Unit 2 Biology AS: Cell Structure, Reproduction, Development and Plant Biodiversity

Cell Theory and the Core Features of Life

The Cell Theory Fundamentals: * All living organisms are composed of one or more cells. * The cell is the basic structural and functional unit of life. * All cells arise from pre-existing cells.
Shared Features of All Cells: * Plasma membrane: Controls the movement of substances in and out of the cell. * Cytoplasm: The site of metabolic reactions. * DNA: Carries genetic information for controlling the cell. * Ribosomes: The site of protein synthesis. * Enzymes: Catalyse reactions essential to life. * Energy release: All cells must carry out respiration (aerobic or anaerobic) to release energy.
Structural Consistency: These core features exist in both prokaryotic and eukaryotic cells, even though structure varies.

Hierarchical Organisation in Multicellular Organisms

Hierarchy levels: 1. Cells: The basic unit of life (e.g., epithelial cells, muscle cells). 2. Tissues: A group of similar cells working together to perform a specific function (e.g., muscle tissue contracts; epithelial tissue lines surfaces). 3. Organs: Made of different tissues working together to carry out a function (e.g., the heart includes muscle tissue, nerve tissue, and connective tissue). 4. Organ Systems: Groups of organs that work together to carry out a broader function (e.g., Circulatory system = heart + blood vessels; Digestive system = stomach, intestines, liver, etc.).
Specialisation: Multicellular organisms rely on cell specialisation and cooperation for survival, as no single cell can carry out all life functions.

Ultrastructure and Function of Eukaryotic Cells

Organelles and Structures: * Nucleus: Surrounded by a nuclear envelope with pores; contains DNA and the nucleolus. It stores genetic material. * Nucleolus: A dense region inside the nucleus that synthesises ribosomal RNA ( $rRNA$ ). * Ribosomes: Small, non-membranous structures, either free or bound to the rough Endoplasmic Reticulum ( $rER$ ). They are the site of protein synthesis. * Rough Endoplasmic Reticulum ( $rER$ ): Membrane-bound sacs with ribosomes attached; synthesises and processes proteins for secretion or membrane use. * Smooth ER ( $sER$ ): Membrane-bound sacs without ribosomes; responsible for lipid synthesis and detoxification. * Mitochondria: Double membrane structure where the inner folds comprise the cristae and the interior space is the matrix. It is the site of aerobic respiration ( $ATP$ production). * Golgi Apparatus: Stacks of flattened sacs (cisternae) with vesicles. It modifies, packages, and transports proteins and lipids. * Lysosomes: Vesicles containing hydrolytic enzymes; they digest old organelles, pathogens, and waste (intracellular digestion). * Centrioles: Cylindrical structures made of microtubules (found in animal cells) involved in spindle formation during cell division.
Cell Type Distinctions: Only animal and plant cells are eukaryotic. Plant cells uniquely include chloroplasts, a large permanent vacuole, and a cellulose cell wall.
Organelle Coordination: Protein synthesis and secretion involve the nucleus $ightarrow$ $rER$ $ightarrow$ Golgi $ightarrow$ vesicle $ightarrow$ plasma membrane.
Compartmentalisation: Organelles provide compartments to increase the efficiency of metabolic processes.

Protein Transport and Secretion Pathways

Detailed Protein Transport Pathway: 1. Transcription in the nucleus: A gene coding for the protein is transcribed into $mRNA$ . 2. $mRNA$ exits the nucleus: The $mRNA$ travels through nuclear pores into the cytoplasm. 3. Translation at ribosomes on the $rER$ : Ribosomes on the $rER$ synthesize the polypeptide chain using the $mRNA$ sequence. 4. Protein enters $rER$ lumen: The polypeptide is threaded into the lumen of the $rER$ during synthesis. 5. Protein folding and modification in the $rER$ : Polypeptides fold into secondary and tertiary structures with chaperone proteins. Carbohydrates may be added to form glycoproteins. 6. Packaging into transport vesicles: Proteins are packaged into transport vesicles that bud off from the $rER$ . 7. Transport to the Golgi apparatus: Vesicles fuse with the cis face of the Golgi apparatus. 8. Further modification and sorting in the Golgi: The Golgi adds groups (e.g., phosphate or sulfate) and sorts proteins by destination. 9. Packaging into secretory vesicles: Proteins are packaged into secretory vesicles at the trans face of the Golgi. 10. Exocytosis: Secretory vesicles fuse with the plasma membrane to release proteins outside the cell.
Extracellular Enzymes: Digestive enzymes like amylase and protease are synthesised and secreted this way to act in the gut.

