Ch 6, A tour of the Cell

I. How we study the Cell. 1. Distinguish between magnification and resolving power.
Magnification is the ratio of an objects image to its real size. Resolving power is a measure of image clarity.

2. Describe the principles, advantages and limitations of the light microscope, transmission electron microscope, and the scanning electron microscope.
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. 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. Scanning electron microscopes (SEMs) are useful for studying surface structures. The SEM has great depth of field, resulting in an image that seems three-dimensional 3. Describe the major steps of cell fractionation and explain why it is a useful technique. 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. 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.

II. A Panoramic View of the Cell

4 . D i s t i n g u i s h b e t w e e n p r o k a r y o t i c a n d e u k a r yo t i c c e l l s . 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. 5.Explai n why there are both upper and lower limits to cell size. A cell can get too small to contain all the components necessary for life. As a cell gets larger, its surface area to volume ratio gets much smaller, which means that it takes too long for substances diffusing into the cell at the membrane (e.g., nutrients or oxygen) to get to all parts of the cell. 6.Explai n the advantages of compartmentalization in eukaryotic cell . Different cell organelles perform different functions, many of which require specialized components for specific targets. Compartmentalization creates appropriate microenvironments for these diverse processes, allows damage limitation, minimizes nonspecific interactions and consequently increased cellular efficiency. For example, all DNA is located in the nucleus which uses a nuclear membrane to regulate the proteins/transcription factors that activate/suppress gene expression.

II. The Nucleus and Ribosomes

7. Describe the structure and function of the nucleus and briefly explain how the nucleus controls protein synthesis in the cytoplasm. The Nucleus: contains the genes of the cell. Its size is about 5um. in diameter. It is surrounded by a lipid bilayer perforated with pores. There is a 20-40 nm. space between the layers of the membrane. Chromosomes are rod shaped structures containing DNA and protein. Chromosomes are usually broken down into chromatin. The Nucleolus is also found in the nucleus. It produces ribosomes at a rate of 10,000 / min. The nucleus controls the cell's functioning through the production of m-RNA. DNA is too large to leave the nucleus. If the program it contains must leave the nucleus, an intermediate must be produced. This intermediate is called m-RNA. m-RNA is formed in the following way, RNA polymerase binds to, a region of the DNA called, the promoter. Here is found the start codon TAC which codes for the amino acid methionine. Once this has been established the m-RNA sequence is produced growing from the 5' - 3' region. This occurs at the rate of 60 nucleotides / sec. The terminator sequence will keep the process from going on indefinitely. The eukaryotic m-RNA must be modified before going to the ribosome, while the prokaryotic does not. 8. Describe the structure and function of a eukaryotic ribosome. The ribosome is made up of two subunits, a large one and a small one. its job is to translate mrna, once it enters the cytoplasm, and make proteins using the information in the mrna

III. The Endomembrane System

9. List the components of the endomembrane system, describe their structures and functions, and summarize the relationship among them. The endomembrane system is the system of internal membranes within eukaryotic cells that divide the cell into functional and structural compartments, or organelles. Prokaryotes do not have an endomembrane system and thus lack most organelles. The endomembrane system also provides a transport system, for moving molecules through the interior of the cell, as well as interactive surfaces for lipid and protein synthesis. The membranes that make up the endomembrane system are made of a lipid bilayer, with proteins attached to either side or traversing them.

The following organelles are part of the endomembrane system: * The plasma membrane is a phospholipid bilayer membrane that separates the cell from its environment and regulates the transport of molecules and signals into and out of the cell. * The nuclear envelope is the membrane around the nucleus of the cell. * The endoplasmic reticulum is a synthesis and transport organelle [the endoplasmic reticulum is an extension of the nuclear envelope]. * The Golgi apparatus acts as the packaging and delivery system for molecules. * Lysosomes are the "digestive" units of the cell. They utilize enzymes to break down macromolecules and also act as a waste disposal system. * Vacuoles act as storage units in some cells. * Vesicles are small membrane-enclosed transport units that can transfer molecules between different compartments. 10. Explain how impaired lysosomal function can cause symptoms of storage diseases. Our lysosomes break down any harmful or unnecessary substances brought into our cells... so if we were to accumulate those harmful substances in our cells, then we would soon be full of toxic materials that our body would be harmed by. 11. Describe the different structures and functions of vacuoles. central vacuole - helps maintain plants' shape and structure by storing water (hypotonic). contractile vacuole - pumps water out of protist cells to maintain a suitable concentration. vacuole - storage for molecules that is a food source for the cell (phagocytosis). 12. Describe the structure of a mitochondrion and explain the importance of compartmentalization in mitochondrial functions. Two membranes, each a phospholipid bilayer with unique embedded proteins, encloses the mitochondrion. A narrow intermembrane space exists between the smooth outer membrane and the convoluted inner membrane, called cristae, create a large surface area and encloses the mitochondrial matrix. Many respiratory enzymes, mitochondrial DNA, and ribosomes are housed in this matrix. Other respiratory enzymes and proteins are built into the inner membrane. 13. Distinguish among amyloplasts, chromoplast, and chloroplasts. Chloroplast is an organelle found in plants and algae cells where photosynthesis occurs. Chromoplasts are plastids responsible for pigment synthesis and storage. Amyloplasts are non-pigmented organelles found in some plant cells. 14. Identify the three functional compartments of a chloroplast. Explain the importance of compartmentalization in the chloroplast function. The stroma is in the inner membrane that is a fluid surrounding a membraneous system of flattened sac called thylakoids, inside of which is the thylakoid space. Photosynthetic enzymes are embedded in the thylakoids, which may be stacked together to form structures called grana.

