CH-4-6 Cell Structure – Understanding Biology : Chapter Notes

This Document Contains Chapters 4 to 6 CHAPTER 4: CELL STRUCTURE WHERE DOES IT ALL FIT IN? The information in Chapter 4 provides details about prokaryotic and eukaryotic cells. It puts the chemistry of the earlier chapters into a picture of the cell. Emphasis is placed on eukaryotic cells because of their complexity and great diversity. Many terms are introduced in the chapter and should be reinforced as much as possible during coverage of the cell in this and other chapters dealing with cell concepts. Chapter 5 is a critical reference when covering the chapters later in the text that describe cell transport, metabolism, cell replication, and genetics. SYNOPSIS All life is composed of cells, individually or as components of multicellular organisms. With certain exceptions, cells are very small. Substances diffuse more rapidly in a small cell, enhancing both its metabolism and its communication with other cells and with its environment. As a cell’s size increases, its volume increases at a much greater rate than its surface area. A cell’s survival depends on its surface, where all molecules enter and exit. If there is too little surface to support the workings of the interior, the cell will die. Many of the structural differences between prokaryotes and eukaryotes are visible at the level of the light microscope; the presence of the nucleus in eukaryotes, for example. The nuclear material in prokaryotes is a single, circular strand of DNA, unencumbered by either proteins or a surrounding membrane and is difficult to see at the same scale. Observation with an electron microscope reveals details about the cytoskeleton and internal membrane systems of the eukaryotes, both absent in prokaryotes. Different kinds of microscopes and different staining procedures can be used to obtain a desired image. On a biochemical level, all of the reactions of a prokaryote, including those associated with ribosomes, occur openly in its cytoplasm, bounded only by invaginations of the plasma membrane. The reactions in a eukaryote are compartmentalized by the endoplasmic reticulum (ER) and by various membrane-bound organelles. Among these organelles are the nucleus, the Golgi apparatus, lysosomes, and microbodies (peroxisomes and glyoxysomes). The smooth and rough ER differ in appearance and function. Rough endoplasmic reticulum possesses ribosomes while smooth endoplasmic reticulum lacks them. Various chemical products are synthesized on the rough endoplasmic reticulum, channeled into the Golgi bodies, and packaged into microbodies and lysosomes. Smooth ER contains embedded enzymes and is involved in carbohydrate and lipid synthesis and detoxification. Some eukaryotic organelles contain DNA, notable among these are the cell’s powerhouses, the mitochondria and the chloroplasts. The cytoskeleton, composed of actin filaments, microtubules, and intermediate filaments, provides a framework to anchor the organelles and give a cell its shape. Microtubules move organelles within a cell assisted by kinesin and dynein proteins. They also provide the characteristic 9+2 arrangement of eukaryotic flagella, cilia, and centrioles. Plant, fungi, and some protists have special adaptations that are lacking in other cells. Plant cells have a large central vacuole which serves as a storage compartment and helps increase the cell’s surface-to-volume ratio. Plants cells and some protists have strong, rigid cell walls composed of cellulose whereas fungi have chitin in their cell walls. Animal cells lack cell walls but have their cytoskeleton linked to the extracellular matrix. LEARNING OUTCOMES 4.1 All Living Organisms Are Composed of Cells 1. Discuss the three principles of the cell theory. 2. Illustrate how the surface-area-to-volume ratio limits cell size. 3. Describe the tools biologists use to visualize cells. 4. Identify similarities found in all cells. 4.2 Prokaryotic Cells Lack Interior Organization 1. Distinguish between bacteria and archaea. 2. Describe the nature of prokaryotic motility. 4.3 Eukaryotic Cells Are Highly Compartmentalized 1. List the structural elements unique to eukaryotic cells. 2. Relate the structure of the nucleus to its function. 3. Describe the structure of a ribosome. 4.4 Membranes Organize the Cell Interior into Functional Compartments 1. Distinguish between rough ER and smooth ER. 2. Explain the role of the Golgi body in the endomembrane system. 3. Explain how cells compartmentalize destructive enzymes. 4.5 Mitochondria and Chloroplasts Are Energy-Processing Organelles 1. Describe the structure of a mitochondrion. 2. Differentiate between mitochondria and chloroplasts. 3. Describe how mitochondria might have evolved from ancient bacteria. 4.6 An Internal Skeleton Supports the Shape of Cells 1. Contrast the structure and function of the three protein fibers of the cytoskeleton. 2. Explain how animal cells use cytoskeletal elements to move materials within the cell. 3. Contrast how an animal cell crawls with how a protist uses flagella to swim. 4.7 Extracellular Structures Protect Cells 1. Contrast primary and secondary plant cell walls. 2. Explain how integrins link the cytoskeleton to the extracellular matrix of animal cells. 4.8 Cell-to-Cell Connections Determine How Adjacent Cells Interact 1. Explain how multicellular organisms are able to differentiate between the cells of different tissues. 2. Relate the structure of different types of junctions to their function. COMMON STUDENT MISCONCEPTIONS There is ample evidence in the educational literature that student misconceptions of information will inhibit the learning of concepts related to the misinformation. The following concepts covered in Chapter 4 are commonly the subject of student misconceptions. This information on “bioliteracy” was collected from faculty and the science education literature. • Cells are within an organism but do not make up the body • All cells are spherical • Cells are 98% water in chemical composition • The cytoplasm is similar to pure water • All animal cells have every type of organelle • Mitochondria are built by the cell • Mitochondria produced all of the cell’s ATP • Prokaryotes produce ATP in mitochondria • All cells have a nucleus • Plant cells do not have mitochondria • Smooth ER and rough ER are separate structures • The Golgi body is an independent organelle unrelated to the ER • All cells of multicellular organisms carry out the same tasks • Plant cells lack protein whereas animal cells are high in protein • Cell walls are the same as plasma membranes • Cell membranes are solid INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE There is a lot of unfamiliar vocabulary in this chapter. Etymology of new words may be helpful. Introduce the plasma membrane carefully. The next two chapters delve into its importance within and between cells. Most students are familiar with simple cell theory. It may be appropriate to discuss Redi’s and Pasteur’s experiments refuting spontaneous generation at this point, when discussing cells originating from other cells. Students have some difficulty with the