CHAPTER 6: A TOUR OF THE CELL The Fundamental Units of Life -All organisms are made of cells -The cell is the simplest living form of matter -All cells are related by their descent from earlier cells -many modifications made -range from single celled organisms to complex organisms with higher levels of cellular organization 6.1: Biologists use microscopes and the tools of biochemistry to study cells -Cell Fractionation: technique using centrifugation that separates cellular components according to their size. This allows researchers to separate specific organelles, etc. for observation. - lower speeds: pellet (precipitate at bottom of test tube) consists of larger cell components - higher speeds: pellet consists of smaller components 6.2: Eukaryotic cells have internal membranes that compartmentalize their functions Comparing Prokaryotic and Eukaryotic Cells -All cells have: a plasma membrane, cytosol, chromosomes (genes in the form of DNA), and ribosomes -DNA: -Eukaryotic: (most) DNA located in membrane bound nucleus -Prokaryotic: DNA is not membrane bound, but concentrated in region called the nucleoid -Cytosol: -Eukaryotic: region between nucleus and plasma membrane, contains membrane-bound organelles -Prokaryotic: takes up the entirety of the cell, does not contain membrane-bound organelles, "organized" into regions -Size: -Eukaryotic: generally larger -Prokaryotic: generally smaller how large a cell is depends on the size of the "machinery" necessary to carry out processes to sustain itself and reproduce, while still remaining practical. -The plasma membrane can only pass a certain amount of a substance at a particular time, so at a certain point, excess surface area of plasma membrane is useless. -The interior volume of cell expands proportionally larger (compared to surface area) as surface area increases. - Smaller cells have a better surface area-to-volume ratio - Cells that have a high exchange rate with their environments increase their surface area-tovolume ratios with extensions called microvilli -These extensions permit expansion of SA without significantly increasing volume. A Panoramic View of the Eukaryotic Cell -Eukaryotic cells have membrane-bound organelles that all the cell to maintain environments within each organelle that benefit their distinct function without harming the rest of the cell's components. -This also allows multiple processes with different environmental requirements to occur simultaneously -These membranes, including the plasma membrane, contain built-in enzymes compatible with their functions. 6.3: The eukaryotic cell's genetic instructions are housed in the nucleus and carried out by the ribosomes The Nucleus: Information Central -Nucleus: generally the largest organelle, houses DNA (genetic information), synthesizes messenger RNA (mRNA) according to DNA templates - mRNA exits to the cytosol to convey DNA message in the synthesis of proteins. -Nuclear Envelope: double layered membrane (2 phosopholipid bilayers) that confines nuclear contents -perforated by nuclear pores for import/export from the nucleus, the two bilayers are continuous through the pores -pore complexes made from proteins line pores -Nuclear Lamina: protein network that lines the internal membrane of the nuclear envelope -maintains structure of the nucleus -Nuclear matrix: protein network throughout the interior nucleus -together the nuclear lamina and matrix are suspected to help orient genetic material for proper function -Chromosomes: organized units of gene carrying DNA, one DNA molecule per chromosome -Chromatin: The complex of DNA and histone proteins that the DNA is coiled around. -chromosomes cannot be distinguished from one another unless preparing for cell division or in the process of dividing. -All species have a characteristic number of chromosomes, and half of that number in their gametes (sex cells) -Nucleolus: structure within nucleus, responsible for ribosomal RNA (rRNA) synthesis from DNA templates and for ribosomal large and small subunit synthesis from proteins and rRNA. -ribosomal subunits exit to the cytoplasm for assembly -depending on species and stage of cell division, there can be two or more nuclei in a cell. Ribosomes: Protein Factories Ribosomes: not organelles because not membrane-bound, made of rRNA and proteins, responsible for protein synthesis. -Cells with high rate of protein synthesis have more ribosomes and prominent nucleoli (ie: pancreas cells) -Two kinds of ribosomes: 1) Free ribosomes: cytosol, enzyme production 2) Bound ribosomes: nuclear envelope and rough endoplasmic reticulum, membranous proteins, packaging