Cell I. Theory A. Robert Hooke was the first to observe cells in 1665, naming the shapes he saw in cork cellulae. This comes down to us as cells. B. Cell theory is the unifying foundation of cell biology 1. The cell theory was proposed to explain the observation that all organisms are composed of cells. 2. In its modern form, cell theory includes the following three principals: a. All organisms are composed of one or more cells, and the life processes of metabolism and heredity occur within these cells. b. Cells are the smallest living things, the basic units of organization of all organisms. c. Cells arise only by division of a previously existing cell. C. Cell size is limited 1. The rate of diffusion is affected by a number of variables, including surface area available for diffusion, temperature, concentration gradient of diffusing substance, and the distance over which diffusion must occur. 2. Larger cells need to synthesize more macromolecules, have a correspondingly higher energy requirements, and produce a greater quantity of waste. 3. The rate at which this transport occurs depends on both the distance to the membrane, as well as the area of membrane available. For this reason, an organism made up of many relatively small cells has an advantage over one compound of fewer, larger cells. 4. The advantage of small cell size is readily apparent in terms of the surface areato-volume ratio. As a cell's size increases, its volume increases much more rapidly than its surface area. 5. The cell surface provides the only opportunity for interaction with the environment, because all substances enter and exit a cell via this surface. D. Microscopes allow visualization of cells and components 1. The reason we can't see such small objects is the limited resolution of the human eye. Resolution is defined as the minimum distance two points can be apart and still be distinguished as two separated points. 2. Modern light microscopes, which operate with visible light, use two magnifying lenses to achieve very high magnification and clarity. 3. Microscopes that magnify in stages using several lenses are called compound microscopes. They can resolve structures that are separated by at least 200 nanometers (nm). 4. Electrons have a much shorter wavelength, and an electron microscope, employing electron beams, has 1000 times the resolving power of a light microscope. 5. Transmission electron microscopes, so called because the electrons used to visualize the specimens are transmitted through the material, are capable of resolving objects only 0.2 nm apart just twice the diameter of a hydrogen atom! 6. A second kind of electron microscope, the scanning electron microscope, beams the electrons onto the surface of the specimen. The electrons reflected back from the surface, together with other electrons that the specimen itself emits as a result of the bombardment, are amplified and transmitted to a screen, where the image can be viewed and photographed. E. All cells exhibit structural similarities 1. Every cell contains DNA, the hereditary molecule. In prokaryotes, the simplest organisms, most of the genetic material lies in a single circular molecule of DNA. It typically resides near the center of the cell in an area called the nucleoid.
Chapter Four: Cell Structure
2. A semifluid matrix called the cytoplasm fills the interious of the cell. The cytoplasm contains all of the sugars, amino acids, and proteins the cell uses to carry out its everyday activities. 3. In eykaryotic cells, in addition to the nucleus, the cutoplasm also contains specialized membrane-bounded compartments called organelles. The part of the cytoplasm that contains organic molecules and iopns in solution is called the cytosol to distinguish it from the larger organelles suspended in this fluid. 4. The plasma membrane encloses a cell and separates its contents from its surroundings. The plasma membrane is a phospholipid bilayer about 5 to 10 nm thick, with proteins embedded in it. 5. Transport proteins help molecules and ions move across the plasma membrane, either from the environment to the interior of the cell or vice versa. Receptor proteins induce changes within the cell when they come in contact with specific molecules in the environment, such as hormones, or with molecules on the surface of neighboring cells. II. Prokaryotic Cells A. Prokaryote cells have relatively simple organization 1. Prokaryotic cells are small, consisting of cytoplasm surrounded by a plasma membrane and encased within a rigid cell wall, with no distinct interior compartments. 2. Prokaryotes are very important in the ecology of living organisms. 3. Although prokaryotic cells do contain complex structures like ribosomes, which carry out protein synthesis, most have no membrane-bounded organelles characteristic of eukaryotic cells. 4. The plasma membrane of a prokaryotic cell carries of some of the functions organelles perform in eukaryotic cells. 