Chapter 6: A Tour of the Cell Flashcards

Fundamental Principles of Cell Biology

• All living organisms are composed of structural and functional units known as cells.

• The cell represents the simplest collection of matter capable of performing all processes associated with life.

• Cellular structure is directly correlated with specific cellular functions; structural features dictate operational capabilities.

• Evolutionary continuity dictates that all contemporary cells are related through descent from earlier ancestral cells.

Scientific Microscopy and Subcellular Visualization

• Visualizing cellular structures requires specialized scientific tools due to the minute physical dimensions of cells:

  • Light Microscopy (LM):

  • Operates by passing visible light through a biological specimen and then through glass lenses, which bend the light to magnify the image.

  • Effectively magnifies biological specimens up to approximately $1,000\times$ their actual size.

  • Resolving power is limited by light wavelength; the minimum resolution limit of a standard light microscope is approximately $200\,\text{nm}$, roughly equivalent to the diameter of a small bacterium.

  • Subcellular structures and most organelles are too small to be resolved using conventional light microscopy.

  • Contrast enhancement techniques include unstained brightfield microscopy, stained brightfield microscopy, and phase-contrast microscopy to improve visual distinction of cellular components.

  • Electron Microscopy (EM):

  • Utilizes focused beams of electrons rather than light, yielding dramatically higher resolution to visualize subcellular ultrastructures.

  • Scanning Electron Microscopy (SEM): Directs an electron beam onto the specimen's surface, producing detailed images with a three-dimensional ($3\text{D}$) appearance. Essential for examining cell surface morphology such as cilia.

  • Transmission Electron Microscopy (TEM): Aims an electron beam through an ultra-thin section of a specimen, utilizing heavy metals to stain cellular structures. Used primarily to study internal cell ultrastructure, such as cross-sectional and longitudinal details of organelles like cilia.

Cell Fractionation and Organelle Isolation

• Cell fractionation is a laboratory technique that disintegrates cells and separates major organelles and subcellular components based on size, density, and mass.

• Differential centrifugation utilizes ultracentrifuges spinning at increasing gravitational forces ($g$) to isolate specific cellular components sequentially:

  • Homogenization: Tissue cells are broken open in a tissue grinder to form a uniform cell homogenate.

  • First Centrifugation Step:

  • Centrifuged at $1,000\,g$ ($1,000\times$ the force of gravity) for $10\,\text{min}$.

  • Resulting pellet is rich in nuclei and heavy cellular debris.

  • Un-pelleted liquid (supernatant) is poured into a new tube for the next step.

  • Second Centrifugation Step:

  • Supernatant is centrifuged at $20,000\,g$ for $20\,\text{min}$.

  • Resulting pellet is rich in mitochondria (and chloroplasts if plant tissue is processed).

  • Supernatant is poured into the next tube.

  • Third Centrifugation Step:

  • Supernatant is centrifuged at $80,000\,g$ for $60\,\text{min}$.

  • Resulting pellet is rich in "microsomes" (fragments of plasma membrane and internal membrane systems).

  • Supernatant is poured into the next tube.

  • Fourth Centrifugation Step:

  • Supernatant is centrifuged at $150,000\,g$ for $3\,\text{hr}$.

  • Resulting pellet is rich in ribosomes.

• Isolating pure organelle fractions enables researchers to biochemically analyze and determine the distinct metabolic functions of each organelle.

Comparative Analysis of Prokaryotic and Eukaryotic Cells

• All living organisms are classified structurally into two fundamental cell types: prokaryotic cells and eukaryotic cells.

• Domain Distribution:

  • Prokaryotic cells comprise organisms within the domains Bacteria and Archaea.

  • Eukaryotic cells comprise protists, fungi, animals, and plants.

• Universal Cellular Features:

  • Plasma membrane: A selective lipid barrier surrounding the cell.

  • Cytosol: A semifluid, jelly-like substance (also termed cytoplasm) suspending cellular elements.

  • Chromosomes: Structures composed of nucleic acids carrying genetic information in the form of genes.

  • Ribosomes: Ribonucleoprotein complexes that synthesize proteins.

• Distinguishing Characteristics of Prokaryotic Cells:

  • Lack a membrane-enclosed nucleus.

  • Genetic material (DNA) is localized to an unbound, concentrated region called the nucleoid.