differences between prokaryotes and eukaryotes, therefore stress nuclear organization and membrane compartmentalization as definitive characteristics. Many texts don’t present much in the way of why cells are the size they are. This is an important concept elaborated on later in this text, in relation to why most animals and some plants have specific size limitations. HIGHER LEVEL ASSESSMENT Higher level assessment measures a student’s ability to use terms and concepts learned from the lecture and the textbook. A complete understanding of biology content provides students with the tools to synthesize new hypotheses and knowledge using the facts they have learned. The following table provides examples of assessing a student’s ability to apply, analyze, synthesize, and evaluate information from Chapter 5. Application • Have students predict which organelles would become more active it the cell was induced to produce more protein secretions. • Ask students to explain which organelles would be damaged if a drug that kills prokaryotes were to end a person’s cells. • Ask students to explain why certain invasive organisms that cause disease in humans produce chemicals that block integrins. Analysis • Ask students to explain the implications of a disease that disrupts the function of the Golgi apparatus. • Ask students to explain the survival advantages of an infectious agent that has the ability to disable lysosomes. • Have students determine some of the consequences of research showing that nicotine reorganizes cytoskeleton structure. Synthesis • Ask students to hypothesize the characteristics of an endosymbiont that purportedly aids feeding in an organism that has no digestive system. • Have students determine the best classification of a cell that has chloroplasts and flagella, but has no cell wall or central vacuole. • Ask students to explain why some cells in an organism can have 100 times more mitochondria than other cells. Evaluation • Ask students to debate the pros and cons of using mechanical devices to replace lost body functions once carried out by cells. • Ask students to evaluate the consequences of a health product claiming to stimulate activity of the mitochondria. • Have students discuss the benefits and risks of producing agricultural animals that have chloroplasts expressed in their skin cells. VISUAL RESOURCES 1. A large, clear plastic bag is a reasonable facsimile of a cell’s plasma membrane. A prokaryote can be represented by a bag with various objects inside to represent their metabolic processes. A large bag with the objects inside of smaller bags represents a eukaryote and its compartmentalizing membrane-bound organelles. One could further place the bag in a box to represent the cell wall of a plant. 2. Fisher educational division sells a superb yet simple model of a lipid bilayer (and it is inexpensive). A saturated salt solution is the cell interior, mineral oil the exterior (the oil floats on the salt solution). Styrofoam balls are one side of the membrane (they float on the oil), plastic balls are the other side (they stay at the salt/oil interface). Plastic rods or straws into the balls serve as the lipid tails. 3. One may want to discuss cell fractionation and gradient centrifugation in relationship to isolating the various cell parts so they can be studied. A short description of various kinds of microscopes (especially the rationale behind why electron microscopes resolve much smaller structures) might be helpful, although this is frequently discussed in the laboratory setting. To a great extent, much of the material in this chapter is supported by laboratory activities where the students can observe many of the larger structures first-hand. 4. Most students mistakenly associate chloroplasts with plants and mitochondria with only animals. Stress that mitochondria are present in virtually all eukaryotes. Remember that these two organelles will be visited again when cell metabolism is discussed. Students may as well learn their structure now as opposed to later when they will be attempting to understand the biochemistry too. 5. Electron micrographs are a must for this material. They can be difficult for students to interpret, therefore accompanying line drawings that simplify the micrograph are beneficial. Or use markers to outline and/or colorize particular structures on either photographs or transparencies. IN-CLASS CONCEPTUAL DEMONSTRATIONS A. Organelle Role Playing Introduction Critical thinking can be done in many ways to encourage student retention of biology concepts. Students can be asked to role model different organelles to learn the function of the organelle and its interconnections with other organelles. This demonstration can be performed in the classroom or outdoors. Materials • Student volunteers to represent one organelle ○ Cell membrane ○ Nucleus ○ Chloroplast ○ Mitochondrion ○ Rough ER ○ Smooth ER ○ Golgi apparatus ○ Lysosome • Colored markers • 8 ½” X 11” sheets of white paper labeled with the name of one organelle ○ Cell membrane ○ Nucleus ○ Chloroplast ○ Mitochondrion ○ Rough ER ○ Smooth ER ○ Golgi apparatus ○ Lysosome Procedure & Inquiry 1. Ask the selected students to quickly design a labeled sign representing their organelle 2. Assign each student to an organelle and hand them the appropriate label. 3. Then ask the student to give a two-minute description of their relationship to the other organelles, for example I take _______ from the nucleus and provide the Golgi apparatus with ______. 4. The other organelles are free to discuss any interrelationships not mentioned by the other organelles. 5. Ask the class to assess the accuracy of the information discussed by the organelles. 6. Then ask the class to do a “Survivor-style” vote to determine which organelle could be “voted out” without outright killing the cell. A. Cytoskeleton in Action Introduction Seeing the activity of an organelle by demonstrating a living model is an excellent means of reinforcing the learning of cell structure. Elodea is a simple to use model for demonstrating cytoskeleton activity. Students can envision the nature and complexity of the cytoskeleton arrangement by tracking the path of chloroplasts traveling around the elodea leaf cytoskeleton. Materials • Microscope attached to a video camera • LCD projector linked to the video camera • Fresh elodea in 300C water • Slide with cover slip • 1 cigarette soaked overnight in 5 ml 30% ethanol solution Procedure & Inquiry 1. Prepare a wet mount of one elodea leave 2. Project a leaf under high magnification for viewing by the class 3. Ask to students to observe and discuss any pattern of movement by the chloroplasts 4. Ask the class to hypothesize why the chloroplasts are being moved around the by cytoskeleton and what factors, such as direction of sunlight irradiation, would affect chloroplast movement 5. Tell the class you are going to add cigarette extract to the elodea 6. Then add on drop of the cigarette solution onto the slide while it is still on the stage 7. Ask the students to observe what happens (the chloroplasts will stop moving) 8. Have the class hypothesize the reason