Comprehensive Biology Notes for University Students

THREE-DOMAIN SYSTEM OF CLASSIFICATION

  • Historical Context: In 1969, Robert Whittaker proposed the Five-Kingdom system. Later, Carl Woese introduced the Three-Domain system based on differences in ribosomal RNA (rRNA) sequences.
  • The Three Domains:
    • Domain Archaea: Includes ancient prokaryotes often living in extreme environments. Derived from the Greek word archaios (ancient).
    • Domain Bacteria: Includes true bacteria (eubacteria), widely distributed across Earth.
    • Domain Eukarya: Includes all eukaryotic organisms (Protists, Fungi, Plants, and Animals).

DOMAIN ARCHAEA

  • Unique Features:
    • Cell Membrane: Linkages are ether-linked lipids (isoprenoid chains) rather than ester-linked fatty acids, making them more stable in extreme heat/acid.
    • Cell Wall Composition: Lacks peptidoglycan (found in Bacteria). Often composed of pseudomurein or S-layers.
    • Genetic Structure: Features unique rRNA sequences and contains introns (like eukaryotes), unlike Bacteria.
    • Metabolism: Capable of methanogenesis (unique to Archaea).
  • Classification Groups:
    • Methanogens: Produce methane as a metabolic byproduct (e.g., Methanosarcina).
    • Extremophiles: Includes Halophiles (salt-loving), Thermophiles (heat-loving), and Acidophiles (acid-loving).

DOMAIN BACTERIA

  • Cell Structure: Prokaryotic; lack membrane-bound organelles.
  • Cell Wall: Composed of Peptidoglycan (Murein).
    • Gram-Positive: Thick layer of peptidoglycan; stains purple.
    • Gram-Negative: Thin peptidoglycan layer with an outer membrane containing lipopolysaccharides; stains pink.
  • Genetic Material: Single circular DNA located in the nucleoid area. Often contains plasmids (small circular DNA for antibiotic resistance).
  • Reproduction: Primarily via Binary Fission.
  • Special Structures:
    • Flagella: Used for motility.
    • Pili/Fimbriae: Help in attachment and conjugation.
    • Endospores: Survival structures produced by genera like Bacillus and Clostridium during harsh conditions.
  • Major Groups:
    • Cyanobacteria: Photosynthetic (e.g., Anabaena, Spirulina).
    • Spirochaetes: Corkscrew-shaped (e.g., Treponema pallidum).
    • Actinomycetes: Branching bacteria (e.g., Streptomyces).
    • Normal Flora: Helpful bacteria residing on/in humans that synthesize vitamins and inhibit pathogens.

DOMAIN EUKARYA AND TAXONOMIC HIERARCHY

  • Eukarya Characteristics: Possess a true nucleus and membrane-bound organelles (mitochondria, ER, Golgi).
  • Taxonomic Hierarchy (Ranked Most General to Most Specific):
    1. Domain: Every living organism belongs to one of three.
    2. Kingdom: Broad groupings (e.g., Animalia).
    3. Phylum: Based on body plan (e.g., Chordata).
    4. Class: (e.g., Mammalia).
    5. Order: (e.g., Primates).
    6. Family: (e.g., Hominidae).
    7. Genus: (e.g., Homo).
    8. Species: Smallest group, defined as organisms that can interbreed and produce fertile offspring (e.g., Homo sapiens).

KINGDOMS OF EUKARYA

  • 1. Kingdom Protista: Primarily aquatic, unicellular or simple multicellular. Examples: Euglena, Amoeba, slime molds.
  • 2. Kingdom Fungi: Chitin-based cell walls, absorptive heterotrophs. Major groups include Zygomycota, Ascomycota, Basidiomycota. Examples: Mushrooms, Yeast, Penicillium.
  • 3. Kingdom Plantae: Photosynthetic autotrophs, cell walls made of cellulose. Groups: Non-vascular (Mosses), Seedless vascular (Ferns), and Seed plants (Gymnosperms and Angiosperms).
  • 4. Kingdom Animalia: Multicellular heterotrophs, no cell walls.

