CAPE Biology Unit 1 Comprehensive Study Notes

Module 1: Cell and Molecular Biology

1.1 Introduction to Biochemistry

Learning Outcomes:

Define biochemistry as the study of biological molecules and their roles in organisms.
State that biological molecules are made of the following elements: $C, H, O, N, S,\text{ and }P$ .
State that many biological molecules are polymers made by joining monomer molecules together.

Chemistry of Life:

Biochemistry: The study of biological molecules and their roles in organisms. These molecules are the building blocks of life, constantly assembled and disassembled.
Metabolism: All chemical reactions occurring in organisms. - Anabolism: Reactions building larger molecules from smaller ones (anabolic reactions). - Catabolism: Reactions breaking down large molecules into smaller ones (catabolic reactions).
Organic Compounds: Complex compounds based on carbon ( $C$ ). Carbon forms strong covalent bonds with itself and other atoms (single and double bonds).
Key Terms: - Chemical element: Pure substance of one type of atom. - Atom: Smallest component of an element; includes a nucleus (neutrons and protons) surrounded by electrons. - Isotope: Atoms of the same element with different numbers of neutrons. - Compound: Substance from two or more elements. - Molecule: Smallest particle retaining substance properties, composed of two or more atoms. - Ion: Atom/molecule that has lost/gained electrons, resulting in a charge. - Ionic bond: Bond between ions with opposite charges. - Covalent bond: Sharing a pair of electrons between atoms.

Macromolecules Summary Table:

Macromolecules	Elements	Sub-unit Molecules	Examples	Roles in Organisms
Carbohydrates	$C, H, O$ (Ratio $1:2:1$ )	Glucose	Starch (amylose/amylopectin), glycogen, cellulose	Energy storage, support
Lipids	$C, H, O$ (High $C:O$ / $H:O$ ratios)	Glycerol, fatty acids, phosphate (phospholipids)	Triglycerides, phospholipids	Energy storage, thermal/electrical insulation, membranes
Proteins	$C, H, O, N, S$	Amino acids (20 types)	Haemoglobin, collagen, amylase, pepsin, insulin, antibodies	Transport, support, catalysts, messengers, protection
Nucleic acids	$C, H, O, N, P$	Nucleotides (5 types)	DNA, RNA (mRNA, tRNA, rRNA)	Information storage/retrieval, protein production

1.2 Water and Hydrogen Bonding

Properties and Structure:

Water forms approx. $70\%$ of animal bodies and $90\%$ of plants.
Structure: Oxygen has a greater attraction for electrons in the covalent bond with hydrogen, making oxygen slightly electronegative ( $\delta-$ ) and hydrogen slightly electropositive ( $\delta+$ ). The molecule is dipolar.
Hydrogen Bonding: Weak bonds (approx. $1/10$ strength of covalent) between $\delta-$ oxygen of one molecule and $\delta+$ hydrogen of another. Each water molecule can bond with up to four others.
Cohesion: Molecules are "sticky" due to hydrogen bonds.

Roles and Environments Table:

Property	Explanation	Roles in Organisms	Roles as Environment
Good Solvent	Charged polar molecules/ions are attracted to weak charges on water.	Solvent within cells and transport media (blood plasma, xylem/phloem).	Solvent for nutrients and gases ( $O_{2}$ , $CO_{2}$ ).
High Specific Heat Capacity	$4.2\,J$ needed to increase $1\,g$ of water by $1^{\circ}C$ .	Limits temperature fluctuations in organisms.	Limits temperature fluctuations in aquatic habitats.
High Latent Heat of Vaporization	Much thermal energy needed to change liquid to vapour.	Efficient cooling (transpiration, sweating).	Shallow habitats (ponds) don't evaporate too quickly.
High Latent Heat of Fusion	Much energy needed to change ice to water (or released when ice forms).	Water in cells stays liquid; prevents ice crystal damage to membranes.	N/A
Density	Ice is less dense than liquid water and floats.	N/A	Ice floating provides buoyancy for aquatic life and insulates water beneath.
Incompressible	Cannot be compressed into smaller volume.	Hydrostatic skeleton (worms); turgidity in plant cells for support.	N/A
High Cohesion	Hydrogen bonds hold molecules together.	Supports columns of water in xylem.	Surface tension allows organisms to live on water surface.

1.3 Carbohydrates - Sugars

General Properties:

Contain $C, H, O$ in general formula $C_{x}(H_{2}O)_{y}$ .

Simple Sugars (Monosaccharides):

Formulas where $x$ is 3–7. Example: Glucose is $C_{6}H_{12}O_{6}$ (a hexose).
Ring Forms: Dependent on $-H$ and $-OH$ groups on Carbon-1 ( $C1$ ). - $\alpha$ -glucose: $-OH$ below the ring. - $\beta$ -glucose: $-OH$ above the ring.
Reducing Sugars: Act as reducing agents (donate electrons) from aldehyde/ketone groups. Glucose and fructose are reducing sugars.