Ultrastructure of Prokaryotic Cells

Key Structures and Descriptions: * Cell wall: Made of peptidoglycan (murein), not cellulose; provides strength and prevents lysis. * Capsule: Outer slimy polysaccharide layer; protects from desiccation, the immune system, and antibiotics. Specifically aids pathogenicity in species like Streptococcus pneumoniae. * Plasmid: Small circular $DNA$ molecule, separate from main $DNA$ ; carries genes for antibiotic resistance. Allows for horizontal gene transfer. * Flagellum: Long protein tail that rotates to enable motility. * Pili (fimbriae): Short protein projections used for attachment or conjugation ( $DNA$ transfer). * Ribosomes: $70S$ type, smaller than eukaryotic $80S$ . * Circular DNA: A single loop of $DNA$ not bound in a nucleus; floats free in the cytoplasm.
Key Notes: Prokaryotes lack a nucleus and membrane-bound organelles. Some form endospores under stress.

Microscopy Principles and Interpretations

Core Definitions: * Magnification: How much larger the image is compared to the actual object. * Resolution: The ability to distinguish two close points as separate.
Calculating Magnification: * $\text{Magnification} = \frac{\text{Image size}}{\text{Actual size}}$ * Units must be consistent (e.g., convert $mm$ to $\mu m$ ).
Electron Micrograph (EM) Identification: * Nucleus: Double membrane with pores; often the largest structure. * Nucleolus: Dense dark region within the nucleus. * Mitochondria: Double membrane with cristae (folded inner membrane). * $rER$ : Flattened sacs with dots (ribosomes) attached. * $sER$ : Flattened sacs without dots. * Golgi: Stacks of flattened sacs with nearby vesicles. * Ribosomes: Tiny dots; visible as polyribosomes in clusters.
Staining Specimens: Stains increase contrast by binding to specific components. * Methylene blue: Binds $DNA$ / $RNA$ (nucleus). * Iodine: Stains starch in plant cells. * Acetic orcein: Binds chromosomes in mitosis.
Core Practical 5 (Light Microscope and Graticule): * Eyepiece graticule: A transparent ruler fitted in the eyepiece. * Stage micrometer: Used to calibrate the graticule to calculate the length per graticule unit. * Drawing Guidelines: Use clear lines, no shading, and include labels ( $nucleus$ , $cytoplasm$ , $cell\,membrane$ ).

Genetic Loci and Meiosis

Locus Definition: A specific, fixed position on a chromosome where a particular gene is located.
Homologous Chromosomes: Carry the same loci and gene order but may carry different alleles.
Role of Meiosis in Genetic Variation: Produces four non-identical haploid gametes. * Independent Assortment (Metaphase I): Homologous chromosomes line up randomly at the equator. Results in $2^n$ combinations, where $n$ is the number of chromosome pairs. * Crossing Over (Prophase I): Non-sister chromatids of homologous chromosomes exchange segments at chiasmata, producing new combinations of alleles (genetic recombination). * Random Fertilisation: The chance fusion of gametes increases random differences across offspring.

Mammalian Gametes and Fertilisation

Sperm Cell Adaptations: * Acrosome: Contains enzymes to digest the zona pellucida. * Nucleus: Haploid ( $n$ ). * Tail: Enables motility. * Mitochondria: Provide $ATP$ for movement. * Streamlined shape: Reduces drag for faster swimming to the egg.
Egg Cell Adaptations: * Zona pellucida: Thick glycoprotein layer protecting the egg and blocking polyspermy. * Cytoplasm: Contains nutrients like lipid granules for embryo growth. * Cortical granules: Release enzymes by exocytosis to harden the zona pellucida. * Large size: Accommodates materials for early embryo divisions.
Mammalian Fertilisation Process: 1. Sperm reaches the egg in the oviduct. 2. Acrosome reaction: Enzymes from the acrosome digest the zona pellucida. 3. Membranes fuse. 4. Cortical reaction: Enzymes released via exocytosis harden the zona pellucida to prevent polyspermy. 5. Fusion of nuclei: Sperm and egg nuclei fuse to form a diploid ( $2n$ ) zygote.