  • Devoid of membrane-bound internal organelles.

• Distinguishing Characteristics of Eukaryotic Cells:

  • Genetic material (DNA) is segregated within a double-membrane-bound organelle called the nucleus, enclosed by a nuclear envelope.

  • Contain extensive internal membrane-bound organelles that compartmentalize specific metabolic functions.

  • Substantially larger in structural volume and physical dimensions than prokaryotic cells.

Surface Area to Volume Dynamics and Cell Size Limits

• Metabolic requirements impose definitive physical upper limits on achievable cell size.

• Plasma Membrane Architecture:

  • Functions as a selective boundary regulating the passage of oxygen, nutrients, and cellular metabolic wastes.

  • Composed fundamentally of a phospholipid bilayer containing hydrophobic interior tails and hydrophilic exterior heads, integrated with dynamic transmembrane and peripheral proteins and exterior carbohydrate side chains.

• Geometric Surface-to-Volume Ratio Principles:

  • As physical volume increases, surface area increases at a proportionally lower rate.

  • Maintaining a high surface-area-to-volume ratio is essential for efficient material exchange across the plasma membrane.

  • Quantitative Comparison Example:

  • Single Large Cube: Dimensions of height = $5$, width = $5$, length = $5$ units (Total volume = $125$ cubic units).

    • Total Surface Area = $5 \times 5 \times 6\,\text{sides} \times 1\,\text{box} = 150$ square units.

    • Surface-to-Volume Ratio = $\frac{150}{125} = 1.2$.

  • Subdivided System of $125$ Small Cubes: Dimensions of height = $1$, width = $1$, length = $1$ unit each (Total volume = $125$ cubic units).

    • Total Surface Area = $1 \times 1 \times 6\,\text{sides} \times 125\,\text{boxes} = 750$ square units.

    • Surface-to-Volume Ratio = $\frac{750}{125} = 6.0$.

  • Division of larger cellular volumes into smaller compartmentalized domains dramatically elevates effective surface area while total volume remains constant, providing sufficient surface area to support cellular metabolism.

Structural Organization and Organelles of Eukaryotic Cells

• Internal biological membranes divide eukaryotic cells into specialized functional compartments called organelles.

• Plant and animal cells share the vast majority of subcellular components, but maintain key distinct structural differences:

• Structures Unique to Animal Cells (Absent in Plant Cells):

  • Lysosomes: Specialized digestive compartments.

  • Centrioles: Paired cylindrical structures within the centrosome organizing microtubule assembly.

  • Flagella: Locomotor structures (present in animal cells and select plant sperm cells).

• Structures Unique to Plant Cells (Absent in Animal Cells):

  • Chloroplasts: Photosynthetic energy conversion organelles.

  • Central Vacuole and Tonoplast: Large storage vacuole enclosed by the tonoplast membrane.

  • Cell Wall: Rigid extracellular protective layer composed of cellulose.

  • Plasmodesmata: Perforated cytoplasmic channels connecting neighboring plant cells.

• Shared Subcellular Components:

  • Nucleus (enclosing nuclear envelope, nucleolus, and chromatin).

  • Plasma membrane.

  • Ribosomes.

  • Endoplasmic Reticulum (divided into Rough ER and Smooth ER).

  • Golgi apparatus.

  • Mitochondria.

  • Peroxisomes.

  • Cytoskeleton (microtubules, microfilaments, intermediate filaments).

  • Centrosome region.

The Nucleus and Ribosomes: Genetic Control and Protein Synthesis

• The Nucleus:

  • Houses the majority of the cell's genetic code (DNA) and serves as the primary command center.

  • Enclosed by the nuclear envelope, a double-membrane barrier consisting of an inner membrane and an outer membrane separated by a narrow space.

  • Nuclear Pores and Pore Complex: Perforated openings spanning the nuclear envelope, lined by a protein structure called the pore complex that regulates entry and exit of proteins, RNA, and macromolecules.

  • Nuclear Lamina: A net-like array of protein filaments lining the inner surface of the nuclear envelope, maintaining mechanical stability and nuclear shape.

  • Chromatin: Structural complex formed by cellular DNA associated with nuclear proteins; condenses into distinct chromosomes during cellular division.

