CAPE Biology Unit 1 Comprehensive Study Notes

Biochemistry is the study of biological molecules and their roles in organisms. These molecules are considered the building blocks of life, constantly being assembled and disassembled through metabolism.
Metabolism is the collective term for all chemical reactions in an organism, divided into two categories: - Anabolism: Reactions that build larger biological molecules from smaller ones (anabolic reactions). - Catabolism: Reactions that break down large biological molecules into smaller ones (catabolic reactions).
All major biological compounds are based on the element carbon, which forms strong covalent bonds with itself and other atoms, producing both single and double bonds.
Inorganic compounds in the air include oxygen, carbon dioxide, nitrogen, and hydrogen. Complex compounds of carbon are categorized as organic compounds.
Key Chemical Terms: - Chemical element: A pure substance consisting of one type of atom. - Atom: The smallest component of an element containing neutrons and protons in a nucleus, surrounded by electrons. - Isotope: Atoms of the same element with different numbers of neutrons. - Molecule: The smallest particle of a substance retaining physical/chemical properties, composed of two or more atoms. - Ion: An atom or molecule that has gained or lost electrons, acquiring a positive or negative charge. - Ionic bond: A chemical bond between two ions with opposite charges. - Covalent bond: A chemical bond involving the sharing of an electron pair between atoms.
Biological macromolecules are often polymers made of repeating sub-units called monomers: - Carbohydrates: Elements C, H, O (ratio $1:2:1$ ). Monomer: Glucose. Sub-types: Starch (amylose/amylopectin), glycogen, cellulose. Roles: Energy storage and support. - Lipids: Elements C, H, O (ratio C:H approx $1:2$ ; high C:O and H:O ratios like $9:1$ or $18:1$ ). Sub-units: Glycerol, fatty acids, phosphate. Examples: Triglycerides, phospholipids. Roles: Energy storage, thermal/electrical insulation, membranes. - Proteins: Elements C, H, O, N, S. Monomer: Amino acids ( $20$ different types). Examples: Haemoglobin, collagen, amylase, pepsin, insulin, antibodies. Roles: Transport, support, catalysts, messengers, protection. - Nucleic Acids: Elements C, H, O, N, P. Monomer: Nucleotides ( $5$ types). Examples: DNA, RNA ( $mRNA$ , $tRNA$ , $rRNA$ ). Roles: Information storage/retrieval, protein production.

Water and Hydrogen Bonding

Water (H2O) forms approximately $70\%$ of animal bodies and $90\%$ of plants.
The water molecule is dipolar: oxygen is slightly electronegative ( $\delta-$ ) and hydrogen is slightly electropositive ( $\delta+$ ). This occurs because oxygen has a greater attraction for covalent bond electrons.
Hydrogen bonds form between the negative charge of oxygen on one molecule and the positive charge of hydrogen on another. Each bond is weak (about $1/10$ the strength of a covalent bond) and frequently breaks/reforms.
Properties of Water: - Solvent: Good for charged substances (ions like $Na^+$ , $Cl^-$ ) and polar molecules (glucose). Carbon dioxide is significantly more soluble than oxygen. - High Specific Heat Capacity: Requires $4.2\,J$ to increase the temperature of $1\,g$ of water by $1\,^{\circ}C$ . This limits temperature fluctuations in organisms. - High Latent Heat of Vaporisation: High energy needed for evaporation, making transpiration and sweating efficient cooling mechanisms. - High Latent Heat of Fusion: High energy needed to melt ice; water in cells stays liquid longer to prevent membrane damage from crystals. - Density: Ice is less dense than water. It acts as insulation for aquatic habitats. Organisms at risk of freezing produce 'anti-freeze' compounds to lower the freezing point of cytoplasm. - Incompressibility: Provides hydrostatic skeletons (sea anemones, worms) and turgidity in plants. - Cohesion: Hydrogen bonds hold molecules together, supporting water columns in xylem and creating surface tension.
Water Reactions: Water splits into hydrogen ions ( $H^+$ ) and hydroxyl ions ( $OH^-$ ). It is used in hydrolysis (e.g., digestion) and photosynthesis (provides ions/electrons).