for the loss of chloroplast movement LABORATORY IDEAS A. Cell Chemistry a. Have students use the microscope to investigate the chemistry of living cells. b. Tell the class that you want students to explore the chemistry of cell components. They should be asked to draw and record in writing their observation of the cells being investigated. c. Provide students with the following materials: i. Microscope ii. 8 microscope slides and cover slips iii. Scalpels iv. Forceps v. Toothpicks vi. Dimethyl Sulfoxide (DMSO) vii. Potassium Iodide (IKI) or Lugol’s solution viii. Concentrated Sudan IV solution ix. Biuret reagent x. Hematoxylin stain xi. Droppers xii. Potato d. Explain to students the different molecules that are detected using the various stains: i. Potassium Iodide - starch ii. Sudan IV solution - lipids iii. Biuret reagent - proteins iv. Hematoxylin stain – nucleic acids e. Tell students that they are going to compare the chemical composition of plant and animal cells. They are going to do this by using potato cells and human cheek cells as models. f. Have students carry out the following procedure: i. Prepare 4 wet mounts of thin potato slivers 1. Add 1 drop DMSO to all slides 2. Add stains: a. 1 drop of potassium Iodide b. 2 drops of sudan IV solution c. 2 drops of Biuret reagent d. 2 drops of hematoxylin stain 3. Students should let slides sit for 1 minute and then observe under the microscope. ii. Prepare 4 wet mounts of cheek cells 1. Carefully remove cheek cells with toothpick 2. Add 1 drop DMSO to all slides 3. Add stains: a. 1 drop of potassium Iodide b. 2 drops of sudan IV solution c. 2 drops of Biuret reagent d. 2 drops of hematoxylin stain 4. Students should let slides sit for 1 minute and then observe under the microscope. g. Ask the students to note any differences in molecular composition between the animal and plant cells. h. Use proper safety precautions and dispose of reagents appropriately according to the MSDS. B. Detection of Catalosomes a. Catalosomes of one of many small vacuoles that carry out specific cell functions. b. Students can investigate the presence of catalosomes using a simple hydrogen peroxide test for the presence of catalase. c. Provide students with the following materials: i. Microscope ii. 2 microscope slides and cover slips iii. Scalpels iv. Forceps v. Medical grade hydrogen peroxide vi. Droppers vii. Dimethyl Sulfoxide (DMSO) viii. Potato ix. Elodea leaves x. Onion roots d. Explain to students they will be looking for organelles called catalosomes and detecting them by looking at metabolic activity of the organelle. e. Then describe that catalase is able to convert hydrogen peroxide into water and oxygen gas. Ask them to hypothesize how they could determine if the reaction is taking place and to what degree it is occurring. f. Instruct students to carry out the following procedure: i. Prepare a wet mounts of potato cells 1. Add 1 drop DMSO to all slides 2. Add hydrogen peroxide and immediately view under the microscope ii. Prepare a wet mounts of elodea cells 1. Add 1 drop DMSO to all slides 2. Add hydrogen peroxide and immediately view under the microscope iii. Prepare a wet mounts of onion root cells 1. Add 1 drop DMSO to all slides 2. Add hydrogen peroxide and immediately view under the microscope g. Ask students to describe where the catalosomes appear to be located in the particular cells and explain any differences seen in catalosome activity between the different specimens. h. Use proper safety precautions and dispose of reagents appropriately according to the MSDS. LEARNING THROUGH SERVICE Service learning is a strategy of teaching, learning and reflective assessment that merges the academic curriculum with meaningful community service. As a teaching methodology, it falls under the category of experiential education. It is a way students can carry out volunteer projects in the community for public agencies, nonprofit agencies, civic groups, charitable organizations, and governmental organizations. It encourages critical thinking and reinforces many of the concepts learned in a course. Students who have successfully mastered the content of Chapter 5 can apply their knowledge for service learning activities in the following ways: 1. Have students take part is a health fair by providing information about the cellular damage caused by smoking. 2. Have students provide background information about stem cells to a civic group. 3. Have students tutor middle school or high school biology students studying cell structure. 4. Have students judge science fair projects related cell structure and function. ETYMOLOGY OF KEY TERMS ana- up; back (from the Greek an- up) archae- first; beginning; principle (from the Greek arche- beginning) -ase enzyme (modern) axo- axis (from the Greek axon- axle or axis) cat- down (from the Greek kata- down) chrom- color (from the Greek chroma- color) cyto- of, or relating to, the cell (from the Greek kytos- cell) endo- within; inside (from the Greek endon- within) eu- good; well; true (from the Greek eu- well) glyco- of, or relating to, sugar (from the Greek glykys- sweet) karyo- nucleus of a cell (from the Greek karyon- nut or kernel) lys (lysis) dissolution; breaking (from the Greek lysis- dissolution) magni- great; large (from the Greek and Latin magnus- great) micro- small; too small to be seen with the naked eye (from the Greek mikros- small) phago eating; devouring (from the Greek phagein- to eat) plasm living substance; tissue (from the Greek plasma- something molded or formed) poly- many (from the Greek polys- many) prote- of, or relating to, protein; first (from the Greek protos- first) some body (from the Greek soma- body) CHAPTER 5: MEMBRANES WHERE DOES IT ALL FIT IN? Chapter 5 takes a more detailed look at the cell by investigating the fine structure and functions of the cell membrane. The discussion of information on the cell membrane provided in Chapter 4 should be briefly reviewed before going into a lecture on Chapter 5. It is also important to stress that the information discussed in this chapter is needed later to understand organismic adaptations and evolution. SYNOPSIS Phospholipids are the foundation of all known biological membranes. The characteristic lipid bilayer forms as a result of the interactions among nonpolar phospholipid tails, polar phospholipid heads, and the surrounding water. The nonpolar tails face inward toward each other while the polar heads face outward toward the water. The arrangement of the lipid bilayer is stable, yet fluid. The membranes of living organisms are assembled from four components. The phospholipid bilayer provides an impermeable flexible matrix in which the other components are arranged. Transmembrane proteins that float within the bilayer are channels through which various molecules pass. A supporting protein network, anchored to the actin filament cytoskeleton, prevents these channels from moving. The glycocalyx consisting of sugars and membrane proteins provide a cell’s identity. All of the cell’s activities are in one way or another tied to the membrane that separates its interior from the environment. Net