Fertilisation in Flowering Plants

Double Fertilisation Process: 1. Pollen grain lands on the stigma. 2. Pollen tube nucleus controls secretion of hydrolytic enzymes to digest the style and create a path (pollen tube) to the micropyle. 3. Generative nucleus divides by mitosis into two male nuclei. 4. One male nucleus fertilises the egg cell to form a diploid ( $2n$ ) zygote. 5. One male nucleus fuses with polar nuclei to form a triploid ( $3n$ ) endosperm (nutritive tissue).
Comparison with Mammals: In plants, the site is the ovule (vs. oviduct) and an extra product (endosperm) is formed.

The Cell Cycle and Mitosis

Interphase ( $\approx 90\%$ of cycle): * $G_1$ phase: Cell growth and protein synthesis (e.g., $DNA\,polymerase$ ). * $S$ phase: $DNA$ replication; chromosomes double. * $G_2$ phase: Preparatory growth, organelle replication, and further protein synthesis.
Mitotic Phase ( $M$ phase): * Mitosis: Division of the nucleus. * Cytokinesis: Division of the cytoplasm into two identical daughter cells.
Mitosis Stages: * Prophase: Chromosomes condense; nuclear envelope breaks down. * Metaphase: Chromosomes line up at the equator, attached to spindle fibres. * Anaphase: Sister chromatids are pulled apart to opposite poles. * Telophase: New nuclear envelopes form; chromosomes decondense.
Core Practical 6 (Root Tip Mitosis): Involves cutting $1\text{--}2\,cm$ from root tips (garlic/onion), treating with $HCl$ to break cell walls, and staining with acetic orcein.

Stem Cells and Medical Applications

Key Classifications: * Stem cell: Undifferentiated cell capable of developing into different types. * Totipotent: Can give rise to any cell type, including placental (extra-embryonic) tissue (e.g., zygote, morula). * Pluripotent: Can give rise to all body cells, but not placental tissue (e.g., inner cell mass of blastocyst).
Embryonic Development: * Morula: Solid ball of totipotent cells formed by mitosis of the zygote. * Blastocyst: Hollow structure with an inner cell mass of pluripotent cells and a surrounding trophoblast (forms placental tissue).
Stem Cells in Medicine: Used for treating degenerative conditions (Parkinson's, diabetes, spinal injuries) and organ regeneration.
Ethical Considerations: * Pro: Saves lives; reduces donor shortages. * Con: Destruction of embryos; moral/religious objections; fear of "designer babies."
$iPSCs$ (Induced Pluripotent Stem Cells): Reprogrammed adult cells that offer a way to avoid the ethical issues of embryonic stem cells.

Cell Specialisation and Gene Expression

Differential Gene Expression: All cells share the same genome, but only specific genes are expressed.
Epigenetic Modification Mechanism: 1. Activation: DNA or histone acetylation. 2. Silencing: Histone or DNA methylation (inhibits $mRNA$ binding).
Proteins and Identity: Active genes are transcribed to $mRNA$ and translated into proteins that define the cell's structure (cytoskeleton) and function (enzymes).
Post-Transcriptional Modification (Alternative Splicing): * Pre- $mRNA$ contains introns (removed) and exons (spliced). * Different combinations of exons joined by spliceosomes produce different mature $mRNA$ molecules. * Allows a single gene to produce multiple proteins (e.g., Tropomyosin in smooth vs. skeletal muscle).

Epigenetics and Inheritance

Phenotype Interaction: $\text{Phenotype} = \text{Genotype} + \text{Environment}$ .
DNA Methylation: Addition of methyl groups ( $CH_3$ ) to cytosine bases (often at CpG sites). Silences genes, such as tumour suppressor genes in cancer.
Histone Modification Details: * Acetylation: DNA wraps loosely; $mRNA$ can bind; gene activated. * Deacetylation/Methylation: DNA wraps tightly; bases not exposed; gene silenced.
Inheritance: Epigenetic marks are passed to daughter cells during division, ensuring liver cells remain liver cells. Some marks contribute to transgenerational effects.

Polygenic Inheritance and Continuous Variation

Monogenic: One gene; Discontinuous variation (e.g., blood group); Bar chart.
Polygenic: Many genes; Continuous variation (e.g., height, skin colour); Normal distribution (bell curve).
Additive Effect: Each gene involved contributes additively. More dominant alleles result in more intense trait expression.

