Comprehensive Study Notes: BIO 001 - BIO 004

BIO 001: Cell and Structural Organisation

Cell Theory and Cell Types

• Modern Cell Theory Tenets:

  • All living organisms are composed of one or more cells.
  • The cell is the basic structural and functional unit of life.
  • All cells arise from pre-existing cells through the process of cell division (Biogenesis).
  • Cells contain hereditary information (DNA) which is passed from cell to cell during cell division.
  • All cells are basically the same in chemical composition in organisms of similar species.
  • Energy flow (metabolism and biochemistry) occurs within cells.

• Prokaryotic Cells:

  • Definition: Cells lacking a membrane-bound nucleus or membrane-bound organelles.
  • Genetic Material: DNA is circular and floats freely in a region called the nucleoid.
  • Size: Generally small, ranging from $0.1 \mu m$ to $5.0 \mu m$ in diameter.
  • Ribosomes: Smaller size, designated as $70S$.
  • Cell Wall: Composed of peptidoglycan (in bacteria).
  • Examples: Bacteria and Archaea.

• Eukaryotic Cells:

  • Definition: Cells containing a defined nucleus and membrane-bound organelles.
  • Genetic Material: Linear DNA organized into chromosomes within the nucleus.
  • Size: Larger, typically $10 \mu m$ to $100 \mu m$.
  • Ribosomes: Larger size, designated as $80S$ (found in the cytosol and on the Rough ER).
  • Examples: Animals, plants, fungi, and protists.

Structure and Functions of Cell Organelles

• The Nucleus:

  • Structure: Surrounded by a double-membrane nuclear envelope with nuclear pores. It contains the nucleolus (site of ribosome synthesis) and chromatin (DNA and proteins).
  • Function: Acts as the control center of the cell, storing genetic information and coordinating activities like growth, metabolism, and reproduction.

• Mitochondria:

  • Structure: Double-membraned; the inner membrane is folded into cristae to increase surface area. The internal space is the matrix.
  • Function: Known as the powerhouse of the cell; the site of aerobic respiration and ATP (adenosine triphosphate) production.

• Chloroplasts (Plant Cells Only):

  • Structure: Double-membraned, containing thylakoid stacks called grana and a fluid called stroma. They contain the pigment chlorophyll.
  • Function: Site of photosynthesis, converting light energy into chemical energy (glucose).

• Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes; involved in protein synthesis and modification.
  • Smooth ER: Lacks ribosomes; involved in lipid synthesis, detoxification of chemicals, and calcium ion storage.

• Golgi Apparatus:

  • Structure: A series of flattened, stacked pouches called cisternae.
  • Function: Modifies, sorts, and packages proteins and lipids received from the ER for secretion or delivery to other organelles via vesicles.

Cell Membrane Structure and Transport

• Fluid Mosaic Model:

  • The membrane is a bilayer of phospholipids with embedded proteins, cholesterol, and carbohydrates.
  • Phospholipids: Have hydrophilic (water-loving) heads and hydrophobic (water-fearing) tails.

• Passive Transport:

  • Diffusion: Movement of molecules from an area of high concentration to an area of low concentration until equilibrium is reached.
  • Osmosis: The diffusion of water molecules across a selectively permeable membrane.
  • Tonicity:
    • Isotonic: Equal solute concentration; no net movement of water.
    • Hypotonic: Lower solute concentration outside; water enters the cell (cell may burst/lyse).
    • Hypertonic: Higher solute concentration outside; water leaves the cell (cell shrivels/plasmolysis).

• Active Transport:

  • Requires energy in the form of $ATP$ to move substances against their concentration gradient (from low to high concentration).
  • Examples: Sodium-Potassium Pump ($Na^+/K^+$ pump).

Tissues in Plants and Animals

• Plant Tissues:

  • Meristematic Tissue: Undifferentiated cells capable of active cell division (apical and lateral meristems).
  • Permanent Tissue: Differentiated cells; includes dermal tissue (protection), ground tissue (storage/photosynthesis), and vascular tissue (Xylem for water and Phloem for food).

• Animal Tissues:

  • Epithelial: Covers body surfaces and lines cavities (e.g., skin, lining of the gut).
  • Connective: Supports and binds other tissues (e.g., bone, blood, cartilage).
  • Muscular: Responsible for movement (Skeletal, Smooth, and Cardiac).
  • Nervous: Conducts electrical impulses for communication (Neurons and Glial cells).

