Cell Biology PDF

# CELLMOL: CELL BIOLOGY ## Reference: Becker's World of the Cell 9th Ed. (Hardin & Bertoni, 2012) ## I. A Preview of the Cell * 1665: Hooke discovered cork cells with 30x magnification * Coined cell from cellula "little rooms" * Leeuwenhoek produced lenses with 300x magnification, becoming th...

# CELLMOL: CELL BIOLOGY ## Reference: Becker's World of the Cell 9th Ed. (Hardin & Bertoni, 2012) ## I. A Preview of the Cell * 1665: Hooke discovered cork cells with 30x magnification * Coined cell from cellula "little rooms" * Leeuwenhoek produced lenses with 300x magnification, becoming the first to observe RBC, sperm, and protists in pondwater * 1830s: compound microscope was built, with increased magnification and resolution * Brown found the nucleus in a plant cell * Nucleus - "kernel" * 1838: Schleiden concludes that all plant tissue is made of cell and embryonic plants arise from a single cell (1st principle.) * 1839: Schwann reports the same with animal cells (2nd principle.) * 1855: Virchow adds the 3rd principle. These three principles make up the cell theory: 1. All organisms consist of 1 or more cells 2. The cell is the basic unit of structure for all organisms 3. All cells arise only from pre-existing cells ## Modern cell biology Cytology + biochemistry + genetics ## 1. Cytology Studies cell structure mainly through use of optical techniques. * From cyto "hollow vessel" * Light microscope was the earliest tool for cytology. * Microtome - rapidly and efficiently prepares very thin tissue slices for microscope observation. * Limit of resolution - how far apart adjacent objects must be to be distinguished from each other. * Resolving power - ability to see fine details. * Lower limit of resolution, lower resolving power. ### Types of microscopy | Microscopy Type | Description | |---|---| | Brightfield (unstained specimen) | Passes light directly through specimen; unless cell is naturally pigmented or artificially stained, image has little contrast. | | Brightfield (stained specimen) | Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved). | | Fluorescence | Shows the locations of specific molecules in the cell. Fluorescent substances absorb ultraviolet radiation and emit visible light. The fluorescing molecules may occur naturally in the specimen but more often are made by tagging the molecules of interest with fluorescent dyes or antibodies. | | Phase contrast | Enhances contrast in unstained cells by amplifying variations in refractive index within specimen; especially useful for examining living, unpigmented cells. | | Differential interference contrast | Also uses optical modifications to exaggerate differences in refractive index. | | Confocal | Uses lasers and special optics to focus illuminating beam on a single plane within the specimen. Only those regions within a narrow depth of focus are imaged. Regions above and below the selected plane of view appear black rather than blurry. | ## 2. Biochemistry * 1828: Friedrich Wöhler synthesized urea, proving that living organisms are governed by principles of chemistry and physics * 1857: Pasteur showed that yeast fermentation produced ethanol * 1897: Eduard and Hans Buchner found that yeast extract fermented without live yeast cells, proving the existence of nonliving biological catalysts - enzymes * 1930s: Gustav Embden and Otto Meyerhof's Embden-Meyerhof pathway for glycolysis * Hans Krebs' Krebs Cycle/TCA Cycle for cellular respiration * Fritz Lipmann showed that ATP is the principal energy storage compound in cells. * Subcellular fractionation - centrifugation; means of separating and isolation subcellular structures and macromolecules * Chromatography - mixture of molecules in solution is progressively fractionated as the solution flows over a stationary absorbing phase. * Electrophoresis - use an electrical field to separate molecules based on mobility; usually to determine sizes of proteins, DNA, RNA. * wherein each gene controls the production of each specific protein. * Double-helix model showed how replication and mutation occur. ## 3. Genetics * 1886: Gregor Mendel laid foundation for "hereditary factors" → genes * 1880: Walther Flemming identified chromosomes and coined mitosis ("thread") * 1900: - George Beadle and Edward Tatum proposed the "one gene - one enzyme concept, ## II. Cell Structure ## Limitations on cell size * Surface area / volume ratio * Exchanges between cell and environment occur on cell surface * Internal volume determines the amount of nutrients that need to be imported and quantity of