St. Mary's University Pre-University Remedial Program Biology Module Comprehensive Notes

THE SCIENCE OF BIOLOGY

• Definition: Biology is a special branch of science that deals with living things, their nature, functions, and interactions with each other and their environment.
• Significance of Biology:
  • Critically affects lives through research on expanding population and diseases like cancer, COVID-19, and AIDS.
  • Opportunities in developmental biology (investigating genes and birth defects) and immunology (cures for cancer, AIDS, or the common cold).
  • Enhances management of natural resources, disease prevention, and quality of life.

THE SCIENTIFIC METHOD

• Concept: Science is a systematically organized body of knowledge regarding nature, society, and thought. It involves the method of investigation, field of investigation, and results of investigation.
• Scientific steps:
  1. Observation: Direct (sensory) or indirect (microscope). Accurate data recording leads to problem identification.
  2. Defining the Problem: Asking questions like "Why," "How," or "When."
  3. Gathering Information and Forming a Hypothesis: Qualitative (color, taste) or quantitative (measurements) data provided. A hypothesis is an intelligent guess or tentative theory characterized by interconnected statements providing solutions.
  4. Inductive vs. Deductive Reasoning:
     • Deductive: General to specific ($All\,animals\,are\,mortal \rightarrow Dogs\,are\,animals \rightarrow Dogs\,are\,mortal$).
     • Inductive: Specific to general ($Apple\,x,\,y,\,z\,are\,sweet \rightarrow All\,apples\,are\,sweet$).
  5. Testing Hypothesis/Experimentation: Involves variables:
     • Independent Variable: Condition changed systematically.
     • Dependent Variable: Variables that change because of the independent variable (e.g., rate of growth).
     • Controlled Variable: Factors kept constant (e.g., light in a growth study).
     • Groups: Experimental (treated) and Control (untreated).
  6. Recording, Analysis, and Interpretation: Organizing data into tables, charts, or graphs.
  7. Drawing Conclusions: Objective analysis of gathered data.
  8. Theory, Principle, Fact, and Law: A hypothesis tested true becomes a theory. If proved invariable, it becomes a fact, principle, or law. Modeling (e.g., Key and Lock model) simplifies ideas.
  9. Evaluation: Repeating experiments for consistent results.
  10. Reporting: Sharing knowledge via journals (e.g., Nature, Science).

BIOLOGY TOOLS AND MICROSCOPY

• Laboratory Tools: Dissecting kit (forceps, scalpel, etc.), Mortar and pestle, Pipette, Microscope (slides, cover slips), Centrifuge, Water-bath, Balance.
• Field Tools: Plant press, Insect net, Secateurs, Altimeter, GIS (Geographical Information System), GPS (Geographical Positioning System), Quadrats, Theodolites.
• Microscopy Concepts:
  • Resolution: Ability to distinguish between two separate objects ($Light\,microscope = 200\,nm;\,Electron\,microscope = 0.5\,nm$).
  • Magnification: Total magnification = $Eye\,piece\,lens \times objective\,lens$.
• Types of Microscopes:
  • Simple: Hand lens ($10\times$ to $20\times$).
  • Compound (Light): Uses two convex lenses and light rays ($max\,1500\times$). Limit of resolution is $0.2\,\mu m$.
  • Electron: Uses electron beams and magnets. TEM (Transmission) for interior details; SEM (Scanning) for 3D surface details.
  • Dissecting: Binocular, moderate magnification ($10\times$).
  • Phase Contrast/Interference: Studies fine structures and contrast in living cells.
• Parts of the Compound Microscope: Arm, Base, Ocular lens ($10\times$), Objective lens ($10\times,\,40\times,\,100\times$), Nose piece, Stage, Coarse/Fine adjustment knobs, Iris diaphragm, Condenser, Mirror, Stage clips.