diffusion occurs when the materials on one side of the membrane have a different concentration than the materials on the other side. Facilitated transport of materials is necessary to control the entrance and exit of particular molecules. Facilitated diffusion is a simple process that utilizes protein carriers that are specific to certain molecules. It is a passive process driven by the concentration of molecules on the inside and the outside of the membrane. Osmosis is a specialized form of diffusion associated specifically with the movement of water molecules. Many cells are isosmotic to the environment to avoid excessive inward or outward movement of water. Other cells must constantly export water from their interior to accommodate the natural inward movement. Most plant cells, on the other hand, are hyperosmotic with respect to their immediate environment. The resulting turgor pressure within the cell pushes the cytoplasm against the cell wall and makes a plant cell rigid. Large molecules enter the cell by endocytosis, a nonselective process. Endocytosis of particulate material is called phagocytosis while endocytosis of liquid material is called pinocytosis. Exocytosis is the reverse mechanism and is used by plants to construct the cell wall and by animals to secrete various internally produced chemicals. Receptor-mediated endocytosis is a complicated mechanism that involves the transport of materials via coated vesicles. Some molecules are transported into or out of the cell independent of concentration. This process requires the expenditure of energy in the form of ATP and is called active transport. Such transport channels are coupled to a sodium¬potassium pump. The proton pump produces ATP through two special transmembrane protein channels through a process called chemiosmosis. LEARNING OUTCOMES 5.1 Membranes Are Lipid Sheets with Proteins Embedded in Them 1. Explain the fluid mosaic model of membrane structure. 2. Describe the four major components of biological membranes. 5.2 Phospholipids Provide a Membrane’s Structural Foundation 1. Explain how lipid bilayers form spontaneously. 5.3 Membrane Proteins Enable a Broad Range of Interactions with the Environment 1. List six key functional classes of membrane proteins. 2. Explain how proteins associate with fluid biological membranes. 5.4 Passive Transport Moves Molecules Across Membranes by Diffusion 1. Explain the importance of a concentration to simple diffusion. 2. Distinguish between simple diffusion and facilitated diffusion. 3. Predict the direction of osmotic movement of water. 4. Discuss three ways organisms maintain osmotic balance. 5.5 Active Transport Across Membranes Requires Energy 1. Distinguish between active transport and facilitated diffusion. 2. Explain the energetics of coupled transport. 5.6 Bulky Materials Cross Membranes Within Vesicles 1. Explain how endocytosis can be molecule-specific. COMMON STUDENT MISCONCEPTIONS There is ample evidence in the educational literature that student misconceptions of information will inhibit the learning of concepts related to the misinformation. The following concepts covered in Chapter 6 are commonly the subject of student misconceptions. This information on “bioliteracy” was collected from faculty and the science education literature. • The lipid layer is a solid surface. • Diffusion only occurs through pores in the membrane. • Any molecule can diffuse across a membrane. • Diffusion and osmosis do not occur together. • Osmosis moves any substance. • Osmosis works by the opposite principles of diffusion. • Particles are not moving back and back during isosmotic conditions. • Diffusion is not temperature dependent. • Active transport only moves against a diffusion gradient. • Gases do not diffuse. • Ions easily pass through a membrane. • All transport proteins require ATP. • Carriers are highly specific to one molecule. • Pinocytosis takes in pure liquids and not solutes. • Turgor is due to osmosis and not due to a diffusion gradient. INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE One could develop a lengthy comparison of a cell and its organelles to a community with respect to energy, transportation, communication, growth, and so forth. Stress the fluidity of the plasma membrane and the regular replacement of its components to ensure constant integrity. It is as though one could remove a chipped brick from a house and replace it with a new one. A completely fluid house would have doors, windows, and walls that moved with respect to the current needs of the occupants and the appearance of the environment. Membrane fluidity is related to the presence of saturated and unsaturated fatty acids in the phospholipid tails. Saturated fats are like books stacked tightly on a shelf. They can’t readily be moved from shelf to shelf and are very rigidly organized. Warped books (unsaturated fats), on the other hand, can’t be as closely packed. It is easier to get one’s fingers between the books and move them around. Do not be confused that a 3-D surface view of a membrane is viewed in a transmission electron microscope rather than a scanning one. The resolution of the TEM is far better (down to 2m), but only a very thin section can be viewed, unlike the SEM which can be used to examine very thick specimens and even whole objects like protozoa, insects, leaves, and flowers. To examine cell membranes and still satisfy the thin layer requirement, it is the cast of the surface that is viewed under the TEM, not the cell surface itself — as would occur if one examined the coated surface of a cryofractured cell with the SEM. Be careful to present hypoosmotic/hyperosmotic as being relative to one another. A solution cannot simply be hypoosmotic unless it is compared to another solution. A cell may be hypoosmotic to its solution, but the solution is also hyperosmotic to the cell. The types of movement of molecules through a membrane are more readily remembered when the students understand what the names mean. Simple diffusion is just that, nothing else assists it. Facilitated diffusion requires the presence of channels that aid in the passage of molecules. Active transport is like any active versus passive mechanism, it requires the expenditure of energy. It is important that students begin to understand how ATP is generated as it will come up again (most notably in the next set of chapters regarding metabolism). Similarly, cell surface receptors and cell surface markers will be discussed in greater depth in a later chapter entitled The Immune System. HIGHER LEVEL ASSESSMENT Higher level assessment measures a student’s ability to use terms and concepts learned from the lecture and the textbook. A complete understanding of biology content provides students with the tools to synthesize new hypotheses and knowledge using the facts they have learned. The following table provides examples of assessing a student’s ability to apply, analyze, synthesize, and evaluate information from Chapter 5. Application • Have students predict the direction of diffusion and osmosis given a cell placed in a concentrated urea solution. • Have students predict