Cell Cycle, Mitosis, and Meiosis

• The Cell Cycle:

  • Interphase: The longest phase, consisting of $G_1$ (growth), $S$ (DNA replication), and $G_2$ (preparation for mitosis).
  • M Phase: Includes Mitosis and Cytokinesis.

• Mitosis (Equational Division):

  • Produces two genetically identical diploid ($2n$) daughter cells.
  • Prophase: Chromosomes condense, spindle forms, nuclear envelope breaks down.
  • Metaphase: Chromosomes align at the equator (metaphase plate).
  • Anaphase: Sister chromatids are pulled apart to opposite poles.
  • Telophase: Nuclear envelopes reform, chromosomes de-condense.

• Meiosis (Reduction Division):

  • Produces four genetically different haploid ($n$) gametes.
  • Meiosis I: Homologous chromosomes separate; includes crossing over in Prophase I for genetic variation.
  • Meiosis II: Sister chromatids separate, similar to mitosis.

BIO 002: Genetics, Evolution and Microorganism

Principles of Inheritance and Genetics

• Mendelian Laws:

  • Law of Dominance: In a heterozygote, one trait will conceal the presence of another trait for the same characteristic.
  • Law of Segregation: During gamete formation, the two alleles for each gene separate so that each gamete receives only one allele.
  • Law of Independent Assortment: Genes for different traits can segregate independently during the formation of gametes.

• Terminology:

  • Genotype: The genetic makeup ($TT, Tt, tt$).
  • Phenotype: The physical expression of the trait (Tall, Short).
  • Homozygous: Having two identical alleles ($TT$ or $tt$).
  • Heterozygous: Having two different alleles ($Tt$).

Chromosomal Basis of Inheritance

• Genes are located on specific locations (loci) on chromosomes.
• Sex Linkage: Genes located on sex chromosomes (X or Y). Examples include Hemophilia and Red-Green colour blindness, more common in males due to having only one X chromosome.
• Linkage and Crossing Over: Genes located close together on the same chromosome tend to be inherited together unless separated by crossing over.

Mutation and Genetic Variation

• Mutation: A permanent change in the DNA sequence.
  • Gene Mutations: Point mutations (substitution) or frameshift mutations (insertion/deletion).
  • Chromosomal Mutations: Changes in number (Aneuploidy like Down Syndrome, Trisomy $21$) or structure (Deletion, Inversion, Translocation).
• Sources of Variation: Independent assortment, crossing over, random fertilization, and mutations.

Evolution and Natural Selection

• Darwin’s Theory of Natural Selection:
  • Overproduction: More offspring are produced than can survive.
  • Variation: Individuals in a population have different traits.
  • Selection: Individuals with favorable traits are more likely to survive and reproduce.
  • Adaptation: Over generations, favorable traits become more common in the population.

Microorganisms and Diseases

• Pathogens: Disease-causing agents.
  • Bacteria: Examples include Tuberculosis ($Mycobacterium \, tuberculosis$) and Cholera ($Vibrio \, cholerae$). Treated with antibiotics.
  • Viruses: Examples include HIV/AIDS and Influenza. Require host cells to replicate; managed with vaccines and antivirals.
  • Fungi: Examples include Ringworm and Athlete’s foot.
  • Protozoa: Examples include Malaria ($Plasmodium$ species, transmitted by Anopheles mosquitoes).

Plant Growth and Physiology

• Nutrition in Plants: Requires macronutrients ($N, P, K, Ca, Mg, S$) and micronutrients ($Fe, Zn, Cu, Mn, B, Mo$).
• Transport System:
  • Xylem: Transports water and minerals upward from roots via transpiration pull.
  • Phloem: Transports sucrose and amino acids from leaves to other parts via translocation.
• Growth Regulators (Phytohormones):
  • Auxins: Promote cell elongation and apical dominance.
  • Gibberellins: Promote stem elongation and seed germination.
  • Cytokinins: Promote cell division and delay senescence.
  • Abscisic Acid (ABA): Inhibits growth; promotes seed dormancy and stomatal closure during stress.
  • Ethylene: Gas that promotes fruit ripening.
• Crop Improvement: Techniques include selective breeding, hybridization, and genetic engineering to improve yield, resistance, and nutritional value.

BIO 003: Plant and Animal Physiology

Photosynthesis and Plant Nutrition

• Overall Equation: $6CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2$
• Light-Dependent Reactions: Occur in thylakoids; produce $ATP$ and $NADPH$, releasing $O_2$ from water splitting (photolysis).
• Light-Independent Reactions (Calvin Cycle): Occur in the stroma; use $ATP$ and $NADPH$ to fix $CO_2$ into glucose.

