bio notes (completed me thinks)

Cell Biology

Microscopes

• Light microscope- Resolving power sufficient to view whole cells and sometimes the nucleus.

  • Sub-cellular detail usually invisible.

  • Resolving Power

    • The ability to distinguish two separate points as distinct.

    • Depends on the wavelength of light used (longer wavelength, lower resolution) and the numerical aperture of the lens.

    • Utilizes visible light.

• Electron microscope- Much higher resolution & magnification; organelles become visible.

  • Key idea: better resolving power (= ability to distinguish two close points).

  • Enhanced Resolution

    • Uses a beam of electrons instead of light.

    • Electrons have a much shorter wavelength than visible light.

    • This allows for significantly higher resolving power, greater magnification, and more detailed images.

Size Calculations

• Formula: $\text{Magnification}=\frac{\text{Image size}}{\text{Object size}}$

• Rearranged for real size: $\text{Object size}=\frac{\text{Image size}}{\text{Magnification}}$

• Always keep units consistent (µm, nm, etc.).

Cell Types

• Eukaryotic (plants, animals): DNA in a nucleus.

• Prokaryotic (bacteria): no nucleus; circular DNA/rings called plasmids.

Universal Organelles/Structures

Transport Across Membranes

Diffusion

• Net movement from high → low concentration (down gradient).

• Passive (no ATP).

• Mechanism

  • Particles possess kinetic energy and move randomly.

  • In a concentration gradient, particles randomly move into areas of lower concentration.

  • The net movement is from higher to lower concentration.

  • Continues until particles are evenly distributed (equilibrium).

Osmosis

• Diffusion of water across a semi-permeable membrane.

• Example: Higher glucose outside cell → water exits cell → mass decreases.

• Mechanism

  • Specific diffusion of water molecules across a partially permeable membrane.

  • Water moves from a region of higher water potential (dilute solution, high free water, low solute) to lower water potential (concentrated solution, low free water, high solute).

  • This is a passive movement.

  • Often facilitated by aquaporins (protein channels).

Factors Increasing Rate

• Larger concentration difference.

• Higher temperature (↑ kinetic energy).

• Larger surface area (villi, alveoli, root hairs).

Osmosis Practical (Potato Cylinders)

1. Cut equal-sized cylinders; weigh (initial mass).

2. Place in varying sucrose concentrations for ≈24 h.

3. Dab, re-weigh.

4. Calculate % change: $\% ext{Change in mass} = \frac{\text{Final mass}-\text{Initial mass}}{\text{Initial mass}}\times100$

5. Plot % change vs. concentration; x-axis intercept ⇒ internal concentration.

Active Transport

• Carrier proteins use ATP to move substances against gradient.

• Example: mineral ions into root hair cells.

• Mechanism

  • Requires energy (ATP) to move substances from lower to higher concentration.

  • Specific carrier proteins in the cell membrane bind the substance.

  • ATP is utilized to change protein shape.

  • Substance is released on the other side of the membrane.

  • Essential for absorption or waste removal when diffusion is insufficient.

Biological Organisation & Digestion

Levels of Organisation

Cells → Tissues → Organs → Organ systems.

Digestive System Highlights

• Mouth/Teeth: Physical breakdown; ↑ surface area for enzymes.

  • Incisors (cut), Canines (tear), Premolars/Molars (grind).

  • Physical Breakdown

    • Chewing (mastication) mechanically breaks down large food pieces.

    • Increases the surface area of the food.

    • Makes food more accessible for chemical digestion by enzymes.

• Stomach: Acidic pH begins protein digestion.

• Liver/Gall Bladder: Produce & store bile; bile neutralises stomach acid & emulsifies fats (↑ SA).

• Small Intestine: Enzymatic breakdown & absorption via villi.

Enzymes

• Biological catalysts; specific (lock-and-key model).

• Lock-and-Key Model

  • Each enzyme has a specific active site with a unique 3D shape.

  • The active site is complementary to a particular substrate molecule.

  • Substrate binds to the active site, forming an enzyme-substrate complex.

  • Enzyme catalyzes the reaction, converting substrate into products.

  • Products are released; the enzyme remains unchanged and reusable.

Effect of Temperature & pH

• Rate ↑ with temperature until optimum; beyond, active site denatures.

• Similar bell-curve vs. pH (both extremes denature).

Amylase Practical

1. Mix starch + amylase at set T or pH.

2. Every 10 s add sample to iodine in spotting tile.

3. Time until iodine stays orange (no starch).

4. Plot time vs. pH or T; lowest time region = optimum (state “between points” per exam rule).

Food Tests

Balanced Diet & Deficiencies

• Carbohydrates: energy.

