The Cell.The Common Denominator of Living Things

4 THE CELL: THE COMMON DENOMINATOR OF LIVING THINGS Cells were discovered by Robert Hooke of England in the mid-seventeenth century, and named by him after the small dormitory-style rooms inhabited by monks. He first saw cell wall remains in thin slices of cork, using a microscope. Around the same time, Anton van Leeuwenhoek of Holland advanced the art of building microscopes, achieving magnification up to 500 times. With these he was able to make detailed studies of living cells. Further study led to the development in the nineteenth century of cell theory:
All living things are composed of one or more cells.
Cells are the basic units of living things and are the site for the reactions of life.
Under today’s conditions, all cells come from preexisting cells. The first tenet encompasses everything from single-celled bacteria to large animals and trees that can have trillions of cells. The second tenet recognizes that individual parts of cells are not by themselves viable. This tenet also excludes viruses from being classified as living things, since they do not metabolize. The third tenet leaves open the possibility of cells arising spontaneously under the conditions of the primitive Earth. The light microscope opened a new world to examination, literally under our noses. Typical cell sizes are about 1 mm for bacteria to 10 mm for most human cells. The human eye can resolve down to only about 100 mm (0.1 mm). The light microscope extends resolution down to 0.2 mm [200 nanometers (nm)], which is half the wavelength of violet light. An advance similar in magnitude to Hooke and Leeuwenhoek’s microscopes occurred in the 1960s with the development of electron microscopes. These can magnify by 30,000 to 100,000 times, yielding resolution down to 2 nm. This is enough to resolve some of the larger macromolecules such as proteins and nucleic acids. Another 65 66 THE CELL: THE COMMON DENOMINATOR OF LIVING THINGS leap was made in 1986, with the development of the atomic force microscope, which can resolve individual atoms and has been used to detect the shape of the DNA helix. These imaging tools, together with biochemical techniques, have led to continual advances in cytology, the study of cells. 4.1 PROKARYOTES AND EUKARYOTES As mentioned in Section 2.4, the highest level of biological classification, the domain, is based on cell type. Bacteria are made of the simpler prokaryotic cell; protists, fungi, plants, and animals are eukaryotic. Prokaryotes are smaller than eukaryotic cells and lack any internal membrane-bound structures. Eukaryotes have organelles, which are specialized structures within the cell that are surrounded by their own membranes, almost like cells within a cell. Some organelles, such as mitochondria, even have their own DNA. It is thought that prokaryotes are relatively primitive life-forms and that eukaryotes may have evolved from a symbiotic association in which an early form of prokaryotic cell incorporated other prokaryotes internally. For example, a large anaerobic prokaryote may have incorporated an aerobic bacterium. The latter eventually became mitochondria, the site of aerobic respiration in eukaryotes. Table 4.1 shows some of the similarities and differences between prokaryotic and eukaryotic cell structures. Figure 4.1 illustrates a typical bacterial (prokaryotic) cell. The nuclear region is not surrounded by a membrane, as it is in eukaryotes. Photosynthetic bacteria include thylakoid membrane structures, an exception to the rule of not having internal membranes. Granules are structures that contain storage projects such as lipids or starches. Bacterial cells are typically about 1 mm in size. Table 4.1 Contrast Between Prokaryotic and Eukaryotic Cells Prokaryotes Structure Cell wall Cell membrane Motility Genetic material Ribosomes Membranous organelles Archaeans Bacteria Eukaryotes Plants Animals Cellulose None No peptidoglycan; Peptidoglycan some have glycoprotein or protein walls Phospholipid bilayer composed of ester-linked straight Lipid biolayer hydrocarbon chains ether-linked branched hydrocarbon chains Flagella Flagella Flagella Flagella or cilia Single circular Single circular Several linear DNA molecules DNA DNA Yes Yes Yes Yes Nuclear envelope, endoplasmic Absent Few: e.g., reticulum, mitochondria, Golgi thylakoids for apparatus, lysosomes, centrioles photosynthesis in cyanobacter Chloroplasts and central vacuoles THE BIOLOGICAL MEMBRANE 67 cell membrane ribosomes cell wall cytoplasm flagellum granules nucleoid thylakoid membrane Figure 4.1 Structure of a prokaryotic cell. Figure 4.2 shows typical plant and animal (eukaryotic) cells. These cells are much more complicated. The nuclear region (nucleus), endoplasmic reticulum, mitochondria, Golgi apparatus, chloroplasts in photosynthetic organisms, and a number of other structures are all surrounded by their own membranes. Eukaryotic cells are usually much larger than prokaryotic cells, on the order of 10 mm in size. Functionally, prokaryotes are capable of a much wider range of basic metabolic processes, including many of environmental importance. These include many processes that catalyze key pathways of the biogeochemical cycles. All chemoautotrophs (organisms that obtain energy from inorganic chemicals) are prokaryotes. These include bacteria that oxidize minerals, such as Fe(II), NH3, H2S, and others. Other major processes limited to prokaryotes are nitrogen fixation and denitrification. Furthermore, with few exceptions, only prokaryotes are capable of using electron substitutes for oxygen, such as nitrate, sulfate, or carbonate, and can live their entire life cycles in the absence of oxygen. However, prokaryotes are specialized, and none can do all of these processes, and most do very few. What specialized advantage do eukaryotes have? One answer is that only eukaryotes form multicellular organisms. 