaped leaves. Paleozoic. Ancestral to conifers.
Geological Time Scale & Plant Evolution
Paleozoic Era
Early land plants (Rhynia-type). Diversification of Pteridophytes. Progymnosperms. Appearance of first seed plants (Cycadofilicales, Cordaitales).
Mesozoic Era ("Age of Gymnosperms")
Dominance of Gymnosperms (Cycads, Conifers, Ginkgoes). Bennettitales flourish. First Angiosperms appear (Cretaceous period).
Cenozoic Era ("Age of Angiosperms")
Rapid diversification and dominance of Angiosperms. Modern conifers and other gymnosperms persist.
Type of Fossils & Study Techniques:
Types: Impressions (imprints), Compressions (carbonized remains), Petrifactions (mineralized, internal structure preserved), Casts/Molds (shape preserved).
Techniques: Thin sectioning (for petrifactions), Peel technique (cellulose acetate peels for compressions/petrifactions), Maceration (isolating cuticles), SEM/TEM for ultrastructure, X-ray analysis.
Angiosperms: The Flowering Plants
Systematics: Study of diversity and evolutionary relationships of plants.
Taxonomic Hierarchy: Kingdom, Division (Phylum), Class, Order, Family, Genus, Species. (e.g., Plantae, Magnoliophyta, Magnoliopsida, Rosales, Rosaceae, Rosa, Rosa indica).
International Code of Nomenclature for algae, fungi, and plants (ICN): Governs scientific naming. Key principles: Priority, Typification (holotype, isotype, etc.), Valid publication, Latin diagnosis (historical), One correct name.
Numerical Taxonomy (Phenetics): Uses overall similarity based on many characters, often computer-aided. Adansonian principles.
Chemotaxonomy: Uses chemical constituents (secondary metabolites like alkaloids, flavonoids, terpenoids; proteins, DNA sequences) for classification.
Evidence from:
Anatomy: Wood structure, stomatal types, trichomes, nodal anatomy.
Embryology: Type of embryo sac development, endosperm formation, embryo development patterns.
Palynology: Pollen morphology (apertures, exine ornamentation).
Cytology: Chromosome number, structure, behavior.
Origin & Evolution: Originated in early Cretaceous or late Jurassic. Exact ancestor debated (possibly related to Bennettitales or Gnetales, or an extinct seed fern group). Rapid diversification - Darwin's "abominable mystery". Key innovations: flowers, enclosed ovules, double fertilization, endosperm, fruits.
Systems of Classification:
Artificial: Linnaeus (based on few characters, e.g., stamen number).
Natural: Bentham & Hooker (based on overall similarity, pre-evolutionary). Widely used in herbaria.
Phylogenetic: Engler & Prantl, Hutchinson, Takhtajan, Cronquist, APG (Angiosperm Phylogeny Group - based on molecular data, cladistics). APG system (I, II, III, IV) is current standard.
Study of Angiospermic Families:
Selected families showcasing diversity (diagnostic features, floral formula/diagrams and economic importance are key aspects of study for each):
E.g., Fabaceae: Papilionaceous corolla, monadelphous/diadelphous stamens, marginal placentation, fruit legume. Economically important for pulses, fodder, timber.
Angiosperm Anatomy & Embryology Highlights:
Anatomical Features
- Stomata & Types: Anomocytic, anisocytic, paracytic, diacytic, graminaceous. Role in gas exchange.
- Trichomes: Glandular (secretory) and non-glandular (protective). Unicellular/multicellular.
- Unusual Secondary Growth: Anomalous patterns in monocots (Dracaena) and dicots (Boerhavia, Bougainvillea) due to abnormal cambial activity.
- Anatomy of C3 and C4 Plants: C4 plants (e.g., maize, sugarcane) show Kranz anatomy (bundle sheath cells with chloroplasts).
- Xylem & Phloem Differentiation: Primary (protoxylem/metaxylem, protophloem/metaphloem) and secondary. Vessel elements and sieve tube members are key components.
- Wood Anatomy: Porous (hardwood, vessels present) vs. non-porous (softwood, vessels absent, only tracheids - gymnosperms). Growth rings, heartwood, sapwood.