waste products to be excreted. * Surface area represents amount of cell membrane available for uptake and excretion. * Smaller cells have higher surface area to volume ratio. * Increase by inward folding/outward protrusion of the cell membrane. * Diffusion rates of molecules * Larger molecule, lower diffusion rate * Bypassed through active transport with carrier proteins or cytoplasmic streaming (active movement and mixing of cytoplasmic contents) ## Need for adequate concentrations of reactants and catalysts * Reactants must collide with and bind to specific enzymes. * Higher reactant concentration → higher collision frequency. * Lower cell volume → lower no. of molecules to synthesize. ## Eukaryotic cells compartmentalize cellular function with organelles. * Organelles - membrane-bounded compartments specialized for specific functions; compartmentalize eukaryotic activities. * Membrane-bounded nucleus * Genetic information is localized to the nucleus, surrounded by a double membrane nuclear envelope. * Includes the nucleolus - site of ribosomal RNA synthesis and ribosome subunit assembly. * Contains DNA-bearing chromosomes dispersed as chromatin throughout the semifluid nucleoplasm. * Absent in prokaryotes - possess the compact structure nucleoid, which is attached to the cell membrane in a particular region. * Use of internal membranes to segregate function. * Organelles are surrounded by their own characteristic membranes/pair of membranes with distinctive chemical composition. * Specialized molecular machinery that perform cellular functions are localized within cytoskeleton. * Several nonmembranous, proteinaceous structures involved in cellular contraction, motility, and the establishment and support of cellular architecture. * Provide scaffolding for intracellular vesicle transport. * Microtubules - found in cilia and flagella. * Microfilaments - found in muscle fibrils and other motility structures. * Intermediate filaments - found in cells subject to stress. * Exocytosis and endocytosis * Exocytosis - membrane-bounded vesicles fuse with the plasma membrane to release contents outside the cell. * DNA organization * Eukaryotes: DNA exists as multiple linear molecules that are complexed with large amounts of proteins known as histones. * Prokaryotes: circular DNA model packed tightly in the cell. * Genetic information segregation. * Prokaryotes: replicate DNA and divide by binary fission. * Eukaryotes: DNA packaged as chromosomes are distributed equally to daughter cells through mitosis/meiosis. * DNA expression * Eukaryotes: DNA → RNA processed and transported to cytoplasm → protein synthesis. * 1 RNA molecule encodes 1 polypeptide. * Prokaryotes: protein synthesis occurs while mRNA still being synthesized. * 1 RNA molecule encodes several polypeptides. * Plasma membrane * Phospholipid, other lipids, and proteins arranged as bilayer. * Phospholipid molecule: hydrophobic "tail" and hydrophilic "head" = amphipathic. * Membrane proteins * Enzymes for catalyzing reactions (e.g. cell wall synthesis) * Anchors for structural elements of the cytoskeleton * Transport proteins for moving ions and hydrophilic solutes across the membrane * Receptors for external chemical signals triggering processes within the cell. ## Nucleus * Bounded by inner and outer nuclear membranes = nuclear envelope. * Has pores that act as channels for water-soluble molecules and supramolecular complexes. * Lined with pore complex - regulates movement of macromolecules through the nuclear envelope. * Transports ribosomal subunits, mRNA, chromosomal proteins, nuclear enzymes. * Contains nucleoli - synthesize and assemble RNA and protein components that form ribosomes. ## Mitochondrion * Found in most eukaryotic cells; site of aerobic respiration. * Double membrane (inner & outer mitochondrial membranes) * Mitochondrial matrix - semifluid material that fills mitochondria and enclosed by inner membrane. * Contains small, circular molecules of DNA, numerous enzymes, and ribosomes. * Contains enzymes and intermediates for important metabolic processes. * Oxidation of sugars to carbon dioxide converts energy from food molecules to ATP. * Located in cristae (infoldings of the inner mitochondrial membrane) * Citric acid cycle and fatty acid oxidation occur in matrix. ## Chloroplast * Site of photosynthesis in plants and algae. * Surrounded by inner and outer membranes * Contains thylakoids - flattened sacs interconnected by stroma thylakoids (tubular membranes); stacked to form a granum. * Reactions that depend directly on solar