  • Nucleolus: Non-membranous structure located within the non-dividing nucleus where ribosomal RNA (rRNA) is synthesized and assembled with proteins into ribosomal subunits.

• Ribosomes:

  • Non-membrane-bound complexes composed of ribosomal RNA (rRNA) and proteins, functioning as protein synthesis factories.

  • Structural composition consists of one large subunit and one small subunit.

  • Function in two distinct cellular locations:

  • Free Ribosomes: Suspended within the cytosol; primarily synthesize proteins that function within the fluid cytosol.

  • Bound Ribosomes: Attached to the exterior surface of the endoplasmic reticulum (ER) or the nuclear envelope; synthesize proteins destined for insertion into membranes, packaging within organelles, or secretion outside the cell.

The Endomembrane System and Metabolic Flow

• The endomembrane system regulates protein traffic and coordinates metabolic pathways within the eukaryotic cell.

• Included Components: Nuclear envelope, Endoplasmic Reticulum (ER), Golgi apparatus, Lysosomes, Vacuoles, and Plasma membrane.

• Members interact through direct physical continuity or through transport vesicles that transfer membrane segments and enclosed lumen materials.

• Endoplasmic Reticulum (ER):

  • Accounts for over half of total membrane area in many eukaryotic cells.

  • Composed of a continuous network of membranous tubules and flattened sacs called cisternae; the internal compartment is termed the ER lumen.

  • Smooth Endoplasmic Reticulum (Smooth ER):

  • Lacks surface-bound ribosomes.

  • Synthesizes lipids, including phospholipids, fatty acids, and steroids.

  • Metabolizes carbohydrates.

  • Stores intracellular calcium ions ($\text{Ca}^{2+}$).

  • Detoxifies drugs and metabolic poisons.

  • Rough Endoplasmic Reticulum (Rough ER):

  • Outer surface is studded with bound ribosomes.

  • Synthesizes proteins and glycoproteins (proteins covalently bonded to carbohydrates).

  • Packages synthesized proteins into transport vesicles formed at specialized transitional ER zones.

  • Functions as the cellular membrane factory, synthesizing membrane phospholipids and proteins.

• Golgi Apparatus:

  • Functions as the receiving, sorting, manufacturing, and shipping center of the cell, composed of stacked flattened membranous cisternae.

  • Exhibits explicit structural and functional polarity:

  • Cis Face: Receiving side located near the ER; transport vesicles from the ER fuse with the cis membrane, adding content and membrane components.

  • Trans Face: Shipping side; gives rise to transport vesicles that pinch off and travel to specific subcellular destinations or fuse with the plasma membrane for secretion.

  • Cisternal Maturation Model: Golgi cisternae physically progress forward from the cis to the trans face, maturing and modifying their internal protein contents progressively.

  • Retrograde Vesicle Transport: Specialized vesicles shuttle specific proteins backward to earlier cisternae or to the ER to recycle functional molecules.

  • Chemical Modification: Modifies carbohydrate portions of glycoproteins, manufactures specific macromolecules, and attaches molecular identification tags to target vesicles to appropriate cellular destinations.

• Lysosomes:

  • Membranous sacs containing acid hydrolytic enzymes utilized for macromolecule digestion ("cellular recycling centers").

  • Maintain optimal activity in acidic microenvironments within the lysosomal lumen.

  • Phagocytosis: Intracellular digestion process where the plasma membrane engulfs food or foreign particles to form a food vacuole; the food vacuole fuses with a lysosome, allowing hydrolytic enzymes to break down engulfed nutrients.

  • Autophagy: Degradative process where lysosomes recycle damaged organelles or cytoplasm components. A double-membrane vesicle surrounds damaged components (e.g., damaged mitochondria or peroxisome fragments) and fuses with a lysosome for breakdown and molecular recycling.

• Vacuoles:

  • Large membrane-bound sacs derived from the ER and Golgi apparatus with diverse operational functions.

  • Food Vacuoles: Formed by phagocytosis to hold engulfed nutritive substances.

  • Contractile Vacuoles: Specialized structures in freshwater protists that accumulate excess water and pump it out of the cell to maintain osmotic homeostasis.

  • Central Vacuoles: Large functional compartment in mature plant cells enclosed by a selective membrane called the tonoplast. Functions in storing organic compounds, inorganic ions, and water, enabling plant cell growth and maintaining turgor pressure.