IV. Other Membranous Organelles

15. Explain the role of the mitochondria and chloroplast. Mitochondria are sometimes called the "energy powerhouse of a cell". It breaks down glucose (C6H12O6) to form energy, Carbon dioxide and water. This process is known as respiration . The chloroplast on the other hand is only found in plants and is the site for photsynthesis where CO2 and water are used to form glucose and Oxygen. Photosynthesis is basically the opposite of respiration Formula for photosynthesis: 6CO2 + 6H2O ---> C6H12O6 + 6O2 Formula for respiration: C6H12O6 + 6O2 --->6CO2 + 6H2O 16. Explain the role of peroxisomes in eukaryotic cells. Perixomes are oxidative organelles filled with enzymes that function in a variety of metabolic pathways, such as breaking down fatty acids for energy or detoxifying alcohol and other poisons.

V. The Cytoskeleton

17. Describe the function of cytoskeleton and motor proteins. It is a network of microtubules, microfilaments, and intermediate filaments that extend throughout the cytoplasm and serve as a variety of mechanical, transport, and signaling functions. (The cytoskeleton is somewhat like a highway - which can be utilized by all the molecular machinery in the cell.) The most obvious function is to give mechanical support to the cell and maintain its shape. This is especially important for animal cells, which lack cell walls. This remarkable strength and resilience of the cytoskeleton as a whole is based on its architecture. Motor protein interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell. Cytoskeletal elements and motor proteins work together with plasma membrane molecules to allow whole cells to move along fibers outside the cell. Motor proteins bring about the bending of cilia and flagella by gripping microtubules within those organelles and sliding them against