• Lipids: energy store, insulation.

• Proteins: growth & repair.

• Vitamins: C (lack → scurvy), D (lack → rickets).

• Minerals: Ca (bones; lack → osteoporosis), Fe (hemoglobin; lack → anaemia).

• Fibre: bowel health.

• Water: universal solvent; all cells need.

Respiratory & Circulatory Systems

Gas Exchange

• Air path: Trachea → Bronchi → Bronchioles → Alveoli.

• Alveoli: massive SA, moist, thin walls → rapid diffusion.

• O$<em>2$ binds hemoglobin → transport; CO$</em>2$ dissolves in plasma → lungs.

Heart & Blood Vessels

• Double circulation: Right side pumps deoxygenated blood to lungs; left pumps oxygenated to body.

• Double Circulation Mechanism

  • Blood passes through the heart twice for each complete body circuit.

  • Pulmonary Circuit: Right side of heart pumps deoxygenated blood to lungs.

    • Blood picks up oxygen and releases carbon dioxide in the lungs.

    • Oxygenated blood returns to the left side of the heart.

  • Systemic Circuit: Left side of heart pumps oxygenated blood to the rest of the body.

    • Deoxygenated blood returns from the body to the right side of the heart.

  • Allows for higher pressure in systemic circulation for efficient blood delivery.

• Major vessels: Vena cava, Pulmonary artery, Pulmonary vein, Aorta.

• Left ventricle thicker (higher pressure to body).

• Pacemaker Cells (Sinoatrial Node)

  • Specialized muscle cells in the sinoatrial (SA) node (right atrium wall).

  • Spontaneously generate electrical impulses.

  • Impulses spread across atria, causing contraction.

  • Impulses travel to AV node and conducting fibers, causing ventricular contraction.

  • This inherent electrical activity sets the basic heartbeat rhythm.

• Blood components: plasma, RBCs, WBCs (lymphocytes & phagocytes), platelets (clotting).

• Coronary arteries feed heart muscle; blockage → CHD/heart attack.

  • Treatments: stents, statins, valve replacement.

Transport in Plants

Xylem vs. Phloem

• Xylem: dead hollow tubes; water/minerals up only (transpiration stream).

• Phloem: living sieve tubes; sugars up & down (translocation).

Transpiration Rate ↑ by

1. Higher temperature.

2. Lower humidity.

3. Greater air movement.

Leaf Structure (cross-section)

• Waxy cuticle: waterproof, reduces evaporation.

• Upper epidermis: transparent.

• Palisade mesophyll: many chloroplasts; main photosynthesis.

• Spongy mesophyll: air spaces for gas exchange.

• Vascular bundle: xylem & phloem.

• Lower epidermis: stomata controlled by guard cells (close at night).

Mineral Deficiencies (Triple)

• Nitrate lack → poor protein synthesis → stunted growth.

• Magnesium lack → chlorosis (yellow leaves).

Disease & Immunity

Non-Communicable

• CVD, diabetes type 2, cancers, liver disease, lung disease.

• Lifestyle factors: diet, smoking, alcohol, inactivity.

• Carcinogens (e.g. ionising radiation) ↑ cancer risk.

Communicable Pathogens

Body Defences

• Barriers: skin, mucus, stomach acid.

• Internal: WBCs

  • Lymphocytes:

    • Recognize specific antigens on pathogens.

    • B-lymphocytes activate, multiply, and differentiate into plasma cells.

    • Plasma cells produce large quantities of specific antibodies.

    • Antibodies: Proteins that bind to pathogens, aiding destruction, neutralizing toxins (antitoxins), or clumping pathogens.

    • T-lymphocytes may directly destroy infected cells.

  • Phagocytes:

    • Engulf and digest pathogens via phagocytosis.

    • Flexible cell membrane surrounds pathogen, forming a vacuole.

    • Vacuole fuses with lysosomes (containing digestive enzymes).

    • Pathogen is broken down and destroyed.

• Immunological Memory

  • After first pathogen exposure, some lymphocytes become memory cells.

  • Memory cells persist long-term in the body.

  • Upon re-encountering the same pathogen, memory cells mount a faster and stronger secondary immune response.

  • Often prevents sickness (immunity).

Vaccination

• Dead/inactive pathogen or mRNA code (e.g. COVID-19) triggers antibody production without disease.

• Vaccination Mechanism

  • Vaccine contains part of a pathogen (weakened, inactive, fragmented) or genetic material (mRNA) for antigens.

  • Introduced into the body, it stimulates the immune system to produce antibodies and memory cells.

