Chapter 6: A Tour of the Cell

Internal membranes compartmentalize the functions of a eukaryotic cell

A eukaryotic cell has extensive and elaborate internal membranes, which partition the cell into compartments. These membranes also participate directly in metabolism, as many enzymes are built into membranes. The compartments created by membranes provide different local environments that facilitate specific metabolic functions, allowing several incompatible processes to go on simultaneously in a cell. The general structure of a biological membrane is a double layer of phospholipids. Other lipids and diverse proteins are embedded in the lipid bilayer or attached to its surface. Each type of membrane has a unique combination of lipids and proteins for its specific functions. For example, enzymes embedded in the membranes of mitochondria function in cellular respiration.

Lysosome

A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to digest macromolecules. Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids. These enzymes work best at pH 5. Proteins in the lysosomal membrane pump hydrogen ions from the cytosol into the lumen of the lysosomes. Rupture of one or a few lysosomes has little impact on a cell because the lysosomal enzymes are not very active at the neutral pH of the cytosol. However, massive rupture of many lysosomes can destroy a cell by autodigestion. Lysosomal enzymes and membrane are synthesized by rough ER and then transferred to the Golgi apparatus for further modification. Proteins on the inner surface of the lysosomal membrane are spared by digestion by their three-dimensional conformations, which protect vulnerable bonds from hydrolysis. Lysosomes carry out intracellular digestion in a variety of circumstances. Amoebas eat by engulfing smaller organisms by phagocytosis. The food vacuole formed by phagocytosis fuses with a lysosome, whose enzymes digest the food. As the polymers are digested, monomers pass to the cytosol to become nutrients for the cell. Lysosomes can play a role in recycling of the cell's organelles and macromolecules. This recycling, or autophagy, renews the cell. During autophagy, a damaged organelle or region of cytosol becomes surrounded by membrane. A lysosome fuses with the resulting vesicle, digesting the macromolecules and returning the organic monomers to the cytosol for reuse. The lysosomes play a critical role in the programmed destruction of cells in multicellular organisms. This process plays an important role in development. The hands of human embryos are webbed until lysosomes digest the cells in the tissue between the fingers. This important process is called programmed cell death, or apoptosis.

Cilia and Flagella

A specialized arrangement of microtubules is responsible for the beating of cilia and flagella. Many unicellular eukaryotic organisms are propelled through water by cilia and flagella. Cilia or flagella can extend from cells within a tissue layer, beating to move fluid over the surface of the tissue. For example, cilia lining the windpipe sweep mucus carrying trapped debris out of the lungs. Cilia usually occur in large numbers on the cell surface. There are usually just one or a few flagella per cell. Flagella are the same width as cilia, but 10-200 microns long. Cilia and flagella differ in their beating patterns. A flagellum has an undulatory movement that generates force in the same direction as the flagellum's axis. Cilia move more like oars with alternating power and recovery strokes that generate force perpendicular to the cilium's axis. In spite of their differences, both cilia and flagella have the same ultrastructure. Both have a core of microtubules sheathed by the plasma membrane. Nine doublets of microtubules are arranged in a ring around a pair at the center. This "9 + 2" pattern is found in nearly all eukaryotic cilia and flagella. Flexible "wheels" of proteins connect outer doublets to each other and to the two central microtubules. The outer doublets are also connected by motor proteins. The cilium or flagellum is anchored in the cell by a basal body, whose structure is identical to a centriole. The bending of cilia and flagella is driven by the arms of a motor protein, dynein. Addition and removal of a phosphate group causes conformation changes in dynein. Dynein arms alternately grab, move, and release the outer microtubules. Protein cross-links limit sliding. As a result, the forces exerted by the dynein arms cause the doublets to curve, bending the cilium or flagellum.

Prokaryote and Eukaryotes Similarity

All cells are surrounded by a plasma membrane. The semifluid substance within the membrane is the cytosol, containing the organelles. All cells contain chromosomes that have genes in the form of DNA. All cells also have ribosomes, tiny organelles that make proteins using the instructions contained in genes.

Metabolic requirements also set an upper limit to the size of a single cell.

