Biology Edexcel Unit 2

Fundamental Principles of Microscopy and Resolution

• Resolution Defined: The shortest distance between two points such that they are perceived by the observer as separate objects. If the distance between two points is less than the resolution limit of the instrument, they will appear as a single, blurry point.
• Magnification Defined: This represents the number of times an image appears larger than the actual object being examined.
• Resolution Calculation: Resolution is mathematically measured as $1/2$ of the shortest wavelength of the light or radiation beam utilized in the microscope.
  • Light Microscope (Optical): Uses a light beam with a shortest wavelength of approximately $400\,nm$. Consequently, its resolution limit is $200\,nm$ ($400\,nm / 2$). The maximum effective magnification is approximately $1500\times$.
  • Electron Microscope: Utilizes electron beams with extremely short wavelengths. This allows for a much higher resolution of $0.5\,nm$. It provides a significantly higher magnification of up to $500,000\times$.
• Relationship between Resolution Value and Clarity: The lower the numerical value of the resolution, the higher the resolution (clarity) of the image. High resolution reduces haziness.

Comparative Analysis: Light vs. Electron Microscopes

• Light Microscope Characteristics:
  • Portability: It is portable and can be moved easily.
  • Cost: Relatively cheap to purchase and maintain.
  • Technical Training: Does not require specialized technical training for basic operation.
  • Specimen State: Can be used to observe living cells and dynamic processes.
  • Color: Displays real colors based on the pigments present in the specimen.
  • Live Observation: Allows for the addition of water droplets to observe cell movement.
• Electron Microscope Characteristics:
  • Portability: Non-portable; requires a fixed, controlled environment.
  • Cost: Very expensive acquisition and maintenance costs.
  • Technical Training: Requires extensive technical training for operation and specimen preparation.
  • Specimen State: Can only observe dead cells because the specimen must be placed in a vacuum.
  • Color: Images are naturally black and white; color must be added digitally afterward.
  • Preparation: The specimen undergoes many chemical and physical treatments, which can lead to the formation of artifacts (structures seen in the image that are not part of the living tissue but are produced during preparation).

Cell Structures and Organelle Classification

• Ultra Cell Structure: Refers to the detailed internal structures of a cell as revealed by an electron microscope.
• Organelle Classification by Membrane:
  • Double-Membrane Bound Organelles: 1. Nucleus; 2. Mitochondria; 3. Chloroplasts; 4. Amyloplasts.
  • Single-Membrane Bound Organelles: 1. Vesicles; 2. Smooth Endoplasmic Reticulum (SER); 3. Rough Endoplasmic Reticulum (RER); 4. Lysosomes; 5. Golgi body; 6. Golgi vesicles; 7. Large Central Vacuole.
  • Non-Membrane Bound Organelles: 1. Centrioles; 2. Nucleolus; 3. Ribosomes.
• Transmission Electron Microscope (TEM): Used specifically for viewing internal structures and internal ultra-cell detail.
• Scanning Electron Microscope (SEM): Used to produce 3D images of the external surfaces of structures.
• Calibration: Involves the alignment of the eyepiece graticule with a stage micrometer to measure cell dimensions accurately.

Detailed Organelle Functions and Protein Synthesis Pathway

• Endoplasmic Reticulum (ER):
  • Rough Endoplasmic Reticulum (RER): Characterized by flattened sacs called cisternae with an inner cisternal space. It is studded with ribosomes, the site of protein synthesis (translation). Polypeptide (pp) chains enter the cisternal space of the RER to be modified (folding into tertiary structures) and then packed into vesicles for transport to the Golgi body.
  • Smooth Endoplasmic Reticulum (SER): Tubular sacs lacking ribosomes. Responsible for the synthesis of lipids and steroidal hormones such as testosterone and oestrogen.
• Golgi Body: A single-membrane bound organelle consisting of flattened sacs with no membrane connections. It collects proteins from the ER to further modify them (e.g., adding carbohydrates to form glycoproteins) and packs them into Golgi vesicles.
  • Secretory Vesicle: Transports contents out of the cell.
  • Lysosome: Remains within the cell for intracellular digestion.
• Protein Transport Pathway: Ribosomes (site of synthesis) $\rightarrow$ Cisternal space of RER (folding/initial modification) $\rightarrow$ Transport vesicles (bud off RER) $\rightarrow$ Cis face (forming face) of Golgi body $\rightarrow$ Golgi cisternae (glycosylation/further modification) $\rightarrow$ Trans face (mature face) $\rightarrow$ Secretory vesicles $\rightarrow$ Plasma membrane (exocytosis requiring ATP).

Energy Production: The Mitochondrion

• Function: The primary site of aerobic respiration to produce ATP ($Adenosine Triphosphate$). Also involved in lipid synthesis.
• Structure:
  • Double Membrane: Inner and outer membranes.
  • Cristae: The folded inner membrane, which increases the surface area for the enzyme ATP synthase.
  • Matrix: Replaces the interior; contains a gel-like substance with $70S$ ribosomes and a loop of mitochondrial DNA.
  • Permeability: The outer membrane is significantly more permeable than the inner membrane.
  • Morphology: Typically rod-shaped, but may look different depending on the angle of the cut or growth stage.

