Study Guide for Cell Biology Final Part 9

Study Guide for Cell Biology Final 103 Chapter 4: 1. What are the four phases that are thought to have led to the appearance of cells on earth? a. The abiotic synthesis of small organic molecules, such as amino acids and nitrogenous bases b. The joining of these small molecules into macromolecules, such as proteins and nucleic acids c. The packaging of the molecules into protocells, droplets with membranes that maintained an internal chemistry different from that of their surroundings d. Origin of self-replicating molecules that eventually made inheritance possible 2. What are the major differences between prokaryotic and eukaryotic cells? What organisms fall into the two divisions? How can the prokaryotes be subdivided? What is the distinction between these two types of prokaryotes? What are the three domains? Give examples of organisms in each. a. The major differences between prokaryotic and eukaryotic cells is that prokaryotes are smaller and don’t have a membrane bound nucleus and eukaryotes are larger and do have a membrane bound nucleus. For example, plant and animal cells are considered to be eukaryotic and bacteria are considered to be prokaryotic. Prokaryotes can then be subdivided into bacteria and archaea. The three domains include Bacteria, Archaea, and Fungi. 3. Which of the following are characteristic of eukaryotes and which are characteristic of prokaryotes: membrane bound nuclei, circular DNA, contains mitochondria, contains cytoskeleton, reproduces by binary fission, performs endocytosis, may contain cell walls, contains ribosomes, contains histones, contains Golgi apparatus, lacks mitochondria, forms gametes by meiosis. 4. Compare the structure of a prokaryotic nucleoid and eukaryotic nuclei. a. A prokaryotic nucleoid is loose DNA that is not protected by a membrane. It is usually in a circular shape. Eukaryotic nuclei are bound by a double bilayer membrane in order to protect the DNA molecules inside. 5. What is the relationship between millimeters, micrometers and nanometers? a. One millimeter is equal to 1/1,000 meters, one micrometer is equal to 1/1,000,000 meters and one nanometer is equal to 1/1,000,000,000 meters 6. What properties do prokaryotic and eukaryotic cells have in common? a. Despite the many differences between prokaryotic cells and eukaryotic cells, there are some similarities. These include both having DNA molecules, ribosomes, and a way to make energy within the cell itself so it doesn’t have to rely on something else for its energy. 7. What is an organelle? a. An organelle is located inside the cell and performs a very specific function. 8. What are the sizes of typical cells? A mitochondrion is 2 micrometers in length. How many nanometers is this? Millimeters? a. The typical size of a cell would be between 10 and 100 micrometers. Since a mitochondrion is 2 micrometers long, it would convert to be 0.002 nanometers and 200 millimeters. 9. Which has a greater surface area to volume ratio, a basketball or baseball? Study Guide for Cell Biology Final 104 a. Without having numbers to work with, my educated guess would be that the basketball has the greater ratio. This is because as the surface area increases from the baseball, the volume either stays the same or decreases, which both would result in a larger SA/V ratio in comparison to the baseball. 10. You are investigating the properties of two cells, Husky and Carver. Husky is a cubeshaped cell that is 20 micrometers long, 20 micrometers wide, and 20 micrometers high. Carver is also cube-shaped cell but is 10 micrometers long, 10 micrometers wide and 10 micrometers high. Calculate the surface area, volume and SA/V ratio for each cell. Which cell has the greatest nutrient demand? Which cell has the greatest surface area? Which cell has the greatest surface area to volume ratio? a. The Husky cell has a volume of 8,000 micrometers3 with a surface area of 2,400 micrometers2. The SA/V ratio then comes to 2,400/8,000 and equals 0.3. the Carver cell has a volume of 1,000 micrometers3 with a surface area of 600 micrometers2. The SA/V ratio then comes to 600/1,000 and equals 0.6. The Husky cell has the largest nutrient demand because it has a greater volume and a greater surface area. The Carver cell though, has the larger SA/V ratio of 0.6 compared to 0.3. 11. Why is it advantageous for a cell to be small? What is the disadvantage of being large? a. Cells are very small in size. This is advantage because then the cells don’t have to send materials as big of a distance as if the cells were larger. The surface area to volume ratio is also larger, which makes it easier for the cell exchange materials between the inside of the cell and the outside through the plasma membrane. The above listed advantages of a small cell size also prove the disadvantages of a cell if it would be large. 