4.2 THE BIOLOGICAL MEMBRANE In many areas of science, it is at the interface where things get interesting, and difficult. Chemical reactions in homogeneous gas or liquid phases are complex enough, but when an interface is present, even the notion of chemical concentration is oversimplified. For example, the pH near the surface of a colloid can vary with distance from the surface. Surface-active agents will distribute themselves differently between the surface and the bulk fluid. Many surfaces act as catalysts. They can be gatekeepers, affecting the transport of substances between phases. The phospholipid bilayer membrane is the major interface formed by living things. It is the structure that separates ‘‘inside’’ from ‘‘outside.’’ By increasing the complexity of the system, it also increases its possibilities. The biological membrane is a flexible sheet forming a closed surface, whose basic structure is formed of a phospholipid bilayer (see Figure 4.3). The capability of phospholipids to form enclosed bilayer vesicles spontaneously was described in Section 3.7.2. The outer membrane of all cells is called the plasma membrane or cell membrane. Similar membranes also enclose cell organelles such as the mitochondria or the nucleus in eukaryotic cells. 68 THE CELL: THE COMMON DENOMINATOR OF LIVING THINGS Figure 4.2 Animal (a) and plant (b) cells. (From Fried, 1990. # The McGraw-Hill Companies, Inc. Used with permission.) Besides being flexible, the phospholipid molecules can move freely within the plane of the membrane, a behavior described as a two-dimensional fluid. Other molecules are intimately associated with the membrane. Eukaryotic membranes can contain large amounts of cholesterol, which increase the fluidity of the membrane. Fatty acids serve the same function in prokaryotes. Globular proteins are embedded in the membrane, somewhat like icebergs floating in the sea. Some penetrate both surfaces of the membrane and participate in the transport of substances across it. Others are embedded in one or the MEMBRANE TRANSPORT Sugar molecules 69 Proteins Phospholipid bilayer Membrane pore Figure 4.3 Plasma membrane structure. (From Van De Graaff and Rhees, 1997. # The McGrawHill Companies, Inc. Used with permission.) other surface and function as chemical receptors or catalytic sites. Biological membranes are asymmetrical. The external surface of the plasma membrane and the internal surface of organelles have carbohydrates bonded to them, forming glycolipids and glycoproteins. The plasma membrane of archaean cells is chemically distinct from eubacterial or eukaryotic cell membranes. Instead of being composed of lipids made from straightchain fatty acids bonded to glycerol by ester bonds, archean membrane lipids are made of the branched hydrocarbon isoprene bonded to glycerol by ether bonds. This structure is thought to give archeans greater physical and chemical resistance to the relatively unfavorable environmental conditions in which they are often found. Membranes are typically less than 10% carbohydrate by mass; the rest of the membrane mass is about equally divided between protein and lipid. In animals, about half the lipid is phospholipid and half is cholesterol. The membrane controls the transport across it of both substances and information. Information is transported in the sense that substances, called ligands, can bind to receptors composed of transmembrane proteins (proteins that penetrate both sides) on one side of the membrane, producing a change in its conformation on the other side. The altered protein can then affect other reactions. This sends a signal across the membrane without a substance actually crossing over. Examples of this are the intercellular messengers called hormones. Insulin, for example, binds to a receptor and causes two separate effects. Primarily, it stimulates plasma membrane mechanisms for the transport of glucose, some ions, and amino acids. Second, it results in changes in intracellular metabolism that result in increased synthesis and storage of protein, glycogen, and lipid. Some toxic substances act by binding with receptors, either by stimulating an inappropriate response directly, or by competing with normal ligands. 