CELLMOLE LECT2 PDF Lecture Notes

LECTURE NOTES 2. Cell and Cell Membranes Tour of the Cell Overview  All organisms are made of cells.  Many organisms are single-celled.  Even in multicellu...

LECTURE NOTES 2. Cell and Cell Membranes Tour of the Cell Overview  All organisms are made of cells.  Many organisms are single-celled.  Even in multicellular organisms, the cell is the basic unit of structure and function.  The cell is the simplest collection of matter that can live.  All cells are related by their descent from earlier cells. A. How We Study Cells 1. Microscopes provide windows to the world of the cell.  The discovery and early study of cells progressed with the invention of microscopes in 1590 and their improvement in the 17th century.  In a light microscope (LM), 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.  Microscopes vary in magnification and resolving power.  Magnification is the ratio of an object’s image to its real size.  Resolving power is a measure of image clarity.  It is the minimum distance two points can be separated and still be distinguished as two separate points.  Resolution is limited by the shortest wavelength of the radiation used for imaging.  The minimum resolution of a light microscope is about 200 nanometers (nm), the size of a small bacterium.  Light microscopes can magnify effectively to about 1,000 times the size of the actual specimen.  At higher magnifications, the image blurs.  Techniques developed in the 20th century have enhanced contrast and enabled particular cell components to be stained or labeled so they stand out.  While a light microscope can resolve individual cells, it cannot resolve much of the internal anatomy, especially the organelles.  To resolve smaller structures, we use an electron microscope (EM), 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. 1   Theoretically, the resolution of a modern EM could reach 0.002 nanometer (nm), but the practical limit is closer to about 2 nm.  Transmission electron microscopes (TEMs) 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 (SEMs) 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.  Electron microscopes reveal organelles that are impossible to resolve with the light microscope.  However, electron microscopes can only be used on dead cells.  Light microscopes do not have as high a resolution, but they can be used to study live cells.  Microscopes are major tools in cytology, the study of cell structures.  Cytology combined with biochemistry, the study of molecules and chemical processes in metabolism, to produce modern cell biology. 2. Cell biologists can isolate organelles to study their functions.  The goal of cell fractionation is to separate the major organelles of the cells so their individual functions can be studied.  This process is driven by an ultracentrifuge, a machine that can spin at up to 130,000 revolutions per minute and apply forces of more than 1 million times gravity (1,000,000 g).  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.  Cell fractionation prepares isolates of specific cell components.  This enables the functions of these organelles to be determined, especially by the reactions or processes catalyzed by their proteins.  For example, one cellular fraction was enriched in enzymes that function in cellular respiration.  Electron microscopy revealed that this fraction is rich in mitochondria. 2   This evidence helped cell biologists determine that mitochondria are the site of cellular respiration.  Cytology and biochemistry complement each other in correlating cellular structure and function. B. A Panoramic View of the Cell 1. Prokaryotic and eukaryotic cells differ in size and complexity.  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.  A major difference between prokaryotic and eukaryotic cells is the location of chromosomes.  In a eukaryotic cell, chromosomes are contained in a membrane-enclosed organelle, the nucleus.  In a prokaryotic cell, the DNA is concentrated in the nucleoid without a membrane separating it from the rest of the cell.  In eukaryote cells, the chromosomes are contained within a membranous nuclear envelope.  The region between the nucleus and the plasma membrane is the cytoplasm.  All the material within the plasma membrane of a prokaryotic cell is cytoplasm.  Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of specialized form and function.  These membrane-bound organelles are absent in prokaryotes.  Eukaryotic cells are generally much bigger than prokaryotic cells.  The logistics of carrying out metabolism set limits on cell size.  At the lower limit, the smallest bacteria, mycoplasmas, are between 0.1 to 1.0 micron.  Most bacteria are 1–10 microns in diameter.  Eukaryotic cells are typically 10–100 microns in diameter.  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. 3  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. 2. 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. C. The Nucleus and Ribosomes 1. The nucleus contains a eukaryotic cell’s genetic library.  The nucleus contains most of the genes in a eukaryotic cell.  