Comprehensive Study Notes: Cell Structure and Function

Introduction to Unit 3: The Study of Living Organisms

• Biology is defined as the study of living organisms. Initial descriptions of their form and appearance highlighted their diversity, but cell theory introduced a unifying principle: the cellular organisation of all life forms.
• This unit explores the structure of cells and cell growth through division.
• The requirement for structural integrity in cellular organisation is a fundamental condition for observing living phenomena, including physiological and behavioural processes.
• Reductionist Biology: This is a physico-chemical approach used to study living organisms. It involves applying the concepts and techniques of physics and chemistry to understand biology at a molecular level.
• Analysis of living tissues for elements and compounds reveals the types of organic compounds present. This allows scientists to investigate the molecular basis of physiological processes such as digestion, excretion, memory, defense, and recognition, as well as abnormal processes in diseased conditions.

G.N. Ramachandran: Pioneer of Structural Biology

• G.N. Ramachandran ($1922-2001$) was an outstanding figure in protein structure and founded the Madras school of conformational analysis of biopolymers.
• Major Contributions:
  • Discovery of the triple helical structure of collagen (published in Nature, $1954$).
  • Analysis of protein conformations using the Ramachandran plot, a seminal tool in structural biology.
• Biographical Details:
  • Born: October $8, 1922$, near Cochin, India.
  • Academic Path: Influenced by his father, a mathematics professor. Graduated top of his class in B.Sc. (Honors) Physics from the University of Madras ($1942$). Received his Ph.D. from Cambridge University ($1949$).
  • Influences: While at Cambridge, he met Linus Pauling. Pauling's work on $\alpha$-helix and $\beta$-sheet structures inspired Ramachandran to solve the structure of collagen.
  • Deceased: April $7, 2001$, at the age of $78$.

The Fundamental Unit of Life: What is a Cell?

• The presence of the cell differentiates living organisms from inanimate (non-living) things. The cell is the basic unit of life.
• Classification by Cell Number:
  • Unicellular organisms: Composed of a single cell. They are capable of independent existence and performing all essential functions of life.
  • Multicellular organisms: Composed of many cells (e.g., humans).
• Definition: A cell is the fundamental structural and functional unit of all living organisms. Any structure less than a complete cell cannot ensure independent living.
• Historical Milestones:
  • Antonie Von Leeuwenhoek: First to see and describe a live cell.
  • Robert Brown: Discovered the nucleus.
  • Technology: The invention and improvement of the microscope, particularly the electron microscope, enabled the study of structural details.

The Formulation and Principles of Cell Theory

• Matthias Schleiden ($1838$): A German botanist who observed that all plants are composed of various kinds of cells that form plant tissues.
• Theodore Schwann ($1839$): A German zoologist who studied animal cells and identified a thin outer layer now called the plasma membrane. He also noted that the cell wall is a unique feature of plant cells. He proposed that the bodies of animals and plants are composed of cells and cell products.
• Rudolf Virchow ($1855$): He provided the final shape to cell theory by explaining that cells divide and new cells are formed from pre-existing cells (Omnis cellula-e cellula).
• Modern Cell Theory:
  1. All living organisms are composed of cells and products of cells.
  2. All cells arise from pre-existing cells.