BIOCHEMICAL MOLECULES: INORGANIC

• Water ($H_2O$): Makes up $60-95\%$ of fresh mass.
  • Properties: Polar, liquid at room temperature, high latent heat of vaporization (sweat cooling), maximum density at $4^\circ C$ (ice floats), high surface tension, low viscosity.
• Mineral Salts:
  • Major Elements: Calcium (Ca - bones, teeth, middle lamella), Sulphur (S - proteins, Co-enzyme A), Nitrogen (N - chlorophyll, DNA), Phosphorus (P - ATP, membranes), Magnesium (Mg - chlorophyll cofactor), Sodium/Potassium (Na/K - nerve impulses/osmotic balance).
  • Trace Elements: Iron (Fe - hemoglobin), Manganese (Mn - photosynthesis), Molybdenum (Mo - nitrogen fixation), Copper (Cu - melanin), Iodine (I - thyroxine).

BIOCHEMICAL MOLECULES: ORGANIC

• Carbohydrates: General formula $C_x(H_2O)_y$.
  • Monosaccharides: Trioses (respiration intermediates), Pentoses (Ribose/Deoxyribose), Hexoses (Glucose, Fructose, Galactose). Energy release: $17\,kJ/g$.
  • Disaccharides: Maltose ($G+G$), Lactose ($G+Gal$), Sucrose ($G+F$). Sucrose is non-reducing.
  • Polysaccharides: Starch (plant store), Glycogen (animal store), Cellulose (cell walls), Chitin (fungi/arthropods), Murein (bacteria).
• Lipids: C, H, O (low O). Hydrophobic.
  • Structure: Triglycerides = $1\,Glycerol + 3\,Fatty\,Acids$. Energy release: $38\,kJ/g$.
  • Saturated vs. Unsaturated: Unsaturated have double bonds ($C=C$) and are liquid at room temp.
• Proteins: Polymers of 20 amino acids. Nitrogen is a key component.
  • Structure: Primary (sequence), Secondary (alpha-helix, beta-pleated sheets), Tertiary (3D globular/fibrous), Quaternary (multiple chains, e.g., hemoglobin).
• Nucleic Acids: Nucleotides made of phosphate + pentose + base (Purines: A, G; Pyrimidines: C, T, U).
  • DNA: Double-stranded, deoxyribose, thymine, stable.
  • RNA: Single-stranded, ribose, uracil, less stable. Types: mRNA (blueprint), tRNA (adapter), rRNA (workbench).

CELL BIOLOGY

• Cell Theory: 1. All organisms consist of one or more cells. 2. Cells are basic units of organization. 3. Cells arise from pre-existing cells.
• Discovery: Robert Hooke (1665 - cork cells), Leeuwenhoek (animalcules), Schleiden/Schwann (1838/39), Virchow (1855).
• Types of Cells:
  • Prokaryotic: No membrane-bound nucleus (e.g., Bacteria).
  • Eukaryotic: True nucleus and organelles (e.g., Animals, Plants, Fungi).
• Organelles:
  • Mitochondria: "Powerhouse," matrix, and cristae; site of ATP production.
  • Ribosomes: Protein synthesis; no membrane.
  • Endoplasmic Reticulum (ER): Rough (translation) and Smooth (lipid synthesis).
  • Golgi Complex: Modifying and packaging products; producing lysosomes.
  • Lysosomes: Hydrolytic enzymes for digestion; found in sperm heads (acrosome).
  • Chloroplasts: Chlorophyll for photosynthesis; stroma and grana.
• Transport Mechanisms:
  • Diffusion: Simple and Facilitated (via carrier proteins).
  • Osmosis: Movement of water. Hypertonic (shrinking/plasmolysis), Hypotonic (turgidity/swelling), Isotonic (balance).
  • Active Transport: Uses ATP (e.g., Sodium-Potassium pump).
  • Bulk Transport: Endocytosis (Phagocytosis - eating; Pinocytosis - drinking) and Exocytosis.
• Cellular Respiration:
  • Aerobic: Glycolysis (cytosol), Krebs Cycle (mitochondria matrix), ETC (inner membrane). Total yield: Approx. $36-38\,ATP$.
  • Anaerobic: Lactic acid fermentation (muscles) or Alcoholic fermentation (yeast yielding ethanol + $CO_2$).

