Chapter 4: The Organization of Cells

The Cell: The Basic Unit of Life

· Which came first, the chicken or the egg? This ancient conundrum applies equally at the cell chemistry level.

· It takes the instructions found in DNA to make protein, and it takes protein to make DNA.

· It takes a series of protein-enzyme catalyzed reactions to make lipid, but without lipid membrane, the compartmentalization necessary for the synthesis of the lipid would not exist. Moreover, without an existing membrane, new lipid and membrane-associated protein cannot organize itself as it is found in living cells.

· See chapter 25 for a discussion of the origin of life

· The cell theory states that all organisms are composed of cells, and all cells come from preexisting cells. It is the basis for studying all life, whether single-celled or multicellular.

Cell size is limited by the surface area-to-volume ratio

· Most cells are tiny, with diameters in the range of 1 to 100 mm.

· The surface of a cell is the area that interfaces with the cell’s environment. The larger the surface area of a cell, the faster a cell can take in substances and remove waste products.

· The volume of a cell is a measure of the space inside a cell. The larger the volume of a cell, the more chemical activity it can have.

· Surface area-to-volume ratio is defined as the surface area divided by the volume. For any given shape, increasing volume decreases the surface area-to-volume ratio (See Figure 4.2.)

· Shape also influences surface area-to-volume ratios.

· A sphere has the least surface area-to-volume ratio of any shape.

· Imagine you have a lump of clay. Fashioning it into a sphere minimizes the surface area.

· Flatten the ball of clay to make a pancake shape, and the surface area increases, while the volume remains the same. Cells like red blood cells flatten into a pancake shape to increase surface area.

· Fashioning the clay into a thin string also increases the surface area without increasing the volume. Nerve cells have this shape, and this allows some of them to be a meter long or more.

· If the clay is spherical but the surface is irregular with many fine projections coming off the surface, surface area is greatly increased. In epithelial cells, such projections are called microvilli.

Microscopes are needed to visualize cells

· The small size of cells makes the use of microscopes necessary to view them. (Figure 4.1 shows the relative sizes of biological objects ranging from atoms to trees.)

· With normal human vision one can resolve objects about 200 mm (0.2 mm) in size. To resolve means to distinguish two separate things. If two objects are too close together, they start to look like one object.

· Light microscopes use glass lenses and visible light, but have resolution limits. The resolving power of light microscopes is typically 0.2 mm (0.2 ´ 10^-6 m), but this depends on the wavelength of the illuminating light. In general, resolution is about 1000 times better than an unaided human eye. Living or killed and fixed cells may be viewed with light microscopes.

· Electron microscopes have magnets rather than glass lenses to focus an electron beam.

· The wavelength of the electron beam is far less than light, and the resulting image resolution is far greater.

· This image is not visible without the use of either film or a fluorescent screen.

· Resolution is about 0.5 nm (0.5 ´ 10^–9 m) or 250,000 times finer than the human eye.

· Subcellular features can only be seen if the cells are killed and fixed with special fixatives and stains.

· The electron beam does not carry color information. All electron micrographs are originally black and white, though false color is often added for clarity.

· See Figure 4.3 for examples of micrographs. Chapter 4 of the Instructor’s Resource CD-ROM includes photographs of light and electron microscopes and examples of light and electron micrographs. The mitosis sequence in Chapter 9 of the IRCD includes examples of fluorescent microscopy.

· Cells are also studied using many other technologies: molecular separation techniques, cell culture, radioisotope labeling, and more.

All cells are surrounded by a plasma membrane

· The plasma membrane is a continuous membrane that surrounds the fluids and other structures of a cell.

· Every cell has a plasma membrane.

· The membrane is composed of a lipid bilayer with proteins floating within it and protruding from it.

· Some proteins associate with the membrane.

· Some proteins traverse the membrane, with one part exposed on the inner cytoplasmic side and the other on the outer face of the cell.

· The plasma membrane acts as a selectively permeable barrier. Some substances can diffuse in and out; others cannot.

· The plasma membrane is an interface for cells where information is received from adjacent cells and extracellular signals.

· The membranes allow the cell to maintain a rather constant internal environment as well as separate and distinct chemical and structural environments.