As a cell increases in size, its volume increases faster than its surface area. Smaller objects have a greater ratio of surface area to volume. The plasma membrane functions as a selective barrier that allows the passage of oxygen, nutrients, and wastes for the whole volume of the cell. The volume of cytoplasm determines the need for this exchange. Rates of chemical exchange across the plasma membrane may be inadequate to maintain a cell with a very large cytoplasm. The need for a surface sufficiently large to accommodate the volume explains the microscopic size of most cells. Larger organisms do not generally have larger cells than smaller organisms—simply more cells. Cells that exchange a lot of material with their surroundings, such as intestinal cells, may have long, thin projections from the cell surface called microvilli. Microvilli increase surface area without significantly increasing cell volume.

Chromatin

As the cell prepares to divide, the chromatin fibers coil up and condense, becoming thick enough to be recognized as the familiar chromosomes.

Microfilaments

Each microfilament is built as a twisted double chain of actin subunits. Microfilaments can form structural networks due to their ability to branch. The structural role of microfilaments in the cytoskeleton is to bear tension, resisting pulling forces within the cell. They form a three-dimensional network just inside the plasma membrane to help support the cell's shape, giving the cell cortex the semisolid consistency of a gel. Microfilaments are important in cell motility, especially as part of the contractile apparatus of muscle cells. In muscle cells, thousands of actin filaments are arranged parallel to one another. Thicker filaments composed of myosin interdigitate with the thinner actin fibers. Myosin molecules act as motor proteins, walking along the actin filaments to shorten the cell.

Eukaryote

In a eukaryotic cell, chromosomes are contained in a membrane-enclosed organelle, the nucleus. Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of specialized form and function. Eukaryotic cells are typically 10-100 microns in diameter.

Prokaryote

In a prokaryotic cell, the DNA is concentrated in the nucleoid without a membrane separating it from the rest of the cell. All the material within the plasma membrane of a prokaryotic cell is cytoplasm. These membrane-bound organelles are absent in prokaryotes. Most bacteria are 1-10 microns in diameter.

Centrsome and centrioles

In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring. Before a cell divides, the centrioles replicate.

actin and myosin

In other cells, actin-myosin aggregates are less organized but still cause localized contraction. A contracting belt of microfilaments divides the cytoplasm of animal cells during cell division. 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. Microfilaments assemble into networks that convert sol to gel. According to a widely accepted model, filaments near the cell's trailing edge interact with myosin, causing contraction. The contraction forces the interior fluid into the pseudopodium, where the actin network has been weakened. The pseudopodium extends until the actin reassembles into a network. In plant cells, actin-myosin interactions and sol-gel transformations drive cytoplasmic streaming. This creates a circular flow of cytoplasm in the cell, speeding the distribution of materials within the cell.

Nucleolus

In the nucleus is a region of densely stained fibers and granules adjoining chromatin, the nucleolus. In the nucleolus, ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm to form ribosomal subunits. The subunits pass through the nuclear pores to the cytoplasm, where they combine to form ribosomes.

endomembrane system

Many of the internal membranes in a eukaryotic cell are part of the endomembrane system. These membranes are either directly continuous or connected via transfer of vesicles, sacs of membrane. The thickness, molecular composition and types of chemical reactions carried out by proteins in a given membrane may be modified several times during a membrane's life. The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane.

The Golgi apparatus is the shipping and receiving center for cell products

Many transport vesicles from the ER travel to the Golgi apparatus for modification of their contents. The Golgi is a center of manufacturing, warehousing, sorting, and shipping. The Golgi apparatus is especially extensive in cells specialized for secretion. The Golgi apparatus consists of flattened membranous sacs—cisternae—looking like a stack of pita bread. The membrane of each cisterna separates its internal space from the cytosol. One side of the Golgi, the cis side, is located near the ER. The cis face receives material by fusing with transport vesicles from the ER. The other side, the trans side, buds off vesicles that travel to other sites. During their transit from the cis to the trans side, products from the ER are usually modified. The Golgi can also manufacture its own macromolecules, including pectin and other noncellulose polysaccharides. The Golgi apparatus is a very dynamic structure. According to the cisternal maturation model, the cisternae of the Golgi progress from the cis to the trans face, carrying and modifying their protein cargo as they move. Finally, the Golgi sorts and packages materials into transport vesicles. Molecular identification tags are added to products to aid in sorting. Products are tagged with identifiers such as phosphate groups. These act like ZIP codes on mailing labels to identify the product's final destination.