energy are localized in the thylakoid membrane system. * Reactions involved in conversion of carbon dioxide to sugar occur in the semifluid stroma that fills the chloroplast interior. * Stroma also contains ribosomes and circular DNA molecules. * Most prominent example of plastids (organelles found in almost all plants, e.g. amyloplasts) ## Network of tubular membranes and cisternae (flattened sacs) that are interconnected in the cytoplasm. * Lumen - internal space enclosed by ER membranes. * Rough ER * Studded with ribosomes on the outer surface that synthesize polypeptides → membrane proteins and secreted proteins * Smooth ER * Synthesis of lipids and steroids (e.g. cholesterol) * Inactivates and detoxifies drugs. ## Golgi apparatus * Stack of flattened vesicles (cisternae) * Processes and packages secretory proteins * Synthesizes complex polysaccharides * Receives proteins from the ER through transition vesicles for modification and processing * Releases processed contents through budding vesicles. * Glycosylation (addition of short-chain carbohydrates to glycoproteins) occurs in rough ER lumen and completed in Golgi apparatus. ## Secretory vesicles * Contain processed secretory proteins and other substances for export from the cell. * Discharge contents by exocytosis. ## Endoplasmic reticulum * Contains small, circular molecules of DNA, numerous enzymes, and ribosomes. * Contains enzymes and intermediates for important metabolic processes. * Oxidation of sugars to carbon dioxide converts energy from food molecules to ATP. * Located in cristae (infoldings of the inner mitochondrial membrane) * Citric acid cycle and fatty acid oxidation occur in matrix. ## Lysosome * Single membrane. * Contains hydrolases for digesting biological molecules (proteins, carbs, fats). * Lysosomal enzymes are synthesized in rough ER, transported to Golgi apparatus, then released into vesicles → lysosomes. * Inner face of membrane is highly glycosylated → protective layer from hydrolytic enzymes. ## Peroxisome * Single membrane * Generates and degrades hydrogen peroxide, a toxic by-product of several normal metabolic reactions. * Catalase - enzyme that decomposes hydrogen peroxide into water and oxygen. * Holds peroxide-generating reactions together with catalase to protect the cell. * In animals: * Especially prominent in liver and kidney cells. * Detoxifies other harmful compounds, e.g. methanol, ethanol, formate, formaldehyde. * Catabolizes unusual substances, e.g. D-amino acids * Plays role in oxidative breakdown of fatty acids (in triacylglycerols, phospholipids, glycolipids) * Breaks down long chains for the mitochondria * In plants: * Glyoxysomes - help convert fat into carbohydrates during germination of fat-storing seeds * Leaf peroxisomes - aid in photorespiration (light-dependent oxygen uptake, carbon dioxide release); catalyze needed reactions. ## Vacuole * For temporary storage/transport in animal and yeast cells. * Some protozoa take up particles by phagocytosis * Plasma membrane folds around particle and pinches off to internalize the particle into a phagosome vacuole. * Phagosome fuses with lysosome to hydrolyze the particle * Most plant cells contain single large vacuole occupying much of the cell's internal volume. * Central vacuole - limited role in storage and intracellular digestion. * Maintains turgor pressure to keep tissue from wilting - high solute concentration moves water into the vacuole, which swells. ## Ribosomes * Site of protein synthesis * More numerous than most other organelles. * Also found in mitochondria and chloroplasts for organelle-specific protein synthesis ## Cytoskeleton * Intricate, three-dimensional array of interconnected proteinaceous structures * Internal framework giving cell distinctive shape and high level of internal organization. * In eukaryotes, framework for positioning and actively moving organelles and macromolecules within the cytosol * Structural elements * Microtubules * Microfilaments. * Intermediate filaments. ## Extracellular matrix / Cell wall * Extracellular structures formed from materials transported outward across the plasma membrane. * For physical cell support. * Extracellular matrix (animal cells) * Consists primarily of collagen fibrils and proteoglycans. * Cell wall (plant and fungal cells) * Primary cell wall is laid down during cell division, while secondary cell wall is formed by deposition of additional material on the inner surface of the primary wall. * Secondary wall may have high content of lignin (component of wood) * Cellulose microfibrils