CAIE AS Level Biology - Comprehensive Theory Notes

The Microscope in Cell Studies

• Temporary Slide Preparation:

  • Cut thin sections of the material for examination.

  • Apply a stain to enhance contrast.

  • Mount the specimen on a clean glass slide.

  • Lower a coverslip over the specimen slowly to prevent drying and trap air bubbles.

• Types of Electron Microscopes:

  • Transmission Electron Microscope (TEM): This provides 2D images and allows for the visualization of internal cellular details.

  • Scanning Electron Microscope (SEM): This produces 3D images but is limited to viewing the surface structures of a specimen.

Magnification and Resolution

• Magnification definitions:

  • The number of times larger an image appears compared to the object's actual size.

  • Determined by the combined power of the objective lens and the eyepiece lens.

• Formula for Calculations:

  • $Actual\,size = \frac{Image\,size}{Magnification}$

• Unit Conversions:

  • $1\,mm = 1000\,\mu m$

  • $1\,\mu m = 1000\,nm$

• Eyepiece Graticule and Stage Micrometer:

  • Eyepiece Graticule: A scale fitted into the microscope eyepiece used for measuring objects; it has no units.

  • Stage Micrometer: An accurate scale (usually in $mm$) used to calibrate the eyepiece graticule for reference dimensions.

  • Calibration must occur at the same magnification used for specimen measurement.

• Microscopy Features Comparison:

  • Light Microscope: Uses light (wavelength $400-700\,nm$); maximum resolution is $200\,nm$; can view alive specimens; produces colored photomicrographs.

  • Electron Microscope: Uses electrons (wavelength $0.1\,nm$); maximum resolution is at least $0.05\,nm$; specimens must be dead; produces black and white electron micrographs.

• Resolution:

  • The ability to distinguish between two separate points.

  • Higher resolution translates to higher detail. A resolution value of $2$ provides greater detail than a value of $10$.

  • Limit of resolution is half the wavelength of the radiation used.

Cell Structure and Organelles

• Ultrastructure: The detailed structure of a cell as revealed by an electron micrograph.

• Organelles: Functionally and structurally distinct parts of a cell, which are usually membrane-bound.

• Cell Surface Membrane ($7\,nm$):

  • Extremely thin with a tri-laminar appearance.

  • Consists of a phospholipid bilayer with hydrophilic phosphate heads facing aqueous environments and hydrophobic tails facing inward.

  • Functions: Barrier, cell signaling, cell recognition (via surface antigens), cell-to-cell adhesion, anchoring the cytoskeleton, and selection of substances entering/leaving.

• Nucleus ($10\,\mu m$):

  • The largest organelle, surrounded by a double-membraned nuclear envelope continuous with the rough endoplasmic reticulum.

  • Nuclear Pores: Gaps allowing exchange. mRNA and ribosomes leave; proteins, nucleotides, ATP, and hormones enter.

  • Chromosomes: Contain hereditary DNA organized into genes.

  • Nucleolus ($0.2-0.5\,\mu m$): Site of ribosome synthesis; contains DNA and RNA.

• Endoplasmic Reticulum (ER):

  • Rough ER (RER): Extensive membrane system with $80S$ ribosomes for protein synthesis. Forms fluid-filled sacs (cisternae) and provides transport pathways. Transport vesicles bud off to join the Golgi body.

  • Smooth ER (SER): Meshwork of tubular membranes without ribosomes; site for lipid and steroid synthesis (e.g., cholesterol, reproductive hormones).

• Golgi Body/Apparatus:

  • Stack of flattened cisternae formed by RER transport vesicles.

  • Functions: Collects, modifies, and sorts molecules. Packages them into Golgi vesicles for secretion (exocytosis) or internal use.

  • Produces lysosomes, glycoproteins, and functional proteins.

• Mitochondria ($1\,\mu m$):

  • Surrounded by a double membrane (envelope); site of aerobic respiration and lipid synthesis.

  • Matrix: Contains $70S$ ribosomes and circular DNA.

  • Cristae: Inner membrane folds increasing surface area.

  • Porin: Transport protein in the outer membrane forming aqueous channels.

  • Inner membrane: Selective barrier controlling ion entrance.

  • ATP (Adenosine Triphosphate): Energy-carrying molecule composed of $3$ phosphate groups, a nitrogenous base, and ribose sugar. Energy is released via reversible hydrolysis to ADP.