Embryology & Reproduction
- Gametophyte Development: Microsporogenesis & male gametophyte (pollen grain with tube nucleus, generative cell -> 2 male gametes). Megasporogenesis & female gametophyte (embryo sac - typically Polygonum type: 8-nucleate, 7-celled).
- Pollination & Fertilization: Transfer of pollen, pollen-pistil interaction. Double fertilization: one male gamete fuses with egg (syngamy -> zygote), other fuses with polar nuclei/secondary nucleus (triple fusion -> primary endosperm nucleus).
- Endosperm: Development (Nuclear, Cellular, Helobial types). Function: nutritive tissue for embryo.
- Embryo Development: Patterns (e.g., Crucifer/Onagrad, Asterad, Solanad, Caryophyllad, Chenopodiad types). Zygote -> proembryo -> globular -> heart-shaped -> torpedo -> mature embryo.
- Polyembryony & Apomixis: Polyembryony (multiple embryos in one seed). Apomixis (asexual seed production, e.g., adventive embryony, parthenogenesis).
- Applications of Palynology: Study of pollen/spores. Used in taxonomy, paleoecology, allergy studies, honey analysis, forensic science, oil exploration.
- Experimental Embryology: In vitro culture of embryos (embryo rescue), ovules, ovaries. Pollen storage, test-tube fertilization (in vitro fertilization).
Plant Resource Development
Plants underpin human civilization. This section explores their domestication, origins, diverse uses, and the importance of ethnobotany and conservation efforts.
Domestication: Process of selecting and adapting wild plants for human cultivation and use, leading to genetic changes (domestication syndrome).
Introduction of Plants: Intentional or accidental movement of plants to new geographical areas where they are not native.
Origin of Cultivated Plants: Tracing the geographical and genetic origins of crop species.
Vavilov’s Centres of Origin: Regions identified by N.I. Vavilov with high genetic diversity of crop plants, considered their primary centres of origin (e.g., Near East, China, Mesoamerica).
Importance of Ethnobotany in Indian Context: Study of traditional knowledge of indigenous communities regarding plant uses (medicinal, food, cultural). India has rich ethnobotanical heritage (e.g., Ayurveda, Siddha). Crucial for bioprospecting, drug discovery, and preserving traditional wisdom.
Energy Plantations: Cultivating fast-growing, high biomass plants (e.g., Jatropha, Pongamia, Leucaena, Eucalyptus) for biofuel production (biodiesel, ethanol, firewood).
Botanical Gardens & Herbaria:
Botanical Gardens: Ex-situ conservation of diverse plant species, research, education, public awareness (e.g., Kew, IBG Kolkata).
Herbaria: Collections of pressed, dried plant specimens, systematically arranged. Essential for taxonomic research, identification, documenting biodiversity (e.g., CAL, BSI).
Plants as Sources: A Diverse Cornucopia
| Category | Examples & Uses |
|---|---|
| Food | Cereals (rice, wheat, maize), pulses (lentils, beans), fruits, vegetables, nuts, millets. |
| Fodder | Grasses (Napier grass), legumes (alfalfa, berseem), tree leaves for livestock. |
| Fibres | Seed (cotton), bast (jute, flax, hemp), leaf (sisal, abaca), coir. For textiles, ropes, paper. |
| Spices | Pepper, cardamom, clove, turmeric, cinnamon, ginger. For flavoring, preservatives, medicinal. |
| Beverages | Tea (Camellia sinensis), Coffee (Coffea arabica), Cocoa (Theobroma cacao). |
| Edible Oils | Groundnut, mustard, sunflower, soybean, coconut, olive, palm oil. For cooking, industrial uses. |
| Drugs | Quinine (Cinchona), Morphine (Papaver), Digoxin (Digitalis), Vincristine (Catharanthus), Aspirin precursor (Salix). |
| Narcotics | Opium (Papaver somniferum), Cannabis (Cannabis sativa), Coca (Erythroxylum coca). (Note: Mentioned for syllabus coverage, not promotion). |
| Insecticides | Pyrethrum (Chrysanthemum cinerariaefolium), Neem (Azadirachta indica - azadirachtin), Rotenone (Derris). |