ANIMALIA CLASSIFICATION (PHYLA)

  • Porifera (Sponges): Asymmetrical, sessile, porous bodies, no true tissues.
  • Cnidaria: Radial symmetry, stingers (nematocysts). Examples: Jellyfish, Hydra, Corals.
  • Platyhelminthes (Flatworms): Bilateral symmetry, acoelomates. Examples: Planaria, Tapeworms.
  • Nematoda (Roundworms): Pseudocoelomates, often parasitic. Example: Ascaris.
  • Mollusca: Soft bodies, often with a shell. Examples: Snails, Octopus.
  • Annelida: Segmented worms. Examples: Earthworms, Leeches.
  • Arthropoda: Jointed appendages, chitinous exoskeleton. Examples: Insects, Spiders, Crabs. Largest phylum.
  • Echinodermata: Spiny-skinned, water vascular system. Examples: Starfish, Sea urchins.
  • Chordata: Possess a notochord, tubular nerve cord, pharyngeal slits, and post-anal tail at some developmental stage.

VERTEBRATE CLASSES

  • Cyclostomata: Jawless fishes (e.g., Lampreys).
  • Chondrichthyes: Cartilaginous skeletal fishes (e.g., Sharks).
  • Osteichthyes: Bony fishes (e.g., Salmon, Rohu).
  • Amphibia: Ectothermic, double-circuit circulation, larval stage in water.
  • Reptilia: Ectothermic, lay amniotic eggs, dry scaly skin.
  • Aves (Birds): Endothermic, feathers, hollow bones for flight, toothless beaks.
  • Mammalia: Endothermic, mammary glands, hair/fur.
    • Monotremes: Egg-laying (Platypus).
    • Marsupials: Pouch-bearing (Kangaroo).
    • Eutherians: Placental (Humans).

CELL BIOLOGY: STRUCTURE AND FUNCTION

  • Cell Theory:

    1. All organisms are composed of one or more cells.
    2. The cell is the basic structural and functional unit.
    3. Cells arise only from pre-existing cells.

  • Microscopy:

    • Magnification: Ratio of image size to actual size.
    • Resolution: Minimum distance between two points to be seen as distinct.
    • Electron Microscope (EM): Uses electron beams. Higher resolution than Light Microscopes. Includes SEM (Scanning) for surfaces and TEM (Transmission) for internal structure.

  • Subcellular Organelles:

    • Nucleus: Contains chromatin (DNA + proteins). Nuclear envelope has nuclear pores with complex subunits.
    • Mitochondria: Site of aerobic respiration. Contains inner folds called cristae and its own DNA.
    • Chloroplasts (Plants): Site of photosynthesis. Features thylakoids stacked into grana within the stroma.
    • Endoplasmic Reticulum (ER): Rough ER (with ribosomes) for protein synthesis; Smooth ER for lipid synthesis and detoxification.
    • Golgi Apparatus: Modifies, sorts, and packages proteins and lipids into vesicles.
    • Lysosomes: Enzymes for intracellular digestion and apoptosis (autophagy).
    • Cytoskeleton: Network of Microfilaments (actin), Microtubules (tubulin), and Intermediate filaments (keratin).

MEMBRANE TRANSPORT AND CELL SIGNALLING

  • Plasma Membrane: Fluid Mosaic Model consisting of a phospholipid bilayer with embedded proteins (Channel, Carrier, Receptor).
  • Passive Transport: Movement down a concentration gradient (No energy).
    • Diffusion: Simple movement of solutes.
    • Facilitated Diffusion: Uses transport proteins.
    • Osmosis: Diffusion of water across a semi-permeable membrane.
      • Hypertonic: High solute (cell shrinks/plasmolysis).
      • Hypotonic: Low solute (cell swells/turgid).
  • Active Transport: Movement against a gradient. Requires energy (ATPATP). Example: Sodium-Potassium Pump (Na+/K+Na^+/K^+ pump).
  • Bulk Transport: Endocytosis (Phagocytosis/Pinocytosis) and Exocytosis.
  • Cell Signalling: Steps: Signal reception →\rightarrow Transduction (relay) →\rightarrow Cellular response.

BIOMOLECULES

  • Carbohydrates: (CH2OCH_2O)n_n.
    • Monosaccharides: Glucose, Fructose, Ribose.
    • Polysaccharides: Starch (energy in plants), Glycogen (energy in animals), Cellulose (plant cell walls).
  • Proteins: Polymers of amino acids linked by peptide bonds.
    • Structure Levels: Primary (sequence), Secondary (alpha helix/beta sheet), Tertiary (3D folding), Quaternary (multiple chains).
    • Enzymes: Biological catalysts. Speed up reactions by lowering Activation Energy. Models: Lock-and-Key vs. Induced Fit.
  • Lipids: Hydrophobic molecules. Includes Acylglycerols (fats/oils), Phospholipids (membranes), Waxes, and Steroids (e.g., Cholesterol).
  • Nucleic Acids:
    • DNA: Double helix, sugar-phosphate backbone, nitrogenous bases (A, T, C, G). Stores genetic info.
    • RNA: Usually single-stranded, contains Uracil (U) instead of Thymine (T). Types: mRNA, tRNA, rRNA.
    • Central Dogma: DNA →\rightarrow (Transcription) →\rightarrow mRNA →\rightarrow (Translation) →\rightarrow Protein.