Errors in Meiosis and Cancer

Non-disjunction: Failure of homologous chromosomes (Meiosis I) or sister chromatids (Meiosis II) to separate properly.
Aneuploidy/Conditions: * Down syndrome: Trisomy $21$ ( $47$ chromosomes). * Turner syndrome: Missing one X in females ( $45, XO$ ). * Klinefelter syndrome: Extra X in males ( $47, XXY$ ). * Patau syndrome: Trisomy $13$ .
Cancer Development: Uncontrolled cell division from mutations. * Proto-oncogenes: Mutate into oncogenes that promote uncontrolled division. * Tumour suppressor genes: Mutations inactivate these, so damaged cells continue dividing.
Tumour Types: * Benign: Slow growth, localised, non-cancerous. * Malignant: Rapid growth, invades tissues, spreads (metastasizes), cancerous.

Plant Structure and Support

Cell Wall Composition: * Cellulose microfibrils: $\beta$ -glucose chains joined by $1,4$ glycosidic bonds; hydrogen bonds provide tensile strength. * Hemicellulose: Short-chain carbohydrates linking microfibrils. * Pectin (calcium pectate): Binds adjacent walls in the middle lamella. * Lignin: Adds rigidity and waterproofs secondary walls; kills the cell to create a hollow xylem vessel.
Tissues: * Xylem: Dead, hollow, lignified vessels. Passive transport of water/minerals via transpiration; provides support. * Phloem: Living sieve tubes and companion cells. Active transport of solutes (translocation). * Sclerenchyma: Dead, elongated cells with thick lignified walls for mechanical strength (purely supportive).
Plant Nutrition Ions: * Nitrate ( $NO_3^-$ ): For amino acids, DNA, and growth. * Calcium ( $Ca^{2+}$ ): Strengthens walls (calcium pectate). * Magnesium ( $Mg^{2+}$ ): Central in chlorophyll for photosynthesis. * Potassium ( $K^+$ ): Regulates stomata. * Phosphate ( $PO_4^{3-}$ ): For DNA, $ATP$ , and phospholipids.

Antimicrobial Properties and Drug Testing

Core Practical 7 (Antimicrobials): * Plants produce secondary metabolites (e.g., garlic, mint) to defend against pathogens. * Measured by the zone of inhibition (diameter in $mm$ ). * Safety: Incubate below $30^{\circ}C$ to avoid pathogenic strains; use aseptic techniques.
Drug Discovery History: William Withering used foxglove extract (digitalis) to treat heart failure (dropsy) via trial and error, documenting dosage vs. toxicity.
Modern Drug Testing Process: * Pre-clinical: Cells, tissues, and animals; tests toxicity. * Phase I: Small group of healthy volunteers; tests safety/dosage. * Phase II: A few hundred patients; assesses efficacy and effective dose; double-blind. * Phase III: Thousands of patients; randomised, double-blind, placebo-controlled; uses statistical tests to compare with existing treatments.

Classification and Biodiversity

Three-Domain System: Bacteria, Archaea, and Eukarya. * Archaea: Ester-linked branched lipids and $70S$ ribosomes; more related to Eukarya. * Bacteria: Peptidoglycan in cell walls; ester-linked unbranched lipids.
Definitions: * Biodiversity: Variety of species, genes, and ecosystems. * Endemism: Species found only in one specific geographic location (e.g., Lemurs in Madagascar).
Hardy-Weinberg Equation: Used to check for stability in allele frequencies ( $p^2 + 2pq + q^2 = 1$ ). * Assumptions: Large population, random mating, no mutation, no migration, no selection.
Speciation: * Allopatric: Geographic isolation (mountains, rivers). * Sympatric: Reproductive isolation (behavioural, temporal, mechanical) in the same area.

Conservation Strategies

Ex situ Conservation: * Seed Banks: Seeds washed, dried, X-rayed, and stored at $-18^{\circ}C$ to $-20^{\circ}C$ . * Cryopreservation: Storage in liquid nitrogen at $-196^{\circ}C$ for indefinite viability. * Zoos and Botanic Gardens: Captive breeding, research, and public education.
Scientific Tools: * Stud Books: Tracking lineage to prevent inbreeding/genetic bottlenecks. * Artificial Insemination ( $AI$ ) and $IVF$ : Boost reproduction when natural mating fails.
Reintroduction: Restoring captive-bred individuals to the wild through habitat preparation and community involvement.