Complex Sugars (Disaccharides):

Formed via condensation reactions (removal of water) creating a glycosidic bond (oxygen bridge).
Sucrose: Formed from glucose + fructose ( $C1-C2$ bond). Used for transport in plant phloem. It is a non-reducing sugar because aldehyde/ketone groups are involved in the bond and unavailable.
Hydrolysis: Addition of water to break a glycosidic bond into monosaccharides.

1.4 Complex Carbohydrates

Polysaccharides:

Storage Polysaccharides (Made of $\alpha$ -glucose): - Amylose (Starch): 1,4 glycosidic bonds, unbranched, forms right-handed helix. Storage in plants. - Amylopectin (Starch): 1,4 and 1,6 glycosidic bonds, branched. Storage in plants. - Glycogen: 1,4 and 1,6 glycosidic bonds, highly branched (more than amylopectin). Storage in animals, fungi, bacteria. "Animal starch."
Structural Polysaccharide: - Cellulose: Made of $\beta$ -glucose monomers. Alternate molecules are flipped $180^{\circ}$ , resulting in a straight (non-helical) chain. Chains bundle into microfibrils via hydrogen bonds. High tensile strength for plant cell walls.

1.5 Lipids

Structure and Types:

Higher ratio of $H:O$ compared to carbohydrates. Non-polar, insoluble in water.
Triglycerides: Glycerol + 3 fatty acids linked by ester bonds via condensation. - Saturated Fatty Acids: Full hydrogen complement; no double bonds between carbons. - Unsaturated Fatty Acids: One or more double bonds in carbon chain. - Function: Long-term energy storage (Adipose tissue in animals; oil droplets in seeds). Highly reduced molecules release more energy per mass than protein or carbs.
Phospholipids: Glycerol + 2 fatty acids + a phosphate-containing group (e.g., Choline). - Amphipathic: Hydrophilic head (phosphate) and hydrophobic tails (fatty acids). - Function: Form the phospholipid bilayer of biological membranes.

Health and Body Mass Index (BMI):

Essential Fatty Acids: Required in diet; cannot be synthesized (e.g., for Vit D absorption).
Obesity: Defined as body mass $>20\%$ above recommended or $BMI > 30$ .
BMI Formula: $BMI = \frac{\text{Body Mass (kg)}}{(\text{Height in metres})^{2}}$ .

1.6 Proteins (1) - Amino Acids

Structure: Central Carbon ( $C$ ), Amine group ( $-NH_{2}$ ), Carboxylic acid group ( $-COOH$ ), and a Residual ( $R$ ) group.
Peptide Bond: Forms between $-COOH$ of one and $-NH_{2}$ of another via condensation. - Dipeptide (2 amino acids); Tripeptide (3); Polypeptide ( $10+$ ).
Importance of R Groups: Determine hydrophobic/hydrophilic regions, ionic interactions, and covalent disulphide bonds (via cysteine's $-SH$ group).

1.7 Proteins (2) - Organization Levels

Primary Structure: Unique sequence of amino acids coded by genes.
Secondary Structure: Coiling or folding into $\alpha$ -helix or $\beta$ -pleated sheet, stabilized by hydrogen bonds between dipolar $-NH$ and $-CO$ groups.
Tertiary Structure: Further folding into a precise 3D shape, stabilized by hydrogen bonds, ionic bonds, hydrophobic interactions, and disulphide bonds ( $S-S$ ).
Quaternary Structure: Combination of two or more polypeptide chains (e.g., Haemoglobin).

Conjugated Proteins: Contain a non-amino acid prosthetic group (e.g., Haem in haemoglobin).

1.8 Proteins (3) - Examples

Haemoglobin: Globular protein, water-soluble. 4 polypeptides ( $2\alpha, 2\beta$ ) each with a Haem group containing $Fe^{2+}$ . Each molecule carries $4\,O_{2}$ . Exhibits allosteric shape changes to ease oxygen binding.
Collagen: Fibrous protein, insoluble. Three identical left-handed helical polypeptides wound into a triple helix. Glycine occurs every 3rd residue for tight packing. Chains are staggered within fibres to avoid weak points. High tensile strength for tendons/ligaments.