• Endosymbiotic Theory: Proposes that mitochondria and chloroplasts originated as bacteria living inside larger cells, explaining their circular DNA and $70S$ ribosomes.

• Ribosomes:

  • Site of translation (mRNA to polypeptides). Composed of rRNA and proteins.

  • 80S Ribosomes: Found in cytoplasm and RER.

  • 70S Ribosomes: Found in chloroplasts and mitochondria.

  • Structure: Small subunit (mRNA binding) and large subunit (joining amino acids).

• Lysosomes ($0.1-0.5\,\mu m$):

  • Single-membrane vesicles containing hydrolytic (digestive) enzymes. Separate from the rest of the cell to prevent autodigestion.

  • Responsible for breaking down old organelles or bacteria (in white blood cells).

• Microtubules:

  • Long hollow tubes ($25\,nm$ diameter) made of alpha and beta tubulin dimers.

  • $13$ protofilaments form a cylinder.

  • Functions: Intracellular transport, determining cell shape, and movement of cilia.

• Centrioles and Centrosomes:

  • Centrosome: A pair of centrioles at right angles; acts as a Microtubule Organizing Center (MTOC).

  • Centriole Structure: $9$ triplets of microtubules. Involved in spindle fiber formation and separating chromatids during division.

• Cilia and Flagella:

  • Cilia: Hair-like structures with a '9+2' microtubule arrangement.

  • Basal Body: Centrioles at the base acting as MTOCs.

• Chloroplasts ($5-10\,\mu m$):

  • Found in plant cells (palisade/spongy mesophyll). Site of photosynthesis.

  • Structure: Double membrane, thylakoids (flattened sacs) stacked into grana, joined by lamellae within the stroma. Contains starch grains, circular DNA, and $70S$ ribosomes.

• Cell Wall ($10\,nm$):

  • Rigid structure containing cellulose fibers. Provides shape, prevents bursting (turgidity), and is freely permeable.

  • Plasmodesmata: Pores allowing cytoplasmic links between neighboring cells.

• Large Vacuole and Tonoplast:

  • Plant vacuole surrounded by the tonoplast membrane. Contains cell sap (sugars, salts, pigments, waste).

Prokaryotes vs Eukaryotes

• Eukaryotes: Organisms with a true nucleus and membrane-bound organelles (animals, plants, fungi, protoctists). Size: $10-100\,\mu m$.

• Prokaryotes: Lack a nucleus and membrane-bound organelles (bacteria). Size: $0.5-5\,\mu m$.

• Detailed Comparison:

  • DNA: Circular and naked in prokaryotes; linear and associated with histones in eukaryotes.

  • Ribosomes: $70S$ ($20\,nm$) in prokaryotes; $80S$ ($25\,nm$) in eukaryotes.

  • Cell Wall: Murein (peptidoglycan) in prokaryotes; cellulose/lignin (plants) or chitin (fungi) in eukaryotes.

  • Division: Binary fission (prokaryotes) vs Mitosis (eukaryotes).

Viruses

• Characteristics: Non-cellular, parasitic, size $20-300\,nm$.

• Structure: DNA or RNA genetic core surrounded by a protein capsid; some possess an outer phospholipid envelope.

• Replication: Hijacks host cell machinery to synthesize viral proteins and nucleic acids.

Biological Molecules and Testing

• Benedict’s Test (Reducing Sugars): Mix equal volume of sample and Benedict's; heat above $80\,^{\circ}\text{C}$. Blue (negative) to green, yellow, orange, or brick-red (positive).

• Benedict’s Test (Non-reducing Sugars): Hydrolyse with HCl, heat, neutralize with NaOH, then perform standard Benedict's test.

• Semi-quantitative Benedict's: Measuring time taken for first color change or using color standards.

• Biuret Test (Proteins): Mix sample with Biuret reagent. Blue (negative) to purple (positive).

• Emulsion Test (Lipids): Dissolve sample in ethanol, then add to cold water. Clear (negative) to milky emulsion (positive).

• Iodine Test (Starch): Add iodine solution. Orange-brown (negative) to blue-black (positive).

Carbohydrates and Lipids

• Monomers and Polymers: Monomers (basic building blocks like glucose, amino acids) join via condensation to form polymers (polysaccharides, proteins).

• Glucose ($C_6H_{12}O_6$): Exists as $\alpha$-glucose (OH group below ring) and $\beta$-glucose (OH group above ring).

• Lipids: Not polymers; made of glycerol and $3$ fatty acids linked by ester bonds.