4.3 MEMBRANE TRANSPORT Membranes also control the transport of substances. This is one of the essential functions of life: the maintenance of different conditions between the interior and exterior of the 70 THE CELL: THE COMMON DENOMINATOR OF LIVING THINGS cell, the distinction between the self and the rest of the world. Many toxic substances also must be transported across membranes to achieve their effect. The simplest mechanism is passive transport, the movement of a chemical from an area of relatively high concentration, through a membrane, to an area of low concentration, by means of molecular diffusion. The transport occurs only when a concentration difference exists between the aqueous phases on the two sides of the membrane. To diffuse across a membrane, a chemical must first dissolve in it. Then, random molecular motion results in a net movement toward the side with the lower concentration. However, molecules that are polar, such as ions or sugars, have very low solubility in the nonpolar interior of the phospholipid bilayer. Thus, the transport of such compounds through the membrane is very slow by this mechanism. Water also moves across membranes by passive transport. The movement is from low solute concentration to high solute concentration. Realize that the higher the concentrations of solutes (ions, proteins, sugars, etc.), the lower the concentration of solvent (water, in this case). From the point of view of the water, the movement is from high concentration (of the water) to low concentration. The passive transport of water due to its concentration gradient is called osmosis. Consider a membrane that is permeable to neutral molecules such as water but impermeable to ions and that separates a solution of fresh water from salt water. The water will move by osmosis from the fresh water (which has a higher water concentration) to the salty side. The flow continues until equilibrium is achieved. If the pressures are equal, osmotic equilibrium means that the concentration of particles is the same on both sides. However, if the system is held at constant volume, the flow results in an increase in pressure on the salty side. The pressure difference across the membrane at equilibrium, p, is related to the difference in the molar concentration of total particles,
c, by a version of the ideal gas law: p ¼
c RT ð4:1Þ The effect of particle concentration is approximately independent of charge or size. For example, a 0:1 M solution of sodium chloride has the same osmolarity as a 0:2 M solution of glucose, because the sodium chloride dissociates to form 0:2 mol of ions per liter. The concentration of particles expressed in moles per liter is called the osmolarity (Osmol/L). For example, blood plasma has a total particle concentration of about 325 mmol per liter (mOsmol/L). This produces an osmotic pressure of about 6000 mmHg (7.9 atm). (This is similar to the osmotic pressure of the ocean during the Precambrian Era, when animals with closed circulation evolved. Since then, the osmotic pressure of seawater has continued to increase about 3.5-fold.) If two solutions with different osmolarities are separated by a barrier to the solutes such as a plasma membrane, the lower-concentration solution is said to be hypotonic to the other. The higher-concentration solution is said to be hypertonic. If the two solutions have the same osmolarity, they are isotonic. Because of osmotic pressure, the total concentration of particles inside a cell must be almost equal to that outside. Otherwise, water would cross the membrane, causing the cell to either shrink or to swell and burst. Plant and bacterial cells are surrounded by rigid cell walls that protect them from bursting, and can therefore exist in a hypotonic solution. A hypertonic solution, however, will cause them to shrink within their cell walls. Cells that have osmotic pressure are said to be turgid. MEMBRANE TRANSPORT 71 Plasma membranes have pores consisting of embedded proteins. In most cells, these allow molecules up to a molar mass of 100 to 200, including water itself, to pass by filtration. The membranes of capillary (blood vessel) cells have larger pores, which allow molecules up to molar mass 60,000 to pass. Molecules too lipophobic for passive diffusion or too large for filtration may still enter the cell by specialized transport systems. These include four types of carrier-mediated transport: facilitated diffusion, active transport, co-transport, and countertransport. In facilitated diffusion the problem of lipophobicity is solved by forming a complex between the solute and a protein in the membrane (the carrier). Random molecular motion then transports the complex to the other face, where the solute is released and the protein is freed for reuse by other molecules. Facilitated diffusion has two important differences from passive diffusion: (1) Because there are a limited number of carriers, at high solute concentrations the carrier protein can become saturated, resulting in a maximum flux. Passive diffusion is limited only by the concentration gradient. (2) Facilitated diffusion is more selective than passive diffusion, since the solute must be able to form a complex with the carrier, and it can be inhibited by competition. An important compound that is carried across membranes by this mechanism is glucose. If it weren’t for protein transporters, membranes would be impermeable to glucose. The hormone insulin affects the permeability of muscle and adipose tissue membranes by increasing the amount of transporter proteins in those membranes. Passive transport, whether membrane or film theory, membrane filtration, or facilitated transport is a physicochemical process and requires no expenditure of energy by