Cells show two organizational patterns

· Living organisms can be classified into one of two major categories based on where, within the cell, the most genetic material is stored. (See Figure 4.4.)

· Organisms called prokaryotes have no nucleus or other membrane-bounded compartments.

· Prokaryotes lack distinct organelles, although some do have invaginous membrane structures.

· Organisms called eukaryotes have a membrane-bounded nucleus.

· Eukaryotic cells usually have other membrane-bounded compartments or organelles as well.

Prokaryotic Cells

· Prokaryotes inhabit the widest range of environmental extremes.

· They can be found living at temperatures above boiling at thermal vents deep in the ocean. They also occur in extremely salty environments.

· Some have been found deep in Earth's crust, far away from the sun, photosynthesizing organisms, and oxygen. These prokaryotes use inorganic, reduced chemicals for an energy source.

All prokaryotic cells share certain features

· All have a plasma membrane.

· All have a region called the nucleoid where the DNA is concentrated.

· The cytoplasm, the plasma-enclosed region of prokaryotes, consists of the nucleoid, ribosomes which are the molecular protein synthesis machines, and a liquid portion called the cytosol.

· The Instructor’s Resource CD-ROM includes several micrographs of prokaryotes, including micrographs of outer membranes, photosynthetic membranes, flagella, and pili.

Some prokaryotic cells have specialized features

· Most prokaryotic cells have a cell wall just outside the plasma membrane. (See Figure 4.4.)

· The cell wall functions to prevent plasma membrane lysis (bursting) when cells are exposed to solutions with lower solute concentrations than the cell interior. It also protects the membrane.

· In most bacteria, (but not in Archaea), the cell wall is made of a polymer of amino sugars called peptidoglycan, which is covalently cross-linked to form one giant molecule around the entire cell.

· Some bacteria have another outer membrane outside the cell wall, a polysaccharide-rich, phospholipid membrane. This membrane has proteins embedded that make it more permeable than the interior membrane.

· Some bacteria have even another layer in addition to a plasma membrane, a cell wall, and an outer membrane. The outermost slimy layer is made of polysaccharides and is referred to as a capsule.

· For some bacteria, this capsule provides a means to escape detection by the immune systems of the animals they infect.

· The capsule can prevent drying out of the cell and help trap other cells for food.

· If the cell loses the capsule, it can survive. Therefore, it is not essential to cell life.

· Some bacteria, including cyanobacteria, can carry on photosynthesis, or the ability to collect solar energy.

· Cyanobacteria have chlorophyll in the infolded plasma membrane for this purpose. (See Figure 4.5.)

· In eukaryotes, separate organelles have specialized membranes for this process.

· Some bacteria have mesosomes, which are involved in cell division or in certain energy-releasing reactions.

· Like the photosynthetic membrane system, they are formed from plasma membrane folding.

· Eukaryotes use mitochondria, separate membrane-bounded organelles, for energy release.

· Some bacteria have flagella. These are locomotary structures that are shaped like a corkscrew. They spin like a propeller to move the bacteria. The flagella bear no structural commonality to the flagella found in eukaryotic cells, such as sperm cells. (See Figure 4.6.)

· Some bacteria have pili, threadlike structures that help bacteria adhere to one another during mating or to other cells for food and protection.

Eukaryotic Cells

· Animals, plants, fungi, and protists have a membrane-bounded nucleus in each of their cells and are classified as eukaryotes.

· Eukaryotic cells tend to be larger than prokaryotic cells.

· Eukaryotic cells have a variety of membrane-bounded compartments called organelles.

· Eukaryotes have a protein scaffolding, called the cytoskeleton, that provides shape and structure to cells, among other functions.

· Figure 4.7 shows the different structures and organelles of eukaryotes. The Instructor’s Resource CD-ROM includes several micrographs of eukaryotic cell structures.

Compartmentalization is the key to eukaryotic cell function

· The subunits, or compartments, within eukaryotic cells are called organelles.

· The nucleus contains most of the cell’s genetic material (DNA).

· The mitochondrion is a power plant and industrial park for the storage and conversion of energy.

· The endoplasmic reticulum and Golgi apparatus make up a compartment where proteins are packaged and sent to appropriate locations in the cell.