5. Because a prokaryotic cell contains no membrane-bounced organelles, the DNA, enzymes, and other cytoplasm constituents have access to all parts of the cell. B. Bacterial cell walls consist of peptidoglycan 1. Most bacterial cells are encased by a strong cell wall. This cell wall is composed of peptidoglycan, which consists of a carbohydrate matrix that is cross-linked by short polypeptide units. 2. Gram-positive bacteria have a thick, single-layered peptidoglycan cell wall that retains a violet dye from the Gram stain, causing the stained cells to appear purple under a microscope. Gram-negative bacteria have evolved a more complex, multilayered cell wall that does not retain the purple due. These bacteria appear red after staining due to a second background dye. C. Some prokaryotes move by means of rotating flagella 1. Flagella are long, threadlike structures protruding from the surface of a cell that are used in locomotion. III. Eukaryotic Cells A. The hallmark of the eukaryotic cell is compartmentalization, which is achieved by an extensive endomembrane system that weaves through the cell interior and by numerous organelles. Organelles are the membrane-bounded structures that form compartments within which multiple biochemical processes can proceed simultaneously and independently. B. Plant cells often have a large, membrane-bounded sac called a central vacuole, which stores proteins, pigments, and waste materials. Both plant and animal cells contain vesicles, smaller sacks that store and transport a variety of materials. Inside the nucleus, the DNA is wound tightly around proteins and packaged into compact units called chromosomes. All eukaryotic cells are supported by an internal protein scaffold, the cytoskeleton. C. The nucleus acts as the information center
1. The largest and most easily seen organelle within a eukaryotic cell is the nucleus. Nuclei are roughly spherical in shape, and in animal cells, they are typically located in the central region of the cell. 2. Many nuclei exhibit a dark-staining zone called the nucleolus, which is a region where intensive synthesis of ribosomal RNA is taking place. 3. The nuclear envelope a.) The surface of the nucleus is bounded by two phospholipids bilayer membranes, which together make up the nuclear envelope. The outer membrane of the nuclear envelope is continuous with the cytoplasm's interior membrane system, called the endoplasmic reticulum. b.) Scattered over the surface of the nuclear envelope are what appear as shallow depressions in the electron micrograph, but are in fact structures called nuclear pores. These pores form 50 to 80 nm apart at locations where the two membrane layers of the nuclear envelope pinch together. c.) The complex allows small molecules to diffuse freely between nucleoplasm and cytoplasm while controlling the passage of proteins and RNA-protein complexes. d.) The inner surface of the nuclear envelope is covered with a network of fibers that make up the nyclear lamina. This is composed of intermediate filament fibers called nuclear lamins. This structure gives the nucleus its shape and its also involved in the deconstruction and reconstruction of the nuclear envelope that accompanies cell division. 4. Chromatin: DNA packaging a.) In both prokaryotes and eukaryotes, DNA contains the hereditary information specifying cell structure and function. In most prokaryotes, the DNA is organized into a single circular chromosome. In eukaryotes, the DNA is divided into multiple linear chromosomes. The DNA is organized with proteins into a complex structure called chromatin. The chromosomes are packaged with proteins called histones into nucleosomes that are formed by DNA being wrapped about histones. b.) Chromatin is usually in a more extended form that allows regulatory proteins to attach to specific nucleotide sequences along the DNA and regulate gene expression. 5. The nucleolus: Ribosomal subunit manufacturing a.) Before cells can synthesize proteins in large quantity, they must first construct a large number of ribosome's to carry out this synthesis. b.) These ribosomal assembly areas are easily visible within the nucleus as one or more dark-staining regions called nucleoli. Nucleoli can be seen under the light microscope even when the chromosomes are uncoiled. D. Ribosomes are the cell's protein synthesis machinery 1. Ribosomes are among the most complex molecular assemblies found in cells. Each ribosome is composed of two subunits and each subunit is composed of a combination of RNA, called ribosomal RNA (rRNA), and proteins. The subunits join to form a functional ribosome only when they are actively synthesizing protieins. This complicated requires process the two other main forms of RNA: messenger RNA (mRNA), which carries coding information from DNA, and transfer RNA (tRNA), which carries amino acids. Ribosomes use the information in mRNA to direct the synthesis of a protein.