proteins, proteins for secretion -structurally identical and interchangeable -cell type and function will determine the ribosomal population within a cell 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell Endomembrane system: nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vesicles/vacuoles, plasma membrane. -protein synthesis and transport, organelle transport, lipid transport, metabolism, and detox functions -system membranes continuous by direct contact or through vesicle (sacs of membrane) transport The Endoplasmic Reticulum: Biosynthetic Factory Endoplasmic Reticulum (ER): extensive membranous network of tubules and sacs called cisternae -membrane separate ER lumen/cisternal space (interior) from cytosol -continuous with nuclear envelope, lumen continuous with intermembrane space (space between exterior and interior membrane) of the nuclear envelope -two regions: Smooth ER (no bound ribosomes) and Rough ER (studded with ribosomes) Functions of Smooth ER: -lipid synthesis: ovaries, testes, adrenal gland -enzymes of smooth ER key in lipid synthesis (oil, steroids, membrane phospholipids) -steroids: vertebrate sex and adrenal hormones -metabolism of carbohydrates -detoxification: liver -enzymes add hydroxyl groups to drugs to increase solubility -drugs can proliferate smooth ER-->increase rate of detox process--> increase drug tolerance->increase tolerance to good drugs (ie: antibiotics) bc enzymes have low substrate specificity -Calcium ion (Ca 2+) storage: muscle cells -Ca 2+ pumped from cytosol into lumen-->nerve cell stimulation--> Ca 2+ rush back into cytosol->muscle contraction - in other cells Ca 2+ release from lumen results in vesicle secretion Functions of Rough ER: -protein secretion: pancreas -Glycoproteins: proteins with covalently bound carbohydrates, carbs attached in ER lumen by enzymes in ER membrane -Proteins released in transport vesicles that "bud" from portion called trasitional ER -membrane factory: -ER membrane grows new membrane, including membrane-bound proteins, expanding itself, then transports portions of its newly formed membrane to other endomembrane organelles. Functions of Smooth ER: -lipid synthesis: ovaries, testes, adrenal gland -enzymes of smooth ER key in lipid synthesis (oil, steroids, membrane phospholipids) -steroids: vertebrate sex and adrenal hormones -metabolism of carbohydrates - -detoxification: liver -enzymes add hydroxyl groups to drugs to increase solubility -drugs can proliferate smooth ER-->increase rate of detox process--> increase drug tolerance->increase tolerance to good drugs (ie: antibiotics) bc enzymes have low substrate specificity -Calcium ion (Ca 2+) storage: muscle cells -Ca 2+ pumped from cytosol into lumen-->nerve cell stimulation--> Ca 2+ rush back into cytosol->muscle contraction - in other cells Ca 2+ release from lumen results in vesicle secretion Functions of Rough ER: -protein secretion: pancreas -Glycoproteins: proteins with covalently bound carbohydrates, carbs attached in ER lumen by enzymes in ER membrane -Proteins released in transport vesicles that "bud" from portion called trasitional ER -membrane factory: -ER membrane grows new membrane, including membrane-bound proteins, expanding itself, then transports portions of its newly formed membrane to other endomembrane organelles. The Golgi Apparatus: Shipping and Receiving Center: Golgi Apparatus: Fedex center of cell, consisting of flat membranous sacs (cisternae), modifies and stores ER products (transported vis vesicles) prior to exportation to other cellular components -cisternae membranes separate interior from cytosol. -Cis face: side closest to ER, receives transport vesicles from ER by fusing with them -Trans face: side furthest from ER, vesicles "bud" from trans face for transport elsewhere -cargo is "tagged" prior to exportation with molecules for recognition by the specified receiver -modifies glycoproteins and synthesizes noncellulose polysaccharides -Cisternal Maturation Model: vesicle movement from the cis face to the trans face, being modified along the way Lysosomes: Digestive Compartments Lysosome: membranous sac of hydrolytic enzymes (perform hydrolysis), digests macromolecules -acidic interior, preferable pH for hydrolytic enzyme (fail safe: hydrolytic enzymes inactive in neutral pH of cytosol) -lysosome membrane and enzymes produced by ER and modified in GA. Phagocytosis: the engulfing of food vesicle or bacterium, performed by unicellular organisms and macrophages ( type of white blood cell) - food vesicle then transported to lysosome for digestion (extraction of nutrients: monomers) Autophagy: the fusing of a membrane containing damaged organelles or cytosol with the lysosome for digestion and harvesting of organic compounds for recycled use within the cell Tay Sachs Disease: lysosomal disorder, non-fuctional or missing lipid enzyme, results in accumulation of lipids in brain cells, resulting in early death. Vacuoles: Diverse Maintenance Compartments Vacuole: large membranous vesicles, formed by the ER and GA -Food vacuoles: products of phagocytosis -Contractile vacuoles: prevalent in unicellular organisms, pump out excess water from cell, maintain [ions] and [molecules] -Enzymatic vacuoles: prevalent in plants and fungi, considered to be a type of lysosome bc of hydrolytic enzymes present. -Storage vacuoles: prevalent in plants, hold stores of organic compounds, poisons that protect from predators, or pigments. -Central vacuoles: prevalent in mature plant cells, formed by the combination of smaller vacuoles, stores sap and serves as storage of inorganic ions, the growth of the central vacuole allows the cell to grow without producing more cytoplasm 6.5: Mitochondria and chloroplasts change energy from one form to another Mitochondria: double membraned organelle (two phospholipid bilayers), performs cellular respiration to produce usable energy (ATP) Chloroplasts: double membraned organelle (two phospholipid bilayers), plants and algae, performs photosynthesis to convert sunlight into chemical energy that produces food for the organism The Evolutionary Origins of Mitochondria and Chloroplasts Endosymbiont Theory: an early eukaryote phagocytized a non-photosynthetic, oxygen-using prokaryotic cell (mitochondria), they began a symbiotic relationship as one cell living inside the other, and eventually evolved to merge into a single organism. One of these newly formed cells eventually phagocytized a photosynthetic prokaryotic cell (chloroplast). -Theory is popular due to structural features of both organelles -both are bound by double membranes -both contain their own ribosomes -both contain their own DNA in the form of plasmids (circular DNA) -both grow and reproduce independently from the rest of the cell. Mitochondria: Chemical Energy Conversion -All eukaryotic cells have mitochondria -# of mitochondria dependent on metabolic activity of cell, -mitochondria form branched tubular networks in cells with multiples -mitochondria not static, they move and change shape -Outer membrane: smooth -Inner membrane: many folds, called cristae, increase SA for cellular respiration (FORM MEETS FUNCTION). -Intermembrane space: between the two membranes -Mitochondrial Matrix: Inside the inner membrane, contains enzymes, DNA and ribosomes Chloroplasts: Capture of Light Energy -chloroplasts contain chlorophyll (green pigment) mandatory for photosynthesis -are found in all green portions of plants/algae -move and change shape within cell -belong to the plastid family of organelles -Two membranes separated by intermembrane space -Thylakoid: stacks of flattened interconnected membranous sacs (stack = granum) -Stroma: fluid between inner membrane and thylakoids, contains DNA, ribosomes and enzymes Peroxisomes: Oxidation Peroxisomes: membrane bound organelle, metabolic function -Enzymes remove H atoms from substrates, transfer them to O2, and make hydrogen peroxide with them (H2O2) -break down fatty acids for fuel -detoxification -H2O2 can be hazardous to other cellular components, peroxisomes can convert to H2O by another enzyme -IMPORTANCE OF COMPARTMENTALIZATION 6.6: The cytoskeleton is a network of fibers that organizes structures and activities in the cell Cytoskeleton: fibrous protein network throughout the cytosol, organizes structures and activities of cell Roles of the Cytoskeleton: Support and Motility -maintain shape using balanced opposing forces -anchor organelles and some cytosolic enzymes -Can alter cell shape by disassembly and reassembly -Movement: movement of the whole cell, movement within the cell -cytoskeleton/motor protein interactions -Manipulation of the plasma membrane Components of the Cytoskeleton Microtubules: thickest, hollow rods, made of tubulin protein (dimer: alpha-tubulin and beta-tubulin) -present in all eukaryotic cells -can grow, reassemble or disassemble by adding or removing tubulin dimers to/from the "plus end" -Shape and support cell -provide tracks for organelles and other materials to travel on using motor proteins -guide vesicles ER --->GA--->plasma membrane -separate chromosomes during cell reproduction -Centrosomes: region near the nucleus that grows microtubules, serve as compression resistance for cell -contains a pair of