  • Achieves this without causing the actual disease.

  • Primes the immune system for a rapid and effective response if the real pathogen is encountered.

Antibiotics & Resistance

• Kill bacteria, not viruses.

• Overuse leads to resistant strains; finish full course.

Drug Development

1. Lab (cells/tissues).

2. Animals.

3. Human trials: blind & double-blind with placebos for unbiased data.

Photosynthesis

• Word: carbon dioxide + water → glucose + oxygen (light).

• Balanced: $6CO<em>2 + 6H</em>2O \xrightarrow{\text{light}} C<em>6H</em>{12}O<em>6 + 6O</em>2$

• Endothermic (requires light energy).

• Process

  • Green plants and some organisms use light energy.

  • Convert carbon dioxide and water into glucose and oxygen.

  • Occurs primarily in chloroplasts, where chlorophyll captures light energy.

  • Involves light-dependent reactions (light energy into chemical energy).

  • Followed by light-independent reactions (glucose synthesis).

Uses of Glucose

1. Respiration.

2. Starch / fat storage.

3. Cellulose (cell walls).

4. Amino acids → proteins (needs nitrates).

Limiting Factors

• Light, CO$_2$, temperature (enzyme-controlled).

• Graph: plateau shows another factor now limiting.

Pondweed Practical

• Measure O$_2$ produced (volume or bubble count).

• Change light intensity (distance).

• Inverse square: $I \propto \frac{1}{d^2}$

Respiration & Metabolism

Aerobic

$C<em>6H</em>{12}O<em>6 + 6O</em>2 \rightarrow 6CO<em>2 + 6H</em>2O + \text{ATP}$

• Occurs in mitochondria; releases energy for muscle contraction, active transport, etc.

Anaerobic (in muscles)

$\text{Glucose} \rightarrow \text{Lactic acid} + \text{ATP (small)}$

• Builds oxygen debt; lactic acid removed by liver post-exercise.

Anaerobic in Yeast (Fermentation)

$\text{Glucose} \rightarrow \text{Ethanol} + CO_2$

• Bread rising, alcohol production.

Metabolism = sum of all reactions

• Examples: glycogen ↔ glucose; fatty acids + glycerol → lipids; amino acids → proteins; deamination → urea.

Homeostasis & Nervous System

Components

Stimulus → Receptor → Coordination centre (CNS) → Effector → Response.

Neurones

• Sensory, relay, motor; synapses use neurotransmitters.

• Reflex arc: bypasses brain → rapid.

Reaction-Time Ruler Test

• Drop ruler; measure catch distance.

• Compute reaction time if needed: $s=\frac{1}{2}gt^2$ (not usually required).

• Test effects of caffeine (stimulant) or depressant.

Brain Structure

• Cerebral cortex: memory, reasoning.

• Cerebellum: balance & coordination.

• Medulla oblongata: involuntary actions, adrenaline release.

• MRI scans map activity; brain surgery risky.

Eye Function

• Accommodation

  • Distant: ciliary relax, suspensory tight → thin lens (low power).

  • Near: ciliary contract, suspensory slack → fat lens (high power).

• Pupil reflex: iris muscles vary aperture.

• Retina: rods (intensity), cones (RGB colour).

• Vision defects: Myopia (short) – concave lens; Hyperopia (long) – convex; laser surgery reshapes cornea.

Thermoregulation

• Too hot: sweating, vasodilation.

• Too cold: vasoconstriction, shivering.

Endocrine System & Blood Glucose

Glucose Control

• High BG → insulin → cells absorb glucose; liver converts to glycogen.

• Low BG → glucagon → glycogen → glucose.

• Diabetes type 1: no insulin (injections). Type 2: insulin resistance (diet/exercise management).

Kidneys & Water Balance (Triple)

• ADH from pituitary controls water re-uptake in kidney tubules.

  • More ADH → more water reabsorbed → concentrated urine.

  • Negative feedback maintains constant blood water potential.

• Dialysis/artificial kidney if failure; urea removal critical.

Reproduction & Hormones

Menstrual Cycle

1. FSH (pituitary): matures follicle.

2. Oestrogen (ovary): thickens uterus; inhibits FSH; triggers LH.

3. LH (pituitary): ovulation.

4. Progesterone (ovary): maintains lining.

Adrenaline Recap

• Increases HR & BR; redirects blood to muscles.

Plant Hormones

Tropism Practical

• Seeds on damp cotton; rotate dish → roots grow downward (positive geotropism).

Meiosis vs. Mitosis

• Meiosis: diploid → 4 haploid gametes; crossing-over adds variation.

• Mitosis: identical clones (asexual reproduction).

