Chapter 6: Metabolism: Energy and Enzymes

Transcription

1 Chapter 6: Metabolism: Energy and Enzymes AP Curriculum Alignment Big Idea 1 explains that metabolic pathways are conserved across all domains of life. This conservation of metabolic pathways is evidence that all life is linked to a common ancestor. All organisms ultimately use ATP as their energy molecule which indicates a common ancestor for all organisms. Chapter 6 explains the fundamentals of energy usage in organisms. The main message from Big Idea 2 is that free energy is used in order to maintain dynamic homeostasis and to grow and reproduce. The exact processes of photosynthesis and cellular respiration are mentioned in this chapter but are detailed in chapters 7 and 8. The fact that biological systems maintain their organization is due to release of free energy in the form of heat to the environment. Therefore organisms do follow the first and second laws of thermodynamics and these laws are detailed in this chapter. Energy can neither be created nor destroyed but can be converted from one form to another form. The most unorganized form of energy is heat and during the conversion process, the energy tends towards disorganization, entropy, so heat is released. Exergonic reactions give off energy and therefore have a negative impact on free energy. Endergonic reactions increase organization and thereby increase free energy. From Big Idea 4, we understand that biological systems interact, and these systems and their interactions produce complex properties. Living systems require a constant continuation of chemical reactions. Each chemical reaction uses an enzyme in order to be energetically efficient. There must be cooperation between the enzyme and the substrate in order for the reaction to occur. Coenzymes and cofactors are cooperating to allow the reactions to occur. The active site of the enzyme may be blocked by inhibitors or changed due to environmental conditions. Allosteric sites may also become filled with inhibitors or enhancers. Chapter 6 describes the activity and limitation of enzymes. Sections of the framework that are applicable to the concepts found in Chapter 6 are shown in the table below: ALIGNMENT OF CONTENT TO THE CURRICULUM FRAMEWORK Big Idea 1: The process of evolution drives the diversity and unity of life. Enduring understanding (EK) 1.B: Organisms are linked by lines of descent from common ancestry. Essential knowledge EK) 1.B.1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. a. Structural and functional evidence supports the relatedness of all domains 3. Metabolic pathways are conserved across all currently recognized domains. Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. Enduring understanding 2.A: Growth, reproduction and maintenance of the 88 Mader, Biology, 12 th Edition, Chapter 6

2 organization of living systems require free energy and matter. Essential knowledge (EK) 2.A.1: All living systems require constant input of free energy. a. Life requires a highly ordered system. 1. Order is maintained by constant free energy input into the system. 2. Loss of order or free energy flow results in death. 3. Increased disorder and entropy are offset by biological processes that maintain or increase order. b. Living systems do not violate the second law of thermodynamics, which states that entropy increases over time. 1. Order is maintained by coupling cellular processes that increase entropy (and so have negative changes in free energy) with those that decrease entropy (and so have positive changes in free energy). 2. Energy input must exceed free energy lost to entropy to maintain order and power cellular processes. 3. Energetically favorable exergonic reactions, such as ATP ADP, that have a negative change in free energy can be used to maintain or increase order in a system by being coupled with reactions that have a positive free energy change. Essential knowledge (EK) 2.A.2: Organisms capture and store free energy for use in biological processes. a. Autotrophs capture free energy from physical sources in the environment. 1. Photosynthetic organisms capture free energy present in sunlight. b. Heterotrophs capture free energy present in carbon compounds produced by other organisms. Big Idea 4: Biological systems interact, and these systems and their interactions possess complex properties. Enduring understanding (EU) 4.B: Competition and cooperation are important aspects of biological systems. Essential knowledge (EK) 4.B.1: Interactions between molecules affect their structure and function. a. Change in the structure of a molecular system may result in a change of the function of the system. b. The shape of enzymes, active sites and interaction with specific molecules are essential for basic functioning of the enzyme. 1. For an enzyme-mediated chemical reaction to occur, the substrate must be complementary to the surface properties (shape and charge) of the active site. In other words, the substrate must fit into the enzyme s active site. 2. Cofactors and coenzymes affect enzyme function; this interaction relates to a structural change that alters the activity rate of the enzyme. The enzyme may only become active when all the appropriate cofactors or coenzymes are present and bind to the appropriate sites on the enzyme. No specific cofactors or coenzymes are within the scope of the course and the AP Exam. c. Other molecules and the environment in which the enzyme acts can enhance or Mader, Biology, 12 th Edition Chapter 6 89