Respiration

• Aerobic Respiration: $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + 36-38 \, ATP$
• Stages:
  1. Glycolysis: Occurs in cytosol; breaks glucose into pyruvate, yielding $2 \, ATP$.
  2. Krebs Cycle: Occurs in mitochondrial matrix; produces electron carriers ($NADH, FADH_2$).
  3. Electron Transport Chain (ETC): Occurs in the inner mitochondrial membrane; produces the bulk of $ATP$.
• Anaerobic Respiration: Occurs without oxygen.
  • Animals: Lactic acid fermentation.
  • Yeast/Plants: Ethanol fermentation.

Human Systems

• Circulatory System: Double circulation. Heart consists of four chambers (Right/Left Atria and Ventricles). Pulmonary circuit to lungs; Systemic circuit to body.
• Respiratory System: Trachea $\\rightarrow$ Bronchi $\\rightarrow$ Bronchioles $\\rightarrow$ Alveoli (site of gas exchange by diffusion).
• Digestive System: Mechanical and chemical breakdown. Enzymes include Amylase (starch), Pepsin (protein in stomach), and Lipase (fats).
• Excretory System: The Nephron is the functional unit of the kidney. Processes include Ultrafiltration, Selective Reabsorption, and Osmoregulation.
• Reproductive System: Production of gametes (Sperm in testes, Ova in ovaries) and hormonal regulation (Testosterone, Estrogen, Progesterone).

Nervous Coordination and Endocrine Control

• Nervous System: Rapid response. Central Nervous System (Brain and Spinal Cord) and Peripheral Nervous System. Nerve impulses travel as action potentials.
• Endocrine System: Slow, long-lasting response using hormones transported in blood.
  • Insulin: Lowers blood glucose (Pancreas).
  • Adrenaline: Fight or flight response (Adrenal glands).

Homeostasis and Enzyme Activity

• Homeostasis: Maintenance of a constant internal environment (e.g., temperature at $37^\circ C$, blood glucose, water potential).
• Enzymes: Biological catalysts.
  • Properties: Protein-natured, specific (Lock and Key model), and sensitive to $pH$ and temperature.
  • Denaturation: Loss of enzyme shape and function due to extreme heat or $pH$ levels.

BIO 004: Ecology, Environment and Practical Skills

Ecosystems and Biodiversity

• Ecosystem Components:
  • Biotic: Producers, Consumers (Primary, Secondary, Tertiary), Decomposers.
  • Abiotic: Sunlight, temperature, soil, water.
• Ecological Relationships:
  • Symbiosis: Mutualism (both benefit), Commensalism (one benefits, one unaffected), Parasitism (one benefits, one harmed).
  • Competition: Resource struggle between organisms.

Food Chains and Webs

• Food Chain: Linear sequence of energy transfer ($\text{Grass} \rightarrow \text{Grasshopper} \rightarrow \text{Frog} \rightarrow \text{Snake} \rightarrow \text{Hawk}$).
• Food Web: Interconnected food chains representing a complex ecosystem.
• Trophic Levels: Only about $10\%$ of energy is transferred to the next level.

Environmental Pollution

• Air Pollution: Greenhouse gases ($CO_2, CH_4$) causing global warming; $SO_2$ causing acid rain.
• Water Pollution: Eutrophication caused by fertilizer runoff, leading to algal blooms and oxygen depletion.
• Soil Pollution: Use of non-biodegradable pesticides and heavy metals.

Classification of Animals

• Invertebrates: Animals without a backbone.
  • Phyla: Porifera (sponges), Cnidaria (jellyfish), Platyhelminthes (flatworms), Nematoda (roundworms), Annelida (segmented worms), Mollusca (snails), Arthropoda (insects, spiders), Echinodermata (starfish).
• Chordates (Vertebrates): Animals with a notochord/backbone.
  • Classes: Pisces (fish), Amphibia (frogs), Reptilia (snakes), Aves (birds), Mammalia (humans).

Physiological Processes and Membrane Transport

• Further Transport Mechanisms:
  • Endocytosis: Cell taking in large particles (Phagocytosis for solids/Pinocytosis for liquids) via vesicles.
  • Exocytosis: Cell releasing materials via vesicles fusing with the plasma membrane.
• Importance of Transport: Essential for nutrient uptake, waste removal, and maintaining ion gradients for nervous and muscular function.