12. What is a virus? Is it considered to be a cell? Why or why not? a. A virus is an infectious agent that is composed of nucleic acid surrounded by protein. It is not a cell because it requires a host in order to fulfill its functions. 13. What is a prion? Is it considered to be a cell? Why or why not? Why is it considered to be an infectious agent? a. A prion is a misfolded protein that can be produced and ingested by the host. It is infectious and not considered a cell. It can be infectious because if several of these proteins gather in the same place of the body, they can change to functions of that specific area. 14. Describe the structure and function of the following eukaryotic cellular structures: membrane, mitochondrion, ribosomes, Golgi complex, rough and smooth endoplasmic reticulum, lysosome, peroxisome, chloroplast, central vacuole, cell wall or nucleus, cytoskeleton. a. Membranes are composed of phospholipid bilayers and serve to protect the cell from extracellular forces. Mitochondrion are similar in size to a bacterium with an inner and outer membrane. They serve to provide energy for the cell. Ribosomes are made up of proteins and RNAs and play a role in protein synthesis. The Golgi complex detoxifies materials and packages materials to be shipped out of the cell. The structure is flattened sacs throughout called cisternae. The rough ER is similar in structure to the Golgi complex, plus it has ribosomes attached to the surface. It functions to Study Guide for Cell Biology Final 105 synthesize proteins. The smooth ER still has a similar structure but synthesizes lipids and not proteins. Lysosomes have a simple structure, membrane bound sac. Their main function is to store hydrolases, which are enzyme that break down biological material. To avoid breaking themselves down, they are surrounded by a layer of phospholipids and carbohydrates. Peroxisomes are very similar to lysosomes to shape and size, though they contain the enzymes needed to neutralize hydrogen peroxide. Chloroplasts are only found in green plant cells. They are full of thylakoids that give them a green pigment and function to provide energy for the cell through photosynthesis. Central vacuoles are used to store water and maintain the turgor pressure in plant cells. Cell walls surround plant cells in order to maintain the cell’s shape. Nuclei are found in both plant and animal cells are function to store genetic information. It is surrounded by a double phospholipid bilayer that has pores in order for the genetic material to leave the nucleus during translation. Cytoskeletons are found in animal cells and have a similar function as a cell wall. They provide structure for the entire cell and are long, thin tubules that attached to the plasma membrane. 15. HOMEWORK ASSIGNMENT: Which cell structures are present in bacteria, amoeba, plants, fungi, and animals? Structure Bacteria Fungi Protist Plant Animal Example E. Coli Yeast Amoeba Spinach Hepatocyte Nucleus X X X X X X X X X DNA RNA X X X X X Cell Wall X X X X X X X X Mitochondria X X Chloroplasts Lysosome X? X X X X X X X X Golgi Apparatus X X X? X Cytoskeleton Plasma Membrane X X X X X Endoplasmic Reticulum X X X X X X X X X Ribosomes Study Guide for Cell Biology Final 106 Chapter 5: 1. Define energy. What are the six kinds of biological work accomplished by cells? a. Energy is defined as the ability to do work. There are six kinds of energy that is accomplished by cells are synthesis, mechanic, transport, heat, electrical, and bioluminescence. 2. How do organisms acquire energy? Define: phototroph and chemotroph. Name some organisms that are examples of phototrophs? Chemotrophs? Compare how they acquire energy. Is energy flow through the biosphere unidirectional or continuous? What about matter? a. Organisms acquire energy by either their diet or the sun. Chemotrophs obtain the energy from their diet and phototrophs do not need to eat because they obtain their energy from the sun. 3. Define thermodynamics and bioenergetics. a. Thermodynamics are the laws that govern energy transformation that accompanies most physical and chemical process. Bioenergetics is the application of thermodynamics to the biological world. 4. Are biological systems open or closed? What is the difference between open and closed systems? a. Open systems interact with the outside environment and closed systems have a sort of barrier separating them from the outside environment. Biological systems are considered to be open systems based on that definition. 