3 inhibit enzyme activity. Molecules can bind reversibly or irreversibly to the active or allosteric sites, changing the activity of the enzyme. d. The change in function of an enzyme can be interpreted from data regarding the concentrations of product or substrate as a function of time. These representations demonstrate the relationship between an enzyme s activity, the disappearance of substrate, and/or presence of a competitive inhibitor. Concepts covered in Chapter 6 also align to the learning objectives that provide a foundation for the course, an inquiry-based laboratory experience, class activities, and AP exam questions. Each learning objective (LO) merges required content with one or more of the seven science practices (SP), and one activity or lab can encompass several learning objectives. The learning objectives and science practices from the Curriculum Framework that pertain to organic chemistry are shown in the table below. Note that other learning objectives may apply as well. LO 1.16 The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. LO 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow and to reproduce. LO 2.2 The student is able to justify a scientific claim that free energy is required for living systems to maintain organization, to grow or to reproduce, but that multiple strategies exist in different living systems. LO 2.3 The student is able to predict how changes in free energy availability affect organisms, populations and ecosystems. LO 4.17 The student is able to analyze data to identify how molecular interactions affect structure and function. Key Concepts Summary Energy in living systems All living systems, from cells to an ecosystem, require free energy to sustain life. Free energy (ΔG) is the amount of energy left to do work after a chemical reaction has occurred. The laws of thermodynamics The first law of thermodynamics is that energy can neither be created nor destroyed but can be changed from one form to another o Some organisms capture solar energy and convert it to chemical energy (carbohydrates) through of photosynthesis. The second law of thermodynamics states that the entropy of the universe if increasing and as energy is changed from one form to another then entropy 90 Mader, Biology, 12 th Edition, Chapter 6

4 increases. o For living systems this means that some energy is lost as the energy of heat because heat is the least organized form of energy. Metabolism Metabolism is the sum total of all reactions in a cell. Reactants are substances that are acted upon in a chemical reaction and products are the substances that are formed in a chemical reaction. ATP, adenosine triphosphate, is the most common energy molecule used by cells. Enzymes and metabolic pathways An enzyme is a molecule that speeds up a chemical reaction without being used up in the process. o Most enzymes are proteins. o Enzymes can be involved in the synthesis or degradation of a substrate. Enzymes have a particular shape so that the active site of an enzyme fits exactly one substrate. o The active site on an enzyme is the location of the substrate binding to that enzyme. o Once the substrate-enzyme binds, the enzyme changes shape slightly in an induced fit. o The induced fit places the substrate in the correct position for facilitating the chemical reaction. Enzymes lower the activation energy, which is the amount of energy that must be added to a reaction for it to occur. Inhibitors are molecules that can combine to the enzyme s active site or to another location that causes a protein shape change. Cofactors are inorganic molecules that some enzymes require in order to make their active sites available. Coenzymes are non-protein organic compounds that are necessary for the functioning of some enzymes and may contribute atoms to the reaction. Oxidation-reduction reactions Oxidation-reduction reactions involve the gain and loss of electrons. OIL RIG: oxidation is loss reduction is gain Oxidation and reduction reactions occur together in the same reaction, hence the term redox reaction. Mader, Biology, 12 th Edition Chapter 6 91

5 Key Terms allosteric site ATP cycle chemical energy coenzymes cofactors competitive inhibitors coupled reaction denaturation endergonic energy energy of activation entropy enzyme enzyme inhibition exergonic first law of thermodynamics free energy kinetic energy metabolic pathway metabolism noncompetitive inhibitors oxidation reactions potential energy reactants reduction reaction ribozyme second law of thermodynamics substrate Teaching Strategies Under Big Idea 4, the AP Biology Investigation Lab Manual contains a lab about enzymes, Investigation 13: Enzyme Activity. This is a great activity to develop students conceptual understanding about enzymes and engage them in inquiry-based learning experiences. Between three and four lab periods should be dedicated to this lab. Prior to completing this lab, students must understand the structure of proteins and how enzymes function. This lab calls for an indicator of enzymatic activity called guaiacol. You may substitute another enzyme lab but review the learning objectives and curriculum that is covered in this lab. It is important that students understand reaction indicators, particularly guaiacol, which is used in the laboratory activity. Cells using molecular oxygen in their metabolism generate small amounts of H2O2 (hydrogen peroxide) which is very toxic. Peroxidase (and other enzymes) speeds up the conversion of H2O2 to water so that the cell is not damaged. Some peroxidase activity can be seen by the generation of O 2 gas but the peroxidase that is extracted from turnips does not generation oxygen gas. Students are going to use a substance called guaiacol as the hydrogen donor (it can also be called a reducing agent) in the lab because it changes color after it loses hydrogens. This is a redox reaction in which H 2 O 2 is reduced and guaiacol is oxidized. Guaiacol turns brown as it loses hydrogens. 92 Mader, Biology, 12 th Edition, Chapter 6

