A Tour of the Cell 2024 PDF

A Tour of the Cell Dr. Faisal Saleh Microscopy Scientists use microscopes to visualize cells too small to see with the naked eye In a light microscope (LM), visible light is passed through a specimen and then through glass lenses Lenses refract (bend) the light, so that the image is...

A Tour of the Cell Dr. Faisal Saleh Microscopy Scientists use microscopes to visualize cells too small to see with the naked eye In a light microscope (LM), visible light is passed through a specimen and then through glass lenses Lenses refract (bend) the light, so that the image is magnified Three important parameters of microscopy Magnification, the ratio of an object’s image size to its real size Resolution, the measure of the clarity of the image, or the minimum distance of two distinguishable points Contrast, visible differences in parts of the sample Light Microscopes (LMs) LMs can magnify effectively to about 1,000 times the size of the actual specimen Various techniques enhance contrast and enable cell components to be stained or labeled Most subcellular structures, including organelles (membrane- enclosed compartments), are too small to be resolved by an LM Recent advances in light microscopy Confocal microscopy and deconvolution microscopy provide sharper images of three-dimensional tissues and cells New techniques for labeling cells improve resolution Electron Microscopes (EMs) Two basic types of electron microscopes (EMs) are used to study subcellular structures Scanning electron microscopes (SEMs) focus a beam of electrons onto the surface of a specimen, providing images that look 3-D Transmission electron microscopes (TEMs) focus a beam of electrons through a specimen Cryo-electron microscopy (cryo-EM) a beam of electrons is passed through the sample to visualize the molecules TEMs are used mainly to study the internal structure of cells Cell Fractionation Cell fractionation takes cells apart and separates the major organelles from one another Centrifuges fractionate cells into their component parts Cell fractionation enables scientists to determine the functions of organelles Biochemistry and cytology help correlate cell function with structure TECHNIQUE Homogenization Tissue cells Homogenate Centrifugation TECHNIQUE (cont.) Centrifuged at 1,000 g (1,000 times the force of gravity) for 10 min Supernatant poured into next tube Differential centrifugation 20,000 g 20 min 80,000 g 60 min Pellet rich in nuclei and cellular debris 150,000 g 3 hr Pellet rich in mitochondria (and chloro- plasts if cells are from a plant) Pellet rich in “microsomes” (pieces of plasma Pellet rich in membranes and ribosomes cells’ internal membranes) Eukaryotic cells have internal membranes that compartmentalize their functions The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells Protists, fungi, animals, and plants all consist of eukaryotic cells Comparing Prokaryotic and Eukaryotic Cells Basic features of all cells Plasma membrane Semifluid substance called cytosol Chromosomes (carry genes) Ribosomes (make proteins) Comparing Prokaryotic and Eukaryotic Cells Prokaryotic cells are characterized by having No nucleus DNA in an unbound region called the nucleoid No membrane-bound organelles Cytoplasm bound by the plasma membrane  Fimbriae Nucleoid Ribosomes Plasma membrane Bacterial chromosome Cell wall Capsule 0.5 m (a) A typical Flagella (b) A thin section rod-shaped through the bacterium bacterium Bacillus coagulans (TEM) Comparing Prokaryotic and Eukaryotic Cells Eukaryotic cells are characterized by having DNA in a nucleus that is bounded by a membranous nuclear envelope Membrane-bound organelles Cytoplasm in the region between the plasma membrane and nucleus Eukaryotic cells are generally much larger than prokaryotic cells The Plasma Membrane The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell The general structure of a biological membrane is a double layer of phospholipids The Plasma Membrane The Plasma Membrane Metabolic requirements set upper limits on the size of cells The surface area to volume ratio of a cell is critical As the surface area increases by a factor of n2, the volume increases by a factor of n3 Small cells have a greater surface area relative to volume  Surface area increases while Geometric relationships total volume remains constant between surface area and volume 5 1 1 Total surface area [sum of the surface areas (height  width) of all box 6 150 750 sides  number of boxes] Total volume [height  width  length  number of boxes] 1 125 125 Surface-to-volume (S-to-V) ratio [surface area  volume] 6 1.2 6 A Panoramic View of the Eukaryotic Cell A eukaryotic cell has internal membranes that partition the cell into organelles Plant and animal cells have most of the same organelles  ENDOPLASMIC RETICULUM (ER) Animal Cell Nuclear Rough Smooth envelope Flagellum ER ER NUCLEUS Nucleolus Chromatin Centrosome Plasma membrane CYTOSKELETON: Microfilaments Intermediate filaments Microtubules Ribosomes Microvilli Golgi apparatus Peroxisome Mitochondrion