General Botany Essentials

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Botany: The Study of Plants Definition: Branch of biology studying plants, including their physiology, structure, genetics, ecology, distribution, classification, and economic importance. Relevance: Crucial in ecology, agriculture, industry, and medicine. Divisions of Natural Sciences Botany is a key component within the natural sciences. Subdivisions of Botany Plant Anatomy: Study of the internal structure of plants. Plant Physiology: Study of plant function and behavior (growth, metabolism, reproduction, defense, communication). Plant Taxonomy: Science of finding, identifying, describing, classifying, and naming plants. Plant Systematics: Reconstructs the evolutionary history of plant life, dividing plants into taxonomic groups using various data. Plant Geography: Study of plant and animal distributions through time. Plant Ecology: Examines relationships between plants and their physical/biotic environment. Plant Morphology: Study of the physical form and external structure of plants. Distinct from anatomy. Plant Genetics: Study of genes, genetic variation, and heredity specifically in plants. Cell Biology: Study of cell structure and function, with the cell as the fundamental unit of life. Economic Botany: Study of the relationship between people and plants. Ethnobotany: Study of a region's plants and their traditional uses by local cultures. Microscopy in Botanical Studies Microscopy: Use of microscopes to view samples invisible to the naked eye. Microscope: Instrument that produces an enlarged image of a minute object. Compound Light Microscope Uses visible light and two lenses (objective and eyepiece) for magnification. Total Magnification: Magnification of objective $\times$ Magnification of ocular (eyepiece). Example: $10\text{x}$ eyepiece with $40\text{x}$ objective = $400\text{x}$ magnification. Four Parameters in Microscopy 1. Magnification: Enlargement of an object's appearance. 2. Resolution: Smallest distance between two points visible as separate. Human eye: $\approx 150 \mu m$. Light microscope: $0.2 \mu m$. Resolving Power: Ability to distinguish two points as separate. 3. Illumination: Light source (transmitted or reflected, white or UV) for visualization. 4. Contrast: Ability to distinguish an object from its surroundings. Enhanced by dyes and stains (e.g., carbol fuchsin, methylene blue, safranin). Microscopy Terminology Numerical Aperture (N.A.): Measure of an objective's light-gathering and fine detail-resolving ability. Working Distance: Linear distance between objective tip and specimen. Refractive Index: Measures light bending of a medium. Immersion Oil: Used to prevent light from bending away from the objective lens, increasing N.A. and resolving power, especially with high magnification. Working Principle of Compound Microscope Specimen on glass slide is positioned between condenser and objective lens. Visible light from base is focused by condenser onto specimen. Objective lens picks up transmitted light, creating magnified primary image in body tube. Ocular lens (eyepiece) further magnifies this image. Higher magnification objectives (e.g., $40\text{x}, 100\text{x}$) are rotated into place. Oil immersion objective ($100\text{x}$) used for very high magnification. Common light microscope is a bright field microscope , producing a darker image against a bright field. Microscope Operation and Image Characteristics Condenser: Usually in highest position; lowering slightly can improve brightness. Aperture Iris Diaphragm: Adjusts to objective magnification (e.g., $4\text{x}, 10\text{x}, 40\text{x}, 100\text{x}$). Image Movement: Appears to move in directions opposite to actual specimen movement (up-down, left-right). Image Orientation: Images viewed through a microscope appear upside down and inverted. Microscope Parts (Examples) Eyepiece (ocular), Revolving nosepiece, Objectives ($4\text{x}, 10\text{x}, 40\text{x}, 100\text{x}$), Condenser (iris diaphragm ring). Coarse adjustment knob, Fine adjustment knob, Stage, Light intensity adjustment knob, Power switch. Diopter adjustment ring, Interpupillary distance adjustment (for binocular). Methods of Sectioning Longitudinal Section: Cut along the length. Tangential Section: Cut along a tangent to the surface. Cross/Transverse Section: Cut perpendicular to the long axis. Diagram Skills for Botanical Drawings Drawing should resemble observation, include details (color, texture, shape). Appropriate size and drawn to scale. All parts labeled as instructed. Include: Title, total magnification, name of specimen, objective used. Relevance of Botany Food: Source of sustenance. Medical Compounds: Many medicines derived from plants. Industrial Byproducts: Timber, paper, dye, textiles. Ecosystem Services: Oxygen production, carbon sequestration, habitat. Cultural, Aesthetics, Educational Benefits: Gardens, parks, research. The Eukaryotic Plant Cell: Structure and Function Learning Objective: Distinguish prokaryotic from eukaryotic