Cellular Maintenance: Lysosomes, Centrioles, and the Nucleus

• Lysosomes: Dark, spherical, single-membrane sacs containing hydrolytic (digestive) enzymes.
  • Functions: 1. Fusing with phagosomes to digest bacteria; 2. Breakdown of worn-out/damaged organelles (autophagy); 3. Programmed cell death (apoptosis); 4. Acrosomal reaction in sperm.
• Centrioles: Composed of $9$ triplets of microtubules (spindle fibers). Two centrioles are arranged at right angles in an area called the centrosome. They act as the microtubule-organizing center to assemble spindle fibers during cell division to separate chromosomes.
• Nucleus: Double-membrane bound with a nuclear envelope and nuclear pores. The outer envelope is continuous with the RER.
  • Chromatin: Loosely coiled DNA associated with histone proteins.
  • Nucleolus: Site of rRNA (ribosomal RNA) formation and the assembly of ribosomal subunits.
  • Functions: DNA within stores genetic codes for protein synthesis and inheritance; the nuclear envelope protects DNA from cytoplasmic enzymes.
• Ribosomes: Non-membrane bound. Site of translation.
  • 80S Ribosomes: Found in eukaryotic RER/cytoplasm ($25\,nm$; subunits $40S$ and $60S$; RNA to protein ratio $1:1$).
  • 70S Ribosomes: Found in mitochondria, chloroplasts, and prokaryotes ($18\,nm$; subunits $30S$ and $50S$; RNA to protein ratio $2:1$).

Prokaryotic Cell Anatomy (Bacteria & Archaea)

• Cell Wall: Provides protection and prevents bursting. Contains peptidoglycan (polysaccharide chains with polypeptide cross-linkages).
• Capsule: A slime layer (starch, glycolipids, or protein) that protects the cell from being engulfed by White Blood Cells (WBCs) and prevents dehydration.
• Pili and Flagellum: Pili are protein threads used for attachment to host cells and sexual reproduction. The flagellum is a helix of flagellin protein that rotates for movement.
• Nucleoid: An area containing a single circular strand of DNA, not protected by a membrane.
• Plasmids: Small, additional circular DNA loops containing genes for specific phenotypic traits (e.g., antibiotic resistance).

The Cell Cycle and Mitosis

• Interphase:
  • G1 Phase: ATP synthesis, protein synthesis, and organelle duplication.
  • S Phase: DNA replication; each chromosome is duplicated into two identical sister chromatids.
  • G2 Phase: Cytoplasm enlargement and duplication of centrioles.
• Mitosis (Nuclear Division):
  • Prophase: Nuclear envelope/nucleolus disappear; chromosomes condense; centrioles move to poles; spindle fibers form.
  • Metaphase: Chromosomes align at the metaphase plate (equator); spindle fibers attach to centromeres.
  • Anaphase: Centromeres break; spindle fibers shorten; sister chromatids are pulled to opposite poles.
  • Telophase: Spindle fibers break down; nuclear envelope/nucleolus reform; chromosomes decondense.
• Cytokinesis: In-tucking of the cell membrane to split the cytoplasm into two identical diploid daughter cells.

Meiosis: Reduction Division and Variation

• Meiosis I:
  • Prophase I: Crossing over occurs (exchange of alleles between homologous non-sister chromatids) creating new allele combinations.
  • Metaphase I: Random alignment (independent assortment) of homologous pairs at the equator.
  • Anaphase I: Homologous chromosomes separate (centromeres do not break).
• Meiosis II: Similar to mitosis; results in four genetically different haploid daughter cells.
• Importance: Produces genetic variation and maintains the chromosome number across generations (preventing doubling during fertilization).

Genetics: Linkage, Loci, and Inheritance

• Locus: The specific physical location of a gene on a chromosome.
• Allele: Alternative versions of a gene.
• Homologous Pairs: Chromosomes with the same genes at the same loci; one paternal and one maternal.
• Sex Linkage: Genes located on sex chromosomes ($X$ or $Y$). Most sex-linked genes are on the $X$ chromosome.
  • Male Expression: Males ($XY$) express recessive $X$-linked traits because they have only one $X$ chromosome. They inherit these from their mothers.
  • Female Carriers: Females ($XX$) can be carriers of recessive alleles if they possess one dominant and one recessive allele.
  • Hemophilia: A classic sex-linked disease causing slowed blood clotting.
• Autosomal Linkage: Genes located on the same non-sex chromosome ($22$ pairs in humans). They do not assort independently unless crossing over occurs. Closer genes have a lower frequency of recombination.

Gametogenesis and Fertilization in Mammals

• Spermatogenesis: Continuous in the testes. Germ cells $\rightarrow$ Spermatogonium $\rightarrow$ Primary spermatocyte ($2n$) $\rightarrow$ Secondary spermatocyte ($n$) $\rightarrow$ Spermatid ($n$) $\rightarrow$ Spermatozoa.
• Oogenesis: Discontinuous in the ovaries. Starts before birth (fetus), pauses at Prophase I. Resumes at puberty, pauses at Metaphase II. Completes only if fertilized.
• Mammalian Fertilization:
  • Capacitation: Chemicals from follicular cells (corona radiata) attract sperm and trigger maturation.
  • Acrosome Reaction: Sperm releases hydrolytic enzymes to digest the zona pellucida.
  • Cortical Reaction: Once one sperm enters, cortical granules release enzymes to thicken the zona pellucida into a tough fertilization membrane to prevent polyspermy.

Plant Reproduction and Anatomy

• Double Fertilization:
  • One male nucleus ($n$) $+$ Egg nucleus ($n$) $\rightarrow$ Diploid Zygote ($2n$