2. Free ribsosomes synthesize proteins that are found in the cytoplasm, nuclear proteins, mitochondrial proteins, and proteins found in other organelles not derived from the endomembrane system. Membrane-associated ribosomes synthesize membrane proteins, proteins found in the endomembrane system, and proteins destined for export from the cell. IV. The Endomembrane System A. The interior of a eukaryotic cell is packaged with membranes so thin that they are invisible under the low resolving power of light microscopes. This endomembrane system fills the cell, dividing it into compartments, channeling the passage of molecules through the interior of the cell, and providing surfaces for the synthesis of lipids and some proteins. B. The largest of the internal membranes is called the endoplasmic reticulum (ER). Like the plasma membrane, the ER is composed of a phospholipids bilayer embedded with proteins. C. Of the many compartments in eukaryotic cells, the two largest are the inner region of the ER, called the cisternal space or lumen, and the region exterior to it, the cytosol, which is the fluid component of the cytoplasm containing dissolved organic molecules such as proteins and ions. D. The rough ER is a site of protein synthesis 1. The rough ER (RER) gets its name from its surface appearance, which is pebbly instead of smooth due to the presence of ribosomes. The RER is not easily visible with a light microscope, but it can be seen using the electron microscope. 2. The proteins synthesized on the surface of the RER are destined to be exported from the cell, sent to lysosomes or vacuoles, or embedded in the plasma membrane. 3. In the ER, newly synthesized proteins can be modified by the addition of shortchain carbohydrates to form glycoproteins. Those proteins destined for secretion are then kept separate from other products and are later packaged into vesicles. The membrane proteins are inserted into the ER's own membrane, which can then expand and pinch off in the form of vesicles to be transferred to other location. E. The smooth ER has multiple roles 1. Regions of the ER with relatively few bound ribosomes are referred to as smooth ER (SER). The SER appears more like a network of tubules than the flattened sacs of the RER. 2. The ratio of SER to RER depends on a cell's function. In multicellular animals such as ourselves, great variation exists in this ratio. F. The Golgi apparatus sorts and packages proteins 1. Flattened stacks of membranes called Golgi bodies can be found within the endomembrane system, often interconnected with one another. The number of Golgi bodies a cell contains ranges from 1 or a few in protests, to 20 or more in animal cells and several hundred in plant cells. They are especially abundant in glandular cells, which manufacture and secrete substances. Collectively, the Golgi bodies are referred to as the Golgi apparatus. 2. A Golgi body has a front and a back, with distinctly different membrane compositions at these opposite ends. The front, or receiving end, is called the cis face, and it is usually located near ER. Materials move to the cis face in transport vesicles that bud off the ER. These vesicles fuse with the cis face, emptying their contents into the interior, or lumen, of the Golgi apparatus. The ER-synthesized molecules then pass through the channels of the Golgi apparatus until they reach the back, or discharging end, called the trans face, where they are discharged in secretory vesicles. 3. The newly formed or altered glycoproteins and glucolipids collect at the ends of the Golgi bodies in flattened, stacked membrane folds called cisternae. Periodically, the membranes of the cisternae push together, punching off small,
membrane-bounded secretoiry vesicles containing the glycoprotein and glycolipid molecules. G. Lysosomes contain digestive enzymes 1. Membrane-bounded digestive vesicles, called lysosomes, are also components of the endomembrane system, and they arise from the Golgi apparatus. They contain high levels of degrading enzymes, which catalyze the rapid breakdown of proteins, nucleic acids, lipids, and carbohydrates. 2. In addition to breaking down organelles and other structures within cells, lysosomes eliminate other cells that the cell has engulfed by phagocytosis. H. Microbodies are a diverse category of organelles 1. Eukaryotic cells contain a variety of enzyme-bearing, membrane-enclosed vesicles called microbodies. Microbodies are found in the cells of plants, animals, fungi and protests. 2. Plant cells have a special type of microbody called a glyoxysome, which contains enzymes that convert fats into carbohydrates. 