cells; describe plant cell components. Key Plant Cell Components Cell Membrane Membranous and Nonmembranous Organelles Cytoplasm Cell Wall 1. The Cell Membrane (Plasma Membrane) Importance: Defines cell boundary, controls material passage, governs cell interactions. Structure: Fluid mosaic model – phospholipid bilayer with anchored proteins. Membrane Lipids Phospholipids (75%): Form bilayer. Head (glycerol + phosphate): Hydrophilic, faces fluid. Tail (two fatty acid chains): Hydrophobic, oriented away from fluid. Cholesterol (20%): Gives fluidity to animal cell membranes. Glycolipids (5%): Two fatty acids + short carbohydrate chains. Membrane Proteins Integral Proteins: Pass all the way through the membrane. Peripheral Proteins: Adhere to the surface. Glycoproteins: Proteins + short carbohydrate chains. Functions: Receptors: Bind chemical messengers (e.g., hormones) for cell communication. Enzymes: Catalyze chemical reactions. Anchor Proteins: Link intracellular with extracellular structures. Transport Proteins: Channel Proteins: Allow passage of water and solutes. Carrier Proteins: Transport substances by changing shape. Protein Pumps: Transport substances against concentration gradient (requires energy). Properties of Membranes 1. Fluidity of Membranes: Permits movement of membrane pieces, allows vesicle formation/fusion. Important for: Transport of materials: Exocytosis: Release materials to outside (secretion). Endocytosis: Materials taken inside cell. Phagocytosis: Solid substances ("cellular eating"). Pinocytosis: Liquid substances ("cellular drinking"). Compartmentalization: Each compartment specialized for a process (e.g., organelles). Phytosterols: Maintain membrane fluidity and stability in plants. 2. Permeability of the Membrane: Selectively permeable. Hydrophobic substances, smaller molecules (e.g., water) diffuse easily. Large hydrophilic substances (e.g., amino acids, glucose) and ions pass via facilitated diffusion or active transport. 2. Cytoplasm Part between cell membrane, nucleus, and vacuole. Components: Cytosol: Fluid portion with water, dissolved solutes, suspended particles. Organelles: Subcellular structures with specific functions. Protoplasm: All substance inside the cell membrane except the vacuole (includes nucleus and cytoplasm). 3. Membranous and Nonmembranous Organelles Membranous Organelles (Endomembrane System) Nucleus: Spherical, double-layered membrane. Outer membrane continuous with ER. Nuclear pores for substance passage. Contains: Nucleoli: Involved in ribosome synthesis and assembly. Chromatin: Tightly coiled DNA and histone proteins. Nucleoplasm: Fluid with water, enzymes, RNA. Endoplasmic Reticulum (ER): Extensive membranous network continuous with nuclear membrane. Rough ER: With ribosomes, synthesizes proteins for secretion. Smooth ER: Lacks ribosomes, synthesizes membrane lipids. Golgi Apparatus (Dictyosomes): Flattened membrane sacs. Receive proteins/lipids from ER, process, sort, and package them for transport or secretion. Cis face: "Entry" side. Trans face: "Exit" side. Importance in plants: Formation of cell plate during cytokinesis, secretion of carbohydrates (nectar, cell wall material). Microbodies: Spherical, single membrane, contain enzymes. Glyoxysomes: Convert stored fats to sugars (important in oily seed germination, e.g., peanut). Peroxisomes: Degrade fatty acids/amino acids, detoxify harmful substances (e.g., $H_2O_2$ converted to $H_2O + O_2$ by catalase). Central Vacuole: Single membrane (tonoplast). Functions: Digestion, storage (ions, sugars, amino acids, waste), maintain cell turgidity, cell growth. Mitochondria: Site of aerobic cell respiration ($C_6H_{12}O_6 + O_2 \rightarrow CO_2 + H_2O + \text{Energy (ATP)}$). Breaks down organic compounds to yield ATP. Has its own DNA and ribosomes; capable of reproduction. Parts: Smooth Outer Membrane: Shape, rigidity, freely permeable. Inner Membrane: Arranged into folds (cristae), site of ATP generation, selectively permeable, rich in enzymes. Matrix: Fluid inner portion. Plastids: Associated with pigments and storage products. Outer and inner membrane, distinct ribosomes and circular DNA; capable of reproduction. Types: Proplastid: Small, undifferentiated, in young cells, can develop into chloroplasts in light. Chloroplast: Site of photosynthesis (solar energy to chemical energy). $CO_2 + H_2O \xrightarrow{\text{sunlight}} C_6H_{12}O_6 + O_2$ Parts: Outer membrane, Inner membrane, Thylakoid (internal system with photosynthetic pigments, site of light reaction and $O_2$ generation), Stroma (fluid, site of $CO_2$ fixation/Calvin cycle and sugar synthesis). Chromoplast: Store pigments (e.g., carotenoids) in flowers/fruits, contain plastoglobuli, transform from chloroplasts during fruit ripening/leaf senescence. Etioplast: Chloroplasts not exposed to light; convert to chloroplasts upon light exposure via cytokinin. Leucoplast: Colorless plastids. Amyloplast: Long-term starch storage (in non-photosynthetic tissues like roots/bark). Layers of starch around hilum. Can