Energy Transducing Organelles: Mitochondria, Chloroplasts, and Peroxisomes

• Mitochondria and chloroplasts convert energy into forms usable by cellular processes; they are autonomous organelles not integrated into the endomembrane system.

• Mitochondria:

  • Sites of cellular respiration, metabolic processes generating ATP by extracting energy from sugars, fats, and other metabolic fuels using oxygen.

  • Enclosed by two distinct biological membranes:

  • Smooth Outer Membrane: Encloses the entire organelle.

  • Convoluted Inner Membrane: Folded into deep infoldings called cristae, maximizing available membrane surface area for ATP synthase enzymes and respiration components.

  • Compartmentalization:

  • Intermembrane Space: Narrow fluid region situated between inner and outer membranes.

  • Mitochondrial Matrix: Internal space enclosed by the inner membrane; contains mitochondrial DNA, free mitochondrial ribosomes, and metabolic enzymes catalyzing chemical steps of cellular respiration.

• Chloroplasts:

  • Specialized photosynthetic organelles belonging to a family of plant structures called plastids; found in leaves, green organs of plants, and algae.

  • Contain the green pigment chlorophyll alongside enzymes and functional molecules required for photosynthetic light capture.

  • Internal Ultrastructure:

  • Outer and Inner Membranes: Separated by a narrow intermembrane space.

  • Thylakoids: Interconnected membranous flattened sacs suspended within the interior; organized into stacks termed grana (singular: granum).

  • Stroma: The fluid-filled space internal to the inner membrane and external to thylakoids; contains chloroplast DNA, ribosomes, and photosynthetic enzymes.

• Peroxisomes:

  • Specialized single-membrane metabolic compartments that perform oxidation reactions, removing hydrogen atoms from substrates and transferring them to oxygen ($\text{O}_2$), producing hydrogen peroxide ($\text{H}_2\text{O}_2$).

  • Destroy toxic chemicals and break down fatty acids.

  • Contain the crucial enzyme catalase, which rapidly converts toxic hydrogen peroxide ($\text{H}_2\text{O}_2$) into harmless water ($\text{H}_2\text{O}$).

Structural Architecture and Dynamics of the Cytoskeleton

• The cytoskeleton is a dynamic network of microscopic fibers extending throughout the cytoplasm, organizing structural framework, anchoring organelles, and facilitating cellular activities.

• Core Functions:

  • Provides mechanical support, structural reinforcement, and shape maintenance.

  • Interacts with ATP-powered motor proteins to generate motility of whole cells and internal structures.

  • Serves as intracellular tracks ("monorails") along which transport vesicles carrying cargo are pulled by motor proteins attached to specific membrane receptors.

  • Helps regulate biochemical and mechanical signaling pathways.

• Three Major Cytoskeletal Elements:

  • Microtubules:

  • Structure: Hollow cylindrical rods constructed from tubulin subunits.

  • Dimensions: Outer diameter measuring approximately $25\,\text{nm}$; lengths range from $200\,\text{nm}$ to $25\,\mu\text{m}$.

  • Functions: Maintaining cell shape, guiding organelle movement, and driving chromosome separation during cell division.

  • Centrosomes and Centrioles: In animal cells, microtubules originate from a centrosome located near the nucleus. Contains a pair of centrioles, each composed of nine sets of triplet microtubules arranged in a ring.

  • Cilia and Flagella:

    • Microtubule-based locomotor appendages protruding from specific cells.

    • Flagella exhibit undulatory motion propelling cells parallel to the flagellum's axis.

    • Cilia exhibit back-and-forth patterns with alternating active strokes and recovery strokes, generating force perpendicular to the cilium's axis.

    • Structural Design: Core of microtubules wrapped by plasma membrane arranged in a "$9+2$" pattern (nine outer microtubule doublets surrounding two central singlet microtubules).

    • Basal Body: Anchors cilia or flagella into the cell, displaying a ring of nine microtubule triplets.

    • Dynein Arm Mechanism: Motor proteins called dynein arms flex using ATP, grabbing, moving, and releasing adjacent doublets. Cross-linking proteins and radial spokes constrain linear sliding, converting dynein forces into bending and wavelike movements.