Overview of Cellular Diversity and Structure

• Model Cells: Plant cells (e.g., onion peel) have a distinct cell wall and an underlying cell membrane. Animal cells (e.g., human cheek cells) have an outer membrane as their delimiting structure.
• Nucleus: A dense membrane-bound structure containing chromosomes, which hold the genetic material, DNA.
• Main Classifications:
  • Eukaryotic cells: Possess membrane-bound nuclei.
  • Prokaryotic cells: Lack a membrane-bound nucleus.
• Cytoplasm: A semi-fluid matrix occupying the cell volume. It is the main arena for cellular activities and chemical reactions required to maintain the living state.
• Organelles:
  • Eukaryotes have membrane-bound organelles: Endoplasmic Reticulum (ER), Golgi complex, lysosomes, mitochondria, microbodies, and vacuoles.
  • Prokaryotes lack these membrane-bound organelles.
  • Ribosomes: Non-membrane bound organelles found in all cells (prokaryotic and eukaryotic). In eukaryotes, they are found in the cytoplasm, chloroplasts, mitochondria, and on rough ER.
  • Centrosome: A non-membrane bound organelle in animal cells that aids in cell division.
• Cell Scale and Measurement:
  • Mycoplasmas (smallest cells): Length of $0.3\,\mu\text{m}$.
  • Bacteria: Typically $3$ to $5\,\mu\text{m}$ (some listed as $1-2\,\mu\text{m}$ in diagrams).
  • Ostrich egg: The largest isolated single cell.
  • Human red blood cells (RBCs): Approximately $7.0\,\mu\text{m}$ in diameter.
  • Nerve cells: Among the longest cells.
  • Cell Shapes: Disc-like, polygonal, columnar, cuboid, thread-like, or irregular; shape often relates to function.

Detailed Study of Prokaryotic Cells

• Organisms: Bacteria, blue-green algae, mycoplasma, and PPLO (Pleuro Pneumonia Like Organisms).
• Characteristics: Generally smaller than eukaryotes and multiply more rapidly. Fundamental organization is similar across varying shapes.
• Bacterial Shapes:
  • Bacillus (rod-like)
  • Coccus (spherical)
  • Vibrio (comma-shaped)
  • Spirillum (spiral)
• Genetic Material: DNA is naked and not enveloped by a nuclear membrane. Most bacteria have a single circular genomic DNA chromosome and many possess smaller circular DNA called plasmids.
• Plasmids: Confer unique phenotypic traits like antibiotic resistance. They are used to monitor bacterial transformation with foreign DNA.
• Cell Envelope Structure:
  • Glycocalyx: Outermost layer. Can be a loose sheath (slime layer) or thick and tough (capsule).
  • Cell Wall: Middle layer. Determines shape and provides structural support to prevent bursting or collapsing.
  • Plasma Membrane: Innermost layer. Selectively permeable and structurally similar to eukaryotic membranes.
• Gram Staining: Classification based on cell envelope differences and staining response.
  • Gram positive: Take up the Gram stain.
  • Gram negative: Do not take up the stain.
• Specialized Structures:
  • Mesosomes: Infoldings of the plasma membrane (vesicles, tubules, lamellae). Functions: Cell wall formation, DNA replication, DNA distribution, respiration, secretion, and increasing surface area/enzymatic content.
  • Chromatophores: Pigment-containing membranous extensions in cyanobacteria.
  • Flagella: Filamentous extensions for motility. Composed of three parts: filament (longest), hook, and basal body.
  • Pili and Fimbriae: Surface structures not involved in motility. Pili are tubular protein structures; fimbriae are bristle-like fibers for attachment to surfaces or host tissues.
• Ribosomes: Associated with the plasma membrane. Size is $15\text{ nm by }20\text{ nm}$. Consist of $50\text{S}$ and $30\text{S}$ subunits, forming $70\text{S}$ prokaryotic ribosomes. Site of protein synthesis. Polyribosomes (polysomes) occur when multiple ribosomes attach to a single mRNA.
• Inclusion Bodies: Reserve material storage (phosphate granules, cyanophycean granules, glycogen granules). Not membrane-bound. Gas vacuoles are found in photosynthetic bacteria (blue-green, purple, and green).

Detailed Study of Eukaryotic Cells

• Organisms: Protists, plants, animals, and fungi.
• Key Features: Extensive compartmentalisation via membrane-bound organelles, organized nucleus with a nuclear envelope, complex locomotory and cytoskeletal structures, and chromosomes for genetic material.
• Differences in Cells:
  • Plant Cells: Have cell walls, plastids, and a large central vacuole.
  • Animal Cells: Have centrioles; lack walls and plastids.