Additional genes are located in mitochondria and chloroplasts.  The nucleus averages about 5 microns in diameter.  The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope.  The two membranes of the nuclear envelope are separated by 20–40 nm.  The envelope is perforated by pores that are about 100 nm in diameter.  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 nuclear side of the envelope is lined by the 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.  Within the nucleus, the DNA and associated proteins are organized into discrete units called chromosomes, structures that carry the genetic information. 4  Each chromosome is made up of fibrous material called chromatin, a complex of proteins and DNA.  Stained chromatin appears through light microscopes and electron microscopes as a diffuse mass.  As the cell prepares to divide, the chromatin fibers coil up and condense, becoming thick enough to be recognized as the familiar chromosomes.  Each eukaryotic species has a characteristic number of chromosomes.  A typical human cell has 46 chromosomes.  A human sex cell (egg or sperm) has only 23 chromosomes.  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.  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. 2. Ribosomes build a cell’s proteins.  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. D. The 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.  In spite of these connections, these membranes are diverse in function and structure.  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. 5  The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane. 1. The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions.  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.  The 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 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.  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.  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. 6   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. 2. 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. 3. Lysosomes are digestive compartments.  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. 7  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. 4. Vacuoles have diverse functions in cell maintenance.  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. E. Other Membranous Organelles 8 1. Mitochondria and chloroplasts are the main energy transformers of cells.  Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work.  Mitochondria are the sites of cellular respiration, generating ATP from the catabolism of sugars, fats, and other fuels in the presence of oxygen.  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.  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.  A typical mitochondrion is 1–10 microns long.  Mitochondria are quite dynamic: moving, changing shape, and dividing.  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.  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.  The chloroplast is 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. 9   Chloroplasts contain the green pigment chlorophyll as well as enzymes and other molecules that function in the photosynthetic production of sugar.  Chloroplasts measure about 2 microns × 5 microns and are found in leaves and other green organs of plants and algae.  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.  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. 2. 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 H 2O2 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. F. The Cytoskeleton  The cytoskeleton is a network of fibers extending throughout the cytoplasm.  The cytoskeleton organizes the structures and activities of the cell. 1. The cytoskeleton provides support, motility, and regulation.  The cytoskeleton provides mechanical support and maintains cell shape. 10  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.  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.  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.  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. 11   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.  They are about 0.25 microns in diameter and 2–20 microns long.  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.  Microfilaments are solid rods about 7 nm in diameter.  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. 12   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.  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.  Intermediate filaments range in diameter from 8–12 nanometers, 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. G. Cell Surfaces and Junctions 1. 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. 13  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. 2. 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. 3. 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. 4. A cell is a living unit greater than the sum of its parts. 14  While the cell has many structures with specific functions, all these structures must work together.  For example, macrophages use actin filaments to move and extend pseudopodia to capture their bacterial prey.  