centrioles: 9 sets of triplet microtubules arranged in a ring -Cilia and Flagella: microtubules arranged in 9 doublets with two individual central rods (called a 9+2 pattern) covered in a sheath of plasma membrane, responsible for motility functions. - extensions can act as locomotive devices for unicellular organisms -locomotive flagella and cilia are anchored by basal bodies (9+0 pattern) within the cell -motile cilia occur in large numbers on the cell surface, and motion to push fluid over cells (falopian tubes, trachea) - a singular cilia may act as a transmitter/receiver for a cell, these are called primary cilium, not usually motile, and have a 9+0 pattern -Movement is governed by motor proteins: -Dyenin: large motor proteins attached along each outer microtubule in each doublet, these proteins have two "feet" that "walk" along the microtubule of the adjacent doublet. -this combined with cross-linking proteins that hold the microtubules in place by linking the doublets with the central microtubules, allows the cilia/flagella to bend Locomotive Flagella video Motile Cilia video Microfilaments: thinnest, solid rods composed of actin protein, appear as linear or branched twisted double chain of actin subunits. -present in all eukaryotic cells -primary function: bear tension (pulling forces) -network of cortical microfilaments just inside the plasma membrane supports cell shape & gives cytoplasmic cortex a gel-like consistency -make up microvilli that line intestinal cells, projections that are for increasing surface area -cell motility: actin filaments in conjunction with myosin filaments -cause muscle contractions -extensions called pseudopodia allow unicellular organisms to pull things toward them -cytoplasmic streaming in plant cells Intermediate Filaments: medium sized, constructed from proteins in keratin family -only found in certain eukaryotic cells -bear tension - don't assemble and diassemble, more permanent, usually remain even after cells die -important for cell structure and anchoring of organelles- "permanent framework of cell" -form a "cage" around nucleus -make up nuclear lamina -anchor microfilaments of microvilli 6.7: Extracellular Components and connections between cells help coordinate cellular activities Extracellular components and connections between cells help coordinate cellular activities -plasma membrane serves as the boundary of the cell -many cells synthesize and secrete material into the extracellular space outside of the plasma membrane Dyenin "wa Cell Walls of Plants Cell wall:extracellular structure in plants, absent in animal cells. made up of cellulose microfibrils -hold cell up from gravity -thicker than plasma membrane -Primary cell wall: young plants, thin and flexible -Middle Lamella: between cell walls of adjacent cells, contains pectin proteins as "glue" -Secondary cell wall: mature cells harden primary cell wall by secreting hardening substances into primary walls, or they add a reinforcement call the secondary cell wall between the primary cell wall and plasma membrane. Plasmodesmatas: perforations between plant cells, provide continuity in membrane, cell wall, and cytoplasm for communication and transport between cells. The Extracellular Matrix (ECM) of Animal Cells: Extracellular Matrix: space between animal cells, consist of glycoproteins and other carb-containing molecules secreted by the cell Collagen: most abundant glycoprotein, forms strong fibers outside of cell -embedded in network of proteoglycans: small core protein, many carb-containing chains covalently bound to it -proteoglycans can form large complexes when they convalently attach to a long polysaccharide molecule Fibronectin: glycoprotein responsible for attaching cells to the ECM -bind integrin proteins: cell surface receptor proteins that extend from one side of the plasma membrane in the ECM to the other in the cytoplasm where they attach to the cytoskeleton -important for communication between ECM and cytoskeleton Cell Junctions: -due to the higher level of cell organization in animals, neighboring cells must interact and communicate Tight Junctions, Desmosomes, and Gap Junctions: -all three common to epitheleal tissues that line internal and external surfaces of the body Tight Junction: cells packed tightly together, bound by proteins, lead to continuous seal that acts as a barrier -skin cells Desomosomes (anchoring): fasten cells together in strong sheets, anchored by keratin in the cytoplasm. -muscle cells Gap Junction (communicating): similar to plasmodesmata, channels connect cytoplasm of adjacent cells for communication -heart muscle
