Cell Structure & Function Essentials

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I. Introduction to Cells & Microscopy A. Cell Theory All living organisms are composed of one or more cells. The cell is the basic unit of life. All cells arise from pre-existing cells. B. Microscopy Techniques Light Microscope (LM): Uses visible light and glass lenses. Max magnification: $\approx 1,000 \times$. Resolution limit: $\approx 0.2 \mu m$ (200 nm), cannot resolve structures smaller than this. Can view living cells and cellular processes (e.g., cell division). Techniques: Bright-field, phase-contrast, differential-interference-contrast, fluorescence, confocal. Electron Microscope (EM): Uses electron beams and electromagnetic lenses. Higher resolution (down to $2 nm$ or less) and magnification ($\approx 100,000 \times$). Specimens must be dead, fixed, and stained (often with heavy metals). Scanning Electron Microscope (SEM): Focuses electron beam on specimen surface, excites secondary electrons, creates 3D image of surface topography. Transmission Electron Microscope (TEM): Passes electron beam through ultra-thin sections of specimen, reveals internal ultrastructure. Advanced Techniques: Fluorescence Microscopy: Uses fluorescent dyes/proteins to label specific molecules/structures. Confocal Microscopy: Uses lasers and pinholes to eliminate out-of-focus light, creating sharper images and 3D reconstructions. Cryo-Electron Microscopy (Cryo-EM): Flash-freezes samples, avoiding chemical fixation/staining, allows visualization of molecules in near-native states. Cell Fractionation: Process of breaking cells apart and separating organelles/subcellular structures based on size and density using a centrifuge. Allows scientists to study the biochemical functions of specific cell components. II. Prokaryotic vs. Eukaryotic Cells A. Fundamental Cell Features (Shared) Plasma Membrane: Selective barrier enclosing the cytoplasm. Cytosol: Semifluid substance within the plasma membrane where organelles are suspended. Chromosomes: Carry genes in the form of DNA. Ribosomes: Complexes that synthesize proteins. B. Prokaryotic Cells (Bacteria & Archaea) Generally smaller ($1-5 \mu m$). No true nucleus; DNA located in a non-membrane-bound region called the nucleoid . No membrane-bound organelles. Cytoplasm lacks extensive internal compartmentalization. Often have a cell wall, capsule, fimbriae, and flagella. C. Eukaryotic Cells (Protists, Fungi, Animals, Plants) Generally larger ($10-100 \mu m$). DNA housed within a membrane-bound nucleus . Contain numerous membrane-bound organelles (e.g., ER, Golgi, mitochondria, lysosomes). Extensive internal compartmentalization allows for specialized functions. Cytoplasm: Refers specifically to the region between the plasma membrane and the nucleus. D. Surface Area to Volume Ratio As a cell increases in size, its volume grows proportionally more than its surface area. A high surface area-to-volume ratio is crucial for efficient exchange of nutrients and waste products across the plasma membrane. Smaller cells generally have a more favorable ratio. Specialized structures like microvilli (e.g., in intestinal cells) increase surface area without significantly increasing volume. III. The Nucleus and Ribosomes A. The Nucleus: Genetic Control Center Nuclear Envelope: Double membrane (each a lipid bilayer) enclosing the nucleus, perforated by nuclear pores , continuous with the ER. Nuclear Lamina: Netlike array of protein filaments lining the inner nuclear membrane; maintains nuclear shape. Chromatin: Complex of DNA and proteins (histones) that makes up eukaryotic chromosomes. Appears as a diffuse mass when the cell is not dividing. Chromosomes: Condensed chromatin structures visible during cell division. Each eukaryotic species has a characteristic number. Nucleolus: Prominent structure within the nucleus; site of ribosomal RNA (rRNA) synthesis and assembly of ribosomal subunits. Function: Stores genetic material (DNA), controls cell's activities by regulating gene expression (e.g., synthesizing mRNA). B. Ribosomes: Protein Synthesis Machinery Structure: Particles made of ribosomal RNA (rRNA) and protein. Not membrane-bound organelles. Location & Function: Free Ribosomes: Suspended in the cytosol; synthesize proteins that function within the cytosol (e.g., enzymes of glycolysis). Bound Ribosomes: Attached to the outside of the endoplasmic reticulum or nuclear envelope; synthesize proteins destined for insertion into membranes, secretion from the cell, or delivery to certain organelles (e.g., lysosomes, Golgi). Ribosomes can switch between free and bound states. IV. The Endomembrane System A network of membranes working together to synthesize proteins, transport proteins into membranes or organelles or out of the cell, metabolize lipids, and detoxify poisons. Components: Nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane. These are either continuous or connected via transfer of vesicles. A. Endoplasmic Reticulum (ER) Extensive