Biology Matters: Exhaustive Study Guide for GCE O- GCE 'O' Level

CELL STRUCTURE AND ORGANISATION

• Cells are the simplest structural and functional units of all living things, often compared to bricks in a building.
• Chemical Factory Analogy: Cells function as chemical factories where chemical reactions occur to take place raw materials, process them into new molecules, and either use them internally or transport them elsewhere.
• Division of Labour: Specialised structures within cells perform specific roles (e.g., mitochondria for energy, chloroplasts for food production) to increase overall efficiency and ensure survival.
• History of Discovery: The term "cells" was introduced by Robert Hooke in 1667 after observing cork bark under a microscope. He saw "closely packed little boxes" which were actually the walls of dead plant cells.
• Microscopy:
  • Light Microscope: Magnifies up to $1000\, \times$. Micrographs provided are in colour.
  • Electron Microscope: Magnifies more than $200000\, \times$. Micrographs are black-and-white (though can be artificially colourised) and show finer details like organelles.
  • Sectioning: Cells are studied via transverse sections (T.S. – cut across) or longitudinal sections (L.S. – cut along the length) to build a 3D model.
• Protoplasm: The mass of living matter in a cell consisting of the cell membrane, cytoplasm, and nucleus. It is a complex jelly-like substance where chemical activities occur.
• Cell Structures and Organelles:
  • Cell Membrane (Cell Surface Membrane): A partially permeable layer made of lipids and proteins. It controls the movement of substances in and out of the cell.
  • Cell Wall: Found only in plant cells; made of cellulose. It is fully permeable, provides protection, and maintains the cell's fixed shape.
  • Cytoplasm: The part of the protoplasm between the cell membrane and the nucleus where most cellular activities occur. It contains organelles.
  • Nucleus: Surrounded by a nuclear membrane. It controls cell activities (growth, repair) and is essential for cell division. Mammalian red blood cells lack a nucleus and cannot divide.
  • Chromosomes: Found in the nucleus as long thread-like structures made of proteins and DNA (deoxyribonucleic acid). Humans have $46$ chromosomes in each body cell. They store hereditary information.
  • Rough Endoplasmic Reticulum (RER): A network of flattened spaces lined with a membrane. It appears rough due to attached ribosomes. It is continuous with the nuclear membrane and transports proteins to the Golgi body.
  • Ribosomes: Small round structures needed for protein synthesis. Ribosomes on the RER make proteins for transport out of the cell; free ribosomes in the cytoplasm make proteins for internal use.
  • Smooth Endoplasmic Reticulum (SER): Tubular and lacks ribosomes. Functions include synthesising fats and steroids (like sex hormones) and detoxification of harmful substances.
  • Golgi Body: Disk-shaped stack of flattened spaces. It chemically modifies substances from the ER, packages them into vesicles, and secretes them out of the cell.
  • Mitochondria (Singular: Mitochondrion): Oval-shaped organelles where aerobic respiration occurs to release energy for growth and reproduction.
  • Chloroplasts: Oval structures in plant cells containing the green pigment chlorophyll, essential for photosynthesis.
  • Vacuoles: Fluid-filled spaces enclosed by a partially permeable membrane. Plant cells have one large sap-filled central vacuole (sugars, mineral salts, amino acids). Animal cells have small, temporary vacuoles (water, food).
• Structural Hierarchy: Cells form tissues (simple or complex like muscular vs. blood/xylem); tissues form organs (stomach, leaf); organs work as organ systems (digestive, shoot system).
• Cell Specialisation (Differentiation):
  • Red Blood Cell: Biconcave shape (high surface area-to-volume ratio for oxygen diffusion), no nucleus (more space for haemoglobin), flexible (squeezes through capillaries).
  • Muscle Cell: Elongated/cylindrical, contains many mitochondria to provide energy for contraction.
  • Root Hair Cell: Long, narrow hair extension to increase surface area-to-volume ratio for faster water and mineral salt absorption.
• Stem Cells: Unspecialised cells with the ability to develop into other specialised types; used in treatments like bone marrow transplants for leukaemia.