Carbohydrates: Sugars and Polysaccharides

Carbohydrates contain C, H, and O with the general formula $C_x(H_2O)_y$ .
Simple Sugars (Monosaccharides): Cx(H2O)y where x is $3$ , $4$ , $5$ , $6$ , or $7$ . - Glucose ( $C_6H_{12}O_6$ ): Exists in ring and straight-chain forms. - Ring forms of glucose: $\alpha$ -glucose (hydroxyl $-OH$ group below the ring at C1) and $\beta$ -glucose ( $-OH$ above the ring at C1). - Hexoses ( $6$ carbons): Glucose, fructose, galactose. Pentoses ( $5$ carbons) are components of nucleotides. Trioses ( $3$ carbons) are metabolic intermediates.
Complex Sugars (Disaccharides): Two monosaccharides joined by a covalent glycosidic bond through a condensation reaction (elimination of water). - Sucrose: Formed from $\alpha$ -glucose and fructose. It is non-reducing, water-soluble, and polar. Plants use it for transport in phloem because it is less reactive than glucose. - Hydrolysis: The addition of water to break a glycosidic bond.
Polysaccharides: Polymers used for energy storage or structure. - Starch (Plants): Composed of Amylose (unbranched unbranched $1,4$ glycosidic bonds, right-handed helix) and Amylopectin (branched, $1,4$ and $1,6$ glycosidic bonds). - Glycogen (Animals/Fungi): Similar to amylopectin but more highly branched ( $1,4$ and $1,6$ bonds). - Cellulose: Unbranched straight chains of $\beta$ -glucose ( $1,4$ bonds) with alternate molecules rotated $180^{\circ}$ . projecting $-OH$ groups form hydrogen bonds between chains to create microfibrils. These arrange in a criss-cross pattern for strength in cell walls.

Lipids and Human Health

Lipids have much higher H:O ratios than carbohydrates. They are non-polar and insoluble in water.
Triglycerides: Glycerol plus three fatty acids joined by ester bonds. - Saturated fatty acids: No double bonds between carbons in the chain, holding maximum hydrogens. - Unsaturated fatty acids: At least one double bond between carbons, resulting in fewer hydrogens. - Efficient for energy storage: Released energy upon oxidation is much higher than carbohydrates/proteins due to high reduction (hydrogen content).
Phospholipids: Glycerol, two fatty acids, and a phosphate group (often with choline). - Structure: Hydrophilic (water-liking) head and two hydrophobic (water-hating) tails. - In water, they form monolayers, micelles (spheres), or bilayers (the basis of biological membranes).
Fat in Diet and Obesity: - Essential fatty acids: Two types humans cannot synthesize and must consume. - Fat-soluble vitamins: $A$ , $D$ , $E$ , and $K$ . - Energy Balance: Positive balance leads to fat storage. Negative balance results in fat usage. - Body Mass Index (BMI): $\text{BMI} = \frac{\text{body mass in kg}}{(\text{height in metres})^2}$ . - BMI Categories: Underweight ( $<20$ ), Acceptable ( $20-25$ ), Overweight ( $25-30$ ), Obese ( $>30$ ), Very Obese ( $>40$ ).

Proteins and Amino Acids

Amino Acid Structure: Central carbon atom attached to an amine group ( $-NH_2$ ), a carboxylic acid group ( $-COOH$ ), a hydrogen atom, and a residual ( $R$ ) group.
Key Amino Acids: - Glycine: Smallest (R is $-H$ ); allows close packing in collagen. - Alanine: Non-polar (R is $-CH_3$ ). - Cysteine: Contains sulfur (R is $-CH_2-SH$ ); forms covalent disulphide bonds.
Peptide Bonds: Form between the carbon of the carboxyl group of one amino acid and the nitrogen of the amine group of another. - $<10$ amino acids: Dipeptide, tripeptide. - $>10$ amino acids: Polypeptide.
Levels of Protein Organisation: - Primary structure: The specific sequence of amino acids and position of disulphide bonds. - Secondary structure: Local folding into $\alpha$ -helices or $\beta$ -pleated sheets, stabilized by hydrogen bonds between $-NH$ and $-CO$ groups. - Tertiary structure: Further folding into a complex 3D shape, stabilized by hydrogen bonds, ionic bonds (between ionized R groups), hydrophobic interactions, and disulphide bonds. - Quaternary structure: Association of two or more polypeptide chains (Identical or different).
Globular vs. Fibrous Proteins: - Globular: Soluble, complex folding, hydrophilic R groups on the surface (e.g., haemoglobin, enzymes). - Fibrous: Insoluble, simple shapes, high tensile strength (e.g., collagen, keratin).
Case Studies: - Haemoglobin: Globular conjugated protein with four polypeptides (two $\alpha$ , two $\beta$ ). Each has a prosthetic haem group with an iron atom ( $Fe^{2+}$ ) at the center. Carries four oxygen molecules. Binding of the first oxygen causes an induced fit change from 'tense' to 'relaxed' state. - Collagen: Three identical left-handed helical polypeptides wound into a triple helix. Glycine occurs every third amino acid. Triple helices are covalently bonded into network fibers ( $300\,nm$ wide) with staggered ends to prevent weakness.