BIOENERGETICS: PHOTOSYNTHESIS AND RESPIRATION

  • Photosynthesis: Converting light energy to chemical energy.

    • Light Reactions (Grana): Photolysis of water releases oxygen and produces ATP and NADPH via non-cyclic and cyclic photophosphorylation.
    • Calvin Cycle (Stroma): Carbon fixation (via RuBisCO), reduction, and regeneration to produce glucose (C6H12O6C_6H_{12}O_6).
    • Photorespiration: Wasteful process where RuBisCO binds oxygen instead of CO2CO_2. C4 and CAM plants evolved adaptations to minimize this.

  • Cellular Respiration: Breaking down glucose to generate ATP.

    • Glycolysis (Cytosol): Splits glucose into 2 Pyruvate. Net yield: 2 ATP, 2 NADH.
    • Krebs Cycle (Mitochondria): Oxidizes acetyl-CoA to CO2CO_2; produces ATP, NADH, and FADH2FADH_2.
    • Electron Transport Chain (ETC): Uses energy from NADH/FADH2FADH_2 to power Chemiosmosis (ATP synthesis via proton gradient). Oxygen is the final electron acceptor, forming water.

HUMAN PHYSIOLOGY SYSTEMS

  • Digestive System:

    • Oral Cavity: Mastication and salivary amylase (digestionofstarchdigestion of starch).
    • Stomach: Gastric juice (HClHCl and Pepsin) for protein digestion.
    • Small Intestine: Duodenum receives bile (lipid emulsification) and pancreatic juice. Major site of absorption via villi.
    • Large Intestine: Water absorption and fecal formation.
    • Liver: Processes nutrients, detoxifies, and stores glycogen.

  • Respiratory System:

    • Pathway: Nasal cavity →\rightarrow Pharynx →\rightarrow Larynx →\rightarrow Trachea →\rightarrow Bronchi →\rightarrow Bronchioles →\rightarrow Alveoli (site of gas exchange).
    • Breathing Mechanism: Diaphragm and intercostal muscles change thoracic volume to create pressure gradients (Negative pressure breathing).
    • Oxygen Transport: 97% carried by Haemoglobin as oxyhaemoglobin.
    • Carbon Dioxide Transport: Mainly as Bicarbonate ions (HCO3−HCO_3^-) in plasma.

  • Circulatory System:

    • Heart: 4 chambers. Double circulation (Pulmonary and Systemic).
    • Cardiac Cycle: Diastole (ventricular filling) and Systole (contraction). Heartbeat initiated by the SA Node (Pacemaker).
    • Blood Vessels: Arteries (carry blood away, thick walls), Veins (carry blood to heart, valves), Capillaries (gas/nutrient exchange).
    • Blood Pressure: Systolic (120 mmHg120\,mmHg) / Diastolic (80 mmHg80\,mmHg). Regulated by ADH and ANH.
    • Lymphatic System: Returns interstitial fluid to blood; involved in immunity via lymph nodes.

  • Skeletal and Muscular System:

    • Bones: Made of compact and spongy tissue; contain osteoblasts (builders) and osteoclasts (removers).
    • Joints: Fibrous (immovable), Cartilaginous (semi-movable), Synovial (movable - includes Hinge and Ball-and-socket).
    • Muscles: Skeletal (striated/voluntary), Smooth (involuntary), Cardiac (branched/involuntary).
    • Muscle Contraction: Sliding Filament Model. Ca2+Ca^{2+} ions bind to troponin, exposing actin sites for myosin cross-bridges. Power stroke uses ATP to slide filaments.

STRUCTURAL AND COMPUTATIONAL BIOLOGY

  • X-Ray Crystallography: Primary tool for determining the 3D structure of proteins by diffracting X-rays through crystals.
  • Bioinformatics: Using computer algorithms to analyze biological data (Genomics/Proteomics).
  • Sequence Homology:
    • Orthologs: Genes in different species evolved from a common ancestor.
    • Paralogs: Genes related by duplication within a genome.
  • Databases: GenBank (DNA sequences), PDB (Protein structures).