Comprehensive Study Notes: Cell Biology, Structure, and Functions

Introduction to Unit 3: Cell Biology and Reductionist Biology

• Definition of Biology: The study of living organisms.
• Unity vs. Diversity: While the form and appearance of living organisms display immense diversity, the cell theory emphasizes the underlying unity of all life forms through their cellular organization.
• Integral Nature of Cellular Organization: Living phenomena (physiological and behavioral processes) require a complete cellular organization to be demonstrated or observed.
• Physico-chemical Approach: One can study physiological and behavioral processes using cell-free systems to describe them in molecular terms.
• Reductionist Biology:     - This approach involves applying the concepts and techniques of physics and chemistry to understand biology.     - It involves analyzing living tissues for elements and compounds to determine the types of organic compounds present.     - It aims to answer the molecular basis of all physiological processes (e.g., digestion, excretion, memory, defense, recognition) and abnormal diseased conditions.
• Unit Overview:     - Chapter 8: Cell: The Unit of Life     - Chapter 9: Biomolecules     - Chapter 10: Cell Cycle and Cell Division

Profile: G.N. Ramachandran (1922–2001)

• Significance: An outstanding figure in protein structure and founder of the 'Madras school' of conformational analysis of biopolymers.
• Key Contributions:     - Discovery of the triple helical structure of collagen (published in Nature in 1954).     - Analysis of allowed protein conformations through the 'Ramachandran plot'.
• Biographical Details:     - Born: October 8, 1922, near Cochin, India.     - Influences: His father, a mathematics professor, shaped his interest in mathematics. He was deeply influenced by Linus Pauling’s publications on $\alpha$-helix and $\beta$-sheet models.     - Education:         - Top-ranking student in B.Sc. (Honors) Physics, University of Madras (1942).         - Ph.D. from Cambridge University (1949).     - Death: Passed away on April 7, 2001, at the age of 78.

What is a Cell?

• Definition: The cell is the basic, fundamental structural and functional unit of all living organisms.
• Classification of Organisms:     - Unicellular: Composed of a single cell. Capable of independent existence and performing all essential functions of life.     - Multicellular: Composed of many cells (e.g., humans).
• Structural Requirement: Anything less than a complete cell structure does not ensure independent living.
• Historical Milestones:     - Antonie Von Leeuwenhoek: First saw and described a live cell.     - Robert Brown: Discovered the nucleus.     - Microscopy: The invention of the microscope and its improvement into the electron microscope revealed structural details of the cell.

Cell Theory

• Contributors:     - Matthias Schleiden (1838): A German botanist who observed that all plants are composed of different kinds of cells forming plant tissues.     - Theodore Schwann (1839): A German zoologist who studied animal cells and discovered they have a thin outer layer now called the plasma membrane. He also concluded that the cell wall is a unique character of plant cells.
• Schwann’s Hypothesis: The bodies of animals and plants are composed of cells and products of cells.
• Refinement by Rudolf Virchow (1855): He explained that cells divide and new cells are formed from pre-existing cells (Omnis cellula-e cellula).
• Modern Cell Theory Principles:     1. All living organisms are composed of cells and products of cells.     2. All cells arise from pre-existing cells.