Biochemical Testing Procedures

Qualitative Tests: - Starch: Iodine in potassium iodide solution. Positive: Yellow-orange to blue-black. - Reducing Sugars: Benedict's solution (alkaline copper sulfate) + heat. Positive: Blue to green/yellow/orange/brick-red precipitate ( $Cu^{2+}$ reduced to $Cu^+$ in copper(I) oxide). - Non-reducing Sugars (Sucrose): Negative Benedict’s test first. Hydrolyse with dilute $HCl$ , boil, neutralize with $NaOH$ or $NaHCO_3$ , then re-test with Benedict’s. Positive: Blue to red signal. - Proteins: Biuret reagent ( $CuSO_4$ and $NaOH$ ). Positive: Blue to violet/lilac/purple. - Lipids: Emulsion test ( $Ethanol$ + water). Positive: White cloudiness/emulsion.
Quantitative Tests: - Semi-quantitative Benedict's: compare test tube color against established glucose standards ( $0.1$ to $50.0\,g\,dm^{-3}$ ). - Quantitative Starch: Prepare starch dilutions (e.g., $0.01$ to $100\,g\,dm^{-3}$ ), add iodine, measure optical density using a colorimeter (absorbance or percentage transmission), and plot a calibration graph.

Cell Structure and Microscopy

Principles of Microscopy: - Resolution: The ability to distinguish detail; limited by the wavelength of radiation. Eye resolution is approx $200\,\mu m$ . - Magnification: Ratio of image size to actual size. $\text{Magnification} = \frac{\text{size of image}}{\text{actual size}}$ .
Microscope Comparison: - Light Microscope: Resolution $200\,nm$ , max magnification $\times 1500$ , uses light ( $400-700\,nm$ ), observes living cells in color. - Electron Microscope: Resolution $0.5\,nm$ , max magnification $\times 250,000$ , uses electron beams ( $1.0\,nm$ ), observes dead specimens in a vacuum (black and white images).
Eukaryotic Organelles: - Nucleus: Stores DNA; contains a nucleolus (ribosome production). - RER: Coated in ribosomes ( $80S$ ); protein synthesis and transport. - SER: Lacks ribosomes; lipid/cholesterol/phospholipid synthesis. - Golgi Body: Modifies/packages proteins into vesicles; makes lysosomes. - Mitochondria: Double membrane, fluid matrix, inner cristae folds; site of aerobic respiration. - Chloroplasts: Site of photosynthesis (plant cells only); contain chlorophyll. - Lysosomes: Contain hydrolytic digestive enzymes. - Centrioles: Assemble spindles for division (animal cells only). - Cell Wall: Cellulose structure (plant cells only) for support and shape.
Prokaryotes vs. Eukaryotes: - Prokaryotes: $0.5-3.0\,\mu m$ , no nucleus (loop of DNA), $70S$ ribosomes, cell wall made of murein (peptidoglycan), may have capsules/flagella. - Endosymbiosis Theory: Proposes that mitochondria and chloroplasts evolved from bacteria that 'invaded' anaerobic ancestral cells. Evidence: they have their own loop of DNA, $70S$ ribosomes, and similar membrane systems.
Tissues and Organs: - Tissue: Groups of similar cells with the same function (e.g., squamous/columnar epithelium, xylem, phloem). - Organ: Structures of different tissues performing complex functions (e.g., leaf, liver, heart).

