A Tour of the Cell PDF

The cell is the smallest unit of an organism and carries out essential functions for life. Life can exist as single-celled or multicellular organisms, such as the Paramecium, plants, and animals. Eukaryotic cells have a nucleus and are found in plants, animals, fungi, and protists. +-------------...

The cell is the smallest unit of an organism and carries out essential functions for life. Life can exist as single-celled or multicellular organisms, such as the Paramecium, plants, and animals. Eukaryotic cells have a nucleus and are found in plants, animals, fungi, and protists. +-----------------------------------------------------------------------+ | LEARNING OBJECTIVES | | =================== | +-----------------------------------------------------------------------+ Microscopy and biochemistry are important techniques in cell biology for visualizing and studying cells (microscopy) and analyzing chemical processes within cells (biochemistry). Prokaryotic and eukaryotic cells differ in terms of the presence of a nucleus and membrane-bound organelles. Animal and plant cells also have distinct characteristics, such as the presence of a cell wall and chloroplasts in plant cells. The nucleus contains genetic material, chromosomes carry genetic information, and ribosomes are responsible for protein synthesis. The endomembrane system, including the endoplasmic reticulum, Golgi apparatus, and vesicles, plays a crucial role in protein synthesis, modification, and transport within the cell. Mitochondria are involved in cellular respiration and energy production, while chloroplasts are responsible for photosynthesis in plant cells. Cytoskeletal fibers, such as microtubules, microfilaments, and intermediate filaments, have different subunits and functions, including providing structural support, facilitating cell division, and enabling cell movement and shape changes. Plant and animal cells have different extracellular components, such as the cell wall in plants and the extracellular matrix in animals. Cell junctions, such as plasmodesmata in plant cells and tight junctions in animal cells, also differ. Cells work together through the coordination of organelles and structures to enhance overall cellular function. +-----------------------------------------------------------------------+ | CONCEPT 6.1 BIOLOGISTS USE MICROSCOPES AND BIOCHEMISTRY TO STUDY CELL | | S. | | ===================================================================== | | == | +-----------------------------------------------------------------------+ Cell biologists use microscopy to investigate the inner workings of cells, which are too small to be seen with the naked eye. Learning how cells are studied is important before understanding cell structure and function. **MICROSCOPY** -------------- Microscopes were developed in the 16th and 17th centuries, enabling the discovery and study of cells. Light microscopes (LM) use visible light and glass lenses to magnify and project images. Magnification, resolution, and contrast are important parameters in microscopy. Magnification is the ratio of image size to real size, while resolution is the minimum distance two points can be separated and still be distinguished. Light microscopes have a resolution limit of about 0.2 micrometers. Staining or labeling cell components enhances contrast in microscopy. Electron microscopes (EM) use a beam of electrons for higher resolution imaging. Recent advancements in light microscopy include fluorescent markers and super-resolution microscopy. Cryo-electron microscopy (cryo-EM) preserves specimens at low temperatures, revealing structures in their cellular environment. Microscopes are essential tools in cytology, and integrating cytology and biochemistry is crucial for understanding cell function.  **CELL FRACTIONATION** ---------------------- Cell fractionation is a technique that separates organelles and subcellular structures for studying cell structure and function. The centrifuge is used to spin disrupted cells, and differential centrifugation separates components based on size. Cell fractionation enables bulk preparation of specific cell components and identification of their functions. It complements biochemistry and cytology in correlating cell function with structure. An example shows how cell fractionation revealed that mitochondria are the sites of cellular respiration. +-----------------------------------------------------------------------+ | CONCEPT 6.2 EUKARYOTIC CELLS HAVE INTERNAL MEMBRANES THAT COMPARTMENT | | ALIZE THEIR FUNCTIONS. | | ===================================================================== | | ====================== | +-----------------------------------------------------------------------+ Cells are the basic units of every organism. Two types of cells: prokaryotic and eukaryotic. Prokaryotic cells in Bacteria and Archaea. Eukaryotic cells in protists, fungi, animals, and plants. \"Protist\" refers to mostly unicellular eukaryotes. **COMPARING PROKARYOTIC AND EUKARYOTIC CELLS** ---------------------------------------------- All cells share basic features: plasma membrane, cytosol, chromosomes, and ribosomes. Prokaryotic cells have DNA concentrated in the nucleoid, while eukaryotic cells have DNA in the nucleus. Eukaryotic cells have membrane-bounded organelles, while prokaryotic cells do not. Eukaryotic cells are generally larger than prokaryotic cells. The surface area to volume ratio is critical for cells and affects material exchange. Cells with high material exchange, like intestinal cells, have microvilli to increase surface area.  **A PANORAMIC VIEW OF THE EUKARYOTIC CELL** ------------------------------------------- Eukaryotic cells have internal membranes called organelles that compartmentalize the cell and support specific metabolic functions. The plasma membrane and organelle membranes participate in the cell\'s metabolism through the presence of enzymes. Biological membranes consist of a double layer of phospholipids and proteins, with each membrane having a unique composition suited to its functions. Chapter 7 will provide a detailed discussion on membranes. Figure 6.8 illustrates the organelles and key differences between animal and plant cells, while the micrographs show cells from different eukaryotic organisms.  +-----------------------------------------------------------------------+ | CONCEPT 6.3 THE EUKARYOTIC CELL'S GENETIC INSTRUCTIONS ARE HOUSED IN | | THE NUCLEUS AND CARRIED OUT BY THE RIBOSOMES. | | ===================================================================== | | ============================================= | +-----------------------------------------------------------------------+ The nucleus houses most of the cell\'s DNA, acting as the control center for gene expression and cellular processes. Ribosomes use DNA information to synthesize proteins, crucial for cell structure and function. **THE NUCLEUS: INFORMATION CENTRAL** ------------------------------------ The nucleus contains most of the genes in the eukaryotic cell and is separated from the cytoplasm by the nuclear envelope, which has pore structures. The nuclear lamina and matrix maintain the shape of the nucleus and organize genetic material. DNA is organized into chromosomes, which are made up of chromatin, a complex of DNA and proteins. Chromosomes condense during cell division. Each eukaryotic species has a characteristic number of chromosomes. The nucleolus synthesizes ribosomal RNA (rRNA) and assembles ribosomes. The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA) from DNA. **RIBOSOMES: PROTEIN FACTORIES** -------------------------------- Ribosomes are complexes made of ribosomal RNAs and proteins that carry out protein synthesis. Ribosomes are not considered organelles and lack a membrane. Cells with high rates of protein synthesis have large numbers of ribosomes and prominent nucleoli. Ribosomes build proteins in two cytoplasmic regions: free ribosomes in the cytosol and bound ribosomes attached to the endoplasmic reticulum or nuclear envelope. Free ribosomes make proteins for intracellular functions, while bound ribosomes make proteins for membrane insertion, organelle packaging, and secretion. Cells specialized in protein secretion, like pancreatic cells, have a high proportion of bound ribosomes.  +-----------------------------------------------------------------------+ | CONCEPT 6.4 THE ENDOMEMBRANE SYSTEM REGULATES PROTEIN TRAFFIC AND PER | | FORMS METABOLIC FUNCTIONS. | | ===================================================================== | | ========================== | +-----------------------------------------------------------------------+ The endomembrane system is a collection of membrane-bounded organelles in eukaryotic cells, including the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, vacuoles, and the plasma membrane. It carries out various tasks such as protein synthesis, transport, lipid metabolism, and detoxification. Membranes within the system are connected physically or through vesicle transfer. Different membranes have unique structures and functions that can be modified. **THE ENDOPLASMIC RETICULUM: BIOSYNTHETIC FACTORY** --------------------------------------------------- The endoplasmic reticulum (ER) is a network of membranes that accounts for over half of the total membrane in eukaryotic cells. The ER consists of tubules and sacs called cisternae, separating the ER lumen from the cytosol. The ER membrane is continuous with the nuclear envelope, and the space between the two membranes is continuous with the ER lumen. There are two regions of the ER: smooth ER and rough ER. Smooth ER is involved in diverse metabolic processes, including lipid synthesis, carbohydrate metabolism, detoxification, and calcium ion storage. Examples of smooth ER functions include the synthesis of sex hormones, detoxification of drugs, and storage of calcium ions in muscle cells. Rough ER is responsible for the synthesis and secretion of proteins, including