MOVEMENT OF SUBSTANCES

• Diffusion: The net movement of particles (atoms, molecules, ions) from a region of higher concentration to a region of lower concentration, moving down a concentration gradient.
• Concentration Gradient: The difference in concentration between two regions. A steeper gradient results in a faster diffusion rate.
• Factors Affecting Diffusion Rate:
  • Concentration Gradient: Higher steepness increases rate.
  • Diffusion Distance: Shorter distances allow faster diffusion.
  • Surface Area-to-Volume Ratio: The larger the ratio, the higher the rate of substance movement in and out of the cell.
• Osmosis: The net movement of water molecules from a region of higher water potential to a region of lower water potential through a partially permeable membrane.
• Water Potential: A measure of the tendency of water molecules to move. Dilute solutions have higher water potential; concentrated solutions have lower water potential.
• Effects of Osmosis on Tissues:
  • Higher Water Potential (outside): Plant cells expand and become turgid (supported by turgor pressure against the inelastic cell wall). Animal cells swell and may burst.
  • Lower Water Potential (outside): Plant cells become flaccid and the cytoplasm shrinks away from the cell wall (plasmolysis). Animal cells shrink and spikes appear (crenation), leading to possible death.
• Active Transport: An energy-consuming process where substances are moved across a membrane against their concentration gradient (from lower to higher concentration). Requires energy from aerobic respiration.
• Examples of Active Transport: Ion uptake by root hairs from soil; glucose uptake by epithelial cells in the villi of the small intestine.

BIOLOGICAL MOLECULES

• Nutrients: Include water (approx. $70\,\%$ of body weight), carbohydrates, fats, and proteins.
• Carbohydrates: Organic molecules made of carbon, hydrogen, and oxygen, with Hydrogen:Oxygen in a $2:1$ ratio.
  • Single Sugars (Monosaccharides): Glucose, fructose. Can pass through cell membranes.
  • Double Sugars (Disaccharides): Maltose ($\text{glucose} + \text{glucose}$), Sucrose ($\text{glucose} + \text{fructose}$).
  • Complex Carbohydrates (Polysaccharides): Starch (plant storage), Glycogen (animal storage in liver/muscles), Cellulose (plant cell walls).
  • Storage Benefits: Starch and glycogen are large, insoluble (no effect on water potential), compact, and easily broken down to glucose.
• Carbohydrate Tests:
  • Benedict's Test (Reducing Sugars): Add Benedict's solution to sample and boil. Brick-red precipitate indicates a large amount; green/yellow/orange indicates traces/moderate amounts.
  • Iodine Test (Starch): Add iodine solution. Change from brown to blue-black indicates starch presence.
• Fats (Lipids): Made of carbon, hydrogen, and oxygen (much less oxygen than carbohydrates). Synthesised from one glycerol and three fatty acid molecules.
  • Functions: Energy storage, insulation (blubber), solvent for vitamins, reducing water loss from skin.
  • Ethanol Emulsion Test: Add ethanol, then water. Presence of a white emulsion indicates fats.
• Proteins: Made of carbon, hydrogen, oxygen, nitrogen (and sometimes sulfur). Synthesised from amino acids.
  • Structure: Amino acids link to form polypeptides, which fold into 3D shapes.
  • Biuret Test: Add biuret solution. Change from blue to violet indicates proteins.

ENZYMES

• Definition: Biological catalysts made of protein that speed up metabolic reactions without being chemically changed.
• Activation Energy: The energy required to start a reaction. Enzymes lower this energy or provide an alternative pathway.
• Digestive Enzymes: Amylase (starch to maltose), Maltase (maltose to glucose), Protease (proteins to polypeptides then amino acids), Lipase (fats to fatty acids and glycerol).
• Nomenclature: Most enzyme names end in "-ase" (e.g., lipase).
• Mode of Action (Lock-and-Key Hypothesis):
  • The substrate (key) fits into the enzyme's active site (lock), forming an enzyme-substrate complex.
  • The reaction converted substrate into products, which leave the active site.
• Characteristics:
  • Speed: Required in minute amounts.
  • Specificity: High specificity due to unique 3D shapes.
  • Temperature: Rate increases with temperature until the optimum ($40-45\,^\circ\text{C}$ for humans). Beyond this, enzymes are denatured.
  • pH: Most have specific optimum pH; changes lead to denaturation (e.g., pepsin at pH 2, salivary amylase at pH 7).
• Denaturation: Irreversible change in 3D structure (loss of active site) caused by high temperature or extreme pH.