Overview of the Cell: Size, Shape, and Basic Structure

• Typical Cell Boundaries:     - Onion cell (Plant): Outer cell wall with a cell membrane just within it.     - Human cheek cell (Animal): Outer cell membrane as the delimiting structure.
• Nucleus: A dense membrane-bound structure containing chromosomes, which in turn contain DNA (genetic material).
• Primary Categorization:     - Eukaryotic: Cells that have membrane-bound nuclei.     - Prokaryotic: Cells that lack a membrane-bound nucleus.
• Cytoplasm: A semi-fluid matrix occupying the cell volume. It is the main arena of cellular activities and chemical reactions required to keep the cell in a 'living state'.
• Organelles:     - Eukaryotic: Endoplasmic reticulum (ER), golgi complex, lysosomes, mitochondria, microbodies, and vacuoles.     - Prokaryotic: Lack membrane-bound organelles.     - Ribosomes: Non-membrane bound organelles found in all cells (prokaryotic and eukaryotic). Within eukaryotes, they are in the cytoplasm, chloroplasts (plants), mitochondria, and on rough ER.     - Centrosome: Non-membrane bound organelle in animal cells that helps in cell division.
• Cell Statistics and Variations:     - Smallest cells: Mycoplasmas ($0.3\,\mu m$ in length).     - Bacteria: Typically $3$ to $5\,\mu m$.     - Largest isolated single cell: Egg of an ostrich.     - Human Red Blood Cells: Approximately $7.0\,\mu m$ in diameter.     - Longest cells: Nerve cells.     - Shapes: Disc-like, polygonal, columnar, cuboid, thread-like, or irregular. Shape often correlates with function.

Prokaryotic Cells

• Examples: Bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms).
• Characteristics:     - Generally smaller and multiply more rapidly than eukaryotic cells.     - Shapes of Bacteria: Bacillus (rod-like), Coccus (spherical), Vibrio (comma-shaped), Spirillum (spiral).     - Cell Wall: Present in all except Mycoplasma.     - Genetic Material: 'Naked' (not enveloped by a nuclear membrane). Genomic DNA is a single chromosome/circular DNA.     - Plasmids: Small circular DNA outside genomic DNA. They confer unique phenotypic characters like antibiotic resistance and are used in bacterial transformation.
• Cell Envelope:     1. Glycocalyx: Outermost. Can be a loose sheath (slime layer) or thick and tough (capsule).     2. Cell Wall: Determines shape and prevents bursting or collapsing.     3. Plasma Membrane: Selectively permeable; interacts with the environment.
• Gram Staining: Based on cell envelope differences and response to stain.     - Gram-positive: Take up the stain.     - Gram-negative: Do not take up the stain.
• Special Structures:     - Mesosome: Infoldings of the cell membrane (vesicles, tubules, lamellae). Help in cell wall formation, DNA replication, distribution, respiration, secretion, and increasing surface area/enzymatic content.     - Chromatophores: Membranous extensions in cyanobacteria containing pigments.     - Flagella: Thin filamentous extensions for motility. Three parts: filament (longest), hook, and basal body.     - Pili and Fimbriae: Surface structures. Pili are tubular (special protein); Fimbriae are bristle-like for attachment to rocks or host tissues.
• Prokaryotic Ribosomes:     - Size: $15\,nm$ by $20\,nm$.     - Subunits: $50S$ and $30S$ (Total = $70S$).     - Polyribosomes / Polysomes: Multiple ribosomes attached to a single mRNA.
• Inclusion Bodies: Free-lying reserve materials (phosphate granules, cyanophycean granules, glycogen granules).
• Gas Vacuoles: Found in blue-green, purple, and green photosynthetic bacteria.

Eukaryotic Cells

• Includes: Protists, plants, animals, and fungi.
• Key Features: Extensive compartmentalization of cytoplasm, organized nucleus with envelope, complex locomotory and cytoskeletal structures.
• Plant vs. Animal Cells:     - Plant Cells: Have cell walls, plastids, and a large central vacuole.     - Animal Cells: Have centrioles; lack cell walls and plastids.

The Cell Membrane

• Composition: Primarily lipids (arranged in a bilayer) and proteins.
• Lipids: Phospholipids with polar heads (outer side) and hydrophobic tails (inner side). Tails consist of saturated hydrocarbons. Also contains cholesterol.
• Protein-Lipid Ratios: Varies by cell. Human erythrocyte (RBC): $52\%$ protein and $40\%$ lipids.
• Membrane Proteins:     - Peripheral: Lie on the surface.     - Integral: Partially or totally buried.
• Fluid Mosaic Model (Singer and Nicolson, 1972):     - Quasi-fluid nature of lipids allows lateral movement of proteins.     - Fluidity is important for cell growth, junction formation, secretion, endocytosis, and division.
• Transport Mechanism:     - Passive Transport: No energy required. Simple diffusion (neutral solutes) and osmosis (water move along concentration gradient).     - Carrier Proteins: Required for polar molecules crossing the nonpolar bilayer.     - Active Transport: Energy dependent (uses ATP). Moves molecules against the gradient (e.g., $\text{Na}^{+}/\text{K}^{+}$ Pump).