5. State the first two laws of thermodynamics. a. The first law of thermodynamics states that energy cannot be created or destroyed and that the total amount of energy in the universe will always remain the same. The second law of thermodynamics states that in every physical or chemical change, the universe tends toward disorder. 6. What is free energy? What is the equation for calculating free energy? Is the change in free energy negative or positive for a spontaneous reaction? What is meant by the term spontaneous reaction? How do energy content and entropy interact to determine whether chemical reactions will proceed to completion? Define: exergonic, endergonic, exothermic, endothermic, entropy, ∆G, ∆H. a. Free energy represents that amount of energy in a system that can do useful work at constant volume and pressure. ∆G = ∆H – T∆S. When ∆G represents a spontaneous reaction, the value of ∆G is a negative number. A spontaneous reaction is one that will definitely occur as written. 7. If the ∆G is positive, is the reaction endergonic or exergonic? If the ∆G is negative? a. If ∆G is a positive number, then the reaction is endergonic and if ∆G is negative, then the reaction is exergonic. Exergonic is when a reaction gives off energy and endergonic is a reaction that requires energy. Exothermic gives off heat and endothermic consumes heat. ∆G refers to the change in free energy and ∆H refers to the change in entropy. 8. Know your symbols! What do the following stand for: E, S, H and G. a. E represents the energy; S represents the entropy; H represents the enthropy; and G represents free energy 9. If entropy is increasing, is the system more or less ordered? a. If entropy is increasing, the system is becoming less ordered. Study Guide for Cell Biology Final 107 10. Do cells carry out endergonic reactions? If so, how? a. Cells carry out exergonic reactions, because they released energy instead of absorbing energy. b. i.e. cell respiration, hydrolysis and photosynthesis 11. Calculate the (∆G) for the following chemical reaction: glutamate + NH3 glutamine + H2O. The reaction occurs at 68F, the change in heat (∆H) = 4103 cal, and the change in entropy (∆S) = 2.4 cal/K. Is this reaction spontaneous? Is it endergonic or exergonic? a. G = 3399.8 cal b. Endergonic, nonspontaneous 12. Calculate the Gibbs free energy change (∆G) for the following chemical reaction: ATP → ADP + Pi. The reaction occurs at 68F, the change in heat (∆H) = 19,070 cal, and the change in entropy (∆S) = 90 cal/K. [Hint: C = (F – 32) * 5/9 and F = C * 9/5 + 32] a. G = -7300 cal b. Exergonic, spontaneous 13. What is the equilibrium constant and how is it determined? a. The equilibrium constant is the concentration of the products divided by the concentration of the reactants when the reaction is at equilibrium. 14. What is the relationship ∆G and the equilibrium constant? a. As the equilibrium constant increases, so does ∆G. 15. What is the difference between ∆G0’ and ∆G’. Which value is more important to a biologist? Why? a. ∆G0’ means that the reaction occurs at standard conditions and a pH of 7. ∆G’ means that the reaction does not occur at standard conditions but it does occur at a pH of 7. Biologists prefer to use ∆G0’ because when studying the body, cells usually maintain standard conditons. 16. For the following equation: 2-phosphoglycerol → 3-phosphoglycerol. At standard conditions: K’eq = [3-phosphoglycerol]/[2-phosphoglycerol] = .65. In the liver cells under steady state conditions, the concentrations are 15 x 10-6 M for 2-phosphoglycerate and 25 x 10-6 M for 3-phosphoglycerate. Calculate ∆G0’ and ∆G’. Why are these values different? What do these numbers tell you? a. G’ = 255.02 b. G’ = 557.43 Study Guide for Cell Biology Final 108 Chapter 6: 1. Identify the major characteristics of protein enzymes. How are enzymes classified? a. Enzymes are characterized based on their primary functions. These functions include the groups oxidoreductases, isomerases, transferases, hydrolases, lyases, and ligases. 2. What effects do enzymes have on a spontaneous reaction? What is the activation energy of a reaction? What effect does an enzyme have on activation energy? Why does lowering activation energy speed up the rate of a reaction? Define the following terms: metastable state, transition state. a. During a spontaneous reaction, enzymes lower the activation energy needed for the reaction to occur. The activation energy is the amount of energy a molecule must produce in order for the reaction to occur. Lowering this activation energy allows for more molecules to reach that level and react. 3. What is the active site of an enzyme? What occurs here? What are three ways enzymes activate substrates and engage in catalysis? a. An enzyme active site is where the substrate will attach. Enzymes work as catalysts by reducing the activation energy needed to a reaction to occur. 