network of membranes, accounts for more than half the total membrane in many eukaryotic cells. Consists of a network of membranous tubules and sacs called cisternae . Lumen (ER Cisternal Space): Internal compartment of the ER, separated from the cytosol. Smooth ER: (Lacks ribosomes) Synthesizes lipids (oils, steroids, phospholipids). Metabolizes carbohydrates. Detoxifies drugs and poisons (especially in liver cells, by adding hydroxyl groups to make substances more soluble). Stores calcium ions (e.g., in muscle cells for contraction). Rough ER: (Studded with ribosomes) Synthesizes secretory proteins (proteins destined for secretion, insertion into membranes, or delivery to other organelles). Ribosomes attach only when synthesizing such proteins. Polypeptides enter ER lumen, fold, and often undergo modifications (e.g., glycosylation to form glycoproteins). A "membrane factory" for the cell: adds membrane proteins and phospholipids to its own membrane. B. Golgi Apparatus Consists of flattened membranous sacs called cisternae , resembling a stack of pancakes. Has distinct structural and functional polarity: Cis face: "Receiving" side, usually located near the ER. Vesicles from ER fuse here. Trans face: "Shipping" side, where vesicles bud off. Functions: Modifies products of the ER (e.g., carbohydrate portions of glycoproteins). Manufactures certain macromolecules (e.g., pectin in plant cell walls). Sorts and packages materials into transport vesicles, adding "molecular tags" (e.g., phosphate groups) to direct vesicles to specific destinations. Cisternal Maturation Model: Cisternae themselves progress from the cis to the trans face, modifying their contents as they move. C. Lysosomes: Digestive Compartments Membranous sac of hydrolytic enzymes that animal cells use to digest macromolecules. Lysosomal enzymes work best in acidic conditions maintained within the lysosome. Functions: Phagocytosis: Engulfment of smaller organisms or food particles, forming a food vacuole that fuses with a lysosome for digestion. Autophagy: Recycling of the cell's own organic material, enclosing damaged organelles or small amounts of cytosol in a double membrane, which then fuses with a lysosome. Defects in lysosomal enzymes can lead to lysosomal storage diseases (e.g., Tay-Sachs disease). D. Vacuoles: Diverse Maintenance Compartments Large vesicles derived from the ER and Golgi apparatus. Food Vacuoles: Formed by phagocytosis; contents digested by lysosomes. Contractile Vacuoles: Pump excess water out of the cell in many freshwater protists, maintaining suitable solute concentration. Central Vacuole (in mature plant cells): Large, often makes up 80% or more of cell volume. Develops by coalescence of smaller vacuoles. Stores water, inorganic ions (e.g., $K^+$, $Cl^-$), pigments, and poisonous compounds (defense against herbivores). Plays a major role in plant cell growth by enlarging, allowing the cell to increase in size with minimal investment in new cytoplasm. V. Energy-Converting Organelles A. Mitochondria: Sites of Cellular Respiration Found in nearly all eukaryotic cells (animal, plant, fungi, protists). Generates ATP by extracting energy from sugars, fats, and other fuels (cellular respiration). Structure: Bounded by two membranes, each a phospholipid bilayer. Outer Membrane: Smooth. Inner Membrane: Highly folded into cristae , which increase surface area. Intermembrane Space: Narrow region between inner and outer membranes. Mitochondrial Matrix: Innermost compartment, contains enzymes for cellular respiration, mitochondrial DNA, and ribosomes. Mitochondria are dynamic, moving, fusing, and dividing. B. Chloroplasts: Sites of Photosynthesis Found in plants and algae; responsible for converting solar energy to chemical energy (photosynthesis). A type of plastid (e.g., amyloplasts store starch, chromoplasts store pigments). Structure: Bounded by two membranes. Stroma: Fluid-filled space outside the thylakoids; contains chloroplast DNA, ribosomes, and many enzymes. Thylakoids: Flattened, interconnected sacs within the stroma. Grana (singular: granum): Stacks of thylakoids. Chlorophyll (green pigment) is located in the thylakoid membranes. C. The Endosymbiont Theory Proposes that mitochondria and plastids (like chloroplasts) originated as prokaryotic cells engulfed by ancestral eukaryotic cells. Evidence: Both organelles have two membranes. Both contain their own circular DNA molecules, similar to bacterial chromosomes. Both have ribosomes similar to prokaryotic ribosomes. Both reproduce independently within the cell by a fission process similar to bacteria. VI. Peroxisomes Specialized metabolic compartments bounded by a single membrane. Contain enzymes that remove hydrogen atoms from various substrates and transfer them to oxygen, producing hydrogen peroxide ($H_2O_2$). Functions: Break down fatty acids for fuel. Detoxify alcohol and other harmful compounds in the liver. Contain the enzyme catalase , which converts toxic $H_2O_2$ into water. Glyoxysomes (in plant