| Timber | Teak (Tectona), Sal (Shorea), Deodar (Cedrus), Pine, Rosewood (Dalbergia). For construction, furniture, paper pulp. |
| Gums | Gum arabic (Acacia senegal), Guar gum, Karaya gum. For food industry, adhesives, pharmaceuticals. |
| Resins | Pine resin (turpentine, rosin), Dammar, Copal. For varnishes, incense, adhesives. |
| Dyes | Indigo (Indigofera), Henna (Lawsonia), Saffron (Crocus), Turmeric, Annatto. Natural colorants. |
| Latex | Natural rubber (Hevea brasiliensis), Gutta-percha, Chicle. For tyres, industrial products. |
| Cellulose | From wood pulp, cotton. For paper, rayon, cellophane, nitrocellulose. |
| Starch & Products | From maize, potato, cassava, wheat. For food, sweeteners (glucose, fructose syrup), adhesives, ethanol. |
| Perfumery | Essential oils from Rose, Jasmine, Sandalwood, Lavender, Vetiver. For perfumes, cosmetics, aromatherapy. |
Morphogenesis & Plant Biotechnology
The development of plant form and structure, and applications in plant tissue culture for propagation and improvement.
Totipotency: Inherent capacity of a plant cell to differentiate and regenerate into a whole plant (Gottlieb Haberlandt). Basis of tissue culture.
Polarity: Axial differentiation (e.g., root-shoot axis) established early in development, maintained in cultured cells/tissues.
Symmetry: Patterns of development (radial, bilateral).
Differentiation: Process by which cells become specialized in structure and function. Dedifferentiation (loss of specialization, e.g., callus formation) and redifferentiation (regaining specialized form from dedifferentiated cells).
Aseptic culture of plant cells, tissues, or organs on defined nutrient media.
Cell Culture: Suspension cultures of single cells or small aggregates.
Tissue/Organ Culture: Explant culture (e.g., leaf, stem, root segments), callus culture, meristem culture (virus-free plants), anther/pollen culture (haploids), ovule/embryo culture.
Protoplast Culture: Isolation (enzymatic removal of cell wall) and culture of protoplasts. Used for fusion.
Somatic Hybrids & Cybrids:
Somatic Hybridization: Fusion of protoplasts from two different plant species/varieties to create hybrids (e.g., Pomato). Overcomes sexual incompatibility.
Cybrids (Cytoplasmic Hybrids): Fusion resulting in nucleus from one parent and cytoplasm from both or one (selectively). Useful for transferring cytoplasmic traits like male sterility.
Micropropagation: Rapid in vitro clonal multiplication of plants. Stages: initiation, multiplication, rooting, acclimatization. For elite genotypes, endangered species, commercial horticulture.
Somaclonal Variation: Genetic variations arising in plants regenerated from tissue culture. Can be a source of novel traits for crop improvement.
Pollen Haploids: Production of haploid plants from anther/microspore culture. Diploidization (e.g., colchicine) yields homozygous diploids quickly, useful in breeding.
Embryo Rescue: Culturing immature embryos from interspecific/intergeneric crosses that would otherwise abort. Overcomes post-zygotic incompatibility.
Botany Paper II
Cell Biology
Exploring the fundamental unit of life: the cell. This section covers its structure, function, organelles, processes, and chromosomal organization.
- Microscopy: Light microscopy (bright-field, phase contrast, fluorescence), Electron microscopy (TEM, SEM).
- Cell Fractionation: Differential and density gradient centrifugation to isolate organelles.
- Staining Techniques: Vital stains, specific stains for DNA (Feulgen), proteins (Coomassie Blue).
- Autoradiography: Using radioactive isotopes to trace metabolic pathways or locate molecules.
- Flow Cytometry: Analyzing and sorting cells based on physical/chemical properties.
Prokaryotic Cells: (e.g., Bacteria) Lack membrane-bound nucleus and organelles. Genetic material in nucleoid. Ribosomes (70S). Cell wall (peptidoglycan in bacteria). Simple structure.