4. Distinguish between the Lock and Key Model and the Induced Fit Model of enzyme action. Which model is considered to be more accurate? Why? a. The Lock and Key model shows the substrate fitting perfectly into the associated enzyme. The Induced Fit model shows the substrate fitting into the enzyme, initiating a conformational change, and releasing two products; this is the most accurate of the two. 5. State the equation for an enzyme catalyzed reaction. a. v = (Vmax[S])/(Km + [S]) 6. How do enzymes affect the ∆G of a reaction, the equilibrium constant, the rate, and the activation energy? a. Enzymes will decrease ∆G, maintain the equilibrium constant, increase the rate, and decrease the activation energy. 7. Define enzyme kinetics. Why is the relationship between reaction velocity and substrate concentration? Define enzyme saturation and explain why is occurs. a. Enzyme kinetics are how we catalyze a reaction rate. Initial reaction velocity will increase as the substrate concentration increases. Enzyme saturation occurs when all the enzymes are in use and the reaction rate plateaus. 8. What is meant by the term Km? Vmax? Why are these important to cell biologists? a. Km is used to describe the Michaelis Constant. Vmax is the maximum velocity that a reaction can have. These are important to cell biologists because then we can estimate the rate of any reaction. 9. State the Michaelis-Menten equation. a. v = (Vmax[S])/(Km + [S]) 10. What is the significance of the double-reciprocal Lineweaver-Burke plot? What is the Lineweaver-Burke equation? What are the axes in the Lineweaver-Burke plot? How do you plot data? How do you determine the Vmax and the Km. a. With the Lineweaver-Burke plot, we are able to plot a reaction as a linear graph. 1/v = (Km/Vmax)(1/[S]) + 1/Vmax. The y-axis is 1/v and the x-axis is Study Guide for Cell Biology Final 109 1/[S]. Vmax is determined by the denominator of the slope and Km is determined by the numerator. 11. Distinguish between reversible and irreversible inhibition. Distinguish between competitive and noncompetitive inhibition. a. Reversible inhibition uses an enzyme that attaches noncovalently and irreversible inhibition uses an enzyme that attaches covalently. Competitive inhibition is when the inhibitor attaches at the active site and noncompetitive inhibition is when the inhibitor attaches at a place that is different from the active site. 12. How are Km and Vmax affected in a reaction in the presence of a competitive inhibitor? A noncompetitive inhibitor? Explain why these effects occur. Be able to identify competitive and non-competitive inhibitors from curves of V vs [S]. a. Km would increase and Vmax would stay the same with a competitive inhibitor. Km would stay the same and Vmax would decrease in the presence of a noncompetitive inhibitor. 13. What affect would raising the enzyme concentration have on Vmax? Km? a. Vmax would increase and Km would stay the same. 14. Describe allosteric regulation. What is allosteric inhibition? Allosteric activation? Which step in a metabolic pathway is regulated and why? Outline the process if feedback inhibition. a. Allosteric regulation makes use of the substrate affinity by regulating the conformation of the enzyme. Activation occurs with an increased affinity and inhibition occurs with a decreased affinity. 15. To increase the rate of a chemical reaction in Organic Chem Lab, Harry Hartline generally heats the reactants. Why does this increase the reaction rate? Why is this an unacceptable way to increase reaction rates in cells? How does the cell overcome this problem? a. Heat allows the molecules to move faster so more of the molecules will exceed the activation energy. This is an ineffective way for cells because too much heat can destroy proteins in the cell. The cell overcomes this problem by using enzymes. 16. What is the purpose of covalent modification of enzymes? What is the role of a protein kinase? A protein phosphatase? Define: phosphorylation, dephosphorylation. a. Covalent modification of enzymes changes the attachment of R groups by cleaving off amino acids from the backbone. Protein kinase uses ATP to remove a hydroxyl group and replace it with a phosphate group. Phosphorylation occurs when adding a phosphate group and dephosphorylation is removing a phosphate group. 