3. Peroxisomes: Peroxide utilization a.) Another type of microbody, a peroxisome, contains enzymes that catalyze the removal of electrons and associated hydrogen atoms. b.) The name peroxisome refers to the hydrogen peroxide produced as a by-product of the activities of the oxidative enzymes in the microbody. I. Plants use vacuoles for storage and water balance 1. Plant cells have specialized membrane-bounded structures called vacuoles. 2. The membrane surrounding this vacuole is called the tonoplast because it contains channels for water that are used to help the cell maintain its tonicity, or osmotic balance. V. Mitochondria and Chloroplasts: Cellular Generators A. Mitochondria metabolize sugar to generate ATP 1. Mitochondria are typically tubular or sausage-shaped organelles about the size of bacteria and found in all types of eukaryotic cells. Mitochondria are bounded by two membranes: a smooth outer membrane, and an inner folded membrane with numerous contiguous layers called cristae. 2. The cristae partition the mitochondrion into two compartments: a matrix, laying inside the inner membrane; and an outer compartment, or intermembrane space, lying between the two mitochondrial membranes. 3. Mitochondria have their own DNA; this DNA contains several genes that produce proteins essential to the mitochondrion's role in oxidative metabolism. 4. A eukaryotic cell does not produce brand-new mitochondria each time the cell divides. Instead, the mitochondria themselves divide in two, doubling in number, and these are partitioned between the new cells. B. Chloroplasts use light to generate ATP and sugars 1. Plant cells and cells of other eukaryotic organisms that carry out photosynthesis typically contain from one to several hundred chloroplasts. Chloroplasts bestow an obvious advantage on the organisms that possess them: They can manufacture their own food. Chloroplasts contain the photosynthetic pigment chlorophyll that gives most plants their green color. 2. In addition to the outer and inner membranes, which lie in close association with each other, chloroplasts have closed compartments of stacked membranes called grana, which lie inside the inner membrane. 3. A chloroplast may contain a hundred or more grana, and each granum may contain from a few to several dozen disk-shaped structures called thylakoids. On the surface of the thylakoids are the light-capturing photosynthetic pigments.
4. A leucoplast that stores starch is sometimes termed an amyloplast. These organelles-chloroplasts, leucoplasts, and amyloplasts-are collectively called plastids. All plastids are produced by the division of existing plastids. C. Mitochondria and chloroplasts arose by endosymbiosis 1. The theory of endosymbiosis proposes that some of today's eukaryotic organelles evolved by a symbiosis arising between two cells that were each freeliving. One cell, a prokaryote, was engulfed by and became part of another cell, which was the precursor to modern eukaryotes. 2. Two key eukaryotic organelles are believed to be the descendants of these endosymbiotic prokaryotes: mitochondria, which are thought to have originatred as bacteria capable of carrying out oxidative metabolism, and chloroplasts, which apparently arose from photosynthetic bacteria. VI. The Cytoskeleton A. The cytoplasm of all eukaryotic cells is crisscrossed by a network of protein fibers that supports the shape of the cell and anchors organelles to fixed locations. This network, called the cytoskeleton, is a dynamic system, constantly forming and dissembling. B. Three types of Fibers compose the cytoskeleton 1. Eukaryotic cells may contain the following three types of cytoskeletal fibers, each formed from a different kind of subunit: actin filaments, microtubules, and intermediate filaments. 2. Actin Filaments (microfilaments) a.) Actin filaments are long fibers about 7 nm in diameter. Each filament is composed of two protein chains loosely twined together like two strands of pears. Each subunit, on the chains is the globular protein actin. Actin filaments exhibit polarity in that they have plus and minis ends. These designate the direction of growth of the filaments. Acrin molecules spontaneously form these filaments, even in a test tube. 3. Microtubules a.) Microtubules, the largest of the cytoskeletal elements, are hollow tubes about 25 nm in diameter, each composed of a ring of 13 protein protofilaments. 4. Intermediate filaments a.) The most durable element of the cytoskeleton in animal cells is a system of tough, fibrous protein molecules twined together in an overlapping arrangement. These intermediate filaments are characteristically 8 to 10 nm in diameter, intermediate in size between acrin filaments and microtubules.