The Cell Wall

• Nature: Non-living rigid structure.
• Function: Gives shape, protects from damage/infection, aids cell-to-cell interaction, acts as a barrier to macromolecules.
• Composition:     - Algae: Cellulose, galactans, mannans, and calcium carbonate.     - Other Plants: Cellulose, hemicellulose, pectins, and proteins.
• Growth Styles:     - Primary Wall: Capable of growth in young cells.     - Secondary Wall: Formed on the inner side as the cell matures.
• Middle Lamella: Layer of calcium pectate that glues neighboring cells together.
• Plasmodesmata: Connect the cytoplasm of neighboring cells.

The Endomembrane System

• Components: Endoplasmic reticulum (ER), golgi complex, lysosomes, and vacuoles. These are grouped because their functions are coordinated.
• Exclusions: Mitochondria, chloroplasts, and peroxisomes (functions are not coordinated with the above).

Endoplasmic Reticulum (ER)

• Structure: Network of tiny tubular structures. Divides space into luminal (inside ER) and extra luminal (cytoplasm).
• Rough ER (RER): Bears ribosomes. Involved in protein synthesis and secretion. Continuous with nuclear outer membrane.
• Smooth ER (SER): Lacks ribosomes. Major site for lipid synthesis. In animals, synthesizes steroidal hormones.

Golgi Apparatus

• History: Discovered by Camillo Golgi (1898).
• Structure: Flat, disc-shaped sacs (cisternae) of $0.5\,\mu m$ to $1.0\,\mu m$ diameter.
• Organization: Concentrically arranged near the nucleus. Distinct cis (convex/forming) face and trans (concave/maturing) face.
• Function: Packaging of materials (vesicles) for delivery or secretion. Modification of proteins. Important site for forming glycoproteins and glycolipids.

Lysosomes

• Formation: Membrane-bound vesicles formed in the Golgi.
• Content: Rich in hydrolytic enzymes (hydrolases: lipases, proteases, carbohydrases).
• Conditions: Optimally active at acidic pH. Capable of digesting carbs, proteins, lipids, and nucleic acids.

Vacuoles

• Structure: Single membrane-bound space called the tonoplast.
• Contents: Water, sap, excretory products, and non-useful materials.
• Plant Specifics: Can occupy up to $90\%$ of the cell volume. Tonoplast pumps ions against concentration gradients (higher concentration inside vacuole).
• Others: Contractile vacuole in Amoeba (osmoregulation/excretion); food vacuoles in protists.

Energy-Transforming Organelles

Mitochondria

• Shape/Size: Sausage-shaped or cylindrical. Diameter: $0.2-1.0\,\mu m$ (average $0.5\,\mu m$); Length: $1.0-4.1\,\mu m$.
• Membranes: Double membrane-bound. Outer membrane is the boundary; Inner membrane forms infoldings called cristae to increase surface area.
• Compartmentalization: Outer compartment and inner compartment (matrix).
• Function: Site of aerobic respiration. Produce energy as ATP ("power houses" of the cell).
• Genetics/Reproduction: Possess a single circular DNA, a few RNA, $70S$ ribosomes, and protein synthesis components. Divide by fission.