Intercellular junctions help integrate cells into higher levels of structure and function

Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact. Plant cells are perforated with plasmodesmata, channels allowing cytosol to pass between cells. Water and small solutes can pass freely from cell to cell. In certain circumstances, proteins and RNA can be exchanged. Animals have 3 main types of intercellular links: tight junctions, desmosomes, and gap junctions. In tight junctions, membranes of adjacent cells are fused, forming continuous belts around cells. This prevents leakage of extracellular fluid. Desmosomes (or anchoring junctions) fasten cells together into strong sheets, much like rivets. Intermediate filaments of keratin reinforce desmosomes. Gap junctions (or communicating junctions) provide cytoplasmic channels between adjacent cells. Special membrane proteins surround these pores. Ions, sugars, amino acids, and other small molecules can pass. In embryos, gap junctions facilitate chemical communication during development.

Peroxisomes generate and degrade H2O2 in performing various metabolic functions.

Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen. An intermediate product of this process is hydrogen peroxide (H2O2), a poison. The peroxisome contains an enzyme that converts H2O2 to water. Some peroxisomes break fatty acids down to smaller molecules that are transported to mitochondria as fuel for cellular respiration. Peroxisomes in the liver detoxify alcohol and other harmful compounds. Specialized peroxisomes, glyoxysomes, convert the fatty acids in seeds to sugars, which the seedling can use as a source of energy and carbon until it is capable of photosynthesis. Peroxisomes are bound by a single membrane. They form not from the endomembrane system, but by incorporation of proteins and lipids from the cytosol. They split in two when they reach a certain size.

Ribosomes

Ribosomes, containing rRNA and protein, are the organelles that carry out protein synthesis. Cell types that synthesize large quantities of proteins (e.g., pancreas cells) have large numbers of ribosomes and prominent nucleoli. Some ribosomes, free ribosomes, are suspended in the cytosol and synthesize proteins that function within the cytosol. Other ribosomes, bound ribosomes, are attached to the outside of the endoplasmic reticulum or nuclear envelope. These synthesize proteins that are either included in membranes or exported from the cell. Ribosomes can shift between roles depending on the polypeptides they are synthesizing.

Plant cells are encased by cell walls

The cell wall, found in prokaryotes, fungi, and some protists, has multiple functions. In plants, the cell wall protects the cell, maintains its shape, and prevents excessive uptake of water. It also supports the plant against the force of gravity. The thickness and chemical composition of cell walls differs from species to species and among cell types within a plant. The basic design consists of microfibrils of cellulose embedded in a matrix of proteins and other polysaccharides. This is the basic design of steel-reinforced concrete or fiberglass. A mature cell wall consists of a primary cell wall, a middle lamella with sticky polysaccharides that holds cells together, and layers of secondary cell wall. Plant cell walls are perforated by channels between adjacent cells called plasmodesmata.

Cytoskeleton

The cytoskeleton is a network of fibers extending throughout the cytoplasm. The cytoskeleton organizes the structures and activities of the cell. The cytoskeleton provides support, motility, and regulation. The cytoskeleton provides mechanical support and maintains cell shape. The cytoskeleton provides anchorage for many organelles and cytosolic enzymes. The cytoskeleton is dynamic and can be dismantled in one part and reassembled in another to change the shape of the cell. The cytoskeleton also plays a major role in cell motility, including changes in cell location and limited movements of parts of the cell. The cytoskeleton interacts with motor proteins to produce motility. Cytoskeleton elements and motor proteins work together with plasma membrane molecules to move the whole cell along fibers outside the cell. Motor proteins bring about movements of cilia and flagella by gripping cytoskeletal components such as microtubules and moving them past each other. The same mechanism causes muscle cells to contract. Inside the cell, vesicles can travel along "monorails" provided by the cytoskeleton. The cytoskeleton manipulates the plasma membrane to form food vacuoles during phagocytosis. Cytoplasmic streaming in plant cells is caused by the cytoskeleton. Recently, evidence suggests that the cytoskeleton may play a role in the regulation of biochemical activities in the cell. There are three main types of fibers making up the cytoskeleton: microtubules, microfilaments, and intermediate filaments.

endoplasmic reticulum

The endoplasmic reticulum (ER) accounts for half the membranes in a eukaryotic cell. The ER includes membranous tubules and internal, fluid-filled spaces called cisternae. The ER membrane is continuous with the nuclear envelope, and the cisternal space of the ER is continuous with the space between the two membranes of the nuclear envelope. There are two connected regions of ER that differ in structure and function. Smooth ER looks smooth because it lacks ribosomes. Rough ER looks rough because ribosomes (bound ribosomes) are attached to the outside, including the outside of the nuclear envelope.

cell franctionation

The goal of cell fractionation is to separate the major organelles of the cells so their individual functions can be studied. Fractionation begins with homogenization, gently disrupting the cell. The homogenate is spun in a centrifuge to separate heavier pieces into the pellet while lighter particles remain in the supernatant. As the process is repeated at higher speeds and for longer durations, smaller and smaller organelles can be collected in subsequent pellets. This enables the functions of these organelles to be determined, especially by the reactions or processes catalyzed by their proteins.