• Glycosidic Bonds: Covalent bonds formed via condensation (removal of water). Broken by hydrolysis.

• Polysaccharides:

  • Starch: Plant storage. Amylose ($\alpha-1,4$ bonds, helical) and Amylopectin ($\alpha-1,4$ and $\alpha-1,6$ bonds, branched).

  • Glycogen: Animal energy storage. Similar to amylopectin but more branched (more $\alpha-1,6$ bonds).

  • Cellulose: In plant cell walls. Made of $\beta$-glucose; alternate molecules rotated $180\,^{\circ}$. Forms microfibrils ($10\,nm$) and fibers ($50\,nm$) via hydrogen bonding.

• Lipid Types:

  • Triglycerides: Glycerol and $3$ fatty acids. Non-polar. Saturated (no C=C) or Unsaturated (C=C present).

  • Phospholipids: Hydrophilic head (phosphate group + glycerol) and two hydrophobic fatty acid tails. Essential for cell membranes.

Proteins

• Structure: Amino acids contain an amine group ($NH_2$), carboxyl group ($COOH$), and variable R-group.

• Peptide Bonds: Formed between the amine group of one amino acid and the carboxyl group of another via condensation.

• Protein Folding Levels:

  • Primary: Unique sequence of amino acids in a polypeptide chain.

  • Secondary: Local folding into $\alpha$-helix (stabilized by H-bonds every $4$ spaces) or $\beta$-pleated sheets.

  • Tertiary: 3D coiling stabilized by hydrogen bonds, disulphide bridges (between cysteines), ionic bonds (between NH2 and COOH groups), and hydrophobic interactions.

  • Quaternary: Arrangement of multiple polypeptide chains (e.g., Haemoglobin).

• Globular vs Fibrous:

  • Globular: Spherical, water-soluble, metabolic roles. Example: Haemoglobin ($4$ chains, each with an iron-containing prosthetic haem group).

  • Fibrous: Long strands, insoluble, structural roles. Example: Collagen ($3$ helical chains; every third amino acid is glycine). Molecules link to form fibrils and fibers.

Water Properties

• Solvent: Polar nature allows electrostatic interactions with other molecules, aiding transport.

• Cohesion and Adhesion: Hydrogen bonding causes molecules to stick together and to walls (e.g., xylem).

• Thermal Properties: High specific heat capacity (limits temperature fluctuations) and high latent heat of vaporization (provides cooling effect through sweating/transpiration).

• Density: Ice is less dense than water, providing insulation for aquatic life.

Enzymes

• Mechanism: Biological catalysts that lower activation energy ($E_a$). They possess an active site complementary to a specific substrate.

• Theories:

  • Lock-and-Key: Active site shape is a perfect fit.

  • Induced Fit: Active site changes shape slightly to fit the substrate more closely.

• Factors Affecting Rate:

  • Temperature: Rate increases with kinetic energy until optimum ($40\,^{\circ}\text{C}$), then decreases as H-bonds break (denaturation).

  • pH: Deviations from optimum disrupt ionic and hydrogen bonds, altering the active site.

  • Concentration: Increasing enzyme or substrate concentration increases rate until sites are saturated ($V_{max}$).

• Inhibition:

  • Competitive: Inhibitor similar to substrate binds to active site; reversible by increasing substrate concentration.

  • Non-competitive: Binds elsewhere, distorting the active site; unaffected by substrate concentration.

  • End-product Inhibition: Form of non-competitive control where the final product inhibits an earlier enzyme.

• Michaelis-Menten Constant ($K_m$): Substrate concentration at $\frac{1}{2} V_{max}$. A lower $K_m$ indicates a higher affinity for the substrate.

• Immobilization: Enzymes trapped in sodium alginate beads. Advantages: easy reuse, product remains enzyme-free, more tolerant to pH and temperature shifts.

Cell Membrane and Transport

• Fluid Mosaic Model: Phospholipids and proteins move via diffusion ('fluid'). Scattered proteins create a 'mosaic' pattern.

• Cholesterol: Regulates fluidity. Prevents rigidity at low temperatures and stabilizes at high temperatures. Improves mechanical stability.

• Glycolipids/Glycoproteins: Form H-bonds with water to stabilize the membrane. Act as signaling receptors, markers for endocytosis, and cell adhesion/recognition antigens.

• Proteins:

  • Channel Proteins: Fixed-shape water-filled pores for ions; can be gated.

  • Carrier Proteins: Change shape to move molecules. Used in both facilitated diffusion and active transport.