MICRO-ORGANISMS

• Groups: Protozoa (unicellular motile eukaryotes), Fungi (yeasts and moulds, saprobionts/parasites), Algae (phototrophs), Viruses (virion with capsid and DNA/RNA), Bacteria (prokaryotes).
• Bacterial Shapes: Cocci (spherical), Bacilli (rods), Spirochaetes (spirals).
• Gram Stain: Primary stain Crystal Violet, Iodine mordant, Ethanol decolorizer, Safranin counterstain. Gram-positive (purple, thick peptidoglycan). Gram-negative (red, outer membrane, endotoxins).
• Pathogens and Transmission: Germ Theory (Koch/Pasteur). Methods: Droplet, contaminated water/food, direct contact, vectors (Mosquito - Malaria; Tsetse fly - Sleeping sickness).
• HIV/AIDS: Retrovirus with RNA and reverse transcriptase. Targets CD4 T-lymphocytes (T-helper cells). Latency phase. Treatment: HAART.
• Biological Cycles:
  • Nitrogen Cycle: Rhizobium (fixation), Nitrosomonas (nitrite), Nitrobacter (nitrate), Pseudomonas (denitrification).
  • Sulphur Cycle: Desulphovibrio (anaerobic decomposition).
• Sterilization: Autoclave ($121^\circ C$, $15\,psi$), UHT ($135-150^\circ C$), Pasteurization ($71.6^\circ C$ for $15\,s$).

GENETICS AND HEREDITY

• DNA Replication: Semiconservative. Enzymes: Helicase (unwinding), DNA Polymerase (synthesis), Ligase (joins Okazaki fragments), Topoisomerase (removes supercoils).
• Protein Synthesis:
  • Transcription: RNA polymerase reads DNA ($3' \rightarrow 5'$) to build mRNA ($5' \rightarrow 3'$).
  • Translation: Ribosome reads mRNA; tRNA brings amino acids; sites A, P, E.
• Genetic Code: Triplet, universal, degenerate, and non-overlapping. Start codon: AUG. Stop: UAA, UAG, UGA.
• Cell Division:
  • Mitosis: One division, 2 identical diploid daughter cells. Used for growth/repair.
  • Meiosis: Two divisions, 4 non-identical haploid gametes. Independent assortment and crossing over cause variation.
• Mendel's Laws: 1. Law of Dominance. 2. Law of Segregation. 3. Law of Independent Assortment.
• Mutations:
  • Numerical: Aneuploidy ($2n+1,\,2n-1$; e.g., Down's syndrome, Turner syndrome), Polyploidy.
  • Structural: Deletion, Duplication, Inversion, Insertion, Translocation.
  • Gene/Point: Substitution, Deletion, Insertion (frameshift).

EVOLUTION

• Theories of Origin: Special Creationism, Spontaneous Generation (disproved by Redi and Pasteur), Eternity of Life, Cosmozoan (Panspermia), Biochemical (Oparin-Haldane - reducing atmosphere).
• Theories of Evolution:
  • Lamarckism: Use and disuse; inheritance of acquired traits ($Giraffe\,neck\,elongation$).
  • Natural Selection (Darwin): V.I.S.T (Variation, Inheritance, Selection, Time). Survival of the fittest.
  • Neo-Darwinism: Modern synthesis combining natural selection with Mendelian genetics and molecular biology.
• Evidence: Paleontology (Fossils - Type I remains, Type II trace), Stratigraphy, Radiocarbon dating ($C_{14}$, max $60,000$ years), Potassium-Argon dating, Comparative Anatomy (Homologous vs. Analogous vs. Vestigial structures).
• Speciation: Allopatric (geographical) vs. Sympatric (seasonal, temporal, behavioral).
• Types of Selection: Directional (shifts to extreme), Stabilizing (favors mean), Disruptive (favors both extremes).
• Human Evolution: 6 million years since common ancestor with Chimpanzees.
  • Key Fossils: Lucy (A. afarensis, Afar, Ethiopia, $3.2$ million years), Ardi (Ar. ramidus, Afar, Ethiopia, $4.4$ million years).
  • Features: Bipedalism, Large Brain (Homo sapiens $1.8-2.3\%$ of mass).