· The lysosome and vacuole are cellular digestive systems, where large molecules are hydrolyzed into usable monomers.

· The chloroplast performs photosynthesis.

· Membranes surrounding these organelles keep inappropriate molecules, which might disturb organelle function, away and act as traffic regulators for raw materials into and out of the organelle.

Organelles that Process Information

· In eukaryotic cells, most DNA, the information-storage molecule, is found in the nucleus.

· Information is translated from the language of DNA into the language of proteins at the ribosomes.

The nucleus stores most of the cell’s DNA

· The nucleus, usually the largest organelle in a cell, is the site of DNA duplication to support cell reproduction.

· The nucleus also plays a role in DNA control of cell activities.

· Within the nucleus is a specialized, non-membrane-bounded region called the nucleolus, where ribosomes, the molecular protein synthesis machinery, are initially assembled.

· Two lipid bilayers form the nuclear envelope.

· The nuclear envelope is perforated with nuclear pores. (See Figure 4.8.)

· Each pore is about 9 nm in diameter. The nuclear pores connect the interior of the nucleus with the rest of the cytoplasm.

· Outer and inner membranes are continuous at these pores.

· A pore complex, consisting of eight very large protein granules arranged in an octagon, surrounds each pore.

· RNA and proteins must pass through these pores to enter or leave the nucleus.

· The DNA of the nucleus is the information molecule that provides the instructions needed for cellular and organismal life.

· It is the RNA, which is generated by using DNA as a template, that actually determines the construction of proteins.

· The nucleus is where the RNA is made, but all proteins are made outside the nucleus. Therefore, the nucleus isolates these two processes.

· At certain sites the nuclear envelope is continuous with another organelle, the endoplasmic reticulum.

· Molecules that are small can enter and leave the nucleus by simple diffusion, but traffic of large molecules is regulated.

· The chromatin consists of diffuse or very long thin fibers in which DNA is bound to proteins. (See Figure 4.9.)

· In humans, there are 46 separate strands of chromatin in each nucleus (with the exception of the sex cells).

· Prior to cell division these condense and organize into structures recognized as chromosomes.

· Surrounding the chromatin is the nucleoplasm within which a network of proteins, the nuclear matrix, organizes the chromatin.

· The nuclear lamina is a meshwork of proteins generated by (reversible) polymerization that maintains the shape of the nuclear envelope and the nucleus. (See Figure 4.10.)

· When the cell is about to divide, the nuclear envelope fragments into pieces of membrane with pore complexes because the nuclear lamina depolymerizes.

· At the end of cell division a nucleus reforms in each of the daughter cells.

Ribosomes are the sites of protein synthesis.

· Ribosomes are tiny granules compared to organelles, but huge compared to proteins.

· In eukaryotes, functional ribosomes are found in three places: free in the cytoplasm, in mitochondria, and bound to the endoplasmic reticulum. They are also found in chloroplasts.

· Ribosomes are the sites of protein synthesis.

· They consist of a certain type of RNA, called ribosomal RNA, and more than 50 other proteins.

The Endomembrane System

· The membrane of eukaryotic cells is synthesized by the endoplasmic reticulum (ER). (See Figure 4.11.)

· There is a direct flow of this membrane to the nuclear envelope, and via small vesicles, to the Golgi apparatus, lysosomes, and plasma membrane.

· These structures together constitute the endomembrane system.

The endoplasmic reticulum is a complex factory

· The ER is a network of interconnecting membranes distributed throughout the cytoplasm.

· The internal compartment, called the lumen, is a separate part of the cell with a distinct protein and ion composition.

· The ER is where most of the membrane of the cell is found.

· Approximately 15% of the entire fluid volume of the cell is inside the ER.

· The ER's folding generates a surface area much greater than that of the plasma membrane.

· At certain sites, the ER membrane is continuous with the outer nuclear envelope membrane.

· The rough ER (RER) has ribosomes attached, which actively synthesize proteins destined for the ER interior or incorporation into the membrane of the ER.

· Some of these membrane and lumen proteins stay with the ER, some are transported to other points of the endomembrane system, and others escape the ER only to be returned.

· Some of the proteins that enter the lumen or face the lumen interior get folded, shaped by disulfide bridges, and/or get carbohydrate groups added.