Protein Synthesis

The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA). The mRNA travels to the cytoplasm through the nuclear pores and combines with ribosomes to translate its genetic message into the primary structure of a specific polypeptide

Nucleus

The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope. The envelope is perforated by pores, continuous with ER At the lip of each pore, the inner and outer membranes of the nuclear envelope are fused to form a continuous membrane. A protein structure called a pore complex lines each pore, regulating the passage of certain large macromolecules and particles.

The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and regulation

Though lacking cell walls, animal cells do have an elaborate extracellular matrix (ECM). The primary constituents of the extracellular matrix are glycoproteins, especially collagen fibers, embedded in a network of glycoprotein proteoglycans. In many cells, fibronectins in the ECM connect to integrins, intrinsic membrane proteins that span the membrane and bind on their cytoplasmic side to proteins attached to microfilaments of the cytoskeleton. The interconnections from the ECM to the cytoskeleton via the fibronectin-integrin link permit the integration of changes inside and outside the cell. The ECM can regulate cell behavior. Embryonic cells migrate along specific pathways by matching the orientation of their microfilaments to the "grain" of fibers in the extracellular matrix. The extracellular matrix can influence the activity of genes in the nucleus via a combination of chemical and mechanical signaling pathways. This may coordinate the behavior of all the cells within a tissue

Vacuoles

Vesicles and vacuoles (larger versions) are membrane-bound sacs with varied functions. Food vacuoles are formed by phagocytosis and fuse with lysosomes. Contractile vacuoles, found in freshwater protists, pump excess water out of the cell to maintain the appropriate concentration of salts. A large central vacuole is found in many mature plant cells. The membrane surrounding the central vacuole, the tonoplast, is selective in its transport of solutes into the central vacuole. The functions of the central vacuole include stockpiling proteins or inorganic ions, disposing of metabolic byproducts, holding pigments, and storing defensive compounds that defend the plant against herbivores. Because of the large vacuole, the cytosol occupies only a thin layer between the plasma membrane and the tonoplast. The presence of a large vacuole increases surface area to volume ratio for the cell.

Chromosomes

Within the nucleus, the DNA and associated proteins are organized into discrete units called chromosomes, structures that carry the genetic information. Each chromosome is made up of fibrous material called chromatin, a complex of proteins and DNA.

Nuclear Lamina

a network of protein filaments that maintains the shape of the nucleus. There is evidence that a framework of fibers called the nuclear matrix extends through the nuclear interior.

Mitochondria and Chloroplasts

are not part of the endomembrane system. In contrast to organelles of the endomembrane system, each mitochondrion or chloroplast has two membranes separating the innermost space from the cytosol. Their membrane proteins are not made by the ER, but rather by free ribosomes in the cytosol and by ribosomes within the organelles themselves. Both organelles have small quantities of DNA that direct the synthesis of the polypeptides produced by these internal ribosomes. Mitochondria and chloroplasts grow and reproduce as semiautonomous organelles. Almost all eukaryotic cells have mitochondria. There may be one very large mitochondrion or hundreds to thousands of individual mitochondria. The number of mitochondria is correlated with aerobic metabolic activity. Mitochondria are quite dynamic: moving, changing shape, and dividing. Like mitochondria, chloroplasts are dynamic structures. Their shape is plastic, and they can reproduce themselves by pinching in two. Mitochondria and chloroplasts are mobile and move around the cell along tracks of the cytoskeleton.

Mitochondria

are the sites of cellular respiration, generating ATP from the catabolism of sugars, fats, and other fuels in the presence of oxygen. have a smooth outer membrane and a convoluted inner membrane with infoldings called cristae. The inner membrane divides the mitochondrion into two internal compartments. The first is the intermembrane space, a narrow region between the inner and outer membranes. The inner membrane encloses the mitochondrial matrix, a fluid-filled space with DNA, ribosomes, and enzymes. Some of the metabolic steps of cellular respiration are catalyzed by enzymes in the matrix. The cristae present a large surface area for the enzymes that synthesize ATP.