Food vacuoles are digested by lysosomes, a product of the endomembrane system of ER and Golgi.  The enzymes of the lysosomes and proteins of the cytoskeleton are synthesized on the ribosomes.  The information for the proteins comes from genetic messages sent by DNA in the nucleus.  All of these processes require energy in the form of ATP, most of which is supplied by the mitochondria.  A cell is a living unit greater than the sum of its parts. Cell Membrane and its Functions Overview  The plasma membrane separates the living cell from its nonliving surroundings.  This thin barrier, 8 nm thick, controls traffic into and out of the cell.  Like all biological membranes, the plasma membrane is selectively permeable, allowing some substances to cross more easily than others. A. Membrane Structure  The main macromolecules in membranes are lipids and proteins, but carbohydrates are also important.  The most abundant lipids are phospholipids.  Phospholipids and most other membrane constituents are amphipathic molecules.  Amphipathic molecules have both hydrophobic regions and hydrophilic regions.  The arrangement of phospholipids and proteins in biological membranes is described by the fluid mosaic model. 1. Membrane models have evolved to fit new data.  Models of membranes were developed long before membranes were first seen with electron microscopes in the 1950s.  In 1915, membranes isolated from red blood cells were chemically analyzed and found to be composed of lipids and proteins.  In 1925, E. Gorter and F. Grendel reasoned that cell membranes must be a phospholipid bilayer two molecules thick.  The molecules in the bilayer are arranged such that the hydrophobic fatty acid tails are sheltered from water while the hydrophilic phosphate groups interact with water. 15   Actual membranes adhere more strongly to water than do artificial membranes composed only of phospholipids.  One suggestion was that proteins on the surface of the membrane increased adhesion.  In 1935, H. Davson and J. Danielli proposed a sandwich model in which the phospholipid bilayer lies between two layers of globular proteins.  Early images from electron microscopes seemed to support the Davson-Danielli model, and until the 1960s, it was widely accepted as the structure of the plasma membrane and internal membranes.  Further investigation revealed two problems.  First, not all membranes were alike. Membranes differ in thickness, appearance when stained, and percentage of proteins.  Membranes with different functions differ in chemical composition and structure.  Second, measurements showed that membrane proteins are not very soluble in water.  Membrane proteins are amphipathic, with hydrophobic and hydrophilic regions.  If membrane proteins were at the membrane surface, their hydrophobic regions would be in contact with water.  In 1972, S. J. Singer and G. Nicolson presented a revised model that proposed that the membrane proteins are dispersed and individually inserted into the phospholipid bilayer.  In this fluid mosaic model, the hydrophilic regions of proteins and phospholipids are in maximum contact with water, and the hydrophobic regions are in a nonaqueous environment within the membrane.  A specialized preparation technique, freeze-fracture, splits a membrane along the middle of the phospholipid bilayer.  When a freeze-fracture preparation is viewed with an electron microscope, protein particles are interspersed in a smooth matrix, supporting the fluid mosaic model. 2. Membranes are fluid.  Membrane molecules are held in place by relatively weak hydrophobic interactions.  Most of the lipids and some proteins drift laterally in the plane of the membrane, but rarely flip- flop from one phospholipid layer to the other.  The lateral movements of phospholipids are rapid, about 2 microns per second. A phospholipid can travel the length of a typical bacterial cell in 1 second.  Many larger membrane proteins drift within the phospholipid bilayer, although they move more slowly than the phospholipids.  Some proteins move in a very directed manner, perhaps guided or driven by motor proteins attached to the cytoskeleton.  Other proteins never move and are anchored to the cytoskeleton. 16  Membrane fluidity is influenced by temperature. As temperatures cool, membranes switch from a fluid state to a solid state as the phospholipids pack more closely.  Membrane fluidity is also influenced by its components. Membranes rich in unsaturated fatty acids are more fluid that those dominated by saturated fatty acids because the kinks in the unsaturated fatty acid tails at the locations of the double bonds prevent tight packing.  The steroid cholesterol is wedged between phospholipid molecules in the plasma membrane of animal cells.  At warm temperatures (such as 37°C), cholesterol restrains the movement of phospholipids and reduces fluidity.  At cool temperatures, it maintains fluidity by preventing tight packing.  Thus, cholesterol acts as a “temperature buffer” for the membrane, resisting changes in membrane fluidity as temperature changes.  To work properly with active enzymes and appropriate permeability, membranes must be about as fluid as salad oil.  