the direction of diffusion and osmosis given a cell placed in a dilute sodium chloride solution. • Ask students explain why patients with severe dehydration are given hypoosmotic drinks. Analysis • Ask students to explain how cell transport is affected if a cell is immersed on a solution that degrades proteins. • Ask students to explain the effects of a toxin that binds up sodium so that it does not pass through the sodium-potassium pump. • Have students determine nature of a toxin that blocks the facilitated diffusion of glucose. Synthesis • Ask students hypothesize the role of an enzyme in the cytoplasm that converts glucose to glycogen upon glucose entering the cell. • Have students to find a use for a large artificial cell membrane capable of pumping sodium and chloride ions in one direction.. • Ask students to explain why human brain cells must rely on the transport capabilities of surrounding cells for obtaining nutrients. Evaluation • Ask students to evaluate the transport properties that a kidney dialysis machine must have to keep a person’s body cells alive. • Ask students to evaluate a claim that drinking too much water can cause swelling of brain cells. • Have students discuss the benefits and risks of drugs that affect the function of the sodium-potassium pump. VISUAL RESOURCES 1. Diffusion can be demonstrated by placing mothballs or perfume in one corner of the lecture hall before lecture begins. As time progresses, have students raise their hands (or colored flags) when they smell the odor. 2. Gortex® is a material that is unidirectionally permeable to water. It allows moisture to pass from the inside (of a jacket or tent) outward, but does not allow rain to penetrate inward. IN-CLASS CONCEPTUAL DEMONSTRATIONS A. Wine from Raisins Introduction Students enjoy and gain educational value from simple classroom demonstrations that show concrete examples of complex topics. Osmosis and diffusion can be boring topics to students without some break in the lecture to observe a simple example. This demonstration uses raisins as a model for understanding osmosis and barriers to osmosis. Materials • Raisins • Acetone • Small beaker • Forceps • 40oC distilled water • 2 Petri plates • Overhead projector Procedure & Inquiry 1. At the beginning of the lecture, tell the class you will be demonstrating a lesson on osmosis. 2. Then immediately, place the two Petri plates on an overhead projector and fill to capacity with the 40oC distilled water. Do not tell the students that the solution is distilled water. 3. Rinse one raisin in acetone telling the class that you are washing the raisin in a solvent. 4. Place that raisin in the one Petri plate. 5. Then place the other raisin in the other Petri plate without doing an acetone rinse. 6. Have the students observe the results. They will notice the acetone-washed raisin swell during the class period as the other does not. 7. Have the students explain the nature of the solution in the Petri dish compared to the raisin. 8. Ask them to explain the role of the solvent in permitting osmosis to occur freely. 9. Have the students hypothesis the unwashed raisin was similar to the protective value of human skin. B. Effect of Temperature on Diffusion Introduction It is important to stress the effects of temperature on diffusion rate. Many organisms maintain a particular body temperature that is favorable to a particular diffusion rate. It also reinforces the principle that diffusion is driven by molecular vibrations that is measured indirectly as temperature. This demonstration is a simple depiction of the influence of temperature on diffusion rate. Materials • Overhead projector • 4 labeled Petri plates ○ One labeled 90 ○ One labeled 40 ○ One labeled RT ○ One labeled Ice • Blue dye in a dropper bottle • 100 ml of 90oC in a small beaker • 100 ml of water in a small beaker chilled in an ice bath • 100 ml of 370C - 400C water in a small beaker • 100 ml of room temperature water in a small beaker Procedure & Inquiry 1. Explain that you will be demonstrating the relationship between temperature and diffusion. 2. Place the four Petri plates on the overhead projector. 3. Add the appropriate water samples in the labeled Petri plates. 4. Tell the students to watch carefully as you slowly add one drop of blue dye to each Petri plate. 5. Ask the students to discuss the importance of the temperature-diffusion relationship to an organism’s survival. LABORATORY IDEAS A. Osmolarity of Plant Cells a. Have students investigate the osmolarity of living tissues using plants cells as a model. b. Tell the class that they will use circular sections of apples to test the isosmolar point of plant tissues. Students should be able to calculate the approximate concentration of solutes in the cytoplasm of apple cells in this investigation. c. Provide students with the following materials: i. Fresh apple ii. 4mm diameter cork borer iii. Small ruler iv. Forceps v. 7 small test tubes vi. Test tube rack vii. Marker viii. A gradient of salt solutions in containers with large droppers: 1. 10% sodium chloride 2. 5 % sodium chloride 3. 2 % sodium chloride 4. 5 % sodium chloride 5. 1 % sodium chloride 6. 0.2% sodium chloride 7. Distilled water d. Have students cut 4mm circles of potato wedges measuring each one before the experiment begins. e. The students should then set up the test tubes so that they are labeled: i. 10% sodium chloride ii. 5 % sodium chloride iii. 2 % sodium chloride iv. 5 % sodium chloride v. 1 % sodium chloride vi. 0.2% sodium chloride vii. Distilled water f. Students should then add 5 ml of the appropriate solution into the test tubes. g. Then have them place one apple circle in each of the tubes and let sit for 15 minutes. h. Next, have the students measure the size of each apple circle. i. They should be asked to conclude the approximate osmolarity of the apple cells based on their findings. They should be encouraged to examine the data of other students to see if there was consistency in the findings. B. Plant model for Diabetes-Induced Dehydration a. Have students use plant cells to understand the dehydrating effects of high blood sugar as found in diabetes. b. Diabetes is indicated by higher than average blood glucose levels for a period after a sugary meal is taken in the body. A typical interpretation of blood glucose levels is given below: c. Tell students that you will be using plants as a model for understanding the effects of high blood sugar on human cells. d. Provide students with the following materials: i. Healthy elodea ii. Microscope iii. 4 microscope slides and cover slips iv. Glucose solutions (each represents a blood glucose condition): 1. 0.8 grams in 400cc of distilled water (normal level) 2. 1.0 grams in 400cc of distilled water (slightly high level) 3. 2.0 grams in 400cc of distilled water (dangerously high level) 4. 