Transmission electron microscopes

are used mainly to study the internal ultrastructure of cells. A TEM aims an electron beam through a thin section of the specimen. The image is focused and magnified by electromagnets. To enhance contrast, the thin sections are stained with atoms of heavy metals.

Scanning electron microscopes

are useful for studying surface structures. The sample surface is covered with a thin film of gold. The beam excites electrons on the surface of the sample. These secondary electrons are collected and focused on a screen. The result is an image of the topography of the specimen. The SEM has great depth of field, resulting in an image that seems three-dimensional.

Chloroplasts

found in plants and algae, are the sites of photosynthesis. They convert solar energy to chemical energy and synthesize new organic compounds such as sugars from CO2 and H2O. one of several members of a generalized class of plant structures called plastids. Amyloplasts are colorless plastids that store starch in roots and tubers. Chromoplasts store pigments for fruits and flowers. Chloroplasts contain the green pigment chlorophyll as well as enzymes and other molecules that function in the photosynthetic production of sugar. The contents of the chloroplast are separated from the cytosol by an envelope consisting of two membranes separated by a narrow intermembrane space. Inside the innermost membrane is a fluid-filled space, the stroma, in which float membranous sacs, the thylakoids. The stroma contains DNA, ribosomes, and enzymes. The thylakoids are flattened sacs that play a critical role in converting light to chemical energy. In some regions, thylakoids are stacked like poker chips into grana. The membranes of the chloroplast divide the chloroplast into three compartments: the intermembrane space, the stroma, and the thylakoid space.

Rough ER

is especially abundant in cells that secrete proteins. As a polypeptide is synthesized on a ribosome attached to rough ER, it is threaded into the cisternal space through a pore formed by a protein complex in the ER membrane. As it enters the cisternal space, the new protein folds into its native conformation. Most secretory polypeptides are glycoproteins, proteins to which a carbohydrate is attached. Secretory proteins are packaged in transport vesicles that carry them to their next stage. Rough ER is also a membrane factory. Membrane-bound proteins are synthesized directly into the membrane. Enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol. As the ER membrane expands, membrane can be transferred as transport vesicles to other components of the endomembrane system.

Smooth ER

is rich in enzymes and plays a role in a variety of metabolic processes. Enzymes of smooth ER synthesize lipids, including oils, phospholipids, and steroids. These include the sex hormones of vertebrates and adrenal steroids. In the smooth ER of the liver, enzymes help detoxify poisons and drugs Frequent use of these drugs leads to the proliferation of smooth ER in liver cells, increasing the rate of detoxification. This increases tolerance to the target and other drugs, so higher doses are required to achieve the same effect. Smooth ER stores calcium ions. Muscle cells have a specialized smooth ER that pumps calcium ions from the cytosol and stores them in its cisternal space. When a nerve impulse stimulates a muscle cell, calcium ions rush from the ER into the cytosol, triggering contraction. Enzymes then pump the calcium back, readying the cell for the next stimulation.

Intermediate Filaments

larger than microfilaments but smaller than microtubules. Intermediate filaments are a diverse class of cytoskeletal units, built from a family of proteins called keratins. Intermediate filaments are specialized for bearing tension. Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes. They reinforce cell shape and fix organelle location.

Microtubules

the thickest fibers, are hollow rods about 25 microns in diameter and 200 nm to 25 microns in length. Microtubule fibers are constructed of the globular protein tubulin. Each tubulin molecule is a dimer consisting of two subunits. A microtubule changes in length by adding or removing tubulin dimers. Microtubules shape and support the cell and serve as tracks to guide motor proteins carrying organelles to their destination. Microtubules are also responsible for the separation of chromosomes during cell division. In many cells, microtubules grow out from a centrosome near the nucleus. These microtubules resist compression to the cell.

Light Microscope

visible light passes through the specimen and then through glass lenses. The lenses refract light such that the image is magnified into the eye or onto a video screen. The minimum resolution of a light microscope is about 200 nanometers (nm) Light microscopes can magnify effectively to about 1,000 times the size of the actual specimen. While a light microscope can resolve individual cells, it cannot resolve much of the internal anatomy, especially the organelles. living cells

electron microscope

which focuses a beam of electrons through the specimen or onto its surface. Because resolution is inversely related to wavelength used, electron microscopes (whose electron beams have shorter wavelengths than visible light) have finer resolution. Theoretically, the resolution of a modern EM could reach 0.002 nanometer (nm), but the practical limit is closer to about 2 nm. dead cells