NUTRITION IN HUMANS

• Stages: Ingestion (food in), Digestion (breakdown), Absorption (nutrients into blood), Assimilation (use by cells), Egestion (removal of waste).
• Digestive Organs:
  • Mouth: Teeth (physical digestion); Salivary glands (saliva with amylase to digest starch).
  • Oesophagus: Moves food via peristalsis.
  • Peristalsis: Rhythmic wave-like muscular contractions. Circular muscles contract (narrowing lumen) while longitudinal muscles relax, pushing food along.
  • Stomach: Secretes gastric juice (hydrochloric acid at pH 2 for pepsin/protease, kills bacteria). Forms chyme.
  • Small Intestine (Duodenum/Ileum): Main site of digestion and absorption. Secretes intestinal juice. Receives pancreatic juice and bile.
  • Liver: Produces bile (alkaline, emulsifies fats); carries out deamination of amino acids (forms urea); detoxification of alcohol; regulates blood glucose.
  • Gall Bladder: Stores bile.
  • Pancreas: Secretes pancreatic juice (amylase, lipase, protease); produces insulin and glucagon.
  • Large Intestine: Colon absorbs water; Rectum stores faeces; Anus performs egestion.
• Digestion Mechanisms:
  • Physical Digestion: Chewing, stomach churning, bile emulsification (breaking fat into tiny droplets to increase surface area).
  • Chemical Digestion: Breakdown of large molecules via enzymes into small soluble ones.
• Absorption in the Small Intestine:
  • Adaptations: Folds/villi/microvilli (increase surface area); one-cell thick epithelium (short diffusion distance); many blood capillaries (glucose/amino acids); lacteals (fats).
• Liver Functions (Exhaustive):
  • Blood Glucose Regulation: Converts glucose to glycogen (insulin) or glycogen to glucose (glucagon).
  • Deamination: Removing amino groups from excess amino acids to form urea ($\text{NH}_2$ removal).
  • Hormone Breakdown: Breaks down hormones after use.
  • Detoxification: Converts harmful substances (alcohol, benzoic acid) into harmless ones.
• Alcohol Consumption Effects:
  • Digestive: Gastric ulcers, liver cirrhosis (replacement of cells with fibrous tissue).
  • Nervous: Depressant (slows brain function), reduced self-control, increased reaction time. Long-term: "Wet brain" (dementia from B1 deficiency), brain shrinkage.

TRANSPORT IN HUMANS

• Blood Components:
  • Plasma: Yellowish liquid transporting blood cells, ions, food, hormones ($\text{CO}_2$, urea, vitamins, proteins).
  • Red Blood Cells (Erythrocytes): Biconcave, no nucleus, contain haemoglobin. Carry oxygen ($\text{haemoglobin} + \text{oxygen} \rightleftharpoons \text{oxyhaemoglobin}$).
  • White Blood Cells (Leukocytes): Phagocytes (engulf bacteria) and Lymphocytes (produce antibodies).
  • Platelets: Fragments involved in blood clotting (catalyse conversion of soluble fibrinogen to insoluble fibrin threads).
• Blood Groups (ABO System):
  • Based on Antigens (A, B) on RBCs and Antibodies (a, b) in plasma.
  • Group O: Universal donor (no antigens).
  • Group AB: Universal acceptor (no antibodies).
  • Agglutination: Clumping of cells when incompatible blood types are mixed (e.g., Antigen A mixed with Antibody a).
• Blood Vessels:
  • Arteries: Carry blood away from heart; thick, muscular, elastic walls to withstand high pressure.
  • Veins: Carry blood back to heart; thin walls, possess valves to prevent backflow.
  • Capillaries: One-cell thick walls, microscopic; allow exchange between blood and tissue fluid.
• Heart Structure:
  • Four chambers: Right/Left Atria (upper), Right/Left Ventricles (lower).
  • Ventricles have thicker walls; Left Ventricle has thickest wall (pumps blood to whole body).
  • Valves: Tricuspid, Bicuspid (mitral), Semi-lunar (aortic and pulmonary).
• Cardiac Cycle: Systole (contraction phase) and Diastole (relaxation phase). Phases: Atria contract, Ventricles contract ('lub'), Ventricles relax ('dub').
• Blood Pressure: Normal approx. $120/80\,\text{mmHg}$ ($120$ systolic, $80$ diastolic).
• Coronary Heart Disease (CHD): Blockage of coronary arteries (atherosclerosis) due to fatty deposits (cholesterol). Risk factors: smoking, sedentary lifestyle, unhealthy diet, age, genetics.