Cells can alter the lipid composition of membranes to compensate for changes in fluidity caused by changing temperatures.  For example, cold-adapted organisms such as winter wheat increase the percentage of unsaturated phospholipids in their membranes in the autumn.  This prevents membranes from solidifying during winter. 3. Membranes are mosaics of structure and function.  A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer.  Proteins determine most of the membrane’s specific functions.  The plasma membrane and the membranes of the various organelles each have unique collections of proteins.  There are two major populations of membrane proteins.  Peripheral proteins are not embedded in the lipid bilayer at all.  Instead, they are loosely bound to the surface of the protein, often connected to integral proteins.  Integral proteins penetrate the hydrophobic core of the lipid bilayer, often completely spanning the membrane (as transmembrane proteins).  The hydrophobic regions embedded in the membrane’s core consist of stretches of nonpolar amino acids, often coiled into alpha helices.  Where integral proteins are in contact with the aqueous environment, they have hydrophilic regions of amino acids.  On the cytoplasmic side of the membrane, some membrane proteins connect to the cytoskeleton. 17   On the exterior side of the membrane, some membrane proteins attach to the fibers of the extracellular matrix.  The proteins of the plasma membrane have six major functions: 1. Transport of specific solutes into or out of cells. 2. Enzymatic activity, sometimes catalyzing one of a number of steps of a metabolic pathway. 3. Signal transduction, relaying hormonal messages to the cell. 4. Cell-cell recognition, allowing other proteins to attach two adjacent cells together. 5. Intercellular joining of adjacent cells with gap or tight junctions. 6. Attachment to the cytoskeleton and extracellular matrix, maintaining cell shape and stabilizing the location of certain membrane proteins. 4. Membrane carbohydrates are important for cell-cell recognition.  The plasma membrane plays the key role in cell-cell recognition.  Cell-cell recognition, the ability of a cell to distinguish one type of neighboring cell from another, is crucial to the functioning of an organism.  This attribute is important in the sorting and organization of cells into tissues and organs during development.  It is also the basis for rejection of foreign cells by the immune system.  Cells recognize other cells by binding to surface molecules, often carbohydrates, on the plasma membrane.  Membrane carbohydrates are usually branched oligosaccharides with fewer than 15 sugar units.  They may be covalently bonded to lipids, forming glycolipids, or more commonly to proteins, forming glycoproteins.  The oligosaccharides on the external side of the plasma membrane vary from species to species, from individual to individual, and even from cell type to cell type within the same individual.  This variation distinguishes each cell type.  The four human blood groups (A, B, AB, and O) differ in the external carbohydrates on red blood cells. 5. Membranes have distinctive inside and outside faces.  Membranes have distinct inside and outside faces. The two layers may differ in lipid composition. Each protein in the membrane has a directional orientation in the membrane.  The asymmetrical orientation of proteins, lipids and associated carbohydrates begins during the synthesis of membrane in the ER and Golgi apparatus.  Membrane lipids and proteins are synthesized in the endoplasmic reticulum. Carbohydrates are added to proteins in the ER, and the resulting glycoproteins are further modified in the Golgi apparatus. Glycolipids are also produced in the Golgi apparatus. 18  When a vesicle fuses with the plasma membrane, the outside layer of the vesicle becomes continuous with the inside layer of the plasma membrane. In that way, molecules that originate on the inside face of the ER end up on the outside face of the plasma membrane. B. Traffic across Membranes 1. A membrane’s molecular organization results in selective permeability.  A steady traffic of small molecules and ions moves across the plasma membrane in both directions.  For example, sugars, amino acids, and other nutrients enter a muscle cell, and metabolic waste products leave.  The cell absorbs oxygen and expels carbon dioxide.  It also regulates concentrations of inorganic ions, such as Na+, K+, Ca2+, and Cl−, by shuttling them across the membrane.  However, substances do not move across the barrier indiscriminately; membranes are selectively permeable.  The plasma membrane allows the cell to take up many varieties of small molecules and ions and exclude others. Substances that move through the membrane do so at different rates.  Movement of a molecule through a membrane depends on the interaction of the molecule with the hydrophobic core of the membrane.  Hydrophobic molecules, such as hydrocarbons, CO2, and O2, can dissolve in the lipid bilayer and cross easily.  