17. Enzymes are characterized by their sensitivity to pH and temperature. Based upon what you know about enzymes and how they work, explain this. What is meant by temperature optimum? pH optimum? a. Since an enzyme is a protein, extreme pH and temperature can cause the enzyme to denaturation, which forces the enzyme to lose its function. Temperature and pH optimum are the levels that an enzyme best functions at. 18. What is a ribozyme? a. A ribozyme is an RNA molecule that is able to function as an enzyme. Study Guide for Cell Biology Final 110 Chapter 7: 1. List the major functions of the plasma membrane and indicate if the functions are carried out by protein, lipid, or carbohydrate. a. The plasma membrane creates a boundary, localizes functions, transport molecules, contains signaling receptors, and plays a role in cell to cell communication. These functions are carried out mostly by proteins. 2. Describe the structure of a lipid bilayer. What type of lipids compose it? How are they oriented? What was the initial evidence that the bilayer exists? What are the forces that hold the bilayer together? a. The lipid bilayer is composed of phospholipids oriented in a way that the hydrophilic heads are facing the aqueous environment and the hydrophobic tails are facing the inside of the membrane. This is held together by hydrophobic forces. 3. What types of movement can membrane lipids perform? Why is membrane fluidity important? a. Membrane lipids can move by lateral diffusion, rotation, and transverse diffusion. Membrane fluidity is important so it is not rigid or fused together. 4. What is the role of cholesterol in membrane mobility? a. Cholesterol stabilizes the membrane and provides rigidity. 5. What is transition temperature? How do fatty acid chain length and saturation affect lipid mobility? Transition temperature? Define: homeoviscous adaptation. What is its purpose? What are lipid rafts? a. The transition temperature is the temperature at which the membrane becomes fluid. The shorter the fatty acid chains, the lower the transition temperature and higher mobility. The more saturated the fatty acid chains, the higher the transition temperature and lower mobility. Homeoviscous adaptation is the compensating for changes in temperature by altering the length and degree of saturation of fatty acids in their membranes. 6. Describe the Fluid Mosaic Model of Membrane structure and identify its components from a diagram. What is the fluid part of the membrane? The mosaic part? a. The Fluid Mosaic Model shows the fluidity of the phospholipids and the mosaic of the scattered proteins, carbohydrates, and sterols. 7. What is the evidence that membrane proteins are mobile? Are all membrane proteins freely mobile? Explain why or why not? a. Not all membrane proteins are mobile. We know this because we can use freeze fracturing to split the membrane in half and look at it under a microscope. 8. Does nonpolar mean hydrophobic or hydrophilic? a. Hydrophobic 9. Distinguish between integral, peripheral, and lipid anchored proteins. How would they differ in the nature of their amino acid R groups? How is each type removed from the membrane? a. Integral proteins are transverse on one or both sides of the membrane. Peripheral proteins are only on one side of the membrane. Lipid anchored proteins are anchored within the periphery of either side of the membrane. Study Guide for Cell Biology Final 111 The R groups would differ based on if it needs to be hydrophilic or hydrophobic. Each type is removed from the membrane by detergents. 10. What is a transmembrane protein? Are transmembrane proteins monotopic? What is the freeze-fracture technique? How does it support the existence of integral proteins? a. A transmembrane protein is a type of integral protein that spans the entire width of the membrane. They are considered to be bitopic. The freezefracture technique involves freezing the cells and slicing open the membrane with a diamond knife to look at the density beneath a microscope. This supports the existence of integral proteins because integral proteins are much more dense than other sections of the membrane. 11. Distinguish between a single pass and a multipass protein. a. A single pass protein only has one subunit that passes through the membrane whereas a multipass protein has more than one subunit that passes through the membrane. 12. How are lipid anchored proteins attached to the membrane? a. They are attached by a covalent bond with a lipid. 13. How are membrane carbohydrates oriented in the membrane? What linkages attach sugars to membrane proteins? What is a glycoprotein? A glycolipid? a. Carbohydrates are attached to the outside of the membrane by a covalent bond. A glycoprotein is a carbohydrate attached to a protein and a glycolipid is a carbohydrate attached to a lipid. 14. What is the glycocalyx? What kinds of cells have this? What functions does it serve? a. The glycocalyx is the glycoprotein and glycolipid covering on epithelial cells for protection. Some bacteria, epithelial and some other cells have this. They serve to protect the underlying cells.