Lysosome Exploring Eukaryotic Cells Animal Cells Fungal Cells 1 m Parent 10 m cell Cell wall Buds Vacuole Cell 5 m Nucleus Nucleus Nucleolus Mitochondrion Human cells from lining Yeast cells budding A single yeast cell of uterus (colorized TEM) (colorized SEM) (colorized TEM)  Nuclear Rough envelope endoplasmic Smooth NUCLEUS Nucleolus reticulum endoplasmic reticulum Plant Cell Chromatin Ribosomes Central vacuole Golgi apparatus Microfilaments Intermediate CYTOSKELETON filaments Microtubules Mitochondrion Peroxisome Plasma membrane Chloroplast Cell wall Plasmodesmata Wall of adjacent cell Exploring Eukaryotic Cells Plant Cells Protistan Cells Flagella 1 m Cell 5 m 8 m Cell wall Nucleus Chloroplast Nucleolus Mitochondrion Vacuole Nucleus Nucleolus Chloroplast Chlamydomonas Cells from duckweed (colorized SEM) Cell wall (colorized TEM) Chlamydomonas (colorized TEM) The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes The nucleus contains most of the DNA in a eukaryotic cell and most of the cell’s genes and is usually the most conspicuous organelle The nuclear envelope encloses the nucleus, separating it from the cytoplasm The nuclear membrane is a double membrane; each membrane consists of a lipid bilayer Ribosomes use the information from the DNA to make proteins  1 m Nucleus The nucleus Nucleolus Chromatin and its Nuclear envelope: envelope Inner membrane Outer membrane Nuclear pore Rough ER Pore complex Surface of nuclear envelope Ribosome Close-up 0.25 m of nuclear Chromatin envelope Pore complexes (TEM) 1 m Nuclear lamina (TEM)  Nucleus Nucleolus Chromatin Nuclear envelope: Inner membrane Outer membrane Nuclear pore Rough ER Pore complex Ribosome Close-up of nuclear Chromatin envelope The Nucleus Pores regulate the entry and exit of molecules from the nucleus The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein In the nucleus, DNA is organized into discrete units called chromosomes Each chromosome is composed of a single DNA molecule associated with proteins The Nucleus The DNA and proteins of chromosomes are together called chromatin Chromatin condenses to form discrete chromosomes as a cell prepares to divide The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis Ribosomes: Protein Factories Ribosomes are particles made of ribosomal RNA and protein Ribosomes carry out protein synthesis in two locations In the cytosol (free ribosomes) On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes) Ribosomes 0.25 m Free ribosomes in cytosol Endoplasmic reticulum (ER) Ribosomes bound to ER Large subunit Small subunit TEM showing ER and ribosomes Diagram of a ribosome The endomembrane system regulates protein traffic and performs metabolic functions in the cell Components of the endomembrane system Nuclear envelope Endoplasmic reticulum Golgi apparatus Lysosomes Vacuoles Plasma membrane These components are either continuous or connected via transfer by vesicles The Endoplasmic Reticulum: Biosynthetic Factory The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells The ER membrane is continuous with the nuclear envelope There are two distinct regions of ER Smooth ER, which lacks ribosomes Rough ER, surface is studded with ribosomes  Smooth ER Nuclear envelope Rough ER Endoplasmic reticulum (ER) ER lumen Cisternae Transitional ER Ribosomes Transport vesicle 200 nm Smooth ER Rough ER Functions of Smooth ER The smooth ER Synthesizes lipids Metabolizes carbohydrates Detoxifies drugs and poisons Stores calcium ions Functions of Rough ER The rough ER Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates) Distributes transport vesicles, proteins surrounded by membranes Is a membrane factory for the cell The Golgi Apparatus: Shipping and Receiving Center The Golgi apparatus consists of flattened membranous sacs called cisternae Functions of the Golgi apparatus Modifies products of the ER Manufactures certain macromolecules Sorts and packages materials into transport vesicles The Golgi Apparatus cis face (“receiving” side of 0.1 m Golgi apparatus) Cisternae trans face (“shipping” side of TEM of Golgi apparatus Golgi apparatus) Lysosomes: Digestive Compartments A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids Lysosomal enzymes work best in the acidic environment inside the lysosome Lysosomes: Digestive Compartments Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole A lysosome fuses with the food vacuole and digests the molecules Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy  1 m Vesicle containing Nucleus two damaged 1 m organelles Mitochondrion fragment Lysosome Peroxisome fragment Digestive enzymes Lysosome Lysosome Plasma membrane Peroxisome Digestion Food vacuole Mitochondrion Digestion Vesicle (a) Phagocytosis (b) Autophagy Vacuoles: Diverse Maintenance Compartments A plant cell or fungal cell may have one or several vacuoles, derived from endoplasmic reticulum and Golgi apparatus Food vacuoles are formed by phagocytosis Contractile vacuoles, found in many freshwater protists, pump excess water out of cells Central vacuoles, found in many