embedded in a matrix of other polysaccharides and small amounts of protein * Connected by plasmodesmata that pass through the fused cell walls * Bacteria and archaea also surrounded by cell wall consisting of peptidoglycans ## III. Membranes ## Cell membrane defines cell * Separates living cell from aqueous environment - thin barrier between ECM and ICM * Extracellular matrix (ECM) – outside * Intracellular matrix (ICM) - inside * Controls traffic in and out of cell * Allows some substances to cross more easily than others. * Hydrophobic (nonpolar) vs hydrophilic (polar) ## Membrane functions | Membrane function | Description | |---|---| | Boundary and permeability barrier | | | Organization and localization of function | | | Transport processes | | | Signal detection | | | Cell-to-cell interactions | | * Define boundaries of the cell and organelles, acting as permeability barriers. * Hydrophobic interior of phospholipid bilayer blocks passage of polar molecules and ions * Plasma membrane - surrounds cell * Intracellular membranes - compartmentalize functions within organelles * Serve as site for specific biochemical functions, e.g. electron transport, protein processing and folding in the ER. * Specific functions for molecules and structures embedded on or localized on membranes * Plant, fungal, bacterial, archaeal plasma membranes contain enzymes for synthesizing cell walls * Vertebrate membranes contain enzymes that secrete materials for the extracellular matrix * Nerve cell membranes contain ion transporters for signal transition to muscles * Possess transport proteins that regulate movement of substances into and out of the cell and its organelles * Gases and very small/lipophilic molecules diffuse across cellular membrane. * Hydrophilic polar/ionic substances transported by specific transport proteins that recognize them. * Aquaporins transport water molecules through kidney cells for urine production. * Transport proteins in muscle cells move calcium ions across membranes for muscle contraction. * Contain protein molecules that act as receptors to detect extracellular signals * Electrical/chemical signals contact the outer cell surface, giving information from the environment. * Signal transduction - specific mechanisms used to transmit signals from the outer surface to the cell interior. * Chemical signal molecules bind to receptors, triggering specific chemical events that lead to changes in cell function. * White blood cell receptors recognize chemical signals from infectious agents, initiating defense response. * Bacteria membrane receptors sense nutrients in the environment that signal the cell to move toward them. * Provide mechanisms for cell-to-cell contact, adhesion, and communication. * Some membrane proteins in animal tissues form adhesive junctions, often mediated by cadherins (membrane proteins) * Membrane proteins may form tight junctions that block the passage of fluid between cells * Gap junctions (animals) and plasmodesmata (plants) mediate intercellular communication. ## Eukaryotic cells use organelles to compartmentalize cellular function. * Lehninger (1983): a membrane enclosed structure that contains enzymes, with specialized functions, found in eukaryotes. * Cell membrane - not organelle; not enclosed as it encloses. * Ribosomes - no membrane. * Sheeler & Bianchi (1983): any subcellular component of a cell performing specialized functions and contains enzymes. ## Models of membrane structure: An experimental approach * Fluid mosaic model is descriptive nature of all biological membranes (plasma, nuclear, etc.) * Overton & Langmuir (1900s): lipids are important components of membranes. * Overton: easy penetration of lipid-soluble substances into cells - implies similar polarity. * Langmuir: phospholipids were amphipathic - Hydrophobic tails away from water * Gorter & Grendel (1925): the basis of membrane structure is a bilayer * Extracted lipids from cells and spread the lipids in a monolayer of water * Lipid film on the water was twice the surface area of the cells - implying double layer/bilayer. * Robertson: all membranes share common underlying structure * Also contain proteins and carbohydrates (glycoproteins, glycolipids, etc.) * Singer & Nicholson: a membrane consists of a mosaic of proteins in a fluid lipid bilayer * The model has two key features: * Fluid lipid bilayer. * Mosaic of proteins attached to or embedded in the bilayer * Unwin & Henderson: most membrane proteins contain transmembrane segments * Integral membrane proteins have one or more hydrophobic