Comprehensive Study Guide on Cell Structure and Cytoplasmic Components

Introduction to Cellular Biology and Microscopy

Cells are the fundamental units of life, characterized by their type, structure, function, and location.
Differentiated cells typically specialize in one activity, although all cells share basic components such as the plasma membrane, cytoplasm, and nucleus.
HeLa cells are a historically significant immortal cell line derived from Henrietta Lacks, an African American woman born in Roanoke, VA, who died at age 31 of cervical cancer. These were the first cancerous cells to produce an immortal line.
Microscopy techniques used for visualizing cells, tissues, and organs include:
- Brightfield Microscopy: Basic light microscopy often using stains to visualize cell boundaries and membrane-associated carbohydrates.
- Fluorescence Microscopy: Uses immunofluorescent staining of membrane proteins or other components.
- Phase Contrast Microscopy: Enhances contrast in transparent specimens.
- Transmission Electron Microscopy (TEM): Visualizes boundaries by depositing heavy metals like osmium in polar regions of membrane lipids; provides trilaminar appearance of membranes.
- Scanning Electron Microscopy (SEM): Provides 3D-like images of surfaces through heavy metal deposition.

Comparative Analysis of Prokaryotic and Eukaryotic Cells

Prokaryotes (Bacteria, Archaea):
- Typical Size: $1-10\,\mu m$ .
- Nucleus: Nucleoid region; no true nucleus with a membrane.
- DNA: Usually circular molecules.
- Synthesis: RNA and protein synthesis are coupled in the cytoplasm.
- Ribosomes: $50S$ and $30S$ subunits.
- Structure: Very few cytoplasmic structures; flagella made of flagellin.
- Division: Binary fission (simple division).
- Organelles: Lack mitochondria and chloroplasts.
Eukaryotes (Protista, Fungi, Plants, Animals):
- Typical Size: $10-100\,\mu m$ (sperm cells are smaller, excluding the tail).
- Nucleus: Real nucleus with a double membrane.
- DNA: Linear molecules organized into chromosomes with histone proteins.
- Synthesis: RNA synthesis occurs inside the nucleus; protein synthesis occurs in the cytoplasm.
- Ribosomes: $60S$ and $40S$ subunits.
- Structure: Highly structured by endomembranes and a cytoskeleton.
- Movement: Flagella and cilia contain microtubules; lamellipodia and filopodia contain actin.
- Division: Mitosis (fission or budding) and Meiosis.
- Mitochondria: Present in numbers ranging from one to several thousand (with rare exceptions).

The Plasma Membrane: Composition and the Fluid Mosaic Model

The Fluid Mosaic Model describes the membrane as "protein icebergs in a sea of lipid."
Fundamental Function: Encloses the cell and organelles, enabling communication and transport between internal and external environments.
Biochemical Composition:
- Lipids: Provide a barrier and enable cellular processes. Major types include Phospholipids (bilayer with hydrophilic phosphate heads and hydrophobic hydrocarbon tails), Glycolipids (localized functions), and Cholesterol (increases fluidity at low temperatures and reduces it at high temperatures; part of lipid rafts).
- Proteins: Functionally classify as Peripheral, Integral (transmembrane), or Lipid-Anchored. Multi-pass membrane proteins result from hydrophobic interactions between lipids and nonpolar amino acids.
- Carbohydrates: Attached to lipids (glycolipids) or proteins (glycoproteins) on the extracellular surface, forming the glycocalyx. Functions include cell recognition and cell adhesion.

Membrane Dynamics: Selective Permeability and Transport

Selective Permeability: Regulates molecular passage across the hydrophobic region of the lipid bilayer.
Passive Transport:
- Simple Diffusion: Movement along a concentration gradient. Includes nonpolar molecules ( $O_2$ , $CO_2$ , $N_2$ , steroids), small polar molecules (urea, ammonia, glycerol, small alcohols), and fat-soluble vitamins.
- Facilitated Diffusion: Requires a protein channel and conformational change to release molecules on the opposite side. Aquaporins (13 known types, 6 in the kidney) facilitate ubiquitous water transport.
Active Transport: Moves molecules against a concentration gradient using energy, usually as ATP.
- Example: $Na^+/K^+$ ATPase transports ions in two directions during one conformational cycle.
Osmosis and Tonicity:
- Isotonic: Normal cell volume.
- Hypertonic: Results in crenation (shriveling) as water leaves the cell.
- Hypotonic: Results in hemolysis (bursting) as water enters the cell.

Intercellular Communication and Signal Transduction

Signal transduction is the process by which cells respond to external stimuli.
Signaling Routes:
- Endocrine: Hormones (e.g., insulin, glucagon) released into the bloodstream.
- Paracrine: Acts on nearby adjacent cells; rapidly metabolized. Synaptic signaling (e.g., neurotransmitters at neuromuscular junctions) is a subtype.
- Autocrine: Cells respond to molecules they produce themselves (e.g., tumor cells producing growth factors).
- Juxtacrine: Contact-dependent signaling. Types include cell-cell signaling (embryogenesis), cell-cell communication (cardiac myocytes), and cell-extracellular matrix signaling (integrins).