The hydrophobic core of the membrane impedes the direct passage of ions and polar molecules, which cross the membrane with difficulty.  This includes small molecules, such as water, and larger molecules, such as glucose and other sugars.  An ion, whether a charged atom or molecule, and its surrounding shell of water also has difficulty penetrating the hydrophobic core.  Proteins assist and regulate the transport of ions and polar molecules.  Specific ions and polar molecules can cross the lipid bilayer by passing through transport proteins that span the membrane.  Some transport proteins, called channel proteins, have a hydrophilic channel that certain molecules or ions can use as a tunnel through the membrane.  For example, the passage of water through the membrane can be greatly facilitated by channel proteins known as aquaporins.  Other transport proteins, called carrier proteins, bind to molecules and change shape to shuttle them across the membrane.  Each transport protein is specific as to the substances that it will translocate. 19   For example, the glucose transport protein in the liver will carry glucose into the cell but will not transport fructose, its structural isomer. 2. Passive transport is diffusion across a membrane with no energy expenditure.  Diffusion is the tendency of molecules of any substance to spread out in the available space.  Diffusion is driven by the intrinsic kinetic energy (thermal motion or heat) of molecules.  Movements of individual molecules are random.  However, movement of a population of molecules may be directional.  Imagine a permeable membrane separating a solution with dye molecules from pure water. If the membrane has microscopic pores that are large enough, dye molecules will cross the barrier randomly.  The net movement of dye molecules across the membrane will continue until both sides have equal concentrations of the dye.  At this dynamic equilibrium, as many molecules cross one way as cross in the other direction.  In the absence of other forces, a substance will diffuse from where it is more concentrated to where it is less concentrated, down its concentration gradient.  No work must be done to move substances down the concentration gradient.  Diffusion is a spontaneous process that decreases free energy and increases entropy by creating a randomized mixture.  Each substance diffuses down its own concentration gradient, independent of the concentration gradients of other substances.  The diffusion of a substance across a biological membrane is passive transport because it requires no energy from the cell to make it happen.  The concentration gradient itself represents potential energy and drives diffusion.  Because membranes are selectively permeable, the interactions of the molecules with the membrane play a role in the diffusion rate.  Diffusion of molecules of limited permeability through the lipid bilayer may be assisted by transport proteins. 3. Osmosis is the passive transport of water.  Differences in the relative concentration of dissolved materials in two solutions can lead to the movement of ions from one to the other.  The solution with the higher concentration of solutes is hypertonic relative to the other solution.  The solution with the lower concentration of solutes is hypotonic relative to the other solution.  These are comparative terms. 20   Tap water is hypertonic compared to distilled water but hypotonic compared to seawater.  Solutions with equal solute concentrations are isotonic.  Imagine that two sugar solutions differing in concentration are separated by a membrane that will allow water through, but not sugar.  The hypertonic solution has a lower water concentration than the hypotonic solution.  More of the water molecules in the hypertonic solution are bound up in hydration shells around the sugar molecules, leaving fewer unbound water molecules.  Unbound water molecules will move from the hypotonic solution, where they are abundant, to the hypertonic solution, where they are rarer. Net movement of water continues until the solutions are isotonic.  The diffusion of water across a selectively permeable membrane is called osmosis.  The direction of osmosis is determined only by a difference in total solute concentration.  The kinds of solutes in the solutions do not matter.  This makes sense because the total solute concentration is an indicator of the abundance of bound water molecules (and, therefore, of free water molecules).  When two solutions are isotonic, water molecules move at equal rates from one to the other, with no net osmosis.  The movement of water by osmosis is crucial to living organisms. 4. Cell survival depends on balancing water uptake and loss.  An animal cell (or other cell without a cell wall) immersed in an isotonic environment experiences no net movement of water across its plasma membrane.  Water molecules move across the membrane but at the same rate in both directions.  The volume of the cell is stable.  The same cell in a hypertonic environment will lose water, shrivel, and probably die.  A cell in a hypotonic solution will gain water, swell, and burst.  