segments that span the lipid bilayer. * Transmembrane segments anchor the protein to the membrane. ## Membrane lipids: the "fluid" part of the model * Cellular membranes are fluid mosaics of lipids and proteins. * Phospholipids are most abundant lipid in plasma membrane - amphipathic. * Lipid composition of different cells * Phosphatidylethanolamine * In human myelin sheath * In E. coli to support high rate of membrane assembly and disassembly in cell division. * Phosphatidylcholine * Produces acetylcholine (neurotransmitter); low concentrations in Alzheimers. * Breaks down fats (e.g. In the liver) * Phosphatidylserine * Important component of myelination * For neuromuscular contraction (brain processing). * Sphingomyelin * Present in myelin sheath of nerve cells * Found in animals only * Intermediate to acetylcholine production: Sphingomyelin → phosphatidylcholine → acetylcholine. * Phosphatidylinositol * Major component of ligands that bind molecules together. * Cell membrane receptors; cell-to-cell communication/recognition. * In eukaryotes only. * Phosphatidylglycerol * Important for membrane integrity and strength. * Protein localization; holds protein in place * Diphosphatidylglycerol (cardiolipin) * Intermediate in phosphatidylglycerol production. * Generates electrochemical/ membrane potential gradient for uneven distribution of ions between ECM and ICM to initiate passive diffusion. ## Lipids move freely within their bilayer * Rotation * Lateral diffusion - most common movement. * Transverse diffusion ("flip-flop") * Peripheral proteins. ## Membranes function properly only in the fluid state * Transition temperature (Tm) - at which it becomes gel → fluid. * Change of state from solid to liquid is called phase transition. ## Membrane proteins: the 'mosaic' part of the model * Lipid rafts/Microdomains - floating lipid molecules on the surface of the cell membrane. * Cell membrane movement trafficking; regulates movement. * If there is too much movement, the surface membrane receptors will miscommunicate or not recognize any communication from the outer membrane at all. * Transmembrane proteins embedded in phospholipid bilayer create semi-permeable channels. * Evidence from freeze-fracture microscopy. ## Membranes contain integral, peripheral, and lipid-anchored proteins * Proteins determine membrane's specific functions - unique collections of proteins to different cell and organelle membranes * Integral membrane proteins possess one or more hydrophobic regions with an affinity for the interior of the lipid bilayer, usually across membrane. * Penetrate bilayer, usually across membrane * Ex. transport channels * 4 types: * Integral monotopic protein * Single pass protein * Multi-pass protein - more single pass proteins * Multi-subunit protein * Peripheral membrane proteins are bound to membrane surfaces through weak electrostatic forces and hydrogen bonds. * Ex. cell surface identity marker (antigens) ## Functions of membrane proteins | Function | Description | |---|---| | Transporter | | | "Channel" | | | Enzyme activity | | | Cell surface receptor | | | "Antigen" | | | Cell surface identity marker | | | Cell adhesion | | | Attachment to the cytoskeleton | | * Cell surface receptor * Cell surface identity marker * Antigen * Cell adhesion * Attachment to the cytoskeleton * ICM in eukaryotes - anchor proteins for cellular movement within * Permeability to polar molecules. * Membranes become semi-permeable via protein channels. * Specific channels allow specific material across cell membrane. * Protein domains anchor molecules * Within membrane * Nonpolar amino acids - hydrophobic * Anchors protein into membrane * Outer surfaces of membrane * Polar amino acids - hydrophilic * Extend into extracellular fluid and into cytosol * Aquaporin - water channel in bacteria * Proton pump channel in photosynthetic bacteria. ## Membrane carbohydrates * Key role in cell-cell recognition * Ability of cell to distinguish one cell from another through antigens. * Basis for rejection of foreign cell by immune system * Lupus - mutation in the membrane protein which causes the immune system to attack one's own cells. ## IV. Membrane Transport ## Permeability of the lipid bilayer * Hydrophobic molecules - lipid soluble; can pass through the membrane rapidly * Polar molecules do not cross membrane rapidly * Ions - do not cross membrane ## Transport processes * Solutes - dissolved ions and small organic molecules * Na+, K+, Ca++, H+, Cl- * Sugars amino acids, nucleotides * Movement of a solute across a membrane