Eukaryotic Cells: (e.g., Plant and Animal cells) True nucleus, membrane-bound organelles. Ribosomes (80S). Complex cytoskeleton.
Plant Cell Specifics: Cell wall (cellulose), large central vacuole, plastids (chloroplasts, chromoplasts, leucoplasts), plasmodesmata. Lack centrioles (most).
Extracellular Matrix (Cell Wall in Plants):
Structure: Primary wall (cellulose, hemicellulose, pectin), Middle lamella (pectin), Secondary wall (cellulose, lignin - in some cells). Plasmodesmata connect adjacent cells.
Functions: Provides structural support, shape, protection; prevents bursting; involved in cell-cell communication.
Cell Membranes (Plasma Membrane): Fluid mosaic model (Singer & Nicolson). Phospholipid bilayer with embedded/associated proteins, cholesterol (animals), phytosterols (plants).
Functions: Selective permeability, transport (passive, active, vesicular), cell adhesion, cell signaling (receptors).
Membrane Transport:
Passive: Simple diffusion, facilitated diffusion (channels, carriers).
Active: Requires energy (ATP pumps, e.g., Na+/K+ pump, H+ pump).
Vesicular Transport: Endocytosis (phagocytosis, pinocytosis, receptor-mediated), Exocytosis.
Cell Organelles: Structure & Function
Site of photosynthesis. Double membrane, stroma, thylakoids (grana). Own DNA, ribosomes.
Site of cellular respiration (ATP synthesis). Double membrane, cristae, matrix. Own DNA, ribosomes.
Network of membranes. RER (ribosomes): protein synthesis/modification. SER: lipid synthesis, detoxification.
Stacks of cisternae. Modify, sort, package proteins and lipids for secretion or delivery to other organelles.
Protein synthesis. Composed of rRNA and proteins. Free or ER-bound (eukaryotes: 80S; prokaryotes, plastids, mitochondria: 70S).
Lysosomes (mainly animal, some plant functional equivalents like vacuoles): Contain hydrolytic enzymes for intracellular digestion.
Peroxisomes: Metabolic compartments; breakdown of fatty acids, detoxification (e.g., H2O2 by catalase). Glyoxysomes in plants (fat to carbohydrate conversion).
Network of protein filaments (microtubules, microfilaments, intermediate filaments). Maintains cell shape, organization, movement of organelles, cell division (spindle).
Nucleus: Contains genetic material (chromatin). Double membrane (nuclear envelope) with nuclear pores.
Nucleolus: Site of ribosome synthesis and assembly.
Communication between cells. Ligands (hormones, growth factors) bind to specific receptors (cell surface or intracellular). Leads to signal transduction pathways altering cell behavior.
Chromatin & Nucleosome: Chromatin is DNA complexed with histone proteins. Basic unit is nucleosome (DNA wrapped around histone octamer). Further packaging into higher-order structures.
Cell Cycle: Interphase (G1, S, G2) and M phase (Mitosis/Meiosis, Cytokinesis). Regulated by cyclins and cyclin-dependent kinases (CDKs).
Mitosis: Somatic cell division. Prophase, Metaphase, Anaphase, Telophase. Produces two genetically identical diploid daughter cells.
Meiosis: Germ cell division. Meiosis I (reductional) and Meiosis II (equational). Produces four genetically distinct haploid cells. Essential for sexual reproduction.
Chromosomal Variations:
Numerical: Aneuploidy (e.g., monosomy 2n-1, trisomy 2n+1), Euploidy (e.g., haploidy n, polyploidy 3n, 4n).
Structural: Deletions, duplications, inversions, translocations. Significance in evolution, speciation, genetic disorders.
Polytene Chromosomes: Giant chromosomes (e.g., in Drosophila salivary glands) formed by repeated DNA replication without separation (endomitosis). Show distinct banding patterns, useful for gene mapping.
B-Chromosomes (Supernumerary): Extra, non-essential chromosomes found in some species. Often heterochromatic, can affect fertility or vigor. Their origin and significance are subjects of research.
