Science Practice Challenge Questions
6.1 Energy and Metabolism
Activation energy is required for a reaction to proceed, and it is lower if the reaction is catalyzed. Sucrose (table sugar) is a disaccharide. When we eat sucrose it is converted to carbon dioxide and water, as with other carbohydrates.
- Identify if the breakdown of sucrose is endergonic or exergonic. Explain the reasoning for your identification.
- Based on your identification, explain if cubes of sugar can be stored in a sugar bowl by creating a diagram similar to Figure 6.10.
- If table sugar is placed in a spoon held over a high flame, the sugar is charred and becomes a blackened mixture composed primarily of carbon. Create a visual representation that includes a chemical equation to explain the role of the flame in this process.
- In terms of your answers to questions 1-3, predict if sugar cubes in a bowl placed in a dish of water can be stored on a table, and justify your prediction.
- [Extension] The energy of activation of a chemical reaction can be determined by measurement of the effect of temperature on reaction rate. The natural logarithm of the reaction rate constant is a linear function of the inverse of the temperature in Kelvin degrees. The negative of the slope of that graph is the energy of activation divided by the universal ideal gas constant, R = 8.314 J/Kmol. Using the following data (R. Wolfenden and Yang Yean, Journal of the American Chemical Society, 2008 Jun 18; 130(24): 7,548–7,549) evaluate the energy of activation of the following reaction.
(a) Construct a graph of ln(rate) versus 1/T(K) and determine the energy of activation for the uncatalyzed reaction.
(b) Based on the data, explain the importance of enzymes for time scales characteristic of living systems on Earth—that is to say, life as we know it.
The time scale required for half of the molecules of initial sucrose to remain can be estimated. The relationship between the half-life and the activation energy is:
At a temperature of 300K, approximately room temperature, RT is equal to 2,494 J/mole.
Physical exercise involves both anabolic and catabolic processes. For each process, explain an expected outcome and describe an example of a specific exercise that can lead to the expected outcome.
6.2 Potential, Kinetic, Free, and Activation Energy
Explanations in science are often constructed by analogy. Explanations of the behavior of a poorly understood phenomenon can often be constructed by analogy to a phenomenon that is well understood. For each of the following cellular functions that require free energy, describe a parallel human activity and identify a source of free energy for that activity. For example, the synthesis of proteins can be expected to proceed as an assembly of a small set of sub-components, just as the construction of a building is accomplished by gathering and joining materials. It is consistent with our analogy to expect that there must be a free-energy resource that is consumed in the synthesis of proteins, just as hydrocarbon fuels are a source of energy for the construction of a building.
6.3 The Laws of Thermodynamics
Each process in Figure 6.8 shows examples of endergonic and exergonic processes.
- For each process, identify if it is endergonic or exergonic, and provide reasoning for your identification that includes your definition of the system.
- For each process, does entropy increase or decrease? Explain your reasoning in terms of changes in the amount of order within the system.
- For each process, is there an input of energy? Explain your reasoning in terms of (a) the source of the energy input into the system and (b) the interaction between the system and its environment that provides that input of energy.
Energy transfers occur constantly in daily activities. Think of two scenarios: cooking on a stove and driving a car. For each scenario, describe the system and explain how the second law of thermodynamics applies to the system in terms of energy input and change in entropy.
Consider a simple process that illustrates the change in entropy when energy is transferred.
Take a block of ice as a system with a temperature of 0°C. This is water as a solid, so it has a high structural order. This means that the molecules are in a fixed position. As a result, the entropy of the system is low.
- Allow the ice to melt at room temperature. Describe changes in the motion and interactions of water molecules before and after melting. Explain where the energy came from whose transfer produced melting. Predict the effect of the energy transfer on the entropy on the system, and justify your prediction.
- Heat the water until the temperature reaches boiling point. Explain what happens to the entropy of the system when the water is heated.
- Continue to heat the water at the constant temperature of the boiling point. Describe changes in the motion and interactions of water molecules before and after boiling. Predict the effect of the energy transfer on the entropy of the system, and justify your prediction.