The Plasma Membrane

• Discovery: Detailed structure identified after the electron microscope ($1950$s) and chemical studies on human RBCs.
• Composition: Primarily lipids and proteins. Phospholipids are arranged in a bilayer with polar heads facing outward and hydrophobic saturated hydrocarbon tails facing inward (protected from aqueous environment). Also contains cholesterol.
• Protein-Lipid Ratios: Varies by cell type. Human erythrocyte membrane is approximately $52\%$ protein and $40\%$ lipid.
• Membrane Proteins:
  • Peripheral proteins: Located on the membrane surface.
  • Integral proteins: Partially or totally buried within the membrane.
• Fluid Mosaic Model (Singer and Nicolson, $1972$): Quasi-fluid nature of lipids allows lateral movement of proteins. Fluidity is vital for cell growth, junction formation, secretion, endocytosis, and division.
• Transport Mechanisms:
  • Passive Transport: Movement without energy. Includes simple diffusion of neutral solutes along a concentration gradient and osmosis (diffusion of water).
  • Facilitated Transport: Polar molecules use carrier proteins to cross the nonpolar bilayer.
  • Active Transport: Energy-dependent ($ATP$ used) movement against a concentration gradient. Example: $\text{Na}^+/\text{K}^+$ Pump.

The Cell Wall

• Nature: A non-living, rigid outer covering for the plasma membrane in fungi and plants.
• Functions: Provides shape, offers mechanical protection, prevents infection, facilitates cell-to-cell interaction, and acts as a barrier to undesirable macromolecules.
• Composition:
  • Algae: Cellulose, galactans, mannans, and calcium carbonate.
  • Plants: Cellulose, hemicellulose, pectins, and proteins.
• Layers:
  • Primary wall: Found in young cells; capable of growth.
  • Secondary wall: Formed on the inner side (towards the membrane) as the cell matures.
  • Middle lamella: Composed of calcium pectate; glues neighbouring cells together.
• Plasmodesmata: Cytoplasmic connections that traverse the cell wall and middle lamella to link neighbouring cells.

The Endomembrane System

• Defined by coordinated functions among specific organelles: Endoplasmic Reticulum (ER), Golgi complex, lysosomes, and vacuoles. Mitochondria, chloroplasts, and peroxisomes are excluded.
• Endoplasmic Reticulum (ER): A network of tubular structures dividing intracellular space into luminal (inside ER) and extra-luminal (cytoplasm) compartments.
  • Rough ER (RER): Studded with ribosomes. Involved in protein synthesis and secretion. Continuous with nuclear outer membrane.
  • Smooth ER (SER): Lacks ribosomes. Major site for lipid synthesis, including steroidal hormones in animals.
• Golgi Apparatus: Discovered by Camillo Golgi ($1898$). Consists of stacked, flat, disc-shaped cisternae ($0.5\,\mu\text{m}$ to $1.0\,\mu\text{m}$ diameter). Features a convex cis (forming) face and concave trans (maturing) face. Functions: Packaging materials into vesicles, modifying proteins, and forming glycoproteins and glycolipids.
• Lysosomes: Membrane-bound vesicles from the Golgi. Contain hydrolytic enzymes (lipases, proteases, carbohydrases) active at acidic pH. Digest carbohydrates, proteins, lipids, and nucleic acids.
• Vacuoles: Tonoplast-bound space containing water, sap, and waste. In plants, can occupy $90\%$ of cell volume. Tonoplast transports ions against gradients. Includes contractile vacuoles (osmoregulation in Amoeba) and food vacuoles (protists).

Mitochondria and Plastids

• Mitochondria:
  • Visibility: Requires specific staining. Variable number and shape (sausage/cylindrical).
  • Size: Diameter $0.2-1.0\,\mu\text{m}$ (avg $0.5\,\mu\text{m}$); Length $1.0-4.1\,\mu\text{m}$.
  • Structure: Double membrane-bound. Outer membrane is continuous; inner membrane forms infoldings called cristae to increase surface area.
  • Function: Site of aerobic respiration and $ATP$ production (‘power houses’).
  • Matrix content: Circular DNA, RNA, $70\text{S}$ ribosomes, and protein synthesis components. Divide by fission.
• Plastids:
  • Found in plants and euglenoides. Large and easily visible.
  • Types based on pigment:
    1. Chloroplasts: Contain chlorophyll and carotenoids for photosynthesis. Lens-shaped, oval, or ribbon-like ($5-10\,\mu\text{m}$ long, $2-4\,\mu\text{m}$ wide).
    2. Chromoplasts: Fat-soluble carotenoid pigments (carotene, xanthophylls) providing yellow, orange, or red colours.
    3. Leucoplasts: Colourless, store nutrients. Amyloplasts (starch), Elaioplasts (oils/fats), Aleuroplasts (proteins).
  • Chloroplast Structure: Double membrane-bound (inner membrane less permeable). Stroma contains enzymes, circular DNA, and $70\text{S}$ ribosomes. Thylakoids are flattened sacs arranged in stacks (grana). Stroma lamellae connect grana.