• Cell Signaling: Ligand binds to complementary receptor, causing a conformational change. Activates G-protein, which triggers a "second messenger" for a signal cascade (amplification).

• Movement Mechanisms:

  • Diffusion: Passive net movement down a concentration gradient. Affected by temperature, surface area, and gradient steepness.

  • Osmosis: Diffusion of water through a selectively permeable membrane from higher water potential ($\psi$, less negative) to lower ($\psi$, more negative).

  • Active Transport: Uses ATP and carrier proteins to move substances against a gradient.

  • Bulk Transport: Exocytosis (secreting materials) and Endocytosis (phagocytosis for solids; pinocytosis for liquids). Requires ATP for vesicle movement.

• Plant Cell Behavior:

  • Turgid: Protoplast pushes against cell wall in high $\psi$.

  • Plasmolysed: Protoplast shrinks away from the wall in low $\psi$.

The Mitotic Cell Cycle

• Chromosomes: Threadlike structures of DNA and histone proteins (chromatin).

• Telomeres: Repeating base sequences at chromosome ends that prevent gene loss and degradation.

• Centromere: Holds two identical chromatids together.

• Stem Cells:

  • Totipotent: Can form any cell (e.g., zygote).

  • Pluripotent: Embryonic cells that cannot form placental tissue.

  • Multipotent: Adult stem cells (e.g., bone marrow) forming limited types.

• Cancer: Mutation in genes controlling division (oncogenes) leads to uncontrolled mitosis and tumors. Malignant tumors can spread via metastasis.

Nucleic Acid and Protein Synthesis

• Nucleotides: Pentose sugar, nitrogenous base, and phosphate group.

• Polynucleotides: Linked by phosphodiester bonds between $3^\prime$ and $5^\prime$ carbons.

• DNA: Two antiparallel strands in a double helix. Nitrogenous bases: Adenine ($A$), Thymine ($T$), Guanine ($G$), Cytosine ($C$). $A-T$ ($2$ H-bonds); $G-C$ ($3$ H-bonds).

• DNA Replication: Semi-conservative process in the $S$ phase. Helicase unzips; DNA polymerase synthesizes strands. The leading strand is continuous; the lagging strand forms Okazaki fragments joined by ligase.

• RNA: Single-stranded, contains ribose and Uracil ($U$) instead of Thymine ($T$).

  • mRNA: Template for translation.

  • tRNA: Carries specific amino acids; has an anticodon.

  • rRNA: Component of ribosomes.

• Genetic Code: Universal, redundant/degenerate, triplet-based (codons).

• Transcription: Occurs in the nucleus. RNA polymerase uses a DNA template to make mRNA. Pre-mRNA undergoes splicing where introns are removed and exons are joined.

• Translation: Occurs in the cytoplasm. mRNA binds to a ribosome. tRNA molecules bring amino acids corresponding to codons. Peptide bonds form between amino acids until a stop codon ($UAA, UAG, UGA$) is reached.

• Mutations:

  • Substitution: Replacement of one base (e.g., sickle cell anemia: thymine replaced by adenine).

  • Insertion/Deletion: Causes frame-shift mutations, altering all subsequent codons.

Transport in Plants

• Tissues: Xylem (dead, lignified, unidirectional water transport) and Phloem (living, bidirectional transport of assimilates).

• Xylem Adaptations: No end walls, no cell contents, lignified walls, pits for lateral movement.

• Phloem Structure: Sieve tube elements (little content, sieve plates) and companion cells (metabolically active, many mitochondria/ribosomes, linked to sieve tubes via plasmodesmata).

• Water Pathways:

  • Apoplast: Movement through cell walls and intercellular spaces.

  • Symplast: Movement through cytoplasm and plasmodesmata.

  • Casparian Strip: Suberin layer in the endodermis that forces water from the apoplast into the symplast.

• Transpiration: Evaporation of water from mesophyll cell walls into air spaces, followed by diffusion through stomata. This creates a transpiration pull maintained by cohesion and adhesion (Cohesion-Tension theory).

• Translocation: Loading of sucrose into phloem. Protons are pumped out of companion cells using ATP. Sucrose is then co-transported back in with protons. This lowers water potential, drawing water from the xylem, increasing hydrostatic pressure, and driving mass flow toward the sink.

• Xerophyte Adaptations: Rolled leaves, thick waxy cuticles, trichomes (hairs), sunken stomata, and reduced leaf size (spines) to minimize water loss.