Plastids

• Found in: All plant cells and euglenoides.
• Types:     1. Chloroplasts: Contain chlorophyll and carotenoids; trap light for photosynthesis.     2. Chromoplasts: Contain fat-soluble carotenoids (carotene, xanthophylls); provide yellow, orange, or red color.     3. Leucoplasts: Colorless storage plastids. Amyloplasts (starch/potato), Elaioplasts (oils/fats), Aleuroplasts (proteins).
• Chloroplast Anatomy:     - Found in leaf mesophyll cells. Lens-shaped ($5-10\,\mu m$ long, $2-4\,\mu m$ wide).     - Double membrane. Space inside is the stroma.     - Thylakoids: Flattened sacs in the stroma. Arranged in stacks called grana.     - Stroma lamellae: Connect thylakoids of different grana.     - Lumen: Space inside the thylakoid.     - Contains: Enzymes for carb/protein synthesis, circular DNA, and $70S$ ribosomes (cytoplasm has $80S$).

Ribosomes and Cytoskeleton

Ribosomes

• History: Dense particles observed by George Palade (1953).
• Composition: RNA and proteins; not membrane-bound.
• Eukaryotic ($80S$): Subunits are $60S$ and $40S$.
• Prokaryotic ($70S$): Subunits are $50S$ and $30S$.
• S (Svedberg’s Unit): Sedimentation coefficient; indirectly measures density and size.

Cytoskeleton

• Components: Microtubules, microfilaments, and intermediate filaments.
• Functions: Mechanical support, motility, maintenance of cell shape.

Locomotory and Structural Organelles

Cilia and Flagella

• Definition: Hair-like outgrowths of cell membrane. Cilia are small (oar-like); flagella are longer.
• Internal Structure (Axoneme): Covered by plasma membrane. Microtubules in a 9+2 array (9 peripheral doublets and 2 central microtubules).
• Components: Central tubules connected by bridges and a sheath; radial spokes connect peripheral doublets to the sheath; linkers connect doublets.
• Origin: Arise from basal bodies (centriole-like structures).

Centrosome and Centrioles

• Composition: Two cylindrical structures (centrioles) surrounded by amorphous pericentriolar materials.
• Arrangement: Centrioles lie perpendicular to each other; "cartwheel" organization.
• Structure: Nine peripheral fibrils of tubulin protein (triplets). Central part is the proteinaceous hub, connected via radial spokes.
• Function: Form basal bodies of cilia/flagella and spindle fibers (spindle apparatus) during animal cell division.

Nucleus and Chromosomes

• History: Described by Robert Brown (1831). Chromatin named by Flemming.
• Interphase Nucleus Components:     - Nuclear Envelope: Two membranes with perinuclear space ($10$ to $50\,nm$) between them. Interrupted by nuclear pores (movement of RNA/protein).     - Nucleoplasm: Contains nucleolus and chromatin.     - Nucleolus: Spherical, non-membrane bound. Site for rRNA synthesis.
• Chromatin: Contains DNA, basic proteins (histones), non-histones, and RNA.
• Chromosomes:     - Human cell has approx. $2\,\text{metres}$ of DNA distributed in $46$ (23 pairs) chromosomes.     - Visible only in dividing cells.     - Centromere (Primary Constriction): Holds two chromatids. Kinetochores (disc-shaped) are on the sides.
• Classification based on Centromere Position:     1. Metacentric: Middle centromere; equal arms.     2. Sub-metacentric: Centromere slightly away from middle; one short, one long arm.     3. Acrocentric: Centromere close to end; one extremely short, one very long arm.     4. Telocentric: Terminal centromere.
• Satellite: Small fragment appearing due to non-staining secondary constrictions at constant locations.

Microbodies

• Membrane-bound minute vesicles containing enzymes; present in both plant and animal cells.

Questions & Discussion (Exercise Summary Items)

• Life Unit: Why is a cell called the basic unit of life? (It is the smallest structure capable of independent existence and metabolic function).
• Division of Labour: How does it exist in multicellular organisms? (Different cells/tissues perform specialized functions like digestion or nerve conduction).
• Organelle Distinctions: Difference between lysosomes and vacuoles? (Lysosomes are for enzymatic digestion; vacuoles are for storage and osmoregulation).
• Identify Wrong/Correct Statements: Robert Brown discovered the nucleus (correct), not the cell (Leeuwenhoek). Prokaryotes lack membrane-bound organelles (correct).