• Advantage sexual: variation/adaptation; advantage asexual: single parent, fast.

Genetics & Inheritance

• Genome = all DNA; Human Genome Project maps ~20 000 genes.

• DNA: double helix of nucleotides (A-T, C-G). Triplet code → amino acid.

• mRNA copies gene → ribosome → protein folding.

  • Gene Expression Process:

    • Transcription:

      • DNA segment (gene) acts as a template for messenger RNA (mRNA) creation.

      • Occurs in the nucleus, catalyzed by RNA polymerase.

    • Translation:

      • mRNA moves to a ribosome in the cytoplasm.

      • Ribosome reads mRNA codons (triplets of nucleotides).

      • Transfer RNA (tRNA) molecules, each with a specific amino acid, match anticodons to mRNA codons.

      • Amino acids link to form a polypeptide chain.

      • Polypeptide folds into a 3D structure to become a functional protein.

• Mutations may alter protein; non-coding DNA regulates gene expression (epigenetics).

Key Terms

• Genotype: allele combination.

• Phenotype: expressed traits.

• Dominant vs. recessive alleles.

• Homozygous (BB / bb) vs. heterozygous (Bb).

Punnett Squares

• Predict probabilities (e.g., 25 % blue eyes from two Bb parents).

• Examples: polydactyly (dominant), cystic fibrosis (recessive).

• Sex determination: XX female, XY male (50 / 50 chance).

Evolution, Selective Breeding & GM

Evidence & Mechanisms

• Darwin: natural selection via random variation.

• Lamark & epigenetics: environment can influence gene activation.

• Antibiotic resistance illustrates rapid evolution in bacteria.

• Species definition: fertile offspring criterion.

Selective Breeding

• Choosing parents with desired traits (dogs, crops); risks ↓gene pool.

Genetic Engineering

1. Restriction enzymes cut desired gene.

2. Insert into vector (plasmid/virus).

3. Vector introduces gene into embryo/cell → transgenic organism.

• Process:

  • Isolation and Cutting the Gene:

    • Identify and isolate specific gene of interest from donor DNA.

    • Use restriction enzymes to precisely cut the gene; these act like molecular scissors.

    • Enzymes create "sticky ends" (short, single-stranded overhangs).

  • Insertion into a Vector:

    • A vector (e.g., bacterial plasmid, modified virus) is cut open with the same restriction enzyme.

    • This creates complementary sticky ends.

    • The isolated gene is inserted into the opened vector.

    • DNA ligase seals the gene into the vector, forming recombinant DNA.

  • Introduction into a Host Cell:

    • Recombinant vector introduced into a host cell (e.g., bacteria, plant, animal embryo).

    • Host cell takes up the modified DNA.

    • New gene integrates into host genome or remains as an independent plasmid.

  • Cloning and Expression:

    • Host cells with recombinant DNA are grown to multiply, replicating the new gene.

    • If producing a substance (e.g., insulin), the gene is expressed to synthesize the protein.

    • If creating a transgenic organism, the host cell develops to carry the new trait.

• Examples: insulin-producing bacteria, golden rice (vitamin A), glowing bunny (jellyfish gene).

Classification

• Linnaean hierarchy: Domain (Archaea, Bacteria, Eukaryota) → Kingdom → … → Species.

• Mnemonic: “King Philip Came Over For Good Soup.”

• Extremophiles: Archaea in harsh conditions.

Ecology & Environment

Interdependence & Factors

• Competition for food, water, light (plants), mates (animals).

• Abiotic: light, temp, moisture, pH, CO$<em>2$, O$</em>2$ .

• Biotic: predation, food availability, pathogens.

Sampling Techniques

• Quadrats: sample ~10 % area; mean × total area = population estimate.

• Transect + quadrats: distribution along gradient.

Food Chains & Trophic Levels

• Producer → Primary consumer → Secondary → Tertiary/Apex.

• Arrows show energy/biomass flow.

Biogeochemical Cycles

• Carbon cycle: respiration, photosynthesis, decomposition.

• Water cycle: precipitation → runoff → ocean → evaporation.

• Decomposition utilised for compost, methane (triple).

Biodiversity & Human Impact

• High biodiversity = ecosystem stability.

• Threats: deforestation, peat bog destruction, pollution, global warming (CO$<em>2$, CH$</em>4$).

Biomass Transfer & Food Security

Pyramid of Biomass

• Draw proportional rectangles for each trophic level.

• % transfer: $\%= \frac{\text{Biomass of next trophic level}}{\text{Biomass of previous trophic level}} \times 100$

• Losses via respiration, excretion (urea, CO$_2$, water), une