Biology: Cell Structure and Functions

Introduction to Cell Biology and Reductionist Biology

• Biology is defined as the study of living organisms. • Historical descriptions based on form and appearance highlighted the diversity of life, but Cell Theory emphasized the underlying unity known as the cellular organization of all life forms. • The integrity of cellular organization is a requirement for living phenomena (physiological and behavioral processes) to be demonstrated or observed. • Reductionist Biology is a physico-chemical approach used to understand biology by applying the concepts and techniques of physics and chemistry. This involves:     • Using cell-free systems to investigate processes.     • Analyzing living tissues for elements and compounds (biomolecules) to describe processes in molecular terms.     • Answering the molecular basis of physiological processes such as digestion, excretion, memory, defense, and recognition.     • Explaining abnormal processes that occur during diseased conditions.

G.N. Ramachandran and Structural Biology

• G.N. Ramachandran ($1922 – 2001$) was an outstanding figure in protein structure and founded the 'Madras school' of conformational analysis of biopolymers. • Personal History:     • Born: October 8, 1922, near Cochin, India.     • Influenced by his father, a mathematics professor.     • Graduated top-rank in B.Sc. (Honors) Physics from the University of Madras in $1942$.     • Received a Ph.D. from Cambridge University in $1949$.     • Deeply influenced by Linus Pauling’s publications on $\alpha$-helix and $\beta$-sheet structures.     • Passed away at age 78 on April 7, 2001. • Scientific Contributions:     • Discovered the triple helical structure of collagen, published in Nature in $1954$.     • Developed the 'Ramachandran plot' to analyze allowed conformations of proteins.

Defining the Cell as the Unit of Life

• The cell is the basic unit of life in all living organisms. Anything less than a complete cell structure does not ensure independent living. • Organismal Types:     • Unicellular Organisms: Composed of a single cell; capable of independent existence and performing all essential life functions.     • Multicellular Organisms: Composed of many cells (e.g., humans). • Discovery Timeline:     • Anton Von Leeuwenhoek: First saw and described a live cell.     • Robert Brown: Discovered the nucleus.     • The invention of the electron microscope allowed for the revelation of intricate structural details.

The Evolution of Cell Theory

• 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 British zoologist who studied animal cells and discovered they had 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: Proposed that the bodies of animals and plants are composed of cells and products of cells. • Rudolf Virchow ($1855$): First explained that cells divide and new cells are formed from pre-existing cells, a concept known as Omnis cellula-e cellula. • Finalized 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 (Size, Shape, and Activity)

• All cells contain a semi-fluid matrix called cytoplasm, which is the main arena of cellular activities and chemical reactions. • Main categories based on nucleus:     • Prokaryotic: Lacks a membrane-bound nucleus; genetic material (DNA) is naked.     • Eukaryotic: Possess a membrane-bound nucleus containing chromosomes with DNA. • Cell Size Specifics:     • Mycoplasmas (smallest cells): $0.3\,\mu m$ in length.     • Bacteria: $3$ to $5\,\mu m$ (typical bacteria are $1$ to $2\,\mu m$).     • PPLO (Pleuro Pneumonia Like Organisms): About $0.1\,\mu m$.     • Viruses (non-cellular): $0.02$ to $0.2\,\mu m$.     • Eukaryotic cells: $10$ to $20\,\mu m$.     • Human Red Blood Cells: $7.0\,\mu m$ in diameter.     • Ostrich Egg: Largest isolated single cell.     • Nerve Cells: Among the longest cells. • Cell Shapes:     • Disc-like, polygonal, columnar, cuboid, thread-like, or irregular.     • Red blood cells: Round and biconcave.     • White blood cells: Amoeboid.     • Columnar epithelial cells: Long and narrow.     • Mesophyll cells: Round and oval.     • Tracheids: Elongated.

Prokaryotic Cells

• Represented by: Bacteria, blue-green algae, mycoplasma, and PPLO. • Bacteria Shapes: 1. Bacillus: Rod-like. 2. Coccus: Spherical. 3. Vibrio: Comma-shaped. 4. Spirillum: Spiral. • Structural Features:     • Cell wall: Surrounds the cell membrane (absent in Mycoplasma).     • Genomic DNA: Single circular DNA/chromosome.     • Plasmids: Small circular DNA outside genomic DNA. They provide unique phenotypic characters like antibiotic resistance and are used to monitor bacterial transformation.     • Mesosomes: Differentiated infoldings of the cell membrane. They exist as vesicles, tubules, and lamellae. Functions include cell wall formation, DNA replication, distribution to daughter cells, respiration, secretion, and increasing surface area/enzymatic content.     • Inclusions: Reserve material stored in the cytoplasm without membranes (e.g., phosphate granules, cyanophycean granules, glycogen granules). Gas vacuoles are found in photosynthetic bacteria.