Genetics, Molecular Biology & Evolution
Understanding heredity, the molecular mechanisms of life, and the processes of evolutionary change.
Development of Genetics: Mendel's laws, contributions of Morgan, Beadle & Tatum.
Gene vs. Allele: Gene is a segment of DNA coding for a functional product. Alleles are alternative forms of a gene.
Pseudoalleles: Closely linked genes with similar functions, appear as alleles due to rare recombination.
Incomplete Dominance & Codominance: Intermediate phenotype; both alleles express.
Multiple Alleles: More than two alleles for a gene in a population (e.g., ABO blood groups).
Polygenic Inheritance & Quantitative Genetics: Traits controlled by multiple genes, showing continuous variation (e.g., height, yield). Multiple factors hypothesis.
Linkage: Tendency of genes on the same chromosome to be inherited together.
Crossing Over: Exchange of genetic material between homologous chromosomes during meiosis, leading to recombination.
Gene Mapping: Determining relative positions of genes on a chromosome using recombination frequencies (map units/cM). Molecular maps use DNA markers.
Sex Chromosomes & Sex-linked Inheritance: Chromosomes determining sex (e.g., X, Y). Inheritance of genes on sex chromosomes (e.g., color blindness).
Sex Determination: Mechanisms like XX/XY, XX/XO, ZW/ZZ. Molecular basis (e.g., SRY gene in mammals). Sex differentiation: development of sexual characteristics.
Mutations: Heritable changes in DNA.
Biochemical Basis: Spontaneous (errors in replication, deamination) or induced (mutagens: physical - UV, X-rays; chemical - base analogs, alkylating agents).
Molecular Basis: Point mutations (substitutions, insertions, deletions), frameshift mutations. Chromosomal mutations (covered in Cell Bio).
Cytoplasmic Inheritance (Extranuclear): Inheritance of traits controlled by genes in mitochondria or chloroplasts. Uniparental (maternal) inheritance is common.
Examples: Mitochondrial diseases in humans, chloroplast-mediated traits in plants (e.g., leaf variegation in Mirabilis jalapa).
Genetics of Male Sterility: Cytoplasmic Male Sterility (CMS) due to mitochondrial genes, often restored by nuclear restorer (Rf) genes. Important in hybrid seed production.
Structure of Nucleic Acids: DNA (double helix, A-T, G-C base pairing) and RNA (single-stranded, U instead of T).
DNA Replication: Semiconservative process, enzymes involved (helicase, primase, DNA polymerase, ligase).
Protein Structure: Primary, secondary, tertiary, quaternary levels.
Protein Synthesis (Translation): Ribosomes, mRNA (template), tRNA (amino acid carrier), genetic code (codons).
Genetic Code: Triplet, non-overlapping, degenerate, universal (nearly).
Gene Expression Regulation (Prokaryotes): Operon model (e.g., Lac operon - inducible, Trp operon - repressible).
Gene Expression Regulation (Eukaryotes): More complex; involves chromatin remodeling, transcription factors, RNA processing (splicing, capping, polyadenylation), post-translational modifications.
Gene Silencing: Mechanisms like RNA interference (RNAi) using siRNA/miRNA to downregulate gene expression.
Multigene Families: Groups of related genes, often arising from duplication (e.g., globin genes, rRNA genes).
Evidences: Fossil record, comparative anatomy (homology, analogy), embryology, biogeography, molecular data (DNA/protein sequences).
Theories:
Lamarckism: Inheritance of acquired characters (discredited).
Darwinism: Natural selection based on variation, overproduction, struggle for existence, survival of the fittest.
Modern Synthetic Theory (Neo-Darwinism): Integrates Darwinian selection with Mendelian genetics, population genetics. Factors: mutation, recombination, gene flow, genetic drift, natural selection.
Mechanisms: Speciation (allopatric, sympatric), adaptive radiation. Hardy-Weinberg equilibrium.
Role of RNA in Origin and Evolution: "RNA world" hypothesis suggests RNA was the primary genetic material and catalytic molecule before DNA and proteins. Ribozymes (catalytic RNA) support this.
Plant Breeding, Biotechnology & Biostatistics
Improving crop plants through traditional and modern techniques, and the statistical tools for analyzing biological data.