is determined by concentration gradient/electrochemical potential * Movement of molecule with no net charge is determined by concentration gradient. * Movement of ion determined by its electrochemical potential = combined effect of concentration gradient and charge gradient. ## Types: * Simple diffusion - directly through membrane (least common) * Facilitated diffusion - passive transport * Active transport - requires energy * Simple diffusion - unassisted movement down the gradient (high → low) * Gases, nonpolar molecules, small polar molecules (water, glycerol, ethanol * Factors affecting diffusion * Size * Polarity * Charge * Always moves solutes toward equilibrium. * Not appropriate for large, polar molecules ## Facilitated diffusion * Protein-mediated movement down a gradient. * Uses transmembrane transport proteins without the use of energy. * Provide a path through the lipid bilayer, allowing "downhill" movement of polar/charged solute. ## Active transport. * Solute is moved up a concentration gradient, away from equilibrium. * Couples endergonic transport to an exergonic process, usually ATP hydrolysis. * Performs 3 important functions: * Uptake of essential nutrients * Removal of wastes * Maintenance of nonequilibrium concentrations of certain ions * Many membrane proteins are called pumps because energy is required to move substances. * Has intrinsic directionality (as opposed to nondirectional diffusion, which is directed by relative concentrations) * 2 types: * Direct active transport - primary * Accumulation of solute molecules on one side of the membrane is coupled directly to an exergonic chemical reaction. * Usually ATP hydrolysis → transport proteins are called transport ATPases/ATPase pumps. * Indirect active transport - secondary * Not powered by ATP * Depends on simultaneous transport of 2 solutes - coupled transport of a solute and an ion * May be symport/antiport * Symport mechanisms: * Na+ (animal) or H+ (other organisms) is continuously pumped out of the cell. * High extracellular concentration of Na+ drives the uptake of sugars and amino acids. * Indirectly related to ATP because the pump that maintains sodium ion gradient is driven by ATP * Ex. exergonic inward movement of protons H+ provides energy to move solute S against its gradient. * Porins * Outer membranes of mitochondria, chloroplasts, and many bacteria * B-barrel protein pore that cross a cellular membrane * Mutations in bacterial porins cause antibiotic resistance * Aquaporins * Assemble in membranes as homotetramers * Each monomer has 6 membrane-spanning a-helical domains * Rapid movement of water molecules * Carrier protein * Transfers large number of both polar and nonpolar molecules * Possesses specific binding site to which solute molecules bind, undergoing conformational change, and are released to the other side * Two conformations: * Conformation A - empty binding site * Conformation B - binding site occupied by the solute * Mediate either passive transport or active transport * Coupled transport * Uniport - only 1 solute transported * Symport - cotransport; 2 solutes moved across a membrane in the same direction * Antiport - countertransport; 2 solutes moved in opposite directions * Erythrocyte glucose transporter * Uniport carrier for glucose * Erythrocyte is capable of glucose uptake by facilitated diffusion because the blood glucose level is much higher than that inside the cell. * Glucose is transported inward by a glucose transporter (GLUT; GLUT1 in erythrocytes) * GLUT1 is an integral membrane protein with 12 transmembrane segments, forming a cavity with hydrophilic side chains. * Transport direction dictated by relative solute concentration * Erythrocyte anion exchange protein * Facilitated diffusion * Chloride-bicarbonate exchanger facilitates reciprocal exchange of Cl and HCO3 ions. * Exchange stops if either anion is absent. * Antiport exchange at 1:1 ratio * "Ping-pong" mechanism * Chloride ion binds on one side of the membrane, causing change into the second conformational state. * Chloride is then moved across the membrane and released. * Chloride release causes protein to bind to bicarbonate, causing shift back to first conformation. * Bicarbonate is released, and the protein is ready to bind chloride again. * In tissues, waste CO2 diffuses into the erythrocytes, where it is converted to HCO3 by the enzyme carbonic anhydrase. * As the concentration of bicarbonate rises, it moves out of the cell, coupled with uptake of Cl to prevent a net charge imbalance. * In the lungs, the entire