glycoproteins. Rough ER also acts as a membrane factory, producing membrane proteins and phospholipids. THE GOLGI APPARATUS: SHIPPING AND RECEIVING CENTER -------------------------------------------------- The Golgi apparatus is responsible for receiving, modifying, and shipping products from the ER. It consists of flattened membranous sacs called cisternae arranged in stacks. The Golgi has a structural directionality with a cis face (receiving) and a trans face (shipping). Transport vesicles move material from the ER to the Golgi, and vesicles bud off from the Golgi to other sites. The Golgi modifies proteins and membrane phospholipids and manufactures macromolecules like polysaccharides. Golgi products, including secretory proteins, are transported to the plasma membrane for secretion. The Golgi operates through cisternal maturation, where the cisternae progress forward from the cis to the trans face, carrying and modifying cargo. Sorting of Golgi products is facilitated by molecular identification tags like phosphate groups.  **LYSOSOMES: DIGESTIVE COMPARTMENTS** ------------------------------------- Lysosomes are membranous sacs containing hydrolytic enzymes used for macromolecule digestion in eukaryotic cells. Lysosomal enzymes work best in an acidic environment found in lysosomes. Excessive leakage from lysosomes can destroy a cell by self-digestion. Lysosomal enzymes and membrane are produced by the rough ER and processed in the Golgi apparatus. Proteins and enzymes on the inner surface of lysosomes are protected from destruction by their three-dimensional shapes. Lysosomes carry out intracellular digestion through processes like phagocytosis (engulfing smaller organisms or food particles) and autophagy (recycling damaged organelles or cytosol). Lysosomes aid in cell renewal by breaking down and releasing small organic compounds for reuse. Lysosomal storage diseases occur when hydrolytic enzymes are lacking, leading to the accumulation of indigestible material and interference with cellular activities. **VACUOLES: DIVERSE MAINTENANCE COMPARTMENTS** ---------------------------------------------- Vacuoles are large vesicles derived from the endoplasmic reticulum and Golgi apparatus, and they have selective membranes that transport solutes. Vacuoles perform various functions in different cells, including food storage, water regulation, enzymatic hydrolysis, and protection against herbivores. Plant vacuoles store organic compounds, pigments, and inorganic ions, and the central vacuole aids in cell growth by absorbing water. The cytosol is located between the central vacuole and the plasma membrane in plant cells.  **THE ENDOMEMBRANE SYSTEM: A REVIEW** ------------------------------------- The endomembrane system is a complex group of organelles that modify, package, and transport proteins and lipids within a cell. Membrane lipids and proteins are synthesized in the endoplasmic reticulum (ER) and then transported to the Golgi apparatus for further modification. As proteins and lipids move through the endomembrane system, their molecular composition and metabolic functions can be altered. Other organelles, such as mitochondria and chloroplasts, are involved in energy transformations. +-----------------------------------------------------------------------+ | CONCEPT 6.5 MITOCHONDRIA AND CHLOROPLASTS CHANGE ENERGY FROM ONE FORM | | TO ANOTHER | | ===================================================================== | | =========== | +-----------------------------------------------------------------------+ Mitochondria and chloroplasts convert energy for cellular work through cellular respiration and photosynthesis, respectively. Mitochondria use oxygen to generate ATP from fuels like sugars and fats. Chloroplasts convert solar energy to chemical energy by synthesizing organic compounds from carbon dioxide and water. Both organelles have similar evolutionary origins, highlighting their shared functions and structures. The peroxisome is an oxidative organelle with a debated evolutionary origin, adding to the ongoing scientific debates in biology.  THE EVOLUTIONARY ORIGINS OF MITOCHONDRIA AND CHLOROPLASTS --------------------------------------------------------- Endosymbiont theory: Eukaryotic cells evolved from a host cell engulfing a non photosynthetic prokaryotic cell, leading to the origins of mitochondria and chloroplasts. Structural features: Mitochondria and chloroplasts have double membranes, ribosomes, and circular DNA molecules, resembling prokaryotes. MITOCHONDRIA: CHEMICAL ENERGY CONVERSION ---------------------------------------- Mitochondria are found in most eukaryotic cells, and their number varies based on metabolic activity. Mitochondria have two membranes, with the inner membrane containing cristae and dividing the mitochondrion into compartments. The matrix, enclosed by the inner membrane, contains enzymes, DNA, and ribosomes. Mitochondria are essential for cellular respiration, with enzymes in the matrix and proteins in the inner