· Some of the proteins that enter the ER have address information that instructs their final destination. By default, those with no address information are transported out of the cell.

· There is a ribosome-free region of the ER called the smooth endoplasmic reticulum (SER).

· The SER of liver cells is the site for the synthesis and hydrolysis of glycogen (animal starch).

· SER of the liver is also the site for drug detoxification (including alcohol) and cholesterol and steroid synthesis.

· Cells that are specialized for synthesizing proteins for extracellular export have extensive ER membrane systems. Examples are the cells of glands.

The Golgi apparatus stores, modifies, and packages proteins

· The Golgi apparatus is difficult to see using standard light microscopy, but clearly visible with the electron microscope. (See Figure 4.12.)

· The Golgi receives its lipid membrane from vesicles that bud off the ER. Proteins are embedded in these vesicles and carried within them.

· The organization of the Golgi varies in different organisms, but always consists of compartments, or cisternae, and small membrane-bounded vesicles.

· In organisms other than vertebrates, compartments are separate and scattered.

· In vertebrates, the Golgi is stacked like pancakes.

· The compartment closest to the nucleus is called the cis region.

· The middle compartment is the medial region.

· The compartment closest to the plasma membrane is the trans region.

· These three parts are the sites of different functions and have different associated enzymes.

· Vesicles from the ER fuse to the cis region. Vesicles from the cis compartment move to the next compartment, the medial region, and then to the trans compartment.

· Modifications and sorting occur during this process. Chemical signals inform the system about the appropriate destinations for the products.

· Some vesicles fuse with the cytoplasmic face of the plasma membrane. (This is where the plasma membrane originates.) The contents of the vesicles are released to the outside of the cell.

· This whole phenomenon of shipping into and out of vesicles is called vesicular trafficking and is somewhat analogous to a conveyer belt flow of materials.

Lysosomes contain digestive enzymes

· Lysosomes are organelles that come in part from the Golgi. They are approximately 1 mm in diameter. (See Figure 4.13.)

· The Golgi creates primary lysosomes, vesicles containing digestive enzymes.

· Food and foreign objects are brought into the cytoplasm through a process called phagocytosis. The resulting phagosomes are vesicles that contain the foreign material.

· Primary lysosomes created by the Golgi fuse with phagosomes to create secondary lysosomes.

· Within the secondary lysosomes, the digestive enzymes hydrolyze macromolecules such as nucleic acids, proteins, lipids, and polysaccharides into monomers. These small molecules diffuse through the lysosome’s membrane into the cytoplasm.

· The remaining undigested material is expelled from the cell when the "used" secondary lysosome fuses with the plasma membrane and releases the undigested contents.

· Lysosomes are also the sites where digestion of spent cellular components occurs, a process called autophagy.

· Cells can take up large molecules and some take up whole cells in a process called endocytosis. Three different types of endocytosis occur.

· One is phagocytosis. (“cell eating”). The cell envelops another cell with its own membrane as it invaginates around it. Not all cells can do this, but it is very common among protists.

· Another is pinocytosis. (“cell drinking”). This is a means of fluid uptake. These vesicles are much smaller.

· The last is receptor-mediated endocytosis. The vesicles are small, like in pinocytosis, but cell surface receptors are involved.

· Cells may also give up water, wastes, and manufactured products of cells (such as hormones) by a process called exocytosis.

Organelles that Process Energy

Mitochondria are energy transformers

· The primary function of mitochondria is to convert the potential energy of fuel molecules into a form that the cell can use.

· Mitochondria are small organelles less than 1.5 mm in diameter, and 2 to 8 mm in length. (See Figure 4.14.)

· Mitochondria have an outer lipid bilayer and a highly folded inner membrane.

· The space between the outer and inner membrane is called the intermembrane space.

· Within the inner membrane is the mitochondrial matrix.

· Mitochondria have a small amount of DNA and some ribosomes located within this matrix.

· The inner deep-folded membrane has embedded proteins, which are important to the functioning of the organelle. The folding gives this membrane a greater surface area on which chemical reactions can occur.

· Mitochondria use simple energy molecules and oxygen to generate ATP from ADP. Most of the oxygen taken in by eukaryotic organisms is used directly by mitochondria.