RESPIRATION IN HUMANS

• Aerobic Respiration: Release of large amount of energy by breakdown of glucose in presence of oxygen.
  • Equation: $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{Energy}$
• Anaerobic Respiration: Release of energy without oxygen. Occurs in muscles during vigorous exercise.
  • Equation: $\text{Glucose} \rightarrow \text{Lactic acid} + \text{small amount of energy}$
• Oxygen Debt: Amount of oxygen needed after exercise to remove lactic acid buildup in the liver.
• Gas Exchange System:
  • Air Passage: Nostrils → Pharynx → Larynx → Trachea → Bronchi → Bronchioles → Alveoli.
  • Trachea: Supported by C-shaped cartilage rings; lined with gland cells (mucus) and ciliated cells (sweep mucus).
  • Alveoli Adaptations: Large surface area (millions of air sacs), one-cell thick walls, thin film of moisture, rich capillary supply.
• Breathing Mechanism:
  • Inspiration (Inhalation): External intercostal muscles contract, internal intercostals relax. Ribs move up/out. Diaphragm contracts/flattens. Thoracic volume increases, pressure decreases, air enters.
  • Expiration (Exhalation): Internal intercostal muscles contract, external intercostals relax. Ribs move down/in. Diaphragm relaxes/arches. Thoracic volume decreases, pressure increases, air forced out.
• Tidal Air: Normal breath volume approx. $500\,\text{cm}^3$.
• Tobacco Smoke Effects:
  • Nicotine: Addictive, increases HR/BP, increases blood clot risk.
  • Carbon Monoxide: Binds permanently to haemoglobin; reduces oxygen transport.
  • Tar: Carcinogen; paralyses cilia, leads to excess mucus.
  • Diseases: Chronic bronchitis, Emphysema (breakdown of alveolar partition walls), Lung cancer.

EXCRETION IN HUMANS

• Excretion: Removal of metabolic waste, toxic substances, and substances in excess (e.g., $CO_2$ via lungs, urea/salts/water via kidneys).
• Urinary System: Kidneys (produce urine), Ureters (transport to bladder), Bladder (storage), Urethra (duct to outside).
• Nephron Structure: Bowman's Capsule (contains glomerulus), Proximal Convoluted Tubule, Loop of Henlé, Distal Convoluted Tubule, Collecting Duct.
• Urine Formation:
  • Ultrafiltration: High pressure in the glomerulus forces small molecules (glucose, water, salts, urea) into the Bowman's capsule, forming glomerular filtrate.
  • Selective Reabsorption: In the nephrons, all glucose/amino acids (active transport), some salts (active transport), and most water (osmosis) are reabsorbed into blood.
• Osmoregulation: Control of water potential in blood via Antidiuretic Hormone (ADH).
  • If water potential is low (sweating): High ADH released → collecting ducts more permeable → more water reabsorbed → small volume of concentrated urine.
• Kidney Failure and Dialysis:
  • Dialysis machine mimics kidney. Dialysis fluid concentration equals blood for glucose/salts to prevent loss but lacks urea to create concentration gradient. Dialysis tubing is long, narrow, and coiled; flow is counter-current to blood flow.