each other. A similiar mechanism involving microfilaments causes muscle cells to contract. Inside the cell, vesicles and other organelles often use motor protein "feet" to "walk" to their destinations along a track provided by the cytoskeleton. (Haha this is very similiar to traintracks [cytoskeleton] and a train [motor proteins] and the passengers [vesicles and other organelles].) 18. Describe the structure, monomers, and function of microtubules, microfilaments, and intermediate filaments. Microtubules are hollow tubules with a diameter of 25 nm that are made up of a and b tubulin heterodimers Microfilaments are two-stranded helices with a diameter of 7 nm (5-9 nm in range) that are made up of actin monomers Intermediate filaments are rope-like fibers with a diameter of about 10 nm that are made up of various proteins, including keratins and vimetins that share common structures, in different cell types. Whereas tubulins and actins are globular proteins, intermediate filament proteins are fibrous proteins. Whereas both microtubules and microfilaments are polar structures, intermediate filaments are non-polarized structures. Various motor proteins or ATPases, including myosins, dyneins and kinesins, are associated with microtubules and microfilaments to convert chemical energy to mechanical work In a typical eukaryotic cell, microtubules are spread out from a structure known as the centrosome or microtubule-organizing center (MTOC); microfilaments are found close to the cell surface (or cell cortex) In specialized cell types, the elements of the cytoskeleton play distinctive roles Microtubules are major components of cilia and flagella, providing for cell motility Microfilaments are major components in muscle cells, providing for muscle contraction Intermediate filaments made up of keratins are major components of epithelial cells, allowing the cell to resist mechanical stress. Microtubules are one of the components of the cytoskeleton. They have a diameter of 25 nm and length varying from 200 nanometers to 25 micrometers. Microtubules serve as structural components within cells and are involved in many cellular processes including mitosis, cytokinesis, and vesicular transport. Microtubules are polymers of - and -tubulin dimers. The tubulin dimers polymerize end to end in protofilaments. The protofilaments then bundle into hollow cylindrical filaments. Typically, the protofilaments arrange themselves in an imperfect helix with one turn of the helix containing 13 tubulin dimers each from a different protofilament. The image above illustrates a small section of microtubule, a few dimers in length. Another important feature of microtubule structure is polarity. Tubulin polymerizes end to end with the subunit of o ne tubulin dimer contacting the subunit of the next. Therefore, in a protofilament, one end will have the subunit exposed while the other end will have the subunit exposed. These ends are designated the () and (+) ends, respectively. The protofilame nts bundle parallel to one another, so in a microtubule, there is one end, the (+) end, with only subunits exposed while the other end, the () end, only has subunits exposed. Microfilaments (or actin filaments) are the thinnest filaments of the cytoskeleton found in the cytoplasm of all eukaryotic cells. These linear polymers of actin subunits are flexible and relatively strong, resisting buckling by multi-piconewton compressive forces and filament fracture by nanonewton tensile forces. Microfilaments are highly versatile, functioning in (a) actoclampin-driven expansile molecular motors, where each elongating filament harnesses the hydrolysis energy of its "on-board" ATP to drive actoclampin endtracking motors to propel cell crawling, ameboid movement, and changes in cell shape, and (b) actomyosin-driven contractile molecular motors, where the thin filaments serve as tensile platforms for myosin's ATP hydrolysis-dependent pulling action in muscle contraction and uropod advancement. Intermediate filaments (IFs) are a family of related proteins that share common structural and sequence features. Intermediate filaments have an average diameter of 10 nanometers, which is between that of actin (microfilaments) and microtubules, although they were initially designated 'intermediate' because their average diameter was between those of narrower microtubules and wider myosin filaments[1]. Most types of intermediate filaments are cytoplasmic, but one type, the lamins, are nuclear. The domain structure of IF molecules is conserved. Each protein has a non-alpha-helical (globular) domain at the N and C-termini which surrounds the alpha-helical rod domain. The basic building block for IFs is a parallel and in register dimer. The dimer is formed through the interaction of the rod domain to form a coiled coil. Cytoplasmic IF assemble into non-polar unit-length filaments (ULF) which then assemble into longer structures. Part of the assembly process includes a compaction step, in which ULF tighten and assume a smaller diameter. The reasons for this compaction are not well understood, and IF are routinely observed to have diameters ranging between 6 and 12nm. The anti-parallel orientation of tetramers means that, unlike microtubules and microfilaments which have a plus end and a minus end, IFs lack polarity. Also, as opposed to actin or tubulin, intermediate filaments do not contain a binding site for a nucleoside triphosphate. Cytoplasmic IF do not undergo treadmilling like microtubules and actin fibers, but they are dynamic. 19. Explain how the ultrastructure of cilia and flagella relate to their functions. cilia are short fibers that are use for attachment to surfaces (biofilms). flagella are longer fibers that are connected to a complex base that rotates. rotation requires atp. this rotation causes the cells to move. cilia are usually dispersed all over the cell's surface. flagella are placed in more distinct areas (on the ends or sides).

VI. Cell Surface and Junctions

20. Describe the development of plant cell walls. The plant cell changes its cell wall architecture during growth and development through synthesis and degradation of wall polysaccharides. Changes of chemical components in the cell wall include not only the synthesis and degradation but also the shift of molecular-weight distribution of certain species of the component polysaccharides. The changes in chemical structure, in turn lead to alteration of physical properties of the cell wall. Changes of physical parameters of cell walls obtained by a physical method accord with the biochemical degradation of polysaccharides. The changes in chemical structures of the cell wall are regulated by plant hormones, stress signals and gene expression. The physical and chemical studies of the cell wall have disclosed that degradation and /or depolymerization of wall polysaccahrides causes decrease in viscosity of the cell wall, leading further extension of the cell wall even under the unchanged osmotic relation. Furthermore, cell walls of outer and inner tissues play different regulatory roles in tissue grown and stem strength was governed by the number of cellulose molecules in the cell wall. 21. Describe the structure and list four functions of the extracellular matrix in animal cells. a. Structure i. Fibronectin attaches to integral plasma membrane proteins ii. Collagen fibers and proteoglycans attach to fibronectin b. Functions i. Anchor and protect cells ii. Direct cell migration during development and healing iii. Control some gene expression iv. Coordinate tissue function 22. Describe the structure of intercellular junctions found in plant and animal cells and relate those structures to their functions. Intercellular Junctions: 1. Tight junctions. bind cells together in such a way that no material can pass through the intercellular spaces. Epithelial cells are held together by tight junctions. 2. Desmosomes: These bind the cells together like rivets. They let material pass through the intracellular spaces. 3. Gap Junctions: They connect cells but allow material to pass from one cell to another through the opening in the center of the joint. They are analogous to the plasmodesmata in plants.