NOTES: Chapter 6 STRUCTURE OF THE CELL

Biology 120 Section 10 J. Greg Doheny NOTES: Chapter 6 STRUCTURE OF THE CELL NOTES Relative sizes of cells: If a Eukaryotic cell was the size of Columbia College, a prokaryotic cell (like a bacterium) would be about the size of a bus, and a virus would be about the size of a tennis ball. i. Eukaryotic Cells: Average 10 um ii. Prokaryotic Cells: Average 0.1 um iii. Viruses: 0.001 um or less Types of Microscopes used by Biologists: i. Brightfield (light) microscope: Specimen is sliced. Must be stained! Resolution limit about 0.1 um. ii. Phase-Contrast (light) microscope: Uses polarized lens filters to create contrast. No need to stain specimens! Advantage: can look at live specimens! Resolution limit: about 0.1 um. iii. Fluorescence Microscope: Uses ultraviolet light instead of visible light. Specimen is stained with fluorescent stains that absorb UV light, and re-emit it at a longer wavelength, in the visible spectrum. Original stains were red (ie-texas Red) and green (fluoroisothiocyanate, or FITC). Immunofluorescence microscopy: attaching fluorescent dyes to antibodies, and then labeling specific cell structures with the antibodies. Co-localization experiments. Resolution limit: about 0.01 um. iv. Scanning Electron Microscope (SEM): Uses a beam of electrons instead of visible or fluorescent light. Enlarges electron beam with magnets instead of glass lenses. For SEM you coat the specimen with metal. Electron beam excites the metal ions, and they re-emit electron beam at a different wavelength. Good for looking at 3D structures and surfaces. Resolution limit: 0.0001 um or less. v. Transmission Electron Microscope (TEM): Uses beam of electrons. Specimen is sliced, and stained with metal salts. Resolution limit: 0.0001 um or less. Cell Structures and Organelles: 1. Plasma membrane: Phospholipid bilayer that separates the cell from the outside world. Phospholipids have a hydrophobic end (the lipids) and a hydrophilic end (the phosphate group). Form a membrane with the water-hating lipids facing inwards and the waterloving phosphates facing outwards. Many proteins are embedded in the membrane, including some that form channels. Many cell receptors, which receive signals from outside the cell are also embedded in the cell membrane. Cell membrane is fluid, and these proteins can move laterally while embedded in the membrane. The mixture of liquids, proteins, and organelles found inside the cell is collectively called the cytoplasm. Just the liquid part of the cytoplasm is called the cytosol. 1

2. Nucleus: Centrally located compartment that contains the DNA (DNA in the form of chromosomes). The mixture of liquid, proteins and DNA inside the nucleus is collectively called the nucleoplasm. The nucleoplasm is surrounded by a double membrane (the nuclear envelope), which is studded with holes called nuclear pore complexes (NPC). NPCs allow messenger RNA (mrna) to get out, and proteins to come in. The inner surface of the nuclear envelope is lined with a nuclear lamina of filaments (like a woven basket). The chromosomes inside the nucleus are unwound, and the DNA is loose. Whether loose or compressed, DNA is associated with proteins. DNA and its closely associated proteins is collectively called chromatin. The main proteins associated with the DNA are called the histone proteins. These are four histone proteins that make up the nucleosomes. Nucleosomes are like microscopic spools that the DNA is wrapped around. DNA is transcribed into mrna by RNA Polymerase enzymes, and transported outside to the cytoplasm via the NPCs. 3. Ribosomes: small anvil shaped organelles where mrna is translated into protein, by linking together chains of amino acids. 4. Endoplasmic Reticulum (ER): network of membranes connected to the nucleus, and often studded with ribosomes. mrna is sent outside the nucleus to the cytoplasm, and is then threaded onto ribosomes embedded in the ER. Proteins are then synthesized, by hooking together chains of amino acids, and sent into the lumen (inside) of the ER. These proteins are then packaged into transport vesicles, and sent to the Golgi Complex for export. Some of the ER is studded with ribosomes, and is called the Rough Endoplasmic Reticulum (RER) because it looks rough under the microscope. ER further from the nucleus often lacks ribosomes, and is called Smooth Endoplasmic Reticulum (SER). Carbohydrates are often added to proteins in the SER to create what are known as glycoproteins (proteins with carbohydrates attached to them). 5. Golgi Complex: (Also called the Golgi Apparatus) A complex of flattened membranes (that look like shelf fungus!). Glycoproteins are sent from the SER to the Golgi Complex in transport vesicles, where they receive additional modifications (more carbohydrates etc.), and are packaged into secretory vesicles (vesicles that are destined to fuse with the outer membrane of the cell) for export out of the cell. Many proteins taken in to the cell must also pass through the Golgi Complex. (Note: this does not apply to phagocytosis, where things taken into the cell are meant to be broken down and eaten.) Thus, the Golgi Complex is sort of a shipping and receiving center for the cell. 6. Lysosomes: The word lyse means to break apart. When food particles are taken into a cell (a process called phagocytosis) the food is engulfed by the cell s plasma membrane, and then that part of the membrane pinches off and becomes a vesicle. Such food vesicles then fuse with lysosomes, that are vesicles filled with digestive enzymes that will break down the food. The interior of lysosomes is also acidic, because the digestive enzymes only work at low ph. This is handy, because, if a lysosome accidentally breaks open inside the cell, the digestive enzymes will not damage the cell, because the ph is too high. 2