mature plant cells, hold organic compounds and water The Plant Cell Vacuole Central vacuole Cytosol Central Nucleus vacuole Cell wall Chloroplast 5 m  Nucleus Rough ER Smooth ER Plasma membrane  Nucleus Rough ER Smooth ER cis Golgi Plasma membrane trans Golgi  Nucleus Rough ER Smooth ER cis Golgi Plasma membrane trans Golgi Mitochondria and chloroplasts change energy from one form to another Mitochondria are the sites of cellular respiration, a metabolic process that uses oxygen to generate ATP Chloroplasts, found in plants and algae, are the sites of photosynthesis Mitochondria and chloroplasts have similarities with bacteria Enveloped by a double membrane Contain free ribosomes and circular DNA molecules Grow and reproduce somewhat independently in cells  Endoplasmic Nucleus reticulum Engulfing of oxygen- Nuclear using nonphotosynthetic envelope prokaryote, which The endosymbiont becomes a mitochondrion theory of the Mitochondrion Ancestor of eukaryotic cells origins of (host cell) mitochondria and Engulfing of chloroplasts in At least photosynthetic prokaryote eukaryotic cells Nonphotosynthetic one cell Chloroplast eukaryote Mitochondrion Photosynthetic eukaryote Mitochondria: Chemical Energy Conversion Mitochondria are in nearly all eukaryotic cells They have a smooth outer membrane and an inner membrane folded into cristae The inner membrane creates two compartments: intermembrane space and mitochondrial matrix Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix Cristae present a large surface area for enzymes that synthesize ATP The Mitochondrion, Site of Cellular Respiration 10 m Intermembrane space Outer Mitochondria membrane DNA Inner Free Mitochondrial membrane ribosomes DNA in the Cristae mitochondrial Nuclear DNA Matrix matrix 0.1 m (a) Diagram and TEM of mitochondrion (b) Network of mitochondria in a protist cell (LM) Chloroplasts: Capture of Light Energy Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis Chloroplasts are found in leaves and other green organs of plants and in algae Chloroplast structure includes Thylakoids, membranous sacs, stacked to form a granum Stroma, the internal fluid The chloroplast is one of a group of plant organelles, called plastids The Chloroplast, Site of Photosynthesis Ribosomes 50 m Stroma Inner and outer membranes Granum Chloroplasts (red) DNA Thylakoid Intermembrane space 1 m (a) Diagram and TEM of chloroplast (b) Chloroplasts in an algal cell Peroxisomes: Oxidation Peroxisomes are specialized metabolic compartments bounded by a single membrane Peroxisomes produce hydrogen peroxide and convert it to water Peroxisomes perform reactions with many different functions How peroxisomes are related to other organelles is still unknown A Peroxisome 1 m Chloroplast Peroxisome Mitochondrion The cytoskeleton is a network of fibers that organizes structures and activities in the cell The cytoskeleton is a network of fibers extending throughout the cytoplasm It organizes the cell’s structures and activities, anchoring many organelles It is composed of three types of molecular structures Microtubules Microfilaments Intermediate filaments The Cytoskeleton 10 m Roles of the Cytoskeleton: Support and Motility The cytoskeleton helps to support the cell and maintain its shape It interacts with motor proteins to produce motility Inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton Recent evidence suggests that the cytoskeleton may help regulate biochemical activities Components of the Cytoskeleton Three main types of fibers make up the cytoskeleton Microtubules are the thickest of the three components of the cytoskeleton Microfilaments, also called actin filaments, are the thinnest components Intermediate filaments are fibers with diameters in a middle range Centrosomes and Centrioles In many cells, microtubules grow out from a centrosome near the nucleus The centrosome is a “microtubule-organizing center” In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring  Centrosome Microtubule Centrosome Centrioles containing a 0.25 m pair of centrioles Longitudinal section of one centriole Microtubules Cross section of the other centriole Cilia and Flagella Microtubules control the beating of cilia and flagella, locomotor appendages of some cells Cilia and flagella differ in their beating patterns Cilia and flagella share a common structure A core of microtubules sheathed by the plasma membrane A basal body that anchors the cilium or flagellum A motor protein called dynein, which drives the bending movements of a cilium or flagellum  Direction of swimming (a) Motion of flagella 5 m Direction of organism’s movement Power stroke Recovery stroke (b) Motion of cilia 15 m  0.1 m Outer microtubule Plasma membrane doublet Dynein proteins Central microtubule Radial spoke Microtubules Cross-linking proteins between outer doublets (b) Cross section of Plasma motile cilium membrane Basal body 0.5 m 0.1 m (a) Longitudinal section Triplet of motile cilium (c) Cross section of basal body Cilia and Flagella How dynein “walking” moves flagella and cilia − Dynein arms alternately grab, move, and release the outer microtubules Protein cross-links limit sliding Forces exerted by dynein arms cause doublets to curve, bending the cilium or flagellum Microfilaments (Actin Filaments) Microfilaments are solid rods about 7 nm in diameter, built as a twisted double chain of actin subunits The structural role of microfilaments is to bear tension, resisting pulling forces within the cell They form a 3-D network called the cortex just inside the plasma membrane to help support the cell’s shape Bundles of microfilaments make up the core of microvilli of intestinal cells  Microvillus A structural Role of Microfilaments Plasma membrane Microfilaments (actin filaments) Intermediate filaments 0.25 m Microfilaments Microfilaments that function in cellular motility contain the protein myosin in addition to actin In muscle cells, thousands of actin filaments are arranged parallel to one another Thicker filaments composed of myosin interdigitate with the thinner actin fibers  Muscle cell 0.5 m Actin filament Myosin filament Myosin head (a) Myosin motors in muscle cell contraction Cortex (outer cytoplasm): gel with actin network 100 m Inner cytoplasm (more fluid) Extending pseudopodium (b) Amoeboid movement Chloroplast 30 m (c) Cytoplasmic streaming in plant cells Microfilaments and motility Muscle cell 0.5 m Actin filament Myosin filament Myosin head (a) Myosin motors in muscle cell contraction Microfilaments Localized contraction brought about by actin and myosin also drives amoeboid movement Pseudopodia (cellular extensions) extend and contract through the reversible assembly and contraction of actin subunits into microfilaments Cytoplasmic streaming is a circular flow of cytoplasm within cells This streaming speeds distribution of materials within the cell In plant cells, actin-myosin interactions and sol-gel transformations drive cytoplasmic streaming Intermediate Filaments Intermediate filaments range in diameter from 8–12 nanometers, larger than microfilaments but smaller than microtubules They support cell shape and fix organelles in place Intermediate filaments are more permanent cytoskeleton fixtures than the other two classes Extracellular components and connections between cells help coordinate cellular activities Most cells synthesize and secrete materials that are external to the plasma membrane These extracellular structures include Cell walls of plants The extracellular matrix (ECM) of animal cells Intercellular junctions Cell Walls of Plants The cell wall is an extracellular structure that distinguishes plant cells from animal cells Prokaryotes, fungi, and some protists also have cell walls The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein Cell Walls of Plants Plant cell walls may have multiple layers Primary cell wall: relatively thin and flexible Middle lamella: thin layer between primary walls of adjacent cells Secondary cell wall (in some cells): added between the plasma membrane and the primary cell wall Plasmodesmata are channels between adjacent plant cells Plant Cell Walls The Extracellular Matrix (ECM) of Animal Cells Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM) The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin ECM proteins bind to receptor proteins in the plasma membrane called integrins Extracellular Matrix (ECM) of an Animal Cell Collagen Polysaccharide EXTRACELLULAR FLUID molecule Proteoglycan Carbo- complex hydrates Fibronectin Core protein Integrins Proteoglycan molecule Plasma membrane Proteoglycan complex Micro- CYTOPLASM filaments The Extracellular Matrix (ECM) of Animal Cells Functions of the ECM Support Adhesion Movement Regulation Cell Junctions Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact Intercellular junctions facilitate this contact There are several types of intercellular junctions Plasmodesmata Tight junctions Desmosomes Gap junctions Plasmodesmata in Plant Cells Plasmodesmata are channels that perforate plant cell walls Through plasmodesmata, water and small solutes (and sometimes proteins and RNA) can pass from cell to cell Cell walls Interior of cell Interior of cell 0.5 m Plasmodesmata Plasma membranes Tight Junctions, Desmosomes, and Gap Junctions in Animal Cells At tight junctions, membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid Desmosomes (anchoring junctions) fasten cells together into strong sheets Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells Tight junctions prevent fluid from moving Tight junction across a layer of cells TEM 0.5 m Tight junction Intermediate filaments Desmosome TEM 1 m Gap junction Ions or small molecules Space TEM between cells Extracellular Plasma membranes matrix of adjacent cells 0.1 m The Cell: A Living Unit Greater Than the Sum of Its Parts Cells rely on the integration of structures and organelles in order to function For example, a macrophage’s ability to destroy bacteria involves the whole cell, coordinating components such as the cytoskeleton, lysosomes, and plasma membrane Coordination of Activities in a Cell