Plastids photosynthesize or store materials

· Plastids are organelles of several types found in eukaryotic plants and some protists.

· Chloroplasts are one type of plastid. (See Figure 4.15.)

· Chloroplasts are the sites where photosynthesis (conversion of light energy to chemical energy) occurs.

· Structurally, chloroplasts are remarkably similar to mitochondria.

· Chloroplasts have special pigments embedded in the membranes of the thylakoid vesicles.

· The chloroplast has an outer lipid bilayer; next is an inner membrane. As with mitochondria, the space between these is the intermembrane space. Next is the stroma, which is the fluid-filled area of the inner membrane. Inside the stroma are the membrane-bounded thylakoids. This is where chlorophyll and other pigments for photosynthesis are embedded.

· Chloroplasts have a small amount of DNA and some ribosomes in the stroma.

· Other plastids found in plants include chromoplasts, such as those that cause the red color of tomatoes. Leucoplasts are plastids specialized for storage of starch and fats.

Mitochondria and chloroplasts may have an endosymbiotic origin

· Organelles with their own DNA? Where did chloroplasts and mitochondria come from?

· One proposal is the endosymbiosis theory.

· The suggestion is that both organelles were formerly prokaryotic organisms that somehow became incorporated into a larger cell.

· This structure was a successful advantage and a symbiotic system evolved.

· Today, both mitochondria and chloroplasts are self-duplicating organelles.

· Chloroplast and mitochondrial DNA, ribosomes, and gene reproduction on the organelle level seem to resemble that of prokaryotes.

· See Figure 4.18 for a simple visual explanation of the endosymbiosis theory.

Other Organelles

Peroxisomes house specialized chemical reactions

· Peroxisomes, also called microbodies, are small organelles (0.2 to 1.7 mm in diameter). These are organelles specialized to compartmentalize toxic peroxides and break them down. (See Figure 4.19.)

· Glyoxysomes are structurally similar organelles found in plants.

Vacuoles are filled with water and soluble substances

· Vacuoles are found in plants and protists. They are filled with an aqueous solution. Plants store wastes and pigments in vacuoles and use them to discourage being eaten by animals or to attract others for pollination and/or seed dispersal. (See Figure 4.20.)

· Vacuoles may develop turgor pressure, a swelling that helps the plant cell maintain support and rigidity.

· Water enters the vacuoles, and turgor pressure builds up as they press against the cell membrane and wall.

· Food vacuoles are formed in single-celled protists. They are similar to the phagosomes mentioned previously.

· The cytoplasm of freshwater protists is generally higher in salt concentration than in their freshwater environment; as a result, water tends to move into the cytoplasm. Many freshwater protists have a contractile vacuole that helps eliminate excess water and restore the proper salt balance in the cytoplasm.

The Cytoskeleton

· The cytoskeleton maintains cell shape and support, provides the mechanisms for cell and organismally controlled movement, and acts as tracks for "motor proteins" that help move materials within cells.

· There are three major types of cytoskeletal components. They are the microfilaments, intermediate filaments, and microtubules. (See Figure 4.21. The mitosis micrographs in Chapter 9 of the Instructor’s Resource CD-ROM are fluorescently stained to show the role of microfilaments and intermediate filaments in mitosis.)

Microfilaments function in support and movement

· Microfilaments may exist as single filaments, in bundles, or in networks. Each is 7 nm in diameter and several mm long.

· A single strand of actin polymer interacts with another to create a double helical microfilament.

· Microfilaments are needed for cell contraction, such as in muscle cells.

· Microfilaments add structure to the plasma membrane and shape to cells. (See Figure 4.23b.)

· They are involved in the flowing movement of cell fluids bearing specific organelles and proteins, a process called cytoplasmic streaming.

· They are also involved in the formation of pseudopodia, cellular extensions seen in the overt appearance of the amoeboid protists and human white blood cells.

· Microvilli are very fine plasma membrane–covered projections that some cells have to increase surface area. Their core is protein cross-linked actin bundles. (See Figure 4.23a.)

Intermediate filaments are tough supporting elements

· Intermediate filaments are found only in multicellular organisms and are ropelike assemblages 8 to 12 nm in diameter.