process is reversed. * Na+/K+ ATPase or pump * In all animal cells, direct active transport by P-type ATPase. * 2 alternative conformational states: * E1 - open to the inside of the cell; high affinity for Na+ ions * E2 - open to the outside of the cell; high affinity for K+ ions * Needed in cells that take up glucose and amino acids even when their concentrations are much lower outside than inside the cells (e.g. intestine). * Steep Na+ gradient maintained across the plasma membrane (via the Na+/K+ pump). * Sodium-dependent glucose transporters (SGLT) responsible for this mechanism. * Na+/glucose symporter * Indirect active transport driving glucose uptake * Bacteriorhodopsin proton pump * Bacteriorhodopsin - small integral membrane protein in the plasma membrane of Halobacterium (archaea) * Retinal - light-absorbing pigment * Has 7 a-helical membrane-spanning segments forming a cylindrical shape * Light driven proton pump. * Uses energy from photons to drive active transport of protons out of the cells. * Creates electrochemical proton gradient that powers synthesis of ATP by ATP synthase ## V. Endomembrane system * Group of membrane-bound organelles in eukaryotes * Modifies, packages, sorts, and transports lipids and proteins ## Endoplasmic reticulum (ER) * Continuous network of flattened sacs, tubules, and vesicles stretching throughout the cytoplasm of the cell. * ER cisternae - membrane bound sacs * ER lumen - space enclosed within * Luminal spaces of RER and SER are connected. * Rough endoplasmic reticulum (RER) * Large flattened sheets with ribosomes attached to its membrane * Translation occurs in the cytosol. * Synthesized proteins move into the lumen. * Transitional elements - subdomain of RER; play role in formation of transition vesicles that shuttle lipids and proteins to Golgi apparatus. * Ribosomes synthesize membrane-bound and soluble proteins. * Processes carbohydrate groups for glycoprotein formation. * Manages polypeptide folding. * Endoplasmic reticulum-assisted degradation (ERAD) * Recognition and removal of misfolded proteins by proteasomes * Assembly of protein complexes - primary, secondary, tertiary * Quaternary processed in the Golgi apparatus. * Smooth endoplasmic reticulum (SER) * Tubular structures; no ribosomes = smooth * Hydroxylation of drugs for easier uptake catalyzed by cytochrome P-450 protein. * Prevalent in hepatocytes * Enzymatic breakdown of stored glycogen. * Present in liver, kidney, intestinal cells * Glucose-6-phosphatase enzyme hydrolyzes phosphate group from glucose-6-phosphate → free glucose and inorganic phosphate * Free glucose leaves cell to enter bloodstream via GLUT2 * Calcium storage. * Sarcoplasmic reticulum in muscle cell contains high concentrations of calcium-building proteins. * Calcium ions pumped into ER by calcium ATPases for muscle fiber contraction. * Biosynthesis of cholesterol and steroid hormones. * Cholesterol hydroxylation → steroid hormone es (e.g. testosterone, estrogen, cortisol) * Biosynthesis of membranes * Fatty acids for membrane phospholipids * Phospholipid translocators (flippases) catalyze translocation (flipping from one side of bilayer to the other) of phospholipids through ER membranes. * Phospholipid exchange proteins convey phospholipid molecules from ER membrane to outer mitochondrial and chloroplast membranes. ## Golgi apparatus * Functionally linked to SER and RER through vesicles * Further processes glycoproteins from ER * Sorts and packages glycoproteins and membrane lipids for transport - membrane and protein trafficking. * Series of flattened membrane-bound cisternae, disk-shaped sacs stacked together (Golgi stack) * Intracisternal space - Golgi apparatus lumen. * Membrane held together by GRASP65 gene protein. * Golgi stack faces: * Cis-Golgi network (CGN) - network of flattened tubules; receive transition vesicles containing lipids/proteins from ER that fuse with its membranes. * Trans-Golgi network (TGN) - proteins/lipids leave in transport vesicles that bud from the tips of TGN cisternae. * Medial cisternae - protein-processing center * 2 models for lipid and protein flow: * Stationary cisternae model * Each stack compartment is stable * Trafficking molecules between cisternae is through shuttle vesicles * Cisternal maturation model * Cisternae are temporary compartments that change from CGN to medial to TGN * Anterograde transport - material from ER → Golgi apparatus → plasma membrane * Retrograde transport - flow of vesicles from Golgi cisternae back to the ER * Glycosylation * addition of carbohydrate