7. Peroxisomes: are smaller vesicles containing enzymes that remove hydrogen groups from various molecules that come into the cell, and transfer them to oxygen to create hydrogen peroxide. Other enzymes then convert the hydrogen peroxide to water and oxygen. Peroxisomes are usually used to detoxify various toxic compounds that enter the cell. 8. Vacuoles: Large compartments inside a cell that are filled with sap (in the case of plant cells) or other liquids (in the case of contractile vacuoles inside protists). The central vacuole of a plant is filled with sap (an aqueous solution of sugars and minerals). The contractile vacuole of a protist can be either filled with more fluid, or emptied of fluid, allowing the protist to maintain the proper osmotic potential (salt balance) inside the cell, similar to the way a fish uses a swim bladder. 9. Mitochondria (Singular: Mitochondrion): small, bean-shaped organelles that generates energy using a process called the Electron Transport Chain (part of the aerobic respiration system). Mitochondria are believed to be endosymbiotic bacteria. Mitochondria have their own, circular chromosome (DNA). Mitochondria are surrounded by two sets of membranes, one belonging to the host, and one belonging to the symbiont. The Electron Transport Chain enzymes are embedded in the mitochondrial membrane, which has been folded into a number of compartments to increase the surface area. The inside of these folded compartments are called cristae. 10. Chloroplasts: Are photosynthetic organelles believed to also be endosymbiotic archaebacteria. Are also enclosed by two sets of membranes, one belonging to the host and the other to the symbiont. Have their own circular DNA chromosome. Have stacks of compartments, called thylakoids, that are filled with the green pigment chlorophyll, which is involved in photosynthesis. Each stack of thylakoids is called a granum. 11. Cytoskeleton: The cell is not just a loose bag of liquid (like a water balloon). It actually has a microscopic skeleton to keep its shape, and allow it to move when necessary. The microscopic skeleton is called the cytoskeleton because it is a skeleton inside the cell s cytoplasm. It consists of three types of filaments: i. Microfilaments (also known as Actin Filaments): are the thinnest (about 7nm wide) and are composed of the protein Actin. Actin filaments both maintain the cell s shape, and are involved in moving things around inside the cell. (mrna molecules are believed to be moved around the cell by actin filaments.) ii. Microtubules: Larger, hollow filaments made of coils of the tubulin protein. They are about 25nm in diameter. Microtubules are involved in cell motility (are inside flagella and cilia), and separate various parts of the cell when the cell divides. Microtubules are sometimes associated with proteins called Motor Proteins, that can slide along the microtubule. iii. Intermediate Filaments: larger than actin filaments and smaller than microtubules (are about 12nm in diameter), are composed of coils of keratin 3