1.9 & 1.10 Biochemical Testing

Test	Reagent	Positive Result	Explanation
Starch	Iodine in $KI$ solution	Yellow-orange to Blue-black	Iodine binds center of amylase helix
Reducing Sugar	Benedict's solution + Boil	Blue to green/yellow/orange/brick-red ppt	$Cu^{2+}$ reduced to $Cu^{+}$ (copper(I) oxide)
Non-reducing Sugar	HCl + Boil, Neutralize ( $NaOH/NaHCO_{3}$ ), then Benedict's	Blue to red ppt	Acid hydrolyzes sucrose to reducing sugars
Protein	Biuret solution ( $CuSO_{4} + NaOH$ )	Blue to Violet/Purple/Lilac	Coloured complex with peptide bonds
Lipids	Ethanol Emulsion (Ethanol then water)	White cloudiness/emulsion	Lipid dissolves in ethanol, precipitates in water

Quantitative Starch Test: Use colorimeter to measure optical density of starch-iodine complex; compare against calibration graph of known dilutions.
Semi-quantitative Benedict's: Compare test result to set of colour standards from known glucose concentrations.

Module 1, Section 2: Cells

2.1 Introduction to Cells

Resolution: Ability to see detail; defined as the minimum distance between two objects to see them as separate. Human eye resolution is $200\,\mu m$ . Light microscope resolution is limited by wavelength ( $200\,nm$ ).
Magnification: Ratio of image size to actual size. - $Magnification = \frac{\text{size of image}}{\text{actual size}}$ .
Light Microscopy: Uses light rays and glass lenses. Max magnification approx. $x1000$ - $x1500$ .

2.2 - 2.4 Electron Microscopy and Cell Structure

Electron Microscope (EM): Uses electron beams (wavelength $1.0\,nm$ ) and magnetic lenses. Resolution is $0.5\,nm$ . Allows viewing of $\text{cell membranes}$ and ribosomes.
Eukaryotic vs. Prokaryotic: - Eukaryotic: ("True nucleus") Complex membrane-bound organelles (mitochondria, RER, Golgi). - Prokaryotic: ("Before nucleus") Simpler, no nucleus. Features: Murein cell wall, 70S ribosomes (smaller than 80S), naked loop of DNA (no histones), and plasmids.
Endosymbiosis: Theory that mitochondria and chloroplasts evolved from prokaryotes invading larger cells. Evidence: they have circular DNA, 70S ribosomes, and specific tRNA.

Organelle Functions:

Rough ER: Protein synthesis (via ribosomes) and transport.
Smooth ER: Synthesis of lipids (fats, phospholipids, cholesterol).
Golgi Body: Modifies/packages proteins; makes lysosomes/secretory vesicles.
Lysosome: Contains hydrolytic enzymes for digestion/waste.
Mitochondria: Site of aerobic respiration ( $ATP$ production).
Centrioles: Organize spindle fibers for nuclear division (animal cells).

2.6 - 2.8 Cell Membranes and Transport

Fluid Mosaic Model: Phospholipid bilayer ("sea") with floating proteins ("mosaic"). - Cholesterol: Regulates fluidity and stabilizes bilayer. - Glycoproteins/Glycolipids: Recognition and receptor sites.
Movement Types: - Simple Diffusion: Passive movement of non-polar/small molecules through bilayer down concentration gradient. - Facilitated Diffusion: Passive, involves channel/carrier proteins for polar molecules. - Osmosis: Diffusion of water through partially permeable membrane from high water potential ( $\psi$ ) to low $\psi$ . - Active Transport: Uses $ATP$ and carrier proteins to move substances against gradient. - Bulk Transport: Endocytosis (entry) and Exocytosis (exit/secretion) using vesicles.
Water Potential ( $\psi$ ): Tendency of water to move. Pure water is $0\,kPa$ . Solutions have negative values. - Plasmolysis: In plants, cell membrane pulls away from wall in concentrated (low $\psi$ ) solutions. - Turgidity: Cell is firm as internal pressure matches external in high $\psi$ environments.

Module 1, Section 3: Enzymes

3.1 Mode of Enzyme Action

Catalysts: Increase reaction rate without being consumed.
Active Site: 3D pocket lined with R-groups. Complementary to substrate shape.
Models: - Lock and Key: Rigid fit. - Induced Fit: Enzyme changes shape slightly to mold around substrate.
Activation Energy: The energy barrier enzymes lower to allow reactions to proceed at biological temperatures.
Turnover Number: Max substrate molecules converted per active site per unit time.

3.5 & 3.6 Factors Affecting Enzyme Activity

Substrate Concentration: Rate increases until all active sites are saturated (Vmax).
Enzyme Concentration: Rate is directly proportional to concentration (if substrate is in excess).
Temperature: - Rate increases with kinetic energy until Optimum (often $40^{\circ}C$ ). - Past optimum, vibration breaks bonds, causing denaturation.
pH: Affects R-group ionization in active site. Change in pH can denature enzymes.
Inhibitors: - Competitive: Compete for active sites. Effect reduced by increasing substrate concentration. - Non-competitive: Bind elsewhere (allosteric site), changing enzyme shape. Effect NOT reduced by more substrate.