HOMEOSTASIS AND HORMONAL CONTROL

• Homeostasis: Maintenance of a constant internal environment (e.g., blood glucose at $70-90\,\text{mg}/100\,\text{cm}^3$, body temp at $37\,^\circ\text{C}$, water potential).
• Principles: Stimulus → Receptor → Control Centre → Corrective Mechanism → Negative Feedback.
• Hormones: Chemical substances produced by endocrine (ductless) glands, carried by blood to specific target organs.
• Islets of Langerhans (Pancreas):
  • Insulin: Lowers blood glucose by increasing cell permeability to glucose, stimulating conversion of glucose to glycogen, increasing respiration.
  • Glucagon: Raises blood glucose by stimulating conversion of glycogen to glucose and lipids/amino acids into glucose.
• Diabetes Mellitus: Type 1 (insufficient insulin); Type 2 (insulin resistance). Risk factors: Obesity, age, sedentary lifestyle, genetics.
• Temperature Regulation (Skin):
  • Hot Weather: Vasodilation (arterioles dilate, more blood to skin surface); active sweat glands (evaporative cooling); decreased metabolic rate.
  • Cold Weather: Vasoconstriction (arterioles constrict, less blood to skin); decreased sweating; increased metabolic rate; shivering.

THE NERVOUS SYSTEM AND THE EYE

• Components: Central Nervous System (Brain and Spinal Cord) and Peripheral Nervous System (Cranial and Spinal Nerves).
• Neurones:
  • Sensory Neurone: Transmits impulses from receptors to CNS.
  • Relay Neurone: Intermediate neurone within CNS.
  • Motor Neurone: Transmits impulses from CNS to effectors.
• Synapse: Tiny gap between two neurones where chemicals transmit impulses.
• Reflex Action: Rapid, automatic response to a specific stimulus without conscious control. Pathway is the Reflex Arc: Receptor → Sensory Neurone → Relay Neurone (CNS) → Motor Neurone → Effector.
• Eye Structure:
  • Sclera: Tough outer coat; Cornea: Refracts light.
  • Choroid: Black pigment (prevents internal reflection), contains blood vessels.
  • Iris: Circular sheet of muscles; Pupil: Hole allowing light entry.
  • Retina: Photoreceptive layer with Rods (dim light, B&W) and Cones (colour, bright light).
  • Fovea: Highest concentration of cones.
  • Ciliary Body: Contains muscles to control lens thickness.
• Pupil Reflex: Bright light → circular muscles contract, radial muscles relax → pupil constricts. Dim light → radial muscles contract, circular muscles relax → pupil dilates.
• Accommodation (Focusing):
  • Distant Object: Ciliary muscles relax → suspensory ligaments taut → lens becomes thin/less convex.
  • Near Object: Ciliary muscles contract → suspensory ligaments slacken → lens becomes thick/more convex.

INFECTIOUS DISEASES IN HUMANS

• Infectious Diseases: Caused by pathogens (viruses, bacteria) and spread via droplets, direct contact, water/food.
• Pathogens:
  • Bacteria: Single-celled, have cell walls, DNA (not in nucleus), plasmids, and ribosomes. Some pathogenic.
  • Virus: Protein coat enclosing genetic material (DNA/RNA); reproduce ONLY in living host cells; lack cell structures.
• Influenza: Caused by influenza virus; spreads by droplets; high fever, aches.
• Pneumococcal Disease: Caused by Streptococcus pneumoniae bacteria; spreads by droplets; pneumonia, respiratory issues.
• Vaccines: Agents resembling pathogens; stimulate white blood cells to produce memory cells and antibodies.
• Antibiotics: Drugs treating bacterial infections by inhibiting cell wall/membrane synthesis, protein synthesis, or enzyme action. Ineffective against viruses (no cell walls/ribosomes).
• Antibiotic Resistance: Caused by misuse/under-dosing; leads to survival of less-sensitive bacteria which multiply.