proteins. Intermediate filaments give structural support to the cell, and form the nuclear lamina. 12. Cell Wall: Only found in plant. The Cell Wall is a layer of cellulose found outside the cell membrane, which gives plant cells their rigid, usually square shape. 13. Extracellular Matrix (ECM): A network of fibers consisting mainly of collagen, elastin and fibronectin that is found outside the cell. The ECM is often used to bundle bunches of cells together into organs, where cells are imbedded inside a network of ECM, and are attached to the ECM proteins via proteins on the cell surface called integrins. Cartilage and tendons in bones are also formed of ECM. Newly formed bone is also made of ECM before it becomes ossified (reinforced with calcium). PRACTICE QUESTIONS Short Answer Questions: 1. Which protein are microfilaments made of? 2. Which type of cytoskeletal filaments can be found inside a flagellum? 3. What is the name of the membrane complex that is continuous with the nucleus, and which is sometimes studded with ribosomes? 4. What shape does a mitochondrial chromosome have? 5. What is the name for the network of flattened membranes which acts as a shipping and receiving center for the cell? 6. What is the name of the green pigment that is involved in photosynthesis inside a chloroplast? 7. What do you call a compartment made from the inwardly folded membrane of a mitochondrion? 8. What is the name for the network of proteins found outside the cell which sometimes forms connective tissue and cartilage? 9. What do you call the flattened green sacks inside of a chloroplast? 10. What are two of the main protein constituents of the ECM? 11. What is the general name for the inside (hollow) part of a tube or a container? 12. What do you call the microscopic spools that DNA is wrapped around? 13. What is the name of the class of proteins found on the surfaces of cells that allows them to attach to the Extracellular Matrix? 14. What is the name for a vesicle containing digestive enzymes and acid? 15. What do you call the process of taking in food from outside the cell by enveloping the food with the plasma membrane, and then pinching off a section of the membrane to form a vesicle? 16. What is the name of the tiny, anvil-shaped organelle on which mrna is translated into protein by linking together chains of amino acids? 17. What is the name for the liquid portion of the cytoplasm? 4

Extended Matching Inventory: Match the Terms to the Definitions. a. Actin i. Golgi b. Centromere j. Heterochromatin c. Chromatin k. Histone d. Collagen l. Integrins e. Cytoplasm m. Intermediate f. Endoplasmic filaments reticulum n. Keratin g. Euchromatin o. Lumen h. Extracellular p. Lysosome matrix q. Microfilaments r. Microtubules s. NPC t. Nuclear lamina u. Nucleosome v. Phagocytosis w. Plasma membrane x. Ribosome y. Telomere z. Tubulin aa. Vesicle 1. Name of a class of proteins that makes up nucleosomes. 2. The type of filaments that make up the nuclear lamina. 3. The protein that microtubules are made of. 4. The type of filaments that are responsible for amoeboid movement. 5. The process of taking food particles into a cell by forming vesicles in the plasma membrane, that then detach and move to the cytoplasm. 6. The protein that microfilaments are made of. 7. A vesicle filled with digestive enzymes and acid. 8. One of the main protein constituents of the ECM. 9. The protein that intermediate filaments are made of. 10. Proteins expressed on the surface of cells that allow the cell to bind to the proteins in the extracellular matrix. 11. The type of filaments that are inside flagella and cilia. 12. A network of proteins in which cells are sometimes embedded, and which sometimes forms connective tissue and/or cartilage. 13. Complex of flattened sacks where glycoproteins are either received for import into the cell, or packaged into secretory vesicles for export out of the cell. 14. Name for a microscopic transporting container. 15. Term that refers to the inside of a tube, such as a blood vessel, or transport vesicle. 16. Network of membranes connected to the nucleus, often studded with ribosomes. mrna is converted to protein, and threaded into the lumen. 17. Small, anvil shaped structure where mrna is translated into protein by linking together chains of amino acids. 18. Name for the phospholipid bilayer that separates the inside of a cell from the outside. 19. The fluid compartment inside the cell membrane, and outside the nucleus. 20. Collective term for DNA and the proteins closely associated with it. 21. The end of a chromosome. 22. Basketlike network of microscopic filaments that lines the inside of the nuclear membrane. 23. A pore complex in the nuclear membrane that allows traffic in and out of the nucleus. 24. Center of a chromosome, composed of DNA and structural proteins. 5

25. Term for the DNA and closely associated proteins that contains the actively transcribed genes. 26. Term for the DNA and closely associated proteins that makes up the structural features of chromosomes, and does not contain actively transcribing genes. 27. Structure made of four proteins that looks like a microscopic spool. DNA is wrapped, periodically around these structures. J. Greg Doheny 2014 6