Movement Across Membranes

Fluid Mosaic Model: A sea of phospholipids in a bilayer ( $7-10\,nm$ wide) with floating transmembrane proteins. Cholesterol stabilizes the bilayer. - Glycoproteins/Glycolipids: Act as receptors for hormones/neurotransmitters and cell recognition sites.
Transport Mechanisms: - Simple Diffusion: Small/non-polar molecules (oxygen, $CO_2$ , ethanol) pass through the bilayer down a concentration gradient. No energy required. - Facilitated Diffusion: Polar molecules/ions use channel proteins or carrier proteins to cross the membrane. - Osmosis: Net movement of water through a partially permeable membrane from high water potential to low water potential. - Active Transport: Movement against a gradient using carrier proteins and energy ( $ATP$ ) from respiration. - Bulk Transport: Endocytosis (taking in large particles via vacuoles) and Exocytosis (exporting materials via vesicles fusing with the cell membrane).
Water Potential ( $\Psi$ ): - Determined by water quantity and solute concentration. Plant cells have pressure potential ( $\Psi_p$ ) exerted by the cell wall. - Turgid: Cell full of water, membrane pushes against wall. $\Psi = 0\,kPa$ when fully turgid. - Plasmolysis: Vacuole shrinks, cytoplasm pulls away from the cell wall in hypertonic (low $\Psi$ ) solutions. Cell is flaccid.

Enzymes: Biological Catalysts

Enzymes are globular proteins that lower the activation energy of metabolic reactions. They are specific due to the shape of the active site.
Models of Action: - Lock and Key: Substrate fits exactly into the active site. - Induced Fit: Enzyme changes shape slightly to mold around the substrate for a tighter fit.
Enzyme examples: - Amylase: Starch $\rightarrow$ maltose. - Catalase: $2H_2O_2 \rightarrow 2H_2O + O_2$ .
Factors Influencing Activity: - Substrate Concentration: Rate increases until active sites are saturated (limiting factor becomes enzyme concentration). - Temperature: Rate increases with kinetic energy until the optimum (usually approx $40\,^{\circ}C$ ). Above this, vibration breaks bonds, leading to denaturation. - pH: Each enzyme has an optimum pH (e.g., Pepsin at $1.0-2.0$ , Catalase at $7.0$ ). Deviations cause R-group interaction breakage and denaturation.
Inhibition: - Competitive: Inhibitor has a similar shape to the substrate and competes for the active site. Effect reduced by increasing substrate concentration. - Non-competitive: Inhibitor binds to an allosteric site, changing the enzyme's overall shape. Effect cannot be overcome by more substrate.

Genetics: DNA, Replication, and Protein Synthesis

Nucleic Acids: Polymers of nucleotides. Nucleotides consist of a pentose sugar, a phosphate group, and a nitrogenous base. - DNA Bases: Adenine, Guanine (purines), Cytosine, Thymine (pyrimidines). - RNA Bases: Adenine, Guanine, Cytosine, Uracil ( $U$ replaces $T$ ).
DNA Structure: Double helix of two antiparallel strands connected by hydrogen bonds (A–T has $2$ bonds; C–G has $3$ ). Sugar-phosphate 'backbone' held by phosphodiester bonds.
DNA Replication: Semi-conservative process. - Helicase separates strands; Topoisomerase unwinds. - DNA Polymerase assembles free nucleotides against template strands in a $5'$ to $3'$ direction. - Meselsohn and Stahl (1958) proven the semi-conservative nature using nitrogen isotopes.
Protein Synthesis: - Transcription (Nucleus): RNA polymerase makes a complementary $mRNA$ copy of the DNA template strand. Transcription factors and promoter sequences regulate the process. - Translation (Ribosomes): $mRNA$ codons are matched by $tRNA$ anticodons carrying specific amino acids. Peptidyl transferase (a ribozyme) forms peptide bonds. The genetic code is degenerate (multiple codons per amino acid) and universal.
From Gene to Phenotype: Genes code for polypeptides. Faulty genes cause disorders: - Albinism: Faulty tyrosinase gene ( $TYR$ ). - Phenylketonuria ( $PKU$ ): Faulty phenylalanine hydroxylase gene ( $PAH$ ).

Cell Division: Mitosis and Meiosis

Mitosis: Maintains genetic stability. Stages: Prophase (condensation), Metaphase (equatorial alignment), Anaphase (chromatid separation), Telophase (nuclear reform). Followed by Cytokinesis.
Cell Cycle phases: $G1$ (growth), $S$ (DNA synthesis), $G2$ (growth), and Mitosis ( $M$ ).
Meiosis: Halves chromosome number for sexual reproduction. Consists of two divisions: - Meiosis I: Homologous chromosomes pair (Bivalents) and separate. Crossing over occurs at chiasmata. - Meiosis II: Sister chromatids separate. Produces four genetically different haploid ( $n$ ) nuclei.
Sources of Variation: Random segregation of chromosomes ( $2^{23}$ combinations in humans) and crossing over.