· These fibrous keratin proteins interact with each other and with other cellular components, particularly those of cell adhesion molecules.

· They are important to the tensile strength of cells, especially for tissues that must stretch, such as muscles.

Microtubules are long and hollow

· Microtubules are hollow cylinders 25 nm thick; they can be several mm in length.

· Microtubules provide a rigid intracellular skeleton for some cells, and they function as tracks that motor proteins can move along in the cell.

· Made from tubulin protein subunits, they regularly form and disassemble as the needs of the cell change.

· Tubulin is a globular protein made of a-tubulin and b-tubulin formed as a dimer (a polymer made up of only two monomers).

· Thirteen rows of tubulin dimers surround and define the central cavity.

· Each microtubule has a + end and a – end.

· Tubulin dimers can be added or subtracted at either end, but the + end is more dynamic. (See Figure 4.25).

Microtubules power cilia and flagella

· Microtubules are structurally essential parts of cilia and flagella, common locomotary appendages of cells.

· Cilia and flagella are plasma membrane–covered cell projections.

· Flagella are usually longer than cilia, and cells that have them usually only have one or two.

· Cilia are usually present in great numbers. (See Figure 4.24.)

· The microtubules in cilia and flagella are arranged in a 9 + 2 array.

· The nine are fused pairs of microtubules (called doublets) arranged to form an outer cylinder.

· Two unfused microtubules (the "2" of the 9 + 2 arrangement) are located in the center of the cylinder.

· At the base of each flagellum or cilium is a basal body. The nine pairs extend into the basal body, which may be the organizing area of these structures.

· In the basal body, there is no central microtubule and each of the nine pairs has an additional microtubule fused with it, making nine triplets instead of doublets.

· In both cilia and flagella, the microtubules are cross-linked by spokes of protein.

· Dynein is a motor protein that drives the cross-linked microtubule pairs past each other, resulting in the bending movement of cilia and flagella. Dynein changes its shape when energy is released from ATP. Many dynein molecules associate along the length of the microtubule pair. (See Figure 4.25).

· Both the plasma membrane and other protein components limit the amount of dynein that can move along the microtubule, so the dynein spokes regulate the amount of cilia or flagella bending.

· Kinesin is another motor protein that moves along microtubules. Kinesin associates with vesicles and moves them in the + direction along microtubule tracks. Dynein also moves vesicles, but in the – direction.

· Centrioles are found in an organizing center near the cell nucleus, and the microtubules that radiate from them help in the movement of chromosomes during cell division. They also provide tracks for intracellular molecular trafficking and help maintain the positions of certain organelles within the cell.

· Most eukaryotic cells have centrioles; exceptions are flowering plants, pine trees and their relatives, and some protists.

· Centrioles are similar to basal bodies, but are located toward the center of the cell.

· Centrioles, like basal bodies, are made of nine sets of three fused microtubules. (See Figure 4.26.)

Extracellular Structures

· Extracellular structures are made by cells of multicellular organisms, but are outside the cell membrane.

The plant cell wall consists largely of cellulose

· In plants, cell walls exist that are made primarily of cellulose. (See Figure 4.27.)

· The cell wall provides a rigid structure for the plasma membrane under turgor pressure, giving important support.

· It is a barrier to many fungi, bacteria, and other organisms that may cause plant diseases.

Multicellular animals have elaborate extracellular matrices

· Multicellular animals have an extracellular matrix. It is composed of fibrous proteins, like collagen, and glycoproteins. (See Figure 4.28.)

· An example is the cartilage of kneecaps and the nose.

· Epithelial cells, line the human body cavity, have a basement membrane of extracellular material called the basal lamina.

· This is extracellular matrix that connects and separates different cells from one another and provides strength.

· Proteoglycan, one component of the extracellular matrix, is huge. One molecule can be as large as 100 million daltons and take up as much space as an entire prokaryotic cell.

The Instructor’s Resource CD-ROM includes micrographs of prokaryotic cells and prokaryotic cellular structures (photosynthetic membranes, pili, etc.); micrographs of eukaryotic cells, organelles, and other substructures; photographs of light and electron microscopes; examples of different types of microscopy; and video microscopy of motor proteins, lamellipodia, organelles, and more.