the cell. Instead, the cell relies on the free energy of the concentration gradient. Another form of carrier-mediated transport, active transport, involves the use of metabolic energy in the form of ATP. Active transport can occur when a membrane-spanning carrier absorbs the substrate from one side of the membrane and uses energy from ATP to pass the substrate through a channel and exude it at the other side. A second active transport mechanism can involve the consumption of a substrate on one side of the membrane, coupled with its production at the other side. The substrate is not really transported across the membrane, but the effect is as though it has been. An example of the latter mechanism is the ‘‘transport’’ of protons across the membrane of bacteria or mitochondria in the respiration process. Active transport is an important mechanism for the transport of natural biochemical compounds in living things. It is the way they obtain nutrients and eliminate waste products. It is also a mechanism for the uptake and excretion of toxins. For example, lead is absorbed by active transport in the intestines. Active transport can move chemicals against a concentration gradient. Active transport has the following characteristics: 1. Chemicals can be moved against electrochemical gradients. 2. Like facilitated diffusion, active transport can be saturated and shows a maximum flux. 3. Also like facilitated diffusion, active transport is highly selective and exhibits competitive inhibition. 4. Active transport requires energy and so can be inhibited by metabolic poisons. Active transport is exploited to transport water passively across membranes by osmosis. For example, the large intestine removes water from its lumen (interior) by using active 72 THE CELL: THE COMMON DENOMINATOR OF LIVING THINGS transport to remove sodium. This decreases the osmolarity in the lumen, and water passively diffuses out to the higher-osmolarity tissues surrounding it. When solutes are transported across a membrane, water will follow if the membrane is permeable to water. Cotransport and countertransport involve two substrates being brought across the membrane by the same carrier at the same time, either in the same direction or in opposite directions, respectively. At least one of the substrates must be transported downgradient and provides the energy to transport the second substrate. For example, a sodium gradient can drive the cotransport of glucose into a cell. A countertransport mechanism exchanges chloride for bicarbonate in the kidney. Since these mechanisms are carrier mediated, they can also be saturated. Another type of specialized transport, limited to eukaryotes, is endocytosis, in which particles are engulfed by cells. The cell accomplishes this by surrounding the particle with part of the plasma membrane, which then pinches off inside the cell, forming a vesicle. If the particle is solid, the process is called phagocytosis; if liquid, it is called pinocytosis. The protozoan amoeba feeds by phagocytosis and the lungs use it to clear themselves of inhaled particulates, incidentally taking up any associated toxins. More details on some membrane transport processes, including ways of describing them mathematically, are given in Section 18.2. 4.4 EUKARYOTIC CELL STRUCTURE AND FUNCTION The emphasis here is on eukaryotic cells. More details on prokaryotic cells are given in Chapter 10. Plants, some fungi, some protists and most prokaryotes form a cell wall outside their plasma membrane. The basic structure in plants is composed of cellulose fibers (cotton is a pure form of cellulose). Besides maintaining cell shape and preventing a cell from rupturing due to osmotic forces, a cell wall provides structural rigidity to multicellular plants. Many plants also lay down a secondary cell wall, which includes lignin, inside the primary wall. Lignin is a polymer of aromatic subunits whose presence increases the toughness of wood. Lignin biodegrades much more slowly in the environment than cellulose does. The degradation products of lignin are thought to be the major source of humic substances, which are the predominant forms of organic matter in soil. The humic substances, in turn, give topsoil its beneficial properties for plant growth and are responsible for the great capacity for soils to absorb nutrients as well as many types of pollutants. Animal cells protect themselves against rupturing from osmotic forces partly by manipulating those forces. Multicellular animals can control the osmotic pressure of their intercellular fluids. In addition, they produce a network of collagen fibers. Collagen consists of polypeptide strands twisted into a ropelike structure. About 25% of the protein in mammals is collagen, and tendons are mostly collagen. The basic matrix of the cell interior is the gel-like cytoplasm, in which the other cell materials and structures are suspended, including the organelles. A three-dimensional lattice of protein fibers called the cytoskeleton gives structure to the cytoplasm and helps orient organelles. Inside cells, the largest and most obvious structure is the nucleus, which contains most of a cell’s DNA. In eukaryotes the nucleus is separated from the cytoplasm by a nuclear membrane, which consists of two phospholipid bilayer