transform into chloroplasts. Statoliths: Special amyloplasts in root caps and shoot nodes, involved in gravity sensing. Elaioplast: Store large amounts of oil. Proteinoplast (Aleuroplast): Store proteins; form aleurone layer in seeds. Non-membranous Organelles Ribosomes: RNA and proteins, important for protein synthesis. Two subunits (large and small). Free Ribosomes: In cytosol. Bound Ribosomes: Attached to ER. Cytoskeleton: Network of protein filaments throughout cytosol. Maintains cell shape, provides support, anchors organelles/enzymes, involved in contractility/movement, intracellular transport. Three kinds of protein filaments: Microfilaments: Thinnest, composed of actin, important for cytoplasmic streaming (cyclosis). Intermediate Filaments: Thicker than microfilaments, thinner than microtubules; anchor organelles, counter mechanical stress. Microtubules: Largest, composed of tubulin, participate in chromosome migration during cell division, form flagella for cell movement. Cytoplasmic Streaming (Cyclosis): Moving currents of cytoplasm, facilitate transport of substances within and between cell/surroundings. 4. Cell Wall Composed of cellulose, hemicellulose, pectin, lignin, and proteins. Three layers: 1. Middle Lamella/Intercellular Layer: Primarily pectin; cements individual cells to form tissues. 2. Primary Cell Wall: First true cell wall, composed of cellulose bound by hemicellulose; develops on newly formed cells. 3. Secondary Cell Wall: Formed on inner surface of primary wall, much thicker, impregnated with lignin (increases strength, waterproofing, pathogen resistance); develops in mature functional cells. Plasmodesmata: Channels through cell walls connecting cytoplasms of adjacent cells. Membrane Transport System Transport Across the Cell Membrane Cell membrane is a selectively permeable boundary. I. Passive Transport: Cell uses no energy. Diffusion Facilitated Diffusion Osmosis II. Active Transport: Cell uses energy (ATP). Protein Pumps Passive Transport Molecules move randomly from high to low concentration. 1. Simple Diffusion: Random movement of molecules from high to low concentration. Factors influencing rate: Distance (shorter = faster), Molecular Size (smaller = faster), Temperature (higher = faster), Steepness of concentration gradient (larger = faster), Membrane surface area (larger = faster). Importance: Gas exchange, transpiration, short-distance transport, attracting pollinators (aroma), fruit ripening (ethylene). Through phospholipid bilayer: Fats, other lipids, small nonpolar molecules can pass directly. Polar molecules, ions, large molecules cannot directly. 2. Facilitated Diffusion: Diffusion of molecules from high to low concentration using transport proteins (channel or carrier proteins). Transports larger or charged molecules. Channel Proteins: Specific channels for specific materials (e.g., water, ions). Carrier Proteins: Change shape to transport molecules. 3. Osmosis: Diffusion of water through a selectively permeable membrane (high to low water concentration). Water moves freely through pores; solutes too large to move. Tonicity of a solution: Determines direction of osmosis by comparing solute concentrations. Hypertonic: More solute, less water. Hypotonic: Less solute, more water. Isotonic: Equal solute, equal water. Effects on cells: Hypotonic solution: Cell gains water. Animal cell lyses; plant cell becomes turgid (firm). Hypertonic solution: Cell loses water. Animal cell shrivels; plant cell plasmolyzes. Importance: Water absorption by roots, nutrient/ion uptake, cell-to-cell water movement, structural support (turgor pressure), stomatal opening/closing. Active Transport Cell uses energy (ATP) to move molecules against their concentration gradient (low to high). Protein Pumps: Carrier proteins that require energy (ATP) to change shape and move molecules (e.g., Sodium/Potassium Pumps). Types: Primary Active Transport: Directly uses ATP. Secondary Active Transport (Coupled Transport/Co-transport): No direct ATP use. Uses movement of one solute down its gradient to move another solute against its gradient. Symporters (Symport): Both molecules transported in the same direction. Antiporters (Antiport): Two ions/solutes pumped in opposite directions. Importance: Mineral uptake by roots (potassium, nitrate, phosphate), loading of sugar from source to sink. Vesicular (Bulk) Transport Moving large molecules into and out of cell via vesicles and vacuoles. Endocytosis: Materials taken inside cell. Phagocytosis: "Cellular eating" (solid substances). Pinocytosis: "Cellular drinking" (liquid substances). Receptor Mediated Endocytosis: Highly specific, receptor proteins bind specific substances. Exocytosis: Materials released from cell. Importance: Cell wall formation, secretion of cuticle/mucilage/nectar, hormone signaling, cell-to-cell communication, defense against pathogens. Membrane Transport Summary Lipids, hydrophobic molecules: Simple diffusion. Ions, hydrophilic and large molecules: Facilitated diffusion or Active transport (requires ATP).