Bulk Transport: Endocytosis and Exocytosis

Endocytosis (Cellular Uptake):
- Phagocytosis: "Cell eating"; engulfment of large particles or bacteria. Performed by specialized cells like macrophages and neutrophils.
- Pinocytosis: "Cell drinking"; non-specific uptake of extracellular fluid via small vesicles.
- Receptor-Mediated Endocytosis: Selective uptake. Example: LDL cholesterol binding to LDL receptors in clathrin-coated pits. The clathrin coat dissociates and is recycled; the vesicle fuses with a primary lysosome to release cholesterol.
Exocytosis (Cellular Secretion):
- Constitutive Secretion: Occurs continuously regardless of external factors.
- Regulated Secretion: Occurs only in response to a specific stimulus, such as a hormone or nerve impulse.

Mitochondria: Structure, Function, and Origin

Structure:
- Dimensions: Approximately $1-2\,\mu m$ long and $0.1-0.5\,\mu m$ in diameter.
- Components: Outer membrane (contains porins), intermembrane space, inner membrane (contains the electron-transport chain, Cytochrome C, and Mitochondrial ATP Synthase/F1 sub-units/lollipops), and the Matrix.
- Cristae: Inward folds of the inner membrane. Most cells have shelf-like cristae; steroid-secreting cells have tubular or vesicular cristae.
- Matrix Components: Tricarboxylic Acid (Krebs) cycle enzymes, circular DNA, ribosomes, and matrix granules containing $Ca^{2+}$ .
Functions:
- ATP production through cellular respiration and metabolism.
- Calcium homeostasis (signaling and muscle contraction).
- Apoptosis: Release of cytochrome c activates cell death pathways.
- Heat production: Thermogenesis in brown adipose tissue.
- Steroid hormone synthesis.
- Regulation of Reactive Oxygen Species (ROS) via antioxidant systems.
Endosymbiotic Theory:
- Proposes mitochondria evolved from a primitive heterotrophic eukaryote engulfing an autotrophic alpha-proteobacterium (symbiont).
- Evidence: Mitochondria only arise from preexisting mitochondria; they possess their own circular DNA genome and protein-synthesizing machinery resembling bacteria; the first amino acid is fMet; protein synthesis is blocked by antibiotics like streptomycin; RNA polymerase is inhibited by rifampicin.

Ribosomes, Protein Folding, and the Proteasome System

Ribosomes:
- Composed of two subunits ( $60S$ and $40S$ ) made of proteins (30 in small, 50 in large) and rRNA (ribozymes).
- Free polysomes synthesize proteins for internal cellular use (e.g., hemoglobin).
Quality Control:
- Chaperones: Proteins that ensure proper folding of newly synthesized proteins.
- Ubiquitin: A small protein that tags denatured, misfolded, or unnecessary proteins for destruction.
Proteasomes:
- Structure: Barrel-shaped core particle consisting of four stacked rings, capped by regulatory particles containing ATPase.
- Degradation Process: Ubiquitin binds to a lysine residue on the target protein → more ubiquitins attach → regulatory particle recognizes the complex → ATPase unfolds the protein → protein translocates into the core → broken into peptides of ~8 amino acids → peptides move to cytosol → ubiquitin is recycled.

The Endoplasmic Reticulum: Rough (RER) and Smooth (SER)

Rough Endoplasmic Reticulum (RER):
- Characteristics: Basophilic staining due to phosphate groups and RNA. Studded with ribosomes.
- Functions: Synthesis of proteins for secretion, isolation from cytosol, insertion into membranes, and assembly of multichain proteins.
- Protein Synthesis Pathway: mRNA codes for a hydrophobic signal sequence → signal recognition particle (SRP) binds sequence and halts translation → SRP receptor (ribophorin) in RER membrane binds complex → SRP is released and translation resumes into RER lumen → signal peptidase cleaves the signal sequence → core glycosylation occurs.
Smooth Endoplasmic Reticulum (SER):
- Functions: Synthesis of phospholipids and steroids; lipid metabolism; glycogen synthesis; drug detoxification (via enzymes like Cytochrome P450).
- Specialization: Sequestration and release of $Ca^{2+}$ in muscle cells (Sarcoplasmic Reticulum).

The Golgi Complex: Modification and Vesicle Targeting

Structure: Stacked cisternae with a Cis face (receiving) and a Trans face (shipping).
Functions: Packaging sequestered proteins, glycosylation, sulfation, and vesicle formation.
Vesicle Coat Proteins:
- Clathrin: Facilitates transport to and from the plasma membrane.
- COP I: Returns processing proteins to organelles (retrograde).
- COP II: Transports proteins from ER to Golgi (anterograde).
Docking Mechanisms:
- SNAREs (Soluble NSF Attachment Protein Receptor): Act like a lock and key.
- v-SNAREs: Targeting proteins located on the transport vesicle membrane.
- t-SNAREs: Located on the target membrane (e.g., pre-synaptic cell membranes).