6 Class time: Six 45 minute class periods Day 1: lecture on energy, laws of thermodynamics, exergonic (exothermic) vs. endergonic (endothermic) reactions, oxidation-reduction reactions, ATP cycle - 25 minutes Demonstration: This website gives a great demonstration of an endergonic reaction that is spontaneous: micreaction-uwdept.ofchemistry.html Day 2: lecture on energy and enzymes 20 minutes Activity 1: Modeling Enzymes -15 minute Lecture on the specific reaction of peroxidase extracted from turnips and the color indicator guaiacol, in preparation for Investigation minutes Day 3: lab safety introduction, and a review of baseline and rate of reactions. Lab activity: Procedure 1 of Investigation 13. Day 4: Procedure 2 of Investigation 13. Students should prepare procedures for completion of the open investigation part of this lab- Designing and Conducting Your Investigation. It is strongly suggested that you approve their design and determine the availability of materials. Day 5: Students complete their own investigation on enzymes (continuation of Investigation 13). Day 6: summative assessment Suggested Approaches Lab work will be crucial to the understanding of enzyme and the effect that the environment can have on enzymatic activity. Student Misconceptions and Pitfalls One of the main student misconceptions about enzymes is that they are living. While enzymes are found in living organisms they are not themselves alive. An enzyme can be denatured not killed since it never was alive in the first place. Modeling an enzyme using pool noodles may help dispel the idea that enzymes are alive. Mader, Biology, 12 th Edition Chapter 6 93

7 Suggested Activities 1. Modeling Enzymes: Students will use paper cut outs to model how enzymes work. 2. Investigation 13 of the AP Biology Investigation Lab Manual: students will follow a prescribed investigative lab as well as complete an open investigation. Modeling Enzymes You can make these pieces shown below by cutting various shapes of pool noodles. Of course other materials can be used, even paper. 1. Give students the pieces of enzyme, substrate and product and ask them to demonstrate how an enzyme works. Note the substrate could also be the product in a different reaction and the product could be the substrate in a different reaction. Enzyme: Substrate 1 Substrate 2 Competitive inhibitor Non-competitive inhibitor Students can demonstrate a hydrolysis-style reaction: 94 Mader, Biology, 12 th Edition, Chapter 6

8 Or, students can demonstrate a dehydration style reaction: 2. Cut a notch in the enzyme pieces. Give the students the notched enzyme and the noncompetitive inhibitor. Ask them to model how a noncompetitive inhibitor would work. 3. Give students the enzyme, substrate, and the competitive inhibitor and ask them to model the activity of a competitive inhibitor. Mader, Biology, 12 th Edition Chapter 6 95

9 Student Edition Chapter Review Answers Answers to Assess Questions 1. c; 2. d; 3. b; 4. d; 5. b; 6. c; 7. d; 8. d; 9. b; 10. a; 11. d; 12. c Answers to Applying the Big Ideas Questions 1. Free energy is the amount of energy left to do work after a reaction occurs and is determined by subtracting the free energy content of the reactants from that of the products. Scientists claim that free energy is required for living systems to maintain organization, to grow, or to reproduce, but multiple strategies for capturing, storing and using it exist in different living systems. In a paragraph, being as specific and detailed as possible, justify this claim using at least THREE examples. Essential Knowledge Science Practice Learning Objective 2.A.1: All living systems require constant input of free energy. 6.1: The student can justify claims with evidence. 2.2: The student is able to justify a scientific claim that free energy is required for living systems to maintain organization, to grow or to reproduce, but that multiple strategies exist in different living systems. 3 points maximum. Examples as evidence of strategies may include (1 point each): Energy capture: When leaf cells photosynthesize, they use solar energy to form carbohydrate molecules from carbon dioxide and water. Carbohydrates are energy-rich molecules because they have many bonds that store energy; carbon dioxide and water are energy-poor molecules, because of the relative lack of bonds. Not all of the captured solar energy becomes carbohydrates; some becomes heat (cells are capable of about 40% efficiency). Energy storage: The reduction of carbon dioxide to form a mole of glucose stores 686 kcal in the chemical bonds of glucose. This is the energy that living organisms utilize to support themselves only because carbohydrates (and other nutrients) can be oxidized in mitochondria. Energy storage: The complete oxidation of a mole of glucose releases 686 kcal of energy, and some of this energy is used to synthesize ATP molecules. If the energy within glucose were released all at once, most would dissipate as heat. So, instead, cells oxidize glucose step by step so the energy is gradually stored and then converted to that of ATP molecules. 96 Mader, Biology, 12 th Edition, Chapter 6