side chains to proteins → glycoproteins * 2 kinds of glycosylation * N-linked - addition of oligosaccharide to the N atom in amino group (asparagine) * O-linked - addition of oligosaccharide to O atom in hydroxyl group (serine/threonine) * Initial glycosylation occurs in the ER * Dolichol phosphate (oligosaccharide carrier) is inserted in the ER membrane. * N-acetylglucosamine and mannose groups are added to phosphate groups of dolichol phosphate. * These are translocated from cytosol to ER lumen by flippase * More mannose and glucose units are added * Core oligosaccharide is transferred as a single unit from dolichol to asparagine residue of recipient protein (N-linked) * Calnexin and calreticulin proteins assist with proper folding during glycosylation - chaperones. * Calnexin ensures that proteins are properly folded before release to Golgi * Calreticulin binds to misfolded proteins for degradation - quality control * Peptide bonds are degraded to allow for recycling of monomers. * BiP chaperone translocates proteins from inside out (lumen → cisternae) * Terminal glycosylations occur in the Golgi * Removal of few carbohydrate units of the core oligosaccharide (mannose) * Complex oligosaccharides can have further addition of n-acetylglucosamine and other monosaccharides (galactose and sialic acid) * Galactosyl transferase marker enzyme unique to Golgi; adds galactose units * Glucan synthetases - produce oligosaccharides from monosaccharides * Glycosyl transferases - attach carbohydrate groups to proteins. ## Protein trafficking * Proteins are tagged for proper transport * Lipids and proteins are selectively packaged into transport vesicles destined for different locations. * Transport vesicles bud from TGN → proteins interact with receptors for delivery * Retention tags prevent some proteins from escaping when vesicles bud from ER membrane. * Retrieval tags bind to transmembrane receptors facing the CGN lumen * Receptor-ligand complex is packaged into transport vesicle for return to ER. * Lysosomal proteins have mannose-6-phosphate tags to ensure transport to lysosomes * Exocytosis and endocytosis * Exocytosis releases intracellular molecules to the exterior of the cell. * Proteins move through secretory pathways: ER → Golgi → secretory vesicles and secretory granules → cell exterior. * Constitutive secretion - secretory vesicles move directly to the cell surface, fusing with plasma membrane to release contents. * Regulated secretion - secretory vesicles fuse with the plasma membrane in response to extracellular signals. * Ex. insulin release from pancreatic ẞ cells in response to glucose * Polarized secretion - secretion is limited to a specific surface of the cell. * Ex. digestive enzymes are released from only the side of the cell that faces the interior of the intestine. * Endocytosis internalizes external materials * Small segment of plasma membrane progressively folds inward and pinches off to form endocytic vesicle * Phagocytosis - ingestion of large particles, macromolecules, or other cells * Ex. protozoa, neutrophils * Phagosome (endocytic vesicle) fuses with late endosome/matures into lysosome for digestion of materials * Receptor-mediated endocytosis - uses receptors on the outer surface of the plasma membrane to internalize specific molecules * Clathrin-dependent endocytosis * Receptor-ligand complexes diffuse into the membrane and are collected in specialized regions called coated pits coated with the protein clathrin * Coated pits pinch off with the protein dynamin to form coated vesicles, which are then uncoated to fuse with an endosome. * Transcytosis - receptor-ligand complexes travel to different regions of the plasma membrane for secretion. * Clathrin-independent endocytosis * Fluid-phase endocytosis - type of pinocytosis for nonspecific internalization of extracellular fluid. * Compensates for membrane segments continuously added to the plasma membrane by exocytosis. * Means for controlling cell's volume ## VI. Cell cycle * M phase - point in the cycle when the cell divides; overlap of two events: mitosis and cytokinesis * Mitosis - division of nucleus * Cytokinesis - division of cytoplasm * Accounts for small portion of total cell cycle * Interphase * Growth phase between divisions * Cellular contents are synthesized continuously. * S phase - amount of nuclear DNA doubles. * GO - cells that become arrested in G1, awaiting signal that triggers reentry into the cell cycle * Terminal differentiation - cells that never divide again (ex. nerve cells) ## Prophase * Toward end of