Prokaryotic Cell Envelope and Appendages

• Cell Envelope Layers (Outermost to Innermost): 1. Glycocalyx: Varies in thickness. Can be a loose sheath (slime layer) or a thick, tough capsule. 2. Cell Wall: Determines shape and provides support to prevent bursting or collapsing. 3. Plasma Membrane: Selectively permeable; similar to eukaryotic membranes. • Gram Staining Procedure:     • Gram-positive: Take up the Gram stain.     • Gram-negative: Do not take up the Gram stain. • Surface Structures:     • Flagella: Filamentous extensions for motility. Composed of three parts: filament (longest), hook, and basal body.     • Pili: Elongated tubular structures made of a special protein; not for motility.     • Fimbriae: Small bristle-like fibers used for attachment to rocks or host tissues. • Ribosomes: 70S ($50S$ and $30S$ subunits). Measured by Svedberg’s Unit (S) as a sedimentation coefficient. Found near the plasma membrane. Site of protein synthesis. • Polyribosomes (Polysomes): A chain of ribosomes attached to a single mRNA for translating mRNA into proteins.

Eukaryotic Cells

• Include: Protists, plants, animals, and fungi. • Key Characteristics:     • Extensive compartmentalization of cytoplasm via membrane-bound organelles.     • Organized nucleus with a nuclear envelope.     • Complex locomotory and cytoskeletal structures.     • Genetic material organized into chromosomes. • Plant vs. Animal Cell Differences:     • Plant cells: Have cell walls, plastids, and a large central vacuole.     • Animal cells: Have centrioles; lack cell walls and plastids.

The Cell Membrane (Plasma Membrane)

• History: Detailed structure studied after the electron microscope ($1950$s). Chemical studies on human RBCs (erythrocytes) revealed the lipid-protein composition. • Composition of Human Erythrocyte Membrane:     • Protein: Approximately $52\,\%$.     • Lipids: Approximately $40\,\%$. • Structure:     • Phospholipid Bilayer: Polar heads point outward; hydrophobic tails (saturated hydrocarbons) point inward to avoid water.     • Cholesterol: Present within the membrane.     • Proteins: Classified as Integral (buried) or Peripheral (on the surface). • Fluid Mosaic Model: Proposed by Singer and Nicolson ($1972$). The quasi-fluid nature of lipids allows lateral movement of proteins (fluidity). Essential for growth, secretion, endocytosis, and division. • Transport Mechanisms:     • Passive Transport: No energy required. Movement along concentration gradients (simple diffusion). Osmosis is the diffusion of water.     • Facilitated Transport: Moves polar molecules through the nonpolar bilayer using carrier proteins.     • Active Transport: Energy-dependent process using ATP to move molecules against their gradient (e.g., $Na^+/K^+$ Pump).

The Cell Wall

• A non-living rigid outer covering for plants and fungi. • Functions: Shape, protection from damage/infection, cell-to-cell interaction, and barrier to macromolecules. • Composition:     • Algae: Cellulose, galactans, mannans, and calcium carbonate.     • Other Plants: Cellulose, hemicellulose, pectins, and proteins. • Layers:     • Primary Wall: Found in young cells; capable of growth.     • Secondary Wall: Formed on the inner side as the cell matures.     • Middle Lamella: Composed of calcium pectate; glues neighboring cells together. • Plasmodesmata: Channels traversing the wall and middle lamella to connect the cytoplasm of neighboring cells.