Ribosomes and the Cytoskeleton

• Ribosomes:
  • Discovered by George Palade ($1953$) as dense particles. Composed of RNA and proteins; no membrane.
  • Eukaryotic: $80\text{S}$ (subunits: $60\text{S}$ and $40\text{S}$).
  • Prokaryotic: $70\text{S}$ (subunits: $50\text{S}$ and $30\text{S}$).
  • 'S' (Svedberg’s Unit): Sedimentation coefficient; measures density and size.
• Cytoskeleton:
  • Proteinaceous network of microtubules, microfilaments, and intermediate filaments.
  • Functions: Mechanical support, motility, and maintenance of cell shape.

Cilia, Flagella, and Centrioles

• Cilia and Flagella:
  • Hair-like outgrowths of cell membrane. Cilia are small (oar-like); flagella are longer.
  • Structure: Covered by plasma membrane. Axoneme core has a $9+2$ array (nine peripheral doublets and two central microtubules). Radial spokes (nine) and linkers connect components. Emerge from centriole-like basal bodies.
• Centrosome and Centrioles:
  • Centrosome contains two perpendicular, cylindrical centrioles surrounded by pericentriolar material.
  • Cartwheel organisation: Nine evenly spaced peripheral triplets of tubulin. Central proteinaceous hub connected to triplets by radial spokes.
  • Functions: Form basal bodies and spindle apparatus/fibres for animal cell division.

The Nucleus and Chromosomes

• Nucleus: Described by Robert Brown ($1831$). Chromatin named by Flemming. Interphase nucleus contains chromatin (nucleoprotein fibres), nuclear matrix, and nucleoli.
• Nuclear Envelope: Two parallel membranes with a perinuclear space ($10$ to $50\text{ nm}$). Contains nuclear pores for two-way movement of RNA and proteins. Outer membrane continuous with ER.
• Nucleolus: Non-membrane bound site for active ribosomal RNA ($rRNA$) synthesis.
• Chromatin/Chromosomes: Chromatin contains DNA, basic proteins (histones), non-histone proteins, and RNA. Human cells have $~2\text{ m}$ of DNA across $46$ ($23$ pairs) chromosomes.
• Chromosome Structure: Primary constriction (centromere) with disc-shaped kinetochores on sides.
• Types of Chromosomes (based on centromere position):
  1. Metacentric: Middle centromere; equal arms.
  2. Sub-metacentric: Slightly off-centre; one short and one long arm.
  3. Acrocentric: Close to the end; one extremely short and one very long arm.
  4. Telocentric: Terminal centromere.
• Satellite: A small fragment formed by non-staining secondary constrictions.
• Microbodies: Membrane-bound vesicles containing enzymes in both plant and animal cells.

Questions & Discussion

• Misconception Check: Robert Brown did not discover the cell; he discovered the nucleus. Cells are not formed de novo from abiotic materials; they arise from pre-existing cells.
• Match the following:
  • Cristae: Infoldings in mitochondria.
  • Cisternae: Disc-shaped sacs in Golgi apparatus.
  • Thylakoids: Flat membranous sacs in stroma.
• Functional Comparisons: Both lysosomes and vacuoles belong to the endomembrane system, but lysosomes focus on macromolecule digestion via hydrolases, while vacuoles handle storage and osmoregulation.
• Uniqueness of Multicellularity: These organisms exhibit division of labour where different cells perform specialized functions.