Module 2: Genetics, Variation, and Natural Selection

1.1 Nucleic Acids

DNA: double helix, antiparallel strands ( $3'$ to $5'$ ). Sugar: Deoxyribose. Bases: $A, T, C, G$ .
RNA: single-stranded. Sugar: Ribose. Bases: $A, U, C, G$ . Types: mRNA, tRNA, rRNA.
Nucleotide: Pentose sugar + Phosphate + Base ( $Purines: A, G$ ; $Pyrimidines: C, T, U$ ).

1.2 DNA Replication

Mechanism: Semi-conservative (one old strand, one new).
Process: Unwinding (Topoisomerase/Helicase) -> Nucleotide assembly against template (DNA Polymerase) -> Phosphodiester bond formation ( $5'$ to $3'$ assembly).

1.3 - 1.5 Protein Synthesis

Transcription (Nucleus): RNA Polymerase produces mRNA from template DNA strand.
Amino Acid Activation (Cytoplasm): Aminoacyl-tRNA synthetase attaches amino acids to tRNA using $ATP$ .
Translation (Ribosome): mRNA codons pair with tRNA anticodons. Peptidyl transferase forms peptide bonds. Start codon: $AUG$ (Methionine).

2.1 - 2.5 Mitosis and Meiosis

Mitosis: Maintains genetic stability. 2 identical diploid daughter nuclei. Stages: Prophase, Metaphase, Anaphase, Telophase.
Meiosis: Halves chromosome number; promotes variation. 4 genetically different haploid nuclei. - Meiosis I: Separation of homologous chromosomes. Site of Crossing Over (Prophase I) and Independent Assortment (Metaphase I). - Meiosis II: Separation of sister chromatids.

3.1 - 3.7 Genetics and Inheritance

Mendel's Laws: - 1st Law (Segregation): Alleles separate into gametes. - 2nd Law (Independent Assortment): Genes on different chromosomes segregate independently.
Ratios: - Monohybrid F2: $3:1$ . - Dihybrid F2: $9:3:3:1$ . - Test Cross (Dihybrid): $1:1:1:1$ . - Codominance: $1:2:1$ .
Epistasis: Interaction between different gene loci. (e.g., Recessive epistasis ratio $9:4:3$ ).
Chi-Squared ( $\chi^{2}$ ) Test: Used to determine if differences between observed ( $O$ ) and expected ( $E$ ) results are significant. $p < 0.05$ = Significant difference.

Module 2, Section 4: Genetic Engineering

4.1 Recombinant DNA Technology

Restriction Enzymes: Cut DNA at specific palindromic restriction sites (Sticky ends vs. Blunt ends).
Vectors: Plasmids, viruses, or liposomes used to move genes into host cells.
Transformation: Host cells taking up recombinant DNA (often via heat shock/calcium ions).

4.2 - 4.4 Applications & Ethics

Gene Therapy: Insertion of functional genes to treat disorders. Somatic (non-inherited) vs. Germ-line (inherited, currently illegal).
Insulin Production: Uses reverse transcriptase to make cDNA from mRNA; inserted into yeast/bacteria.
GMO Examples: Bt cotton (pest resistance), Golden Rice (Vitamin A), Transgenic goats (antithrombin in milk).

Module 2, Section 5: Natural Selection

Variation: Intraspecific (within species) vs. Interspecific (between species). - Discontinuous: Qualitative (bar charts, e.g., blood groups). - Continuous: Quantitative (histograms, polygenic, environment-influenced, e.g., height).
Mutation: Substitution, Frameshift, or Chromosome (Aneuploidy like Down's Syndrome ( $Trisomy 21$ )).
Selection Types: - Stabilizing: Favours mean (Horseshoe crab). - Directional: Favours one extreme (Peppered moth/Galapagos finches). - Disruptive: Favours both extremes (African seedcracker).

Module 3: Reproductive Biology

Asexual: Binary fission (bacteria), Budding (yeast), Fragmentation (Spirogyra), Spore formation (Rhizopus).
Plant Reproduction: Pollination (Self/Cross) -> Pollen tube growth -> Double Fertilization ( $Zygote (2n)$ and $Endosperm (3n)$ ).
Human Reproduction: - Gametogenesis: Spermatogenesis (4 equal sperm) vs. Oogenesis (1 large oocyte, 3 polar bodies). - Hormonal Control: Hypothalamus ( $GnRH$ ) -> Pituitary ( $FSH, LH$ ) -> Gonads (Testosterone/Oestrogen/Progesterone).