For organisms living in an isotonic environment (for example, many marine invertebrates), osmosis is not a problem.  The cells of most land animals are bathed in extracellular fluid that is isotonic to the cells.  Organisms without rigid walls have osmotic problems in either a hypertonic or hypotonic environment and must have adaptations for osmoregulation, the control of water balance, to maintain their internal environment.  For example, Paramecium, a protist, is hypertonic to the pond water in which it lives.  In spite of a cell membrane that is less permeable to water than other cells, water still continually enters the Paramecium cell. 21   To solve this problem, Paramecium cells have a specialized organelle, the contractile vacuole, which functions as a bilge pump to force water out of the cell.  The cells of plants, prokaryotes, fungi, and some protists have walls that contribute to the cell’s water balance.  A plant cell in a hypotonic solution will swell until the elastic cell wall opposes further uptake.  At this point the cell is turgid (very firm), a healthy state for most plant cells.  Turgid cells contribute to the mechanical support of the plant.  If a plant cell and its surroundings are isotonic, there is no movement of water into the cell. The cell becomes flaccid (limp), and the plant may wilt.  The cell wall provides no advantages when a plant cell is immersed in a hypertonic solution. As the plant cell loses water, its volume shrinks. Eventually, the plasma membrane pulls away from the wall. This plasmolysis is usually lethal. 5. Specific proteins facilitate passive transport of water and selected solutes.  Many polar molecules and ions that are normally impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane.  The passive movement of molecules down their concentration gradient via transport proteins is called facilitated diffusion.  Two types of transport proteins facilitate the movement of molecules or ions across membranes: channel proteins and carrier proteins.  Some channel proteins simply provide hydrophilic corridors for the passage of specific molecules or ions.  For example, water channel proteins, aquaporins, greatly facilitate the diffusion of water.  Many ion channels function as gated channels. These channels open or close depending on the presence or absence of a chemical or physical stimulus.  If chemical, the stimulus is a substance other than the one to be transported.  For example, stimulation of a receiving neuron by specific neurotransmitters opens gated channels to allow sodium ions into the cell.  When the neurotransmitters are not present, the channels are closed.  Some transport proteins do not provide channels but appear to actually translocate the solute- binding site and solute across the membrane as the transport protein changes shape.  These shape changes may be triggered by the binding and release of the transported molecule.  In certain inherited diseases, specific transport systems may be defective or absent.  Cystinuria is a human disease characterized by the absence of a protein that transports cysteine and other amino acids across the membranes of kidney cells.  An individual with cystinuria develops painful kidney stones as amino acids accumulate and crystallize in the kidneys. 22 6. Active transport uses energy to move solutes against their gradients.  Some transport proteins can move solutes across membranes against their concentration gradient, from the side where they are less concentrated to the side where they are more concentrated.  This active transport requires the cell to expend metabolic energy.  Active transport enables a cell to maintain its internal concentrations of small molecules that would otherwise diffuse across the membrane.  Active transport is performed by specific proteins embedded in the membranes.  ATP supplies the energy for most active transport.  ATP can power active transport by transferring a phosphate group from ATP (forming ADP) to the transport protein.  This may induce a conformational change in the transport protein, translocating the solute across the membrane.  The sodium-potassium pump actively maintains the gradient of sodium ions (Na+) and potassium ions (K+) across the plasma membrane of animal cells.  Typically, K+ concentration is low outside an animal cell and high inside the cell, while Na+ concentration is high outside an animal cell and low inside the cell.  The sodium-potassium pump maintains these concentration gradients, using the energy of one ATP to pump three Na+ out and two K+ in. 7. Some ion pumps generate voltage across membranes.  All cells maintain a voltage across their plasma membranes.  Voltage is electrical potential energy due to the separation of opposite charges.  The cytoplasm of a cell is negative in charge compared to the extracellular fluid because of an unequal distribution of cations and anions on opposite sides of the membrane.  The voltage across a membrane is called a membrane potential, and ranges from −50 to −200 millivolts (mV). The inside of the cell is negative compared to the outside.  The membrane potential acts like a battery.  