NUTRITION AND TRANSPORT IN FLOWERING PLANTS

• Leaf Internal Structure: Cuticle, Upper/Lower Epidermis, Palisade Mesophyll (tightly packed, many chloroplasts), Spongy Mesophyll (irregular cells, many air spaces), Stomata (surrounded by guard cells).
• Stomata Control: Guard cells photosynthesise → higher glucose/lower water potential → water enters by osmosis → cells become turgid and curved → stoma opens.
• Transport Tissues:
  • Xylem: Dead cells, empty lumen, walls thickened with lignin (mechanical support). Transports water/minerals from roots to leaves.
  • Phloem: Living sieve tubes (thin cytoplasm, sieve plates) and companion cells (provide energy via mitochondria). Transports sugars/amino acids.
• Organisation: In stems, vascular bundles arranged in a ring (xylem inside, phloem outside). In roots, xylem and phloem in central core.
• Photosynthesis:
  • Equation: $6CO_2 + 6H_2O \xrightarrow{\text{light, chlorophyll}} C_6H_{12}O_6 + 6O_2$
  • Fate of Glucose: Respiration, starch (storage), cellulose (walls), sucrose (transport), fats, or proteins.
  • Limiting Factors: Light intensity, $CO_2$ concentration, Temperature.
• Translocation: Transport of sucrose/amino acids via phloem. Studied via ringing experiments, aphid stylet analysis, and radioisotopes ($^{14}C$).
• Transpiration: Loss of water vapour from aerial parts via stomata. Creates Transpirational Pull (suction force).
  • Factors: Increases with wind speed, temperature, light intensity; decreases with humidity.
  • Wilting: Occurs if transpiration rate exceeds water absorption rate; leads to flaccid cells.

ORGANISMS AND THEIR ENVIRONMENT

• Trophic Levels: Producers (level 1), Primary Consumers (level 2), Secondary, etc. Decomposers return nutrients.
• Energy Flow: Non-cyclical ($90\,\%$ loss between levels as heat/waste); the Sun is the principle input.
• Pyramid of Biomass: Always broad at base; represents total dry mass.
• Pyramid of Numbers: Can be inverted (e.g., one tree supporting many insects).
• Carbon Cycle: Photosynthesis removes $CO_2$; Respiration, Decomposition, and Combustion return it.
• Carbon Sinks: Forests and Oceans (absorb approx. $1/3$ of human emissions).
• Global Warming: Caused by greenhouse gases ($CO_2$, methane) from deforestation and fossil fuel burning. Leads to climate change, rising sea levels, coral bleaching.
• Pollution:
  • Sewage / Fertiliser: Eutrophication (nutrient excess → algae bloom → plant death → bacteria multiply → oxygen used up → fish die).
  • Insecticides (DDT): Bioaccumulation (buildup in one individual) and Biomagnification (increasing concentration up the food chain).
• Conservation: Sustaining biodiversity for gene pools, economic use (food/materials), research, and ecosystem stability.

MOLECULAR GENETICS AND INHERITANCE

• DNA Structure: Double helix made of nucleotides ($\text{sugar} + \text{phosphate} + \text{base}$). Complementary bases: Adenine-Thymine (A-T), Cytosine-Guanine (C-G).
• Gene: Unit of inheritance; sequence of DNA nucleotides coding for one polypeptide.
• Genetic Engineering: Transfer of genes across species. Example: Transgenic bacteria producing insulin using human insulin gene inserted into a plasmid vector via restriction enzymes (producing sticky ends) and DNA ligase.
• Monohybrid Inheritance: Crossing contrasting traits.
  • Alleles: Alternative forms of a gene (Dominant vs. Recessive).
  • Genotype: Genetic makeup (Homozygous DD/dd vs. Heterozygous Dd).
  • Phenotype: Expressed physical trait.
• Codominance: Both alleles expressed in phenotype (e.g., AB blood group, roan coat in cattle).
• Multiple Alleles: Genes with $>2$ alleles (Blood group system alleles $I^A, I^B, I^O$).
• Sex Determination: Male ($XY$), Female ($XX$). Sperm determines baby's sex.
• Variation:
  • Discontinuous: Clear-cut types (blood group), controlled by single genes.
  • Continuous: Range of values (height), controlled by many genes + environment.
• Mutation: Spontaneous change in gene sequence (Sickle cell anaemia) or chromosome number (Down syndrome – extra chromosome $21$). Increase rate by mutagens (UV, X-rays, tar).
• Natural Selection: Survival of the fittest. Individuals with favourable traits survive, reproduce, and pass on genes, leading to evolution (gradual change over time). Examples: antibiotic-resistant bacteria, peppered moths, Darwin's finches.