A Tour of the Cell


I.         Prokaryotic and eukaryotic cells differ in size and complexity.

            A.        All cells are surrounded by a plasma membrane. A semifluid substance within the membrane, called the cytosol, contains the organelles.

            B.        All cells contain chromosomes that have genes in the form of DNA.

            C.        All cells also have ribosomes, tiny organelles that make proteins using the instructions contained in genes.

            D.        A major difference between prokaryotic and eukaryotic cells is the location of chromosomes.

                        1.         In a eukaryotic cell, chromosomes are contained in a membrane-enclosed organelle, the nucleus.

                        2.         In a prokaryotic cell, the DNA is concentrated in the nucleoid without a membrane separating it from the rest of the cell.

            E.        The region between the nucleus and the plasma membrane is the cytoplasm.

                        1.         All the material within the plasma membrane of a prokaryotic cell is cytoplasm.

                        2.         Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of specialized form and function.

                                    a.         These membrane-bound organelles are absent in prokaryotes.

            F.        Eukaryotic cells are generally much bigger than prokaryotic cells.

II.        The ability of a cell to carry out metabolism set limits on cell size.

            A.        As a cell increases in size, its volume increases faster than its surface area because smaller objects have a greater ratio of surface area to volume.

            B.        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.

            C.        Rates of chemical exchange across the plasma membrane may be inadequate to maintain a cell with a very large cytoplasm.

            D.        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. Rather, they have more cells.

            E.        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.

III.       A eukaryotic cell has extensive and elaborate internal membranes, which partition the cell into compartments.

            A.        These membranes also participate directly in metabolism, as many enzymes are built into membranes.

            B.        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.

IV.      The nucleus and ribosomes

            A.        The nucleus contains most of the genes in a eukaryotic cell. Additional genes are located in mitochondria and chloroplasts.

                        1.         The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope.

                                    a.         The envelope is perforated by pores. At the lip of each pore, the inner and outer membranes of the nuclear envelope are fused to form a continuous membrane.

                                    b.         A protein structure called a pore complex lines each pore, regulating the passage of certain large macromolecules and particles.

                                    c.         The nuclear side of the envelope is lined by the nuclear lamina, a network of protein filaments that maintains the shape of the nucleus.

                        2.         Within the nucleus, the DNA and associated proteins are organized into discrete chromosomes. Each chromosome is made up of fibrous material called chromatin, a complex of proteins and DNA.

                        3.         In the nucleus is a region of densely stained fibers and granules adjoining chromatin, the nucleolus.

                                    a.         In the nucleolus, ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm to form ribosomal subunits.

                                    b.         The subunits pass through the nuclear pores to the cytoplasm, where they combine to form ribosomes.

            B.        Ribosomes build a cell’s proteins.

                        1.         Ribosomes, containing rRNA and protein, are the organelles that carry out protein synthesis.

                        2.         Cell types that synthesize large quantities of proteins (e.g., pancreas cells) have large numbers of ribosomes and prominent nucleoli.

                        3.         Some ribosomes, free ribosomes, are suspended in the cytosol and synthesize proteins that function within the cytosol.

                        4.         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.

                        5.         Ribosomes can shift between roles depending on the polypeptides they are synthesizing.

V.        The Endomembrane System

            A.        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.

            B.        The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane.

                        1.         The endoplasmic reticulum (ER) manufactures membranes and performs many other biosynthetic functions. The endoplasmic reticulum accounts for half the membranes in a eukaryotic cell.

                                    a.         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.

                                    b.         There are two connected regions of ER that differ in structure and function.

                                                (1)       Smooth ER looks smooth because it lacks ribosomes.

                                                (2)       Rough ER looks rough because ribosomes (bound ribosomes) are attached to the outside, including the outside of the nuclear envelope.

                                    c.         The smooth ER is rich in enzymes and plays a role in a variety of metabolic processes.

                                                (1)       Enzymes of smooth ER synthesize lipids, including oils, phospholipids, and steroids

                                                (2)       In the smooth ER of the liver, enzymes help detoxify poisons and drugs such as alcohol and barbiturates. 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.

                                                (3)       Smooth ER stores calcium ions.

                                                            (a)       Muscle cells have a specialized smooth ER that pumps calcium ions from the cytosol and stores them.

                                                            (b)       When a nerve impulse stimulates a muscle cell, calcium ions rush from the ER into the cytosol, triggering contraction.

                                                            (c)       Enzymes then pump the calcium back, readying the cell for the next stimulation.