4.0 grams in 400cc of distilled water (severely high level) v. Instruct students to prepare four slides labeling them with a glucose level amount from the samples provided above. vi. They should then place several drops of the appropriate solutions on a slide. vii. Have the students place one elodea leaf on each slide to observe under the microscope. viii. They should record their results and determine effects high sugar concentrations in blood would have on cells and tissues. LEARNING THROUGH SERVICE Service learning is a strategy of teaching, learning and reflective assessment that merges the academic curriculum with meaningful community service. As a teaching methodology, it falls under the category of experiential education. It is a way students can carry out volunteer projects in the community for public agencies, nonprofit agencies, civic groups, charitable organizations, and governmental organizations. It encourages critical thinking and reinforces many of the concepts learned in a course. Students who have successfully mastered the content of Chapter 5 can apply their knowledge for service learning activities in the following ways: 1. Have students talk to youth sports groups about the benefits of proper hydration. 2. Have students design an electronic presentation on cell transport for use by teachers at local schools. 3. Have students tutor middle school or high school biology students studying cell transport. 4. Have students judge science fair projects related to cell transport. ETYMOLGY OF KEY TERMS amphi- two; both (from the Greek amphi- on both sides) calyx cup-like; covering (from the Greek kalyx- husk) endo- within; inside (from the Greek endon- within) exo- outside; external (from the Greek exo- outside) glyco- of, or relating to, sugar (from the Greek glykys- sweet) hyper- over; above (from the Greek hyper- above) hypo- under; below (from the Greek hypo- below) integral part of the whole; necessary (from the Latin intangere- untouched or undivided) iso- equal; same (from the Greek isos- equal) osmo- pertaining to the movement of fluids through membranes (from the Greek osmos- push or thrust) -pathic feeling; suffering (from the Greek pathos- suffering or feeling) peripheral on the outskirts; near the outer boundary (from the Greek peri- around and pherein- to bear, used together, the Greek peripheria signified circumference) phago- eating; devouring (from the Greek phagein- to eat) pino- drinking (from the Greek pinein- to drink) port to carry (from the Latin portare- to carry) sym/syn- with; together (from the Greek syn- together) trans- across, through (from the Latin trans- across or through) uni- one (from the Latin unus- one) CHAPTER 6: ENERGY AND METABOLISM WHERE DOES IT ALL FIT IN? Chapter 6 builds upon the cell anatomy coverage of Chapter 4 and provides students with details of cellular energy concepts needed understand the metabolic pathways that run a cell. It is a critical step into Chapter 7. By this point of the books students have been given many terms and concepts the must now be put together to give a complete picture of the cell and cell interactions that build the higher hierarchical levels. It is important to briefly highlight the information in the previous chapters for students to gain a better understanding of the concepts in Chapter 6. Chapter 6 is critical for students to understand other concepts that integrate cell function to homeostasis and development. SYNOPSIS Living organisms transform potential energy into kinetic energy to survive, grow, and reproduce. The energy that the earth receives from the sun is transformed into heat energy as it warms the continents and the oceans. Various kinds of photosynthetic organisms also absorb this energy and convert it to potential energy in the form of chemical bonds. Oxidation-reduction reactions are a class of reactions that pass electrons from one molecule to another. A molecule that is oxidized loses an electron; one that is reduced gains an electron. Oxygen is the most common electron acceptor in biological systems. Since the transfer of electrons is accompanied by a transfer of protons in the form of H+ ions, oxidation generally involves the removal of hydrogen atoms and reduction involves the addition of hydrogen atoms. In biological systems, oxidation-reduction reactions are coupled to one another. In photosynthesis, carbon dioxide is reduced to form glucose, storing energy. In cellular respiration, the oxidation of glucose releases energy. The First Law of Thermodynamics states that energy can be transformed from one state to another, but cannot be created or destroyed. The Second Law of Thermodynamics states that objects tend to move from a state of greater order to one of lesser order. Thus entropy, the measure of disorder in a system, is constantly increasing. The amount of free energy available to form chemical bonds is equal to the energy within a cell that is available to do work (enthalpy) minus the product of temperature and entropy. A reaction proceeds spontaneously when its change in free energy is a negative number. The products of exergonic reactions contain less free energy than the reactants. Such reactions proceed spontaneously and release the excess usable free energy. The products of endergonic reactions have more free energy than the reactants, do not occur spontaneously, and require an input of energy to proceed. Fortunately, even exergonic reactions require an input of a small amount of activation energy to get started. Otherwise all combustible materials would have burned up long ago. This activation energy is required to destabilize the existing chemical bonds; something that occurs more readily in the presence of a catalyst. The chief energy currency of cells is the molecule adenosine triphosphate, ATP. This molecule is composed of a five-carbon backbone to which a nitrogenous adenine base and a chain of three phosphate groups are attached. The covalent bonds linking the phosphate groups are high ¬energy bonds that are readily broken to release 7.3 kcal/mole of energy. All cells use ATP to drive their endergonic reactions. Cells do not store large amounts of ATP but possess a pool of ADP and phosphates so that they can make ATP whenever it is needed. Enzymes are biological catalyzing agents generally in the form of proteins and having names ending in -ase. An enzyme brings two substances together in the proper orientation and stresses certain bonds. It does not force a reaction to occur in a single direction but enhances the reaction in both directions. Although many reactions involve discrete enzymes, many complex pathways depend on multienzyme complexes to efficiently carry out their sequential reactions. Certain RNA reactions possess unique RNA catalysts called ribozymes, giving strength to the argument that RNA evolved prior to proteins. Enzyme activity is altered by several factors including temperature and hydrogen ion concentration (pH). A competitive inhibitor binds at the same site as the substrate, effectively inhibiting the reaction. Non¬competitive inhibitors and activators bind to the allosteric site to alter reaction rates. Various cofactors are associated with most enzymes and may be in the form of metal ions or nonprotein, organic molecules called coenzymes. One of the more important coenzymes is nicotinamide adenine dinucleotide (NAD+), a hydrogen acceptor that, when reduced, becomes NADH. This molecule is responsible for carrying the energy of an electron and a hydrogen throughout the cell. Living organisms organize their metabolic activities in reaction chains called biochemical pathways. The first metabolic pathways were anaerobic since oxygen was not present in the early atmosphere of the earth. The product of one reaction becomes the substrate for the next. The step-wise nature of a biochemical pathway reflects its evolution. Organisms rarely evolve new processes completely independent of other processes; rather they utilize the machinery that already exists and add to it or alter it slightly. The addition of new processes generally occurs at the beginning of the pathway; such a pathway evolves backwards. The final reactions evolved first, the beginning reaction is the most recent adaptation. The stepwise progression of pathways allows for more precise regulation. LEARNING OUTCOMES 6.1 Energy Flows Through Living Systems 1. Differentiate between kinetic and potential energy. 