- Introduction: Bringing new plant varieties from outside. Quarantine is crucial.
- Selection:
Mass Selection: Based on phenotype from mixed populations.
Pure Line Selection: From self-pollinated crops, selecting superior homozygous lines.
Clonal Selection: For vegetatively propagated crops. - Hybridization: Crossing genetically diverse parents.
Pedigree Method: Selection in segregating generations, detailed records.
Bulk Method: Generations advanced in bulk, selection in later stages.
Backcross Method: Transferring specific genes (e.g., disease resistance) from donor to recurrent parent. - Mutation Breeding: Inducing mutations (X-rays, gamma rays, EMS) to create variability.
- Polyploidy Breeding: Creating polyploids (e.g., colchicine treatment). Autopolyploids (e.g., triploid watermelon), Allopolyploids (e.g., Triticale).
- Male Sterility: Using CMS or GMS systems for easier hybrid seed production.
- Heterosis Breeding (Hybrid Vigour): Exploiting superiority of F1 hybrids over parents.
- Use of Apomixis in Plant Breeding: Fixing heterosis by asexual seed production.
DNA Sequencing: Methods like Sanger sequencing, Next-Generation Sequencing (NGS) for determining DNA base order.
Genetic Engineering - Methods of Gene Transfer:
Indirect: Agrobacterium-mediated transformation (using Ti plasmid).
Direct: Biolistics (gene gun), electroporation, microinjection.
Transgenic Crops & Biosafety: Crops with foreign genes (e.g., Bt cotton for insect resistance, Golden Rice for Vitamin A).
Biosafety Aspects: Concerns about gene flow, impact on non-target organisms, allergenicity. Regulatory frameworks (e.g., GEAC in India).
Molecular Markers in Plant Breeding: DNA-based markers to identify genetic variation.
Types: RFLP (Restriction Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA), AFLP (Amplified Fragment Length Polymorphism), SSR (Simple Sequence Repeats/Microsatellites), SNP (Single Nucleotide Polymorphism).
Applications: Genetic diversity analysis, marker-assisted selection (MAS), QTL mapping.
Tools & Techniques:
Probes: Labeled DNA/RNA segments to detect specific sequences.
Southern Blotting: Detecting specific DNA fragments. (Northern for RNA, Western for proteins).
DNA Fingerprinting: Identifying individuals based on unique DNA patterns (e.g., using SSRs, VNTRs).
PCR (Polymerase Chain Reaction): Amplifying specific DNA segments.
FISH (Fluorescence In Situ Hybridization): Locating specific DNA sequences on chromosomes.
Measures of Central Tendency & Dispersion: Mean, median, mode. Variance, Standard Deviation (SD), Coefficient of Variation (CV) - measures spread of data.
Tests of Significance: Used to determine if observed differences are statistically significant or due to chance.
Z-test: For large samples, when population SD is known.
t-test: For small samples, comparing means (paired, unpaired).
Chi-square (χ2) test: For categorical data, testing goodness-of-fit, independence of attributes.
Probability and Distributions:
Probability: Likelihood of an event.
Normal Distribution: Bell-shaped curve, common for continuous data.
Binomial Distribution: For discrete data with two outcomes (e.g., success/failure).
Poisson Distribution: For rare events in a continuum.
Correlation and Regression:
Correlation: Measures strength and direction of linear relationship between two variables (correlation coefficient 'r').
Regression: Predicts value of one variable based on another (regression equation, line of best fit).
Physiology & Biochemistry
Exploring the life processes of plants: water relations, nutrition, metabolism, growth, and responses to environment.
Water Relations: Water potential (Ψw = Ψs + Ψp + Ψg), osmosis, diffusion, imbibition. Absorption of water by roots. Ascent of sap (cohesion-tension theory). Transpiration (stomatal regulation, factors affecting).
Mineral Nutrition: Essential macro- (C,H,O,N,P,K,S,Ca,Mg) and micro- (Fe,Mn,Zn,Cu,B,Mo,Cl,Ni) nutrients. Roles and deficiency symptoms.