- [Extension/Connection] Molecules of water have simple responses to heating: The molecules move faster and interact less strongly with other neighboring molecules. Consider the primary producers of an aquatic ecosystem in summer. Describe the source of energy transfer to the system of photosynthetic plants and algae. Predict changes in the system in response. Explain what happens to the entropy of this trophic level when energy transfer occurs. Now consider the primary producers and their aqueous environment as the system. Explain what happens to the entropy of this system composed of photosynthetic organisms and their abiotic environment.
- Predict the change in entropy of the system when both autotrophs and their abiotic environment are considered. Justify your prediction. Predict the signs of the entropy changes in both biotic and abiotic components of this system. Predict the relative magnitudes of these entropy changes, and justify your prediction.
6.4 ATP: Adenosine Triphosphate
The sodium-potassium pump is an example of free-energy coupling. The free energy derived from exergonic ATP hydrolysis is used to pump sodium and potassium ions across the cell membrane. The hydrolysis of one ATP molecule releases 7.3 kcal/mol of free energy (ΔG = -7.3 kcal/mol). If it takes 2.1 kcal/mol of free energy to move one Na+ across the membrane (ΔG = +2.1 kcal/mol), how many sodium ions could be moved by the hydrolysis of one ATP molecule? Show your calculations to provide reasoning for your answer.
Is the EA for ATP hydrolysis in cells likely relatively low or high compared to the EA for the combustion of gasoline in an internal combustion engine?
- Explain your reasoning in terms of the relative stabilities of ATP and gasoline compared to air in which no catalysts are present.
- Describe how the role of the enzyme ATPase in the hydrolysis of ATP in a cell differs from a spark in the cylinder of an internal combustion engine.
- Describe a strategy for collecting data that can be used to measure the energies of activation (EA) of each of these two processes with instruments that can measure concentrations of reactions produced in each system.
Vitamin B12 is a co-enzyme involved in a wide variety of cellular processes. Synthesis of vitamin B12 occurs only in bacteria; in animals, these bacteria populate anaerobic environments in the gut. Consequently, vegan diets in developing nations and diets common to developing nations provide no source of B12. Researchers (Ghosh et al. http://dx.doi.org/10.3389/fnut.2016.00001]) found that rats whose diets contained limited (L) and no (N) B12 displayed symptoms that were not observed in the control group (C) whose diet included B12 and was otherwise identical. Chemical analysis of adipocytokines in the plasma after feeding periods of 4 and 12 weeks are shown in the following table.
|Adipocytokines Tissue of origin||Feeding duration (weeks)||C||L||N|
The sample size for these data are small: n = 6, within each group. Also shown in the table are cells in which these cytokine messages originate. Adipose cells store fats. Monocytes are white blood cells of the immune system. Over the 12 weeks of feeding, the weights of all three groups were equivalent, while the percent of body fat increased relative to the control for the rats fed a diet of limited and no B12: 40% (N) and 20% (L), respectively.
- Identify which adipocytokines show significant increases, relative to the control group, after only 4 weeks of treatment. Justify your identification.
- Identify which adipocytokines show only significant increases, relative to the control group, after 12 weeks of treatment. Justify your identification.
- Identify which adipocytokines show significant increases, relative to the control group, after 4 weeks of treatment but no further increase after 12 weeks. Justify your identification.
Adipocytokines are chemical messengers that regulate metabolism and blood vessel production and dilation. High concentrations of adipocytokines are commonly found among individuals with abnormal autoimmune response. Monocyte chemoattractant protein 1 (MCP-1) is involved in the trafficking or guiding of monocytes to damaged tissue, as in a wound. In mice, leptin receptors of cells in the hypothalamus suppress hunger. Interleukin (IL-6) is released to initiate and then regulate inflammation in response to an infection. The mice in this study were not infected or wounded.
- Construct an explanation, with reasoning based on the evidence provided by these data, for the observed variations in adipocytokines.
Many noncommunicable diseases are associated with abnormal autoimmune responses, and the number of diseases that involve abnormal autoimmune response is increasing. Many autoimmune diseases, such as diabetes and heart disease, occur in developed nations at a much higher frequency than in developing nations.
- Evaluate, based on these data concerning the effect of restrictions on the availability of B12, the following question: Does the increased lack of exposure to pathogens in developed nations lead to reduced or abnormal immune response?
Using an example, explain how enzyme feedback inhibition regulation regulates a cellular process.