membrane involved in energy production. Mitochondria exhibit dynamic behavior, such as movement, shape changes, and fusion or division. CHLOROPLASTS: CAPTURE OF LIGHT ENERGY ------------------------------------- Chloroplasts contain chlorophyll and other molecules for photosynthesis. Chloroplasts are lens-shaped organelles found in leaves, green organs, and algae. Chloroplast structure includes an envelope with two membranes, thylakoids, and stroma. Thylakoids are flattened sacs that can stack into grana. Chloroplast space is divided into intermembrane space, stroma, and thylakoid space. Chloroplasts convert light energy to chemical energy during photosynthesis. Chloroplasts exhibit dynamic behavior, changing shape, growing, and reproducing. Chloroplasts, mitochondria, and other organelles move along the cytoskeleton. Chloroplasts are a type of plastid, related to amyloplasts and chromoplasts. Amyloplasts store starch, while chromoplasts produce pigments.  PEROXISOMES: OXIDATION ---------------------- Peroxisomes are specialized metabolic compartments bounded by a single membrane. They contain enzymes that remove hydrogen atoms from substrates and transfer them to oxygen, producing hydrogen peroxide as a by-product. Peroxisomes have various functions, including the breakdown of fatty acids and detoxification of harmful compounds. They also contain enzymes that convert hydrogen peroxide to water, preventing toxicity. Glyoxysomes, a type of peroxisome found in plant seeds, initiate the conversion of fatty acids to sugar. +-----------------------------------------------------------------------+ | CONCEPT 6.6 THE CYTOSKELETON IS A NETWORK OF FIBERS THAT ORGANIZES ST | | RUCTURES AND ACTIVITIES IN THE CELL. | | ===================================================================== | | ==================================== | +-----------------------------------------------------------------------+ Organelles in eukaryotic cells are organized by the cytoskeleton, challenging previous beliefs (evidence: advancements in microscopy). The cytoskeleton is a network of protein fibers that supports cell structure and facilitates movement and division (evidence: extends throughout the cytoplasm, role in organizing structures and activities). Bacterial cells also have a cytoskeleton constructed of similar proteins, showing evolutionary conservation (evidence: proteins similar to eukaryotic ones).  ROLES OF THE CYTOSKELETON: SUPPORT AND MOTILITY ----------------------------------------------- The cytoskeleton provides mechanical support and maintains cell shape, especially in animal cells without walls. Its strength and resilience come from its architecture, which is stabilized by opposing forces. The cytoskeleton anchors organelles and enzyme molecules within the cell. It is dynamic, allowing for quick dismantling and reassembly, leading to changes in cell shape. Cell motility involves the interaction of the cytoskeleton with motor proteins. Cytoskeletal elements, motor proteins, and plasma membrane molecules enable cell movement. Motor proteins use the cytoskeleton as a track to transport vesicles and organelles. The cytoskeleton manipulates the plasma membrane, forming phagocytic vesicles. Intermediate filaments are a diverse class of cytoskeletal elements found only in some animal cells, including vertebrates. They have a larger diameter than microfilaments but smaller than microtubules. Intermediate filaments are constructed from specific molecular subunits, such as keratins. Unlike microfilaments and microtubules, intermediate filaments are more permanent fixtures of cells. They play a crucial role in reinforcing cell shape and fixing the position of certain organelles, like the nucleus. The various types of intermediate filaments function together as the permanent framework of the entire cell. COMPONENTS OF THE CYTOSKELETON ------------------------------ The cytoskeleton consists of three main types of fibers: microtubules, microfilaments, and intermediate filaments. Microtubules are hollow rods made of tubulin proteins and provide shape, support, and tracks for organelle movement in the cell. They grow by adding tubulin dimers and have a plus end and a minus end. Centrosomes with centrioles initiate microtubule growth in animal cells.  Cilia and flagella are cellular extensions containing microtubules. They have different beating patterns and are involved in cell locomotion and fluid movement. Cilia can also act as signal-receiving antennae for the cell.  Microfilaments are thin solid rods made of actin proteins. They provide structural support, contribute to cell motility and contraction, and form networks and bundles. Intermediate filaments are fibers with intermediate diameters. They provide mechanical strength and maintain cell shape and integrity. Intermediate filaments are a diverse class of cytoskeletal elements found only in some animal cells, including vertebrates. They have a larger diameter than microfilaments but smaller than microtubules. Intermediate filaments are constructed from specific molecular subunits, such as keratins. Unlike microfilaments and microtubules, intermediate filaments are more permanent fixtures of cells. They play a crucial role in reinforcing cell shape and fixing the position of certain organelles, like the nucleus. The various types of intermediate filaments function together as the permanent framework of the entire cell.  +-----------------------------------------------------------------------+ | CONCEPT 6.7 EXTRACELLULAR COMPONENTS AND CONNECTIONS BETWEEN CELLS HE | | LP COORDINATE CELLULAR ACTIVITIES. | | ===================================================================== | | ================================== | +-----------------------------------------------------------------------+ The plasma membrane is the boundary of the living cell and regulates the movement of substances in and out of the cell. Cells synthesize and secrete materials outside the cell, which are important for cell biology. Extracellular structures like the extracellular matrix, cell walls, and extracellular vesicles play roles in cell adhesion, signaling, and communication. CELL WALL OF PLANTS ------------------- The cell wall is an extracellular structure that protects plant cells, maintains their shape, and prevents excessive water uptake. Cell walls are not exclusive to plant cells and are also present in prokaryotes, some protists, and fungi. Plant cell walls are thicker than the plasma membrane and have a variable chemical composition. They are composed of microfibrils made of cellulose, embedded in a matrix of polysaccharides and proteins. Plant cells have primary and secondary cell walls, with the middle lamella, rich in pectins, gluing adjacent cells together. Some plant cells strengthen their walls by secreting hardening substances, while others add a secondary cell wall. Secondary walls, often deposited in multiple layers, provide strong and durable protection and support. THE EXTRACELLULAR MATRIX (ECM) OF ANIMAL CELLS ---------------------------------------------- Animal cells have an extracellular matrix (ECM) composed of glycoproteins and carbohydrate-containing molecules. The ECM provides structural support and regulatory functions. Collagen is the most abundant glycoprotein in the ECM, forming strong fibers outside the cells. It accounts for about 40% of the total protein in the human body. Proteoglycans, consisting of a small core protein with attached carbohydrate chains, are also present in the ECM. They can form large complexes when multiple proteoglycan molecules attach to a single polysaccharide molecule. Some cells are attached to the ECM through glycoproteins like fibronectin, which bind to integrin receptor proteins on the cell surface. Integrins transmit signals between the ECM and the cytoskeleton, allowing the ECM to regulate a cell\'s behavior. The ECM plays a crucial role in cell migration, gene activity, and protein production. It can influence cell behavior by matching the orientation of microfilaments to the fibers in the ECM and by transmitting signals that trigger changes in the cytoskeleton and gene expression. Understanding the composition and function of the ECM, including collagen, proteoglycans, and integrins, is important for comprehending the structural and regulatory roles of the ECM in cell biology. The ECM coordinates cellular processes within tissues.  CELL JUNCTIONS -------------- Cells in animals and plants are organized into tissues, organs, and organ systems, with tissues being groups of cells that work together to perform specific functions. Plant cell walls contain plasmodesmata, which are channels that connect neighboring cells, allowing for communication and transport between cells. Plasmodesmata unify most of the plant into one living continuum, as they share the same internal chemical environment. Animal cells have three main types of cell junctions: tight junctions, desmosomes, and gap junctions. These junctions are especially common in epithelial tissue, which lines the external and internal surfaces of the body. Gap junctions in animal cells are similar to plasmodesmata in plant cells, as they also allow for communication and transport between adjacent cells, although they consist of proteins forming a connecting pore rather than being lined with membrane.  +-----------------------------------------------------------------------+ | CONCEPT 6.8 A CELL IS GREATER THAN THE SUM OF ITS PARTS | | ======================================================= | +-----------------------------------------------------------------------+ The structure of a cell is correlated with its function, as seen in the compartmental organization and organelle architecture. Cellular processes are integrated, as exemplified by the coordination of activities in a macrophage cell to defend against infections. Understanding the role of biological molecules and structures in a cell is crucial for comprehending its internal organization and processes.