2. Differentiate between oxidation and reduction reactions. 6.2 The Laws of Thermodynamics Govern All Energy Changes 1. Define thermodynamics, and state the First Law of Thermodynamics. 2. Define entropy, and state the Second Law of Thermodynamics. 3. Use the definition of free energy to differentiate between endergonic and exergonic reactions. 6.3 ATP Is The Energy Currency of Cells 1. Explain how the phosphate groups of ATP store potential energy. 2. Distinguish which bonds in ATP are “high energy.” 6.4 Enzymes Speed Chemical Reactions by Lowering Activation Energy 1. Explain how catalysts increase the rate of chemical reactions. 2. Explain how enzymes lower activation energies, and the consequences of doing so. 3. Differentiate between an enzyme’s active site and its substrate-binding site. 4. Describe the different types of molecules that may act as enzymes. 5. Explain the effects of temperature and pH on an enzyme-catalyzed reaction. 6.5 Metabolism Is the Sum of a Cell’s Chemical Activities 1. Describe how chemical reactions can be organized into pathways. 2. Explain the function of allosteric proteins. COMMON STUDENT MISCONCEPTIONS There is ample evidence in the educational literature that student misconceptions of information will inhibit the learning of concepts related to the misinformation. The following concepts covered in Chapter 6 are commonly the subject of student misconceptions. This information on “bioliteracy” was collected from faculty and the science education literature. • Spontaneous reactions “do not require energy to occur”. It is important to remind students that ALL reactions require an input of energy in the form of activation energy. • ATP gives energy to a cell. • ATP is produced in the body and not in the cell. • ATP production increases with calories taken in the diet. • All enzymes are killed by heating. • Enzymes are so highly selective that they only bind to one type of substrate. • Enzymes cannot bind to products of their reaction. • Organisms dot not obey the laws of thermodynamics. INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE As seen in figure 6.3, the condition of one’s bedroom, office, or desk is related to the Second Law of Thermodynamics. There is a tendency for each of them to become more disorganized (increased entropy). Cleanup and organization requires the input of energy. It is easier to see how reactions with negative free energy occur spontaneously if the equation is presented as DG = DH + (–TDS). For DG to be negative, disordering influences (–TDS) must be larger than ordering influences (DH). In relation to oxidation/reduction reactions, think of the reverse of what is expected. In reduction, an electron is GAINED. When oxygen does what it is best at, accepting electrons, it is REDUCED. The lock and key analogy to enzyme action can be extended to include a master key system. Sometimes a key opens only one specific lock. A master or submaster key may be able to open several locks in a specific series. In addition, some high security doors may require two or more locks to be unlocked to gain access. This is similar to how cofactors help control enzyme activity. A multienzyme complex can be likened to a separate key ring used to open a series of rooms in a certain building. I personally keep my work, home, and car keys on separate rings. It makes any entry less cumbersome and prevents me from losing everything all at once should I leave a set of keys somewhere! On a social comparison, a catalyst is like a good party host/hostess (or a romantic match maker). He/she introduces two individuals that otherwise might not meet. The host/ess is not “used up” in the process, but if there are too many unfamiliar individuals, the host/ess can become “saturated” trying to pair up the guests. HIGHER LEVEL ASSESSMENT Higher level assessment measures a student’s ability to use terms and concepts learned from the lecture and the textbook. A complete understanding of biology content provides students with the tools to synthesize new hypotheses and knowledge using the facts they have learned. The following table provides examples of assessing a student’s ability to apply, analyze, synthesize, and evaluate information from Chapter 6. Application • Have students explain why an animal benefits from eating foods high in free energy. • Have students explain why certain vitamins are known to regulate the rate of certain metabolic pathways. • Ask students explain why any environmental factor that slows down diffusion would affect enzyme function. Analysis • Ask students to explain why reptiles move into the sunlight after eating a large meal. • Ask students to explain may many plant seeds produce chemicals that inhibit enzymes involved in starch digestion. • Ask students hypothesize the purpose of designing drugs that fit into the allosteric site of certain types of enzymes. Synthesis • Ask students to design an experiment that tests whether an enzymatic reaction is being carried out by proteins or by nucleic acids. • Have students explain some researcher believe that metabolic pathways existed before organisms had protein enzymes. • Ask students the value of a drug that blocks the enzymatic degradation of fats. Evaluation • Ask students to evaluate that statement that the heat produced during metabolism is not wasted energy. • Ask students to come up with commercial uses of enzymes taken from organisms that live in temperatures that exceed 200oC. • Have the students evaluate the claims that heating an injury increases the healing ability of the body. VISUAL RESOURCES 1. Any wooden or plastic interlocking puzzle can be used to show how an enzyme catalyzes a reaction by stressing bonds and altering chemical shapes. The puzzle cannot be taken apart until one knows the special twist or trick to it. Finding this may take hours. Once it is known, the puzzle can be done very rapidly — like an enzyme catalyzing a reaction. 