The membrane potential favors the passive transport of cations into the cell and anions out of the cell.  Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane.  One is a chemical force based on an ion’s concentration gradient.  The other is ann electrical force based on the effect of the membrane potential on the ion’s movement.  An ion does not simply diffuse down its concentration gradient but diffuses down its electrochemical gradient. 23   For example, there is a higher concentration of Na+ outside a resting nerve cell than inside.  When the neuron is stimulated, a gated channel opens and Na+ diffuse into the cell down their electrochemical gradient. The diffusion of Na+ is driven by their concentration gradient and by the attraction of cations to the negative side of the membrane.  Special transport proteins, electrogenic pumps, generate the voltage gradient across a membrane.  The sodium-potassium pump in animals restores the electrochemical gradient not only by the active transport of Na+ and K+, setting up a concentration gradient, but because it pumps two K+ inside for every three Na+ that it moves out, setting up a voltage across the membrane.  The sodium-potassium pump is the major electrogenic pump of animal cells.  In plants, bacteria, and fungi, a proton pump is the major electrogenic pump, actively transporting H+ out of the cell.  Proton pumps in the cristae of mitochondria and the thylakoids of chloroplasts concentrate H + behind membranes.  These electrogenic pumps store energy that can be accessed for cellular work. 8. In cotransport, a membrane protein couples the transport of two solutes.  A single ATP-powered pump that transports one solute can indirectly drive the active transport of several other solutes in a mechanism called cotransport.  As the solute that has been actively transported diffuses back passively through a transport protein, its movement can be coupled with the active transport of another substance against its concentration gradient.  Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive the active transport of amino acids, sugars, and other nutrients into the cell.  One specific transport protein couples the diffusion of protons out of the cell and the transport of sucrose into the cell. Plants use the mechanism of sucrose-proton cotransport to load sucrose into specialized cells in the veins of leaves for distribution to nonphotosynthetic organs such as roots. 9. Exocytosis and endocytosis transport large molecules across membranes.  Small molecules and water enter or leave the cell through the lipid bilayer or by transport proteins.  Large molecules, such as polysaccharides and proteins, cross the membrane via vesicles.  During exocytosis, a transport vesicle budded from the Golgi apparatus is moved by the cytoskeleton to the plasma membrane.  When the two membranes come in contact, the bilayers fuse and spill the contents to the outside.  Many secretory cells use exocytosis to export their products.  During endocytosis, a cell brings in macromolecules and particulate matter by forming new vesicles from the plasma membrane. 24  Endocytosis is a reversal of exocytosis, although different proteins are involved in the two processes.  A small area of the plasma membrane sinks inward to form a pocket.  As the pocket deepens, it pinches in to form a vesicle containing the material that had been outside the cell.  There are three types of endocytosis: phagocytosis (“cellular eating”), pinocytosis (“cellular drinking”), and receptor-mediated endocytosis.  In phagocytosis, the cell engulfs a particle by extending pseudopodia around it and packaging it in a large vacuole.  The contents of the vacuole are digested when the vacuole fuses with a lysosome.  In pinocytosis, a cell creates a vesicle around a droplet of extracellular fluid. All included solutes are taken into the cell in this nonspecific process.  Receptor-mediated endocytosis allows greater specificity, transporting only certain substances.  This process is triggered when extracellular substances, or ligands, bind to special receptors on the membrane surface. The receptor proteins are clustered in regions of the membrane called coated pits, which are lined on their cytoplasmic side by a layer of coat proteins.  Binding of ligands to receptors triggers the formation of a vesicle by the coated pit, bringing the bound substances into the cell.  Receptor-mediated endocytosis enables a cell to acquire bulk quantities of specific materials that may be in low concentrations in the environment.  Human cells use this process to take in cholesterol for use in the synthesis of membranes and as a precursor for the synthesis of steroids.  Cholesterol travels in the blood in low-density lipoproteins (LDL), complexes of protein and lipid.  These lipoproteins act as ligands to bind to LDL receptors and enter the cell by endocytosis.  In an inherited disease called familial hypercholesterolemia, the LDL receptors are defective, leading to an accumulation of LDL and cholesterol in the blood.  This contributes to early atherosclerosis. ------ BIOL 107 Cell and Molecular Biology 2024-2025 1S MTh 9:00–10:30; BQRST1&2 25