Transport in Mammals

• System: Closed, double circulation (pulmonary and systemic circuits).

• Blood Vessels:

  • Arteries: Thick muscular and elastic walls to withstand high pressure. Narrow lumen.

  • Veins: Thinner walls, wide lumen, valves to prevent backflow.

  • Capillaries: Single layer of endothelial cells ($7\,\mu m$ lumen) for rapid exchange.

• Blood Composition: Plasma (solutes), Red Blood Cells ($RBCs$, biconcave, no nucleus, transport $O_2$), White Blood Cells ($WBCs$, immunity), and Platelets (clotting).

• Oxygen Transport: Haemoglobin binds oxygen to form oxyhaemoglobin. High $pCO_2$ causes haemoglobin to release $O_2$ more readily (Bohr effect).

• Carbon Dioxide Transport:

  • $10\%$ as carbaminohaemoglobin.

  • $5\%$ dissolved in plasma.

  • $85\%$ as hydrogencarbonate ions ($HCO_3^-$). Carbonic anhydrase catalyzes the formation of carbonic acid, which dissociates. $Cl^-$ ions move into RBCs to maintain charge (Chloride shift).

• Heart Structure: Four chambers. Right side (deoxygenated), Left side (oxygenated, thicker muscular wall). Atrioventricular valves (bicuspid/mitral on left, tricuspid on right) and Semi-lunar valves (at exits).

• Cardiac Cycle:

  • Atrial Systole: Atria contract; blood to ventricles.

  • Ventricular Systole: Ventricles contract; blood to arteries. AV valves shut.

  • Diastole: Heart muscles relax.

• Control of Heartbeat: Myogenic. Sinoatrial node (SAN) sets the rhythm. Atrioventricular node (AVN) delays the impulse by $0.1\,s$ before it travels down the septum via Purkyne tissue to the ventricle base.

Gas Exchange

• System Components: Trachea and Bronchi (contain C-shaped/irregular cartilage for support), Bronchioles (no cartilage, smooth muscle to adjust diameter), and Alveoli (gas exchange surface).

• Epithelium: Ciliated cells move mucus; Goblet cells secrete sticky mucin (glycoproteins) to trap particles.

• Alveoli Adaptations: Extremely thin walls (one cell thick), surrounded by capillaries, contain elastic fibers for recoil, and have a large surface area.

Infectious Diseases

• Cholera: Bacterium Vibrio cholerae; faecal-oral transmission. Secretes choleragen toxin; causes severe diarrhea and dehydration.

• Malaria: Protoctist Plasmodium species; vector transmission by female Anopheles mosquitoes. Affects liver and RBCs; causes fever and anemia. Difficult to vaccinate against due to antigenic variation and multiple life stages.

• HIV/AIDS: Virus; transmission via bodily fluids. Attacks T-helper cells. No cure; treated with Zidovudine to inhibit reverse transcriptase.

• Tuberculosis ($TB$): Bacteria Mycobacterium tuberculosis; aerosol transmission. Affects lungs. Treated with DOTS (long course of multiple antibiotics).

Antibiotics and Immunity

• Penicillin: Inhibits transpeptidase enzyme, stopping cross-link formation in bacterial peptidoglycan cell walls. Osmotic pressure causes the weakened cell to lyse. Does not affect viruses (no metabolism or cell walls).

• Resistance: Develops via mutation and selection pressure. Spread through vertical transmission (asexual) or horizontal transmission (conjugation via plasmids).

• Immune System Cells:

  • Phagocytes: Neutrophils (early response, ingest bacteria) and Monocytes/Macrophages (long-lived, antigen-presenting cells).

  • Lymphocytes: B-cells (produce antibodies, differentiate into plasma and memory cells) and T-cells (Helper T secrete cytokines; Killer/Cytotoxic T destroy infected cells).

• Antibodies: Quaternary globular glycoproteins (immunoglobulins). Y-shaped with a variable region (antigen-binding sites) and a constant region. Work via neutralization, agglutination, and tagging for phagocytosis.

• Monoclonal Antibodies ($MABs$): Produced by fusing a spleen plasma cell with a cancerous myeloma cell to create a hybridoma. Used for diagnosis (locating clots/cancer) and therapy (marking cancer cells).

• Immunity Types:

  • Active: Produced by person's own immune system (Natural-infection; Artificial-vaccine).

  • Passive: Antibodies provided from external source (Natural-breast milk/placenta; Artificial-antitoxin injection).