  • Microfilaments (Actin Filaments):

  • Structure: Solid linear rods constructed as a twisted double chain of actin protein subunits.

  • Dimensions: Diameter measuring approximately $7\,\text{nm}$.

  • Functions: Bear mechanical tension (resisting pulling forces); form a dynamic three-dimensional structural network (cortex) beneath the plasma membrane to support cell shape. Core support for intestinal microvilli.

  • Motility and Contraction:

    • Interdigitate with thicker filaments composed of the motor protein myosin in muscle cells to produce contraction.

    • Amoeboid Movement: Extension and retraction of pseudopodia ("false feet") through local assembly and disassembly of actin networks; transitions between outer gel-like cortex and inner fluid sol cytoplasm.

    • Cytoplasmic Streaming: Circular flow of cytoplasm within large plant cells, driven by actin-myosin interactions along parallel actin filaments, speeding material distribution.

  • Intermediate Filaments:

  • Structure: Fibrous proteins supercoiled into structural cables.

  • Dimensions: Middle-range diameters measuring between $8\text{--}12\,\text{nm}$.

  • Functions: Specially adapted for bearing tension, reinforcing overall cell shape, and anchoring the nucleus and other organelles permanently in position.

  • Represent more permanent cytoskeletal fixtures compared to dynamic microtubules and microfilaments.

Extracellular Components and Intercellular Junctions

• Specialized extracellular structures and physical connections coordinate activities between neighboring cells within tissues and organs.

• Plant Cell Walls:

  • Extracellular protective layer surrounding plant cells, preventing excess water absorption, maintaining cell shape, and providing structural resistance against gravity.

  • Composed of microfibrils of cellulose embedded in a matrix of proteins and polysaccharides.

  • Multi-layered Structural Organization:

  • Primary Cell Wall: Relatively thin and flexible wall layer secreted first by young growing cells.

  • Middle Lamella: Thin layer rich in sticky polysaccharides (pectins) located between primary walls of adjacent cells, gluing them together.

  • Secondary Cell Wall: Thickened layer added between the plasma membrane and primary cell wall in mature plant cells.

• Extracellular Matrix (ECM) of Animal Cells:

  • Replaces cell walls in animal tissues, consisting of an elaborate structural network of secreted glycoproteins and carbohydrate-containing molecules.

  • Major Components: Collagen fibers embedded in a network of proteoglycan complexes.

  • Adhesion and Signaling: Fibronectin molecules attach ECM networks to integrins, transmembrane receptor proteins anchored to cytoskeletal microfilaments.

  • Functions: Mechanical support, cellular adhesion, tissue movement, and cell-signaling regulation.

• Intercellular Junctions:

  • Physical structural channels and junctions allowing neighboring cells in tissues to adhere, interact, and communicate directly.

  • Plasmodesmata (Plants): Open channels perforating plant cell walls; plasma membranes of adjacent cells line each channel, allowing water, small solutes, proteins, and RNA molecules to pass freely between cytosol of adjacent cells.

  • Animal Cell Junctions:

  • Tight Junctions: Plasma membranes of adjacent cells are tightly pressed together and bound by specific proteins, forming continuous fluid-tight seals that prevent leakage of extracellular fluid across cell layers.

  • Desmosomes (Anchoring Junctions): Fasten cells together into strong sheets, anchored into the cytoplasm by intermediate filaments (e.g., keratin).

  • Gap Junctions (Communicating Junctions): Consist of membrane proteins surrounding a central pore, creating open cytoplasmic channels between adjacent cells for passage of ions, sugars, amino acids, and small signaling molecules.

Systemic Integration of Cellular Functions

• The cell operates as an integrated living unit where individual organelles and structural elements do not act in isolation.

• High-level functions require coordinated cooperation across multiple organelles, membranes, and cytoskeletal structures.

• Example Application: A white blood cell macrophage phagocytosing and destroying pathogenic bacteria relies on total cellular coordination:

  • Plasma membrane extends pseudopodia driven by actin microfilament rearrangement.

  • Bacterial particles are ingested into a food vacuole.

  • Vesicles move along microtubule monorails propelled by motor proteins.

  • Lysosomes fuse with the food vacuole to deliver acid hydrolytic enzymes for digestion.

  • Energy required for all involved processes is continuously supplied in the form of ATP generated by cellular respiration within mitochondria.