Lysosomes and Phagosomes: Intracellular Digestion and Disease

Lysosomes: Membrane-bound vesicles produced by the ER and Golgi containing over 50 hydrolytic enzymes (acid pH optima).
- Enzyme Classes: Proteases (Cathepsins), Lipases, Esterases, Nucleases (DNases, RNases), Saccharidases (Glucosidases), and Acid Phosphatase.
- Types: Primary lysosomes (inactive, homogeneous appearance) and Secondary lysosomes (active, mottled appearance after fusion with phagosomes).
- Pathways: Endocytosis, Phagocytosis, and Autophagy (digesting old organelles like mitochondria).
Lysosomal Malfunction Diseases:
- Pompe’s Disease: Missing alpha-glycosidase; glycogen buildup damages heart and breathing muscles.
- Tay-Sachs Disease: Missing Hexosaminidase A; fatty protein buildup in the brain. High prevalence in Jewish populations of Central/Eastern European descent, French Canadians in Quebec, Old Order Amish in PA, and Cajuns in LA.
- Gout: Hyperuricemia leading to crystals piercing lysosomal membranes in joints and kidneys, releasing enzymes.

Peroxisomes: Metabolism and Detoxification

Peroxisomes (Microbodies): Produced only on the SER. They generate and break down $H_2O_2$ .
Enzymatic Functions:
- Fat-to-carbohydrate conversion.
- Detoxification: In the liver, peroxisomes oxidize $5-25\%$ of consumed alcohol.
- Reactive Oxygen Species Management: Enzymes remove H atoms to form $H_2O_2$ ; Catalase then converts $H_2O_2$ to $H_2O$ and oxygen.
Enzymes: Urate Oxidase, Hydroxyacid Oxidase, D-Amino Acid Oxidase, Catalase.
Zellweger’s Syndrome: A rare, fatal genetic disorder affecting the brain, liver, and kidneys caused by malformed peroxisomes due to gene mutations.

The Cytoskeleton: Microfilaments and Actin Dynamics

Microfilaments: ~ $5\,nm$ in diameter.
Structure: double-helical linear array of globular (G) actin monomers forming filamentous (F) actin polymers.
Functions: Contraction, cell adhesion, shape changes, and motility (e.g., white blood cells chasing bacteria).
Cytokinesis: An equatorial actomyosin ring contracts to divide daughter cells.
Treadmilling: Continuous assembly (polymerization) at the (+) end and disassembly (depolymerization) at the (-) end.
Actin-Binding Proteins: Profilin, Thymosin, Formins, ARPs, Myosin, Gelsolin.
Stabilization: Microvilli core microfilaments insert into the terminal web, stabilized by spectrin at the cell membrane.
Inhibition: Cytochalasin prevents F-actin polymerization.

The Cytoskeleton: Intermediate Filaments

Intermediate Filaments: ~ $10\,nm$ in diameter. Provide tensile strength and resist cell deformation.
Assembly: $\alpha$ -helical monomer → coiled-coil dimer → staggered tetramer → overlapping long polymers → side-by-side sheets → twisted intermediate filaments. These lack polarity (no + or - ends).
Cell-Specific Types:
- Cytokeratin: Epithelial cells (found in tonofilaments of desmosomes).
- Vimentin: Connective tissue cells.
- Desmin: Muscle cells.
- Glial Fibrillary Acidic Protein (GFAP): Glial cells (Astrocytes).
- Neurofilament Protein: Neurons.

The Cytoskeleton: Microtubules, Centrioles, and Motility Structures

Microtubules: ~ $25\,nm$ in diameter.
Structure: Heterodimers of $\alpha$ - and $\beta$ -tubulin assemble into protofilaments; 13 protofilaments form one microtubule. They exhibit treadmilling with growth at the (+) end.
Microtubule Organizing Center (MTOC): Organizes microtubules around a centriole surrounded by satellite bodies (containing $\gamma$ -tubulin). The (-) end is directed toward the centriole.
Centrioles: Occur in pairs at right angles. Self-duplicate during G2 phase. Organize the Golgi and vesicles.
Motility Structures:
- Axoneme: Core of cilia and flagella. Structure is 9 doublets + 2 single microtubules ( $9+2$ arrangement). Includes dynein arms (motor), nexin bridges, and radial links.
- Basal Body: Found at the base of cilia.
Microtubule Motor Proteins:
- Kinesin: Moves vesicles toward the (+) end (away from MTOC).
- Dynein: Moves toward the (-) end (toward MTOC).
Antimicrotubule Drugs:
- Colchicine: Binds tubulin heterodimers to prevent assembly.
- Nocodazole: Causes depolymerization of existing microtubules.
- Taxol: Binds to microtubules to prevent depolymerization (stabilizes them).
- Vinblastine/Vincristine: Aggregate tubulin to prevent assembly.