2. Pipe cleaners or modeling clay are excellent materials that can be molded to 3-D models that help students visualize enzymatic interactions with substrates. IN-CLASS CONCEPTUAL DEMONSTRATIONS A. “Hot and Cold” Reactions: Demonstrating Endothermy and Exothermy Introduction A fun visual demonstration is a proven way to reinforce learning of energy concepts. This demonstration shows students the temperature changes associated with endothermic and exothermic reactions. -Endothermy Materials • Approximately 64g of barium hydroxide octahydrate • Approximately 30g of ammonium nitrate • 250 ml Erlenmeyer flask • Thermometer • Glass stirring rod • Distilled water • Well-vented area Procedure & Inquiry 1. Add 150 ml of water to the flask. 2. Add solid barium hydroxide octahydrate to the flask. 3. Place thermometer in the flask and tell the initial temperature to the class. 4. Add ammonium nitrate to Erlenmeyer flask and stir 5. Stir the two components together. 6. After 30 seconds ammonia vapors will exit the flask. 7. Read the temperature change to the class after this point. 8. Ask students what type of reaction took place. 9. Ask the students to think of possible ways endothermic reactions can be used in everyday life. 10. Dispose of materials appropriately according to institutional chemical waste policies. -Exothermy Materials • Supersaturated sodium acetate • Thermometer • Sodium acetate crystals • 250 mL Erlenmeyer flask • Glass stirring rod Procedure & Inquiry 1. Add 150ml of supersaturated sodium acetate to flask. 2. Add thermometer and announce temperature to class. 3. Add a large crystal of sodium acetate to the flask. 4. A long crystalline spike should form from the crystal. 5. Start announcing the temperature change to the class as heat is produced. 6. Ask students what type of reaction took place. 7. Ask the students to think of possible ways exothermic reactions can be used in everyday life. 8. Dispose of materials appropriately according to institutional chemical waste policies. B. Clay Enzymes with a Charge Introduction A quick demonstration of enzyme specificity can be demonstrated using clay and magnets to demonstrate the induced fit model of enzyme function. This demonstration should be done during a discussion of active site action. Materials • Three different colors of modeling clay • Small cylindrical magnets marked with white correction fluid to show the positive and negative poles. Procedure & Inquiry 1. Mold a large wad of clay into a virtual enzyme with a square indentation representing the active site. Place five magnets into the active site. One magnet should be placed in each wall with the negative poles facing out. 2. Tell the class that this now represents an enzyme active site. 3. Then tell the class you are going to make to potential substrates. 4. Form one substrate using another color of clay. Make the clay into a square that would fit into the active site. Add five magnets to the clay block. The magnets should be placed with the positive poles facing out. 5. Place the “substrate” into the “active site” showing how shape and charge create a best fit. 6. Next, form the other substrate using the remaining color of clay. Make the clay into a square that should fit into the active site. Add five magnets to the clay block. The magnets should be placed with the negative poles facing out. 7. Place the “substrate” into the “active site” showing how it is almost impossible to get a good charge fit. 8. Ask the class to explain the cause of the charges in the active site. 9. Ask the class to discuss other factors besides shape and charge that may affect the interaction between the active site and substrate. LABORATORY IDEAS Commercial Applications of Enzymes a. Have students investigate one commercial use of enzymes using a long-term project that they can monitor for a period of time. b. Tell the class that they will be using enzymes to as a way of recycling paper into animal feed. This process is used in many countries where animal feed is expensive and waste disposal is prohibitive because of a lack of landfill space. c. Students should be able to make a setup that degrades the paper into slurry useful as an animal nutrient. d. Provide students with the following materials: i. Amylase powder or liquid ii. Cellulase powder or liquid iii. Protease powder or liquid iv. Pectinase powder or liquid v. Phosphate buffer 1. Monosodium phosphate, monohydrate 58.4 2. Disodium phosphate, heptahydrate 154.7 3. Mixed together in 1 liter of distilled water vi. Test tubes vii. Test tube rack viii. 1cm2 pieces of newspaper e. Ask students to test the effectiveness of particular types of enzymes on degrading waste paper into animal feed. f. Have them research the chemistry of newspaper and the activity of each enzyme supplied for the study. g. Then ask the students to select and enzyme or enzyme mixture the completely degrades the paper into a solution that be turned into animal feed. LEARNING THROUGH SERVICE Service learning is a strategy of teaching, learning and reflective assessment that merges the academic curriculum with meaningful community service. As a teaching methodology, it falls under the category of experiential education. It is a way students can carry out volunteer projects in the community for public agencies, nonprofit agencies, civic groups, charitable organizations, and governmental organizations. It encourages critical thinking and reinforces many of the concepts learned in a course. Students who have successfully mastered the content of Chapter 6 can apply their knowledge for service learning activities in the following ways: 1. Have students talk to youth sports groups about misconceptions of energy supplements and athletic performance. 2. Have students design prepare a talk for seniors groups about the effectiveness, benefits, and risks of nutritional supplements that supply “energy”. 3. Have students tutor middle school or high school biology students studying cell energy concepts. 4. Have students judge science fair projects related to cell function. ETYMOLOGY OF KEY TERMS alkal(i)- basic or alkaline; a substance that can neutralize an acid to produce a salt (from the Arabic al-qali- salt wort ashes) allo- divergence; difference from; other (from the Greek allos- other) ana- up; back (from the Greek an- up) -ase enzyme (modern) -bolic proceeding; moving (from the Greek bole- throw) cat- down (from the Greek kata- down) dynamic changing; active; characterized by energy (from the Greek dynamikos- force or power) end(o)- within; inside (from the Greek endon- within) equi- equal (from the Latin aequus- equal) -ergonic relating to energy; transfer of energy (from the Greek ergon- work) ex(o)- outside; external (from the Greek exo- outside) -ism the state of (from the Greek ismos- state of) libri balance (from the Latin libra- balance) lys (lysis) dissolution; breaking (from the Greek lysis- dissolution) meta- change; transformation; following something in a series (from the Greek meta- change or after) steric pertaining to the spatial arrangement of atoms in molecules (derived from stereo, which is from the Greek stereos- solid) thermo- indicating heat (from the Greek therme- heat) Instructor Manual for Understanding Biology Kenneth Mason, George Johnson, Jonathan Losos, Susan Singer 9780073532295, 9781259592416