seeds): Convert fatty acids to sugars to provide energy for the seedling until it can photosynthesize. VII. The Cytoskeleton A network of fibers extending throughout the cytoplasm; organizes cell structures and activities, anchoring many organelles. Functions: Mechanical support for the cell, maintains cell shape, provides anchorage for organelles, involved in cell motility (often interacting with motor proteins), regulates biochemical activities. A. Three Main Types of Cytoskeletal Fibers Feature Microtubules Microfilaments (Actin Filaments) Intermediate Filaments Structure Hollow tubes; walls consist of 13 columns of tubulin dimers Two intertwined strands of actin Fibrous proteins supercoiled into thicker cables Diameter Largest: 25 nm with 15 nm lumen Smallest: 7 nm Middle range: 8–12 nm Protein Subunits $\alpha$-tubulin and $\beta$-tubulin dimers Actin Diverse (e.g., keratins, vimentin, lamins); depend on cell type Main Functions Maintain cell shape (compression-resisting girders) Cell motility (cilia, flagella) Chromosome movements in cell division Organelle movements (e.g., vesicle transport) Cell plate formation (plants) Maintain cell shape (tension-bearing elements) Changes in cell shape Muscle contraction (with myosin) Cytoplasmic streaming (plants) Cell motility (amoeboid movement, pseudopodia) Cleavage furrow formation (animal cell division) Maintain cell shape (tension-bearing elements) Anchorage of nucleus and other organelles Formation of nuclear lamina More permanent than other two types B. Centrosomes and Centrioles Centrosome: Region near the nucleus in animal cells; considered the "microtubule-organizing center." Contains a pair of centrioles , each composed of nine sets of triplet microtubules arranged in a ring. Centrioles replicate before cell division. Not essential for microtubule organization in all eukaryotes (e.g., plants lack them). C. Cilia and Flagella Locomotor appendages of some cells (e.g., sperm, protists). Flagella: Usually long and few per cell; undulating motion. Cilia: Usually short and numerous; back-and-forth motion (like oars). Can also function as signal-receiving antennae (primary cilia). Structure: Both have a "9 + 2" arrangement of microtubules (nine doublets surrounding two central singlets) in the axoneme. Anchored to the cell by a basal body , structurally similar to a centriole ("9 + 0" triplet arrangement). Movement is driven by the motor protein dynein , which "walks" along adjacent microtubules using ATP. VIII. Extracellular Components & Cell-Cell Junctions A. Cell Walls of Plants Rigid extracellular structure that distinguishes plant cells from animal cells. Functions: Protects the plant cell, maintains its shape, prevents excessive water uptake, provides support against gravity. Composition: Primarily cellulose microfibrils embedded in a matrix of other polysaccharides and proteins. Layers: Primary Cell Wall: Relatively thin and flexible layer secreted by a young plant cell. Middle Lamella: Thin layer rich in sticky polysaccharides (pectins) that glues adjacent cells together. Secondary Cell Wall: (Some plant cells) Deposited between the plasma membrane and the primary wall after cell growth has stopped; often strong and durable (e.g., in wood). B. The Extracellular Matrix (ECM) of Animal Cells Elaborate network of macromolecules outside the plasma membrane, providing support, adhesion, movement, and regulation. Composition: Primarily glycoproteins (e.g., collagen is the most abundant, forming strong fibers; fibronectin connects cells to the ECM) and proteoglycans (carbohydrate-protein complexes). Integrins: Cell-surface receptor proteins that span the plasma membrane, connecting the ECM to the cytoskeleton. They transmit signals between the ECM and the cytoskeleton, influencing cell behavior. Functions: Support, adhesion, movement, regulation (influences gene activity, cell differentiation). C. Intercellular Junctions Facilitate direct physical contact and communication between adjacent cells. Plasmodesmata (Plants): Channels through cell walls that connect the cytoplasm of adjacent plant cells. Allow free passage of water, small solutes, and sometimes proteins and RNA molecules. Animal Cell Junctions: Tight Junctions: Plasma membranes of adjacent cells are tightly pressed together, sealed by specific proteins. Prevent leakage of extracellular fluid across a layer of epithelial cells (e.g., in the intestine, bladder). Desmosomes (Anchoring Junctions): Fasten cells together into strong sheets. Intermediate filaments (e.g., keratin) anchor desmosomes in the cytoplasm. Abundant in tissues subjected to mechanical stress (e.g., muscle cells, skin). Gap Junctions (Communicating Junctions): Provide cytoplasmic channels between adjacent cells (similar to plasmodesmata in plants). Consist of specialized membrane proteins surrounding a pore. Allow passage of ions, sugars, amino acids, and other small molecules. Crucial for communication in many tissues (e.g., heart muscle for coordinated contractions).