Ion Transport: Uptake of mineral ions (passive and active). Apoplast and symplast pathways. Role of Casparian strip.
Photosynthesis:
Photochemical Reactions (Light Reactions): Pigment systems (PS I, PS II), electron transport chain, non-cyclic and cyclic photophosphorylation (ATP, NADPH production).
Carbon Fixation Pathways (Dark Reactions): C3 cycle (Calvin cycle), C4 cycle (Hatch-Slack pathway, Kranz anatomy), CAM pathway (Crassulacean Acid Metabolism).
Phloem Transport: Translocation of organic solutes (sucrose). Mass flow hypothesis (Munch hypothesis).
Respiration:
Aerobic: Glycolysis, pyruvate oxidation (link reaction), Krebs cycle (TCA cycle), Electron Transport Chain (ETC) and Oxidative Phosphorylation (ATP synthesis).
Anaerobic Respiration & Fermentation: Lactic acid and alcoholic fermentation.
Photorespiration (C2 Cycle): In C3 plants, RuBisCO oxygenase activity. Occurs in chloroplast, peroxisome, mitochondrion. Reduces photosynthetic efficiency.
Chemiosmotic Theory & ATP Synthesis: Proton gradient across inner mitochondrial/thylakoid membrane drives ATP synthase.
Lipid Metabolism: Synthesis of fatty acids, triglycerides. β-oxidation (breakdown of fatty acids). Glyoxylate cycle in germinating fatty seeds.
Nitrogen Fixation & Metabolism:
Nitrogen Fixation: Biological (symbiotic - Rhizobium; non-symbiotic - Azotobacter, cyanobacteria) and non-biological. Nitrogenase enzyme.
Nitrogen Metabolism: Nitrate assimilation (nitrate reductase, nitrite reductase), ammonia assimilation (GS-GOGAT pathway, GDH pathway). Synthesis of amino acids.
Enzymes & Coenzymes: Biological catalysts (proteins). Lock-and-key/induced fit models. Factors affecting activity (temp, pH, substrate conc.). Enzyme kinetics (Km, Vmax). Coenzymes (vitamins, NAD, FAD).
Energy Transfer & Conservation: ATP as energy currency. Redox reactions.
Importance of Secondary Metabolites: Terpenoids, phenolics, alkaloids. Roles in defense, allelopathy, attraction of pollinators, human uses (drugs, flavors).
Pigments as Photoreceptors:
Plastidial Pigments: Chlorophylls, carotenoids (light harvesting in photosynthesis).
Phytochrome: Red/far-red light photoreceptor (Pr, Pfr forms). Controls seed germination, flowering, photomorphogenesis.
Cryptochromes & Phototropins: Blue light photoreceptors (phototropism, stomatal opening).
Plant Movements:
Tropic: Directional growth responses (phototropism, gravitropism, thigmotropism).
Nastic: Non-directional responses (nyctinasty - sleep movements, seismonasty - touch response).
Photoperiodism & Flowering: Response to day/night length. Short-day plants (SDP), long-day plants (LDP), day-neutral plants (DNP). Florigen concept.
Vernalization: Cold treatment to induce/promote flowering.
Senescence: Programmed aging and death of plant parts or whole plant. Role of ethylene.
Growth Substances (Phytohormones):
Auxins (IAA): Cell elongation, apical dominance, rooting.
Gibberellins (GA): Stem elongation, seed germination, flowering.
Cytokinins (Zeatin): Cell division, delay senescence, shoot initiation.
Abscisic Acid (ABA): Stress hormone, dormancy, stomatal closure.
Ethylene: Fruit ripening, senescence, abscission.
Applications in Agri-horticulture: Rooting, fruit setting/ripening, weed control, tissue culture.
Growth Indices: Measures of plant growth (e.g., RGR, NAR, LAI). Growth movements (nutation).
Stress Physiology: Plant responses to adverse conditions.
Heat Stress: Heat shock proteins (HSPs), membrane stability.
Water Stress (Drought/Flooding): Osmotic adjustment, ABA accumulation, antioxidant systems.
Salinity Stress: Ion toxicity, osmotic stress. Salt exclusion/compartmentation.