BIOTECHNOLOGY

• Traditional: Yeast fermentation (Anaerobic: $Glucose \rightarrow Ethanol + CO_2$). Injera (ershoo), Tej, Wine, Beer. Yoghurt (irgo - Lactobacillus), Cheese (ayib).
• Modern: Industrial fermenters (oxygen, stirrers, cooling jackets).
• Genetic Engineering: Restriction endonucleases (cutting), Ligase (pasting), Vectors (Plasmids/Viruses). Transgenic organisms.
• Medical Applications: Humulin (synthetic insulin), Penicillin (Fleming, 1928), Gene Therapy, ELISA ($early\,diagnosis$), PCR ($nucleic\,acid\,amplification$).
• Biofuels: Biogas (Methane $50-80\%$), Bio-ethanol (carbon-neutral).

HUMAN BIOLOGY AND HEALTH

• Nutrition: Macronutrients vs. Micronutrients.
  • Energy: Carbohydrate ($17\,kJ/g$), Proteins ($17\,kJ/g$), Lipids ($38\,kJ/g$).
  • Deficiencies: Protein (Kwashiorkor/Marasmus), Vitamin A (Night blindness), Vitamin C (Scurvy), Vitamin D (Rickets), Iodine (Goiter), Iron (Anemia).
• Diseases: NCDs (Cardiovascular, Cancer, Diabetes Type I/II, Obesity - $BMI > 30$).
• Digestive System: Teeth (Enamel, Dentine, Pulp). Peristalsis. Gastric juice (HCl + Pepsin). Bile (liver - emulsification). Villi and Microvilli (absorption).
• Respiratory System: Nasal cavity, Pharynx, Trachea ($C-shaped\,cartilage$), Bronchioles, Alveoli. Tidal volume ($500\,cm^3$).
• Circulatory System: Double circulation. Arteries (away, thick walled), Veins (toward, valves), Capillaries. Heart (Diastole - relax, Systole - contract). Blood (Plasma, RBC - $120\,day\,life$, WBC, Platelets). ABO Blood groups.
• Control Systems:
  • Nervous Control: Neurons (sensory, inter, motor), synapses, myelin sheath. CNS (brain/spinal cord) vs. PNS.
  • Hormonal Control: Pituitary (master), Thyroid (thyroxine), Pancreas (insulin/glucagon), Adrenal (adrenalin), Gonads.
• Reproductive System: Male (Testes, Vas Deferens, Prostate), Female (Ovaries, Fallopian tubes, Uterus - endometrium, Vagina).

PLANT BIOLOGY

• Photosynthesis: $6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$.
  • Light-dependent: Photolysis of water, produce ATP/NADPH.
  • Light-independent: Carbon fixation in Stroma.
• Transport: Xylem (passive water move, transpiration stream, adhesion/cohesion) vs. Phloem (active translocation of sugars).
• Growth/Response: Tropisms (Phototropism, Geotropism, Hydrotropism).
• Plant Hormones: Auxins (IAA - elongation, apical dominance), Gibberellins (stem elongation), Cytokinins (cell division), ABA (dormancy/leaf fall), Ethylene (fruit ripening).

ECOLOGY AND CONSERVATION

• Ecosystem Structures: Trophic levels (Producers, Consumers - primary/secondary, Decomposers). Energy flow is unidirectional.
• Cycles: Carbon, Nitrogen, Phosphorus, Sulphur, Water.
• Ecological Succession: Primary (on bare rock, pioneer community) vs. Secondary (on cleared land). Climax community.
• Biomes: Terrestrial (Desert, Tundra, Taiga, Forest, Rainforest) and Aquatic (Marine/Freshwater).
• Biodiversity: Simpson's Index ($d = \frac{N(N-1)}{\sum n(n-1)}$).
• Ethiopian Context: High endemicity (Teff, Enset, Walia Ibex, Ethiopian Wolf). Threats: Deforestation, overgrazing, population growth.
• Pollution: Global Warming ($CO_2$, methane), Acid Rain ($SO_2$, nitrogen oxides).