                                    d.         Rough ER is especially abundant in cells that secrete proteins.

                                                (1)       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.

                                                (2)       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.

                                                (3)       Rough ER is also a membrane factory.

                                                            (a)       Membrane-bound proteins are synthesized directly into the membrane.

                                                            (b)       Enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol.

                                                            (c)       As the ER membrane expands, membrane can be transferred as transport vesicles to other components of the endomembrane system.

                                    e.         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.

                                                (1)       The Golgi is a center of manufacturing, warehousing, sorting, and shipping and is especially extensive in cells specialized for secretion.

                                                (2)       The Golgi apparatus consists of flattened membranous sacs called cisternae which look like pancakes.

                                                (3)       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.

                                                (4)       The Golgi sorts and packages materials into transport vesicles.

                                                            (a)       Molecular identification tags are added to products to aid in sorting.

                                                            (b)       Products are tagged with identifiers such as phosphate groups. These act like postal codes on mailing labels to identify the product’s final destination.

                                    f.         Lysosomes are digestive compartments.

                                                (1)       A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to digest macromolecules.

                                                (2)       Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids. These enzymes work best at pH 5.

                                                            (a)       Proteins in the lysosomal membrane pump hydrogen ions from the cytosol into the lumen of the lysosomes.

                                                            (b)       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.

                                                            (c)       However, massive rupture of many lysosomes can destroy a cell by autodigestion.

                                                (3)       Proteins on the inner surface of the lysosomal membrane are spared by digestion by their three-dimensional conformations, which protect vulnerable bonds from hydrolysis.

                                                (4)       Lysosomes carry out intracellular digestion in a variety of circumstances.

                                                            (a)       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.

                                                            (b)       Lysosomes can play a role in recycling of the cell’s organelles and macromolecules. 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.

                                                            (c)       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.

                                    g.         Vesicles and vacuoles (larger versions) are membrane-bound sacs with varied functions.

                                                (1)       Food vacuoles are formed by phagocytosis and fuse with lysosomes.

                                                (2)       Contractile vacuoles, found in freshwater protists, pump excess water out of the cell to maintain the appropriate concentration of salts.

                                                (3)       A large central vacuole is found in many mature plant cells. 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.

                                                (4)       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.

VI.      Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work.

            A.        Mitochondria and chloroplasts are not part of the endomembrane system.

            B.        In contrast to organelles of the endomembrane system, each mitochondrion or chloroplast has two membranes separating the innermost space from the cytosol.

            C.        Their membrane proteins are not made by the ER, but rather by free ribosomes in the cytosol and by ribosomes within the organelles themselves.

                        1.         Both organelles have small quantities of DNA that direct the synthesis of the polypeptides produced by these internal ribosomes.

                        2.         Mitochondria and chloroplasts grow and reproduce as semiautonomous organelles.

            D.        There may be one very large mitochondrion or hundreds to thousands of individual mitochondria. The number of mitochondria is correlated with aerobic metabolic activity.

            E.        Mitochondria have a smooth outer membrane and a convoluted inner membrane with infoldings called cristae. The inner membrane divides the mitochondrion into two internal compartments.

                        1.         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.

            F.        The chloroplast is one of several members of a generalized class of plant structures called plastids.

            G.        The contents of the chloroplast are separated from the cytosol by an envelope consisting of two membranes separated by a narrow intermembrane space.

            H.        Inside the innermost membrane is a fluid-filled space, the stroma, in which float membranous sacs, the thylakoids.

                        1.         The stroma contains DNA, ribosomes, and enzymes.

                        2.         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.

            I.         Mitochondria and chloroplasts are mobile and move around the cell along tracks of the cytoskeleton.

VII.     Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen.

            A.        An intermediate product of this process is hydrogen peroxide (H2O2), a poison. The peroxisome contains an enzyme that converts H2O2 to water.

            B.        Some peroxisomes break fatty acids down to smaller molecules that are transported to mitochondria as fuel for cellular respiration.

            C.        Peroxisomes in the liver detoxify alcohol and other harmful compounds.

VIII.    The Cytoskeleton

            A.        The cytoskeleton is a network of fibers extending throughout the cytoplasm and it organizes the structures and activities of the cell.

            B.        It provides mechanical support and maintains cell shape.

            C.        The cytoskeleton provides anchorage for many organelles and cytosolic enzymes.

            D.        The cytoskeleton is dynamic and can be dismantled in one part and reassembled in another to change the shape of the cell.

            E.        The cytoskeleton interacts with motor proteins to produce motility.

                        1.         Cytoskeleton elements and motor proteins work together with plasma membrane molecules to move the whole cell along fibers outside the cell.