Metal Stress: Heavy metal toxicity, phytochelatins, metallothioneins.
Fruit & Seed Physiology:
Fruit Development & Ripening: Changes in color, texture, flavor. Climacteric (ethylene-dependent) vs. non-climacteric fruits. Molecular basis (gene expression changes). Manipulation (controlled ripening, storage).
Seed Dormancy: Physical, physiological. Breaking dormancy (scarification, stratification, hormones).
Seed Storage: Orthodox (low moisture) vs. recalcitrant seeds. Factors affecting viability.
Seed Germination: Water imbibition, enzyme activation, mobilization of reserves, embryo growth.
Ecology & Plant Geography
Study of interactions between plants and their environment, plant communities, ecosystems, conservation, and plant distribution.
Concept of Ecosystem: Biotic and abiotic components interacting. Structure (species composition, stratification) and function (energy flow, nutrient cycling, productivity).
Ecological Factors:
Climatic: Light, temperature, water, wind.
Edaphic: Soil formation, composition, pH, texture.
Biotic: Interactions (competition, predation, mutualism, parasitism).
Concepts & Dynamics of Community: Plant community attributes (species diversity, dominance, structure). Ecological niche.
Plant Succession: Gradual process of change in species composition over time. Primary (on bare areas) vs. Secondary (after disturbance). Climax community. Hydrosere, Xerosere.
Concepts of Biosphere: Global sum of all ecosystems.
Ecosystems Conservation: Importance of maintaining ecosystem health and services.
Pollution & Control: Air, water, soil pollution. Sources, effects, control measures.
Phytoremediation: Use of plants to remove/degrade pollutants (e.g., heavy metals, organic contaminants).
Plant Indicators: Species whose presence, abundance, or health indicates specific environmental conditions (e.g., pollution, soil type).
Environment (Protection) Act, 1986 (India): Umbrella legislation for environmental protection. Aims, key provisions for pollution control, hazardous substance management.
Forest Types of India: Tropical (evergreen, deciduous, thorn), Montane (temperate, alpine), Mangrove. Ecological and economic importance.
Afforestation, Deforestation, Social Forestry: Planting trees, clearing forests, community-based forestry for local needs and environmental benefits.
Endangered Plants & Endemism:
IUCN Categories: Extinct, Critically Endangered, Endangered, Vulnerable, etc. Red Data Books list threatened species.
Endemism: Species restricted to a specific geographic area. Hotspots of biodiversity.
Biodiversity & its Conservation: Levels (genetic, species, ecosystem).
In-situ Conservation: Protecting species in their natural habitats (National Parks, Sanctuaries, Biosphere Reserves - Protected Area Network).
Ex-situ Conservation: Protecting species outside natural habitats (Botanical gardens, seed banks, cryopreservation, tissue culture).
Convention on Biological Diversity (CBD): International treaty for conservation, sustainable use, and equitable sharing of benefits from genetic resources.
Farmers’ Rights & Intellectual Property Rights (IPR): Rights of farmers regarding seeds and traditional knowledge. IPR (patents, plant variety protection) related to plant genetic resources and innovations. PPV&FR Act in India.
Concept of Sustainable Development: Development meeting present needs without compromising future generations' ability to meet their own needs. Balancing economic, social, environmental aspects.
Biogeochemical Cycles: Movement of elements (Carbon, Nitrogen, Phosphorus, Sulphur) through biotic and abiotic components of ecosystems.
Global Warming & Climatic Change: Greenhouse effect, rising temperatures, impacts on plant distribution, phenology, agriculture. Invasive species facilitated by climate change.
Invasive Species: Non-native species that spread and cause ecological/economic harm (e.g., Lantana camara, Parthenium hysterophorus).
Environmental Impact Assessment (EIA): Process to predict and evaluate environmental consequences of proposed projects, suggesting mitigation measures.
Phytogeographical Regions of India: Major botanical zones based on climate, vegetation, and floristic composition (e.g., Western Himalayas, Eastern Himalayas, Indus Plain, Gangetic Plain, Deccan, Malabar, Andaman & Nicobar).