The Endomembrane System

• Components (coordinated functions): ER, Golgi complex, Lyososomes, and Vacuoles. (Note: Mitochondria, chloroplasts, and peroxisomes are not included). • Endoplasmic Reticulum (ER):     • Tiny tubular structures dividing the cell into luminal (inside ER) and extra-luminal (cytoplasm) spaces.     • Rough ER (RER): Ribosomes attached; specialized for protein synthesis and secretion.     • Smooth ER (SER): No ribosomes; site for lipid synthesis and steroidal hormone synthesis in animals. • Golgi Apparatus:     • Discovered by Camillo Golgi ($1898$).     • Consists of flat disc-shaped cisternae ($0.5\,\mu m$ to $1.0\,\mu m$ diameter) stacked parallel.     • Faces: Convex cis (forming face near ER) and concave trans (maturing face).     • Function: Packaging and modifying materials (proteins/lipids) into vesicles. Form glycoproteins and glycolipids. • Lysosomes:     • Membrane-bound vesicles from the Golgi.     • Rich in hydrolytic enzymes (hydrolases: lipases, proteases, carbohydrases) active at acidic pH. Digest carbs, proteins, lipids, and nucleic acids. • Vacuoles:     • Membrane-bound space (tonoplast). In plants, occupies up to $90\,\%$ of cell volume.     • Facilitates transport of ions against concentration gradients into the vacuole.     • Amoeba: Contractile vacuole for osmoregulation and excretion. Food vacuoles formed in protists.

Mitochondria and Plastids

• Mitochondria:     • Not easily visible without staining. Shape: Sausage-shaped or cylindrical ($0.2-1.0\,\mu m$ diameter; $1.0-4.1\,\mu m$ length).     • Structure: Double-membrane. Inner membrane forms infoldings called cristae to increase surface area for ATP production (Power Houses).     • Matrix contains: Single circular DNA, RNA, 70S ribosomes, and protein synthesis machinery.     • Division: Occurs via fission. • Plastids (Plant cells and Euglenoids): 1. Chloroplasts: Contain chlorophyll and carotenoids for photosynthesis. Found in mesophyll cells ($5-10\,\mu m$ long, $2-4\,\mu m$ wide). Numbers range from $1$ (Chlamydomonas) to $20-40$ (mesophyll).         • Structure: Double-membrane. Stroma (inner space) contains thylakoids (flattened sacs) stacked as grana. Stroma contains circular DNA, 70S ribosomes, and enzymes for carb/protein synthesis. 2. Chromoplasts: Contain fat-soluble carotenoids (carotene, xanthophylls); provide yellow, orange, or red colors. 3. Leucoplasts (Colorless):         • Amyloplasts: Store starch (e.g., potato).         • Elaioplasts: Store oils and fats.         • Aleuroplasts: Store proteins.

Ribosomes and Cytoskeleton

• Ribosomes:     • Discovered by George Palade ($1953$). Granular particles made of RNA and proteins. Non-membrane bound.     • Eukaryotic: 80S (subunits: $60S$ and $40S$).     • Prokaryotic: 70S (subunits: $50S$ and $30S$). • Cytoskeleton:     • Network of proteinaceous structures: Microtubules, microfilaments, and intermediate filaments.     • Functions: Mechanical support, motility, and maintenance of cell shape.

Cilia, Flagella, and Centrosomes

• Cilia and Flagella:     • Outgrowths of cell membrane. Cilia (oar-like) for movement; Flagella (longer) for cell movement.     • Axoneme structure: $9+2$ array (nine pairs of peripheral doublets and two central microtubules).     • Contains central sheath, radial spokes ($9$), and interdoublet linkers. Emerge from basal bodies. • Centrosome and Centrioles:     • Contains two perpendicular cylindrical centrioles surrounded by pericentriolar material.     • Cartwheel organization: Nine evenly spaced peripheral triplets of tubulin. Central hub connected to triplets by radial spokes.     • Functions: Form basal bodies and spindle apparatus during animal cell division.

The Nucleus and Chromosomes

• Structure:     • Described by Robert Brown ($1831$).     • Nuclear Envelope: Two parallel membranes with perinuclear space ($10$ to $50\,nm$). Nuclear pores allow bidirectional movement of RNA and proteins.     • Nucleoplasm: Contains nucleolus and chromatin. Nucleolus is the site of active rRNA synthesis.     • Chromatin: Named by Flemming. Contains DNA, basic proteins (histones), non-histone proteins, and RNA. • DNA Content: A single human cell contains approximately $2\,m$ of DNA distributed across $46$ ($23$ pairs) of chromosomes. • Chromosome Classification (By Centromere Position): 1. Metacentric: Middle centromere; equal arms. 2. Sub-metacentric: Centromere slightly off-center; one short arm, one long arm. 3. Acrocentric: Centromere close to end; extremely short and very long arm. 4. Telocentric: Terminal centromere.     • Kinetochores: Disc-shaped structures on the sides of the centromere.     • Satellite: Small fragment resulting from a secondary constriction at a constant location.