                        2.         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.

                        3.         Inside the cell, vesicles can travel along cytoskeleton “monorails.”

                        4.         The cytoskeleton manipulates the plasma membrane to form food vacuoles during phagocytosis.

                        5.         Cytoplasmic streaming in plant cells is caused by the cytoskeleton.

                        6.         There are three main types of fibers making up the cytoskeleton: microtubules, microfilaments, and intermediate filaments.

                                    a.         Microtubules, the thickest fibers, are hollow rods about 25 microns in diameter and 200 nm to 25 microns in length.

                                                (1)       Microtubule fibers are constructed of the globular protein tubulin. Each tubulin molecule is a dimer consisting of two subunits.

                                                (2)       A microtubule changes in length by adding or removing tubulin dimers.

                                                (3)       Microtubules shape and support the cell and serve as tracks to guide motor proteins carrying organelles to their destination.

                                                (4)       Microtubules are also responsible for the separation of chromosomes during cell division.

                                                (5)       In many cells, microtubules grow out from a centrosome near the nucleus. In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring.

                                                (6)       A specialized arrangement of microtubules is responsible for the beating of cilia and flagella.

                                                            (a)       A flagellum has an undulatory movement that generates force in the same direction as the flagellum’s axis.

                                                            (b)       Cilia move more like oars with alternating power and recovery strokes that generate force perpendicular to the cilium’s axis.

                                                            (c)       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.

                                                            (d)       The cilium or flagellum is anchored in the cell by a basal body, whose structure is identical to a centriole.

                                                            (e)       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.

                                                            (f)        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.

                                    b.         Microfilaments are solid rods about 7 nm in diameter.

                                                (1)       Each microfilament is built as a twisted double chain of actin subunits.

                                                (2)       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.

                                                (3)       Microfilaments are important in cell motility, especially as part of the contractile apparatus of muscle cells.

                                                            (a)       In muscle cells, thousands of actin filaments are arranged parallel to one another.

                                                            (b)       Thicker filaments composed of myosin interdigitate with the thinner actin fibers.

                                                            (c)       Myosin molecules act as motor proteins, walking along the actin filaments to shorten the cell.

                                                (4)       A contracting belt of microfilaments divides the cytoplasm of animal cells during cell division.

                                                (5)       Localized contraction brought about by actin and myosin also drives amoeboid movement.

                                                            (a)       Pseudopodia, cellular extensions, extend and contract through the reversible assembly and contraction of actin subunits into microfilaments.

                                                            (b)       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.

                                    c.         Intermediate filaments range in diameter from 8–12 nanometers, larger than microfilaments but smaller than microtubules.

                                                (1)       Intermediate filaments are a diverse class of cytoskeletal units, built from a family of proteins called keratins.

                                                (2)       Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes. They reinforce cell shape and fix organelle location.

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

            A.        The primary constituents of the extracellular matrix are glycoproteins, especially collagen fibers, embedded in a network of glycoprotein proteoglycans.

            B.        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.

            C.        The interconnections from the ECM to the cytoskeleton via the fibronectin-integrin link permit the integration of changes inside and outside the cell.

            D.        The ECM can regulate cell behavior.

                        1.         Embryonic cells migrate along specific pathways by matching the orientation of their microfilaments to the “grain” of fibers in the extracellular matrix.

                        2.         The extracellular matrix can influence the activity of genes in the nucleus via a combination of chemical and mechanical signaling pathways.

                        3.         This may coordinate the behavior of all the cells within a tissue.

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

            A.        Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact.

            B.        Plant cells are perforated with plasmodesmata, channels allowing cytosol to pass between cells.

                        1.         Water and small solutes can pass freely from cell to cell.

                        2.         In certain circumstances, proteins and RNA can be exchanged.

            C.        Animals have 3 main types of intercellular links: tight junctions, desmosomes, and gap junctions.

                        1.         In tight junctions, membranes of adjacent cells are fused, forming continuous belts around cells. This prevents leakage of extracellular fluid.

                        2.         Desmosomes (or anchoring junctions) fasten cells together into strong sheets, much like rivets. Intermediate filaments of keratin reinforce desmosomes.

                        3.         Gap junctions (or communicating junctions) provide cytoplasmic channels between adjacent cells.

                                    a.         Special membrane proteins surround these pores.

                                    b.         Ions, sugars, amino acids, and other small molecules can pass.

                                    c.         In embryos, gap junctions facilitate chemical communication during development.