Inheritance and Genetic Engineering

Mendel’s Laws: Law of Segregation (alleles separate) and Law of Independent Assortment (unlinked genes separate independently).
Patterns: - Monohybrid: $3:1$ ratio in $F2$ . - Dihybrid: $9:3:3:1$ ratio in $F2$ . - Codominance: Both alleles expressed (e.g., Mirabilis jalapa flowers: red, white, pink). - Sex Linkage: Genes on X-chromosome (e.g., Haemophilia, color blindness). - Multiple Alleles: e.g., ABO blood groups ( $I^A$ , $I^B$ are codominant, $I^O$ is recessive). - Epistasis: Interaction where one gene masks another (e.g., flower color in Collinsia parviflora). $9:4:3$ or $9:3:4$ ratios.
Chi-Squared ( $\chi^2$ ) Test: $\chi^2 = \sum \frac{(O-E)^2}{E}$ . Used to determine if results differ significantly from expected ratios. A value with $p < 0.05$ is significant.
Genetic Engineering: Recombinant DNA technology. - Restriction Enzymes: Cut DNA at palindromic restriction sites (blunt or sticky ends). - Vector: Transports gene (Plasmids, viruses, liposomes). - Ligase: Joins DNA fragments. - Reverse Transcriptase: Makes $cDNA$ from $mRNA$ (used for human insulin production). - Gene Therapy: Transferring functioning genes into patients (e.g., SCID, Cystic Fibrosis).
GMO Examples: Bt crops (insect resistance), Herbicide resistance (Soya), Golden Rice (vitamin A precursors), Transgenic animals (antithrombin in goat milk).

Variation, Selection and Speciation

Variation Types: - Discontinuous: Clear categories, monogenic (e.g., blood groups, ear lobe attachment). - Continuous: Range of phenotypes, polygenic, affected by environment (e.g., height, milk yield).
Selection Types: - Stabilising: Favors the intermediate form (e.g., horseshoe crab, warbler wing length). - Directional: Favors one extreme due to environmental change (e.g., Darwin’s finches during drought, peppered moth melanism). - Disruptive: Favors both extremes, selecting against the middle (e.g., African seedcracker beaks).
Natural Selection Examples: Kettlewell’s moths (industrial melanism), antibiotic resistance in bacteria (vertical and horizontal transmission), guppies in Trinidad (predation affects maturation size).
Mutations: Chromosome mutations (Aneuploidy like Down's Syndrome $2n=47$ ; Polyploidy) and Gene mutations (Substitution, Frameshift, Stutter/repeat).
Speciation: Formation of new species. - Allopatric: Geographical isolation (e.g., snapping shrimps at Isthmus of Panama). - Sympatric: Within the same area (e.g., polyploidy in Spartina cord grass, Lonicera fly hybrids).

Reproductive Biology

Asexual Reproduction: Produces clones. Methods: Binary fission (bacteria), Budding (yeast, Aiptasia), Fragmentation (Spirogyra), Spores (Rhizopus).
Plant Sexual Reproduction: - Pollen produced in anthers (pollen mother cell $\xrightarrow{meiosis}$ tetrad). - Embryo sac in ovule (mother cell $\xrightarrow{meiosis}$ $4$ cells $\xrightarrow{3\,degenerate}$ 1\,cell\,\xrightarrow{mitosis}$ 8\,nuclei).\n - Double Fertilisation: One male gamete fuses with ovum (2n $zygote); one fuses with two polar nuclei ($ 3n endosperm).\n- Human Reproduction:\n - Gametogenesis: Spermatogenesis (equal division) and Oogenesis (unequal division; arrested in meiosis I until menstrual cycle).\n - Fertilisation: Occurs in the oviduct. Involves capacitation, acrosome reaction, and cortical reaction (to prevent polyspermy).\n - Internal Development: Blastula implants in endometrium. Placenta (maternal/foetal tissue) provides gas exchange, nutrition (glucose by facilitated diffusion), and hormone secretion (hCG, progesterone, oestrogen).
Hormonal Control: - GnRH (Hypothalamus) \rightarrow$$ FSH/LH (Anterior Pituitary). - Males: Negative feedback of testosterone and inhibin. - Females: Complex cycle (Follicular, Ovulation, Luteal phases). LH surge triggers ovulation.
Maternal Behavior: Alcohol (Foetal Alcohol Syndrome), Nicotine (restricts blood flow/oxygen transport), Carbon monoxide (carboxyhaemoglobin), Folic acid (prevents spina bifida).