10 Energy use in coupled reactions (exergonic + endergonic) with ATP in chemical work: ATP (ATP ADP) supplies the energy needed to synthesize macromolecules (anabolism) that make up the cell. Energy use in coupled reactions (exergonic + endergonic) with ATP in transport work: ATP(ATP ADP) supplies the energy needed to pump substances across the plasma membrane, particularly important in nerve conduction. Energy use in coupled reactions (exergonic + endergonic) with ATP in mechanical work: ATP (ATP ADP) supplies the energy needed to permit muscles to contract, cilia and flagella to beat, chromosomes to move, and so forth. In most cases, ATP is the immediate source of energy for these processes. 2. Nicotinamide adenine dinucleotide (NAD + ) is involved with many types of oxidation reactions where alcohols are converted to ketones or aldehydes. It is noted in the lab that in the absence of niacin, the rate of hydrogen transfer as seen in cellular respiration by NAD + is greatly reduced and cells do not thrive. a) Based on the lab observations described above, analyze the role niacin and NAD + play in metabolic reactions? b) Explain how this relates to how molecular interactions affect structure and function. Essential Knowledge Science Practice Learning Objective 4.B.1: Interactions between molecules affect their structure and function. 5.1: The student can analyze data to identify patterns or relationships. 4.17: The student is able to analyze data to identify how molecular interactions affect structure and function. 3 points maximum. Description of the roles played by molecules and the explanation of how interactions affect structure and function: Descriptions molecule roles (1 point each) Niacin is a vitamin (small, organic molecule required in trace amounts) and is required for the synthesis of coenzyme NAD + as it becomes part of the coenzyme s structure. Explanation of how interactions affect structure and function (1 point each) Vitamins are often components of coenzymes. The vitamin becomes part of a coenzyme s molecular structure. The vitamin niacin is part of the coenzyme NAD +. If a vitamin is not available, enzymatic activity will decrease and the result will be a vitamin-deficiency disorder. (Not Mader, Biology, 12 th Edition Chapter 6 97

11 necessary to know, but possible answer includes that a niacin deficiency results in a skin disease called pellagra.) NAD+ is a nonprotein organic molecule called a coenzyme, which is a type of cofactor. It participates in enzymatic reactions of cellular respiration by being present in the active site so that the enzyme works properly. There is a strong relationship between enzyme shape and its function, and enzyme shape (and therefore function) is influenced by other molecules, such as the substrate, cofactors, coenzymes and other molecules. Many enzymes require the presence of a non-protein organic molecule (coenzyme) at the active site in order to work properly. They participate in the reaction and ay even accept or contribute atoms to the reaction. For an enzyme-mediated chemical reaction to occur, the substrate must be complementary to the surface properties (shape and charge) of the active site. In other words, the substrate must fit into the enzyme s active site. Cofactors and coenzymes affect enzyme function; this interaction relates to a structural change that alters the activity rate of the enzyme. The enzyme may only become active when all the appropriate cofactors or coenzymes are present and bind to the appropriate sites on the enzyme. The change in function of an enzyme can be interpreted from data regarding the concentrations of product or substrate as a function of time. 98 Mader, Biology, 12 th Edition, Chapter 6

12 3. In targeted therapy used to treat cancer, drugs target certain parts of the cell and the signals that are needed for cancer to develop and grow. Some targeted therapies make use of enzyme inhibitors that target enzymes such as DNA polymerase, an enzyme required for DNA replication. In a paragraph, describe how enzyme inhibitors function and explain why this method of cancer treatment is a viable option. Essential Knowledge Science Practice Learning Objective 3.A.1: DNA, and in some cases RNA, is the primary sources of heritable information 6.5: The student can evaluate alternative scientific explanations. 3.1: The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information. 3 points maximum. Description of how enzyme inhibitors function (1 point each): Enzyme inhibition occurs when a molecule (the inhibitor) binds to an enzyme and decreases the activity. Enzyme inhibition can occur through noncompetitive inhibition where the inhibitor binds to the enzyme at a location (allosteric site) other than the active site and changes the enzyme s shape, or through competitive inhibition where the inhibitor is in the active site so that a substrate cannot bind. Explanation of why this method of cancer treatment is a viable option (1 point each): DNA polymerase is an enzyme required for DNA replication so inhibiting this enzyme (students will not know necessarily if this is competitive or noncompetitive) will inhibit replication. DNA replication ensures continuity of hereditary information, so if there is no DNA replication, the growth and spread of cancer would halt. Some DNA polymerase inhibitors can also be used to stop the replication and spread of bacteria. Similarly, DNA interference could also occur by limiting the availability of cofactors needed by DNA polymerase, or by targeting other enzymes. Mader, Biology, 12 th Edition Chapter 6 99

13 Answers to Applying the Science Practices Questions Think Critically 1. Student graphs may reflect the increase in cells active with an increase in concentration of ATP, or they may reflect the increase in flagella beat frequency as concentration of ATP increases. These may also be shown together on the same graph. Not only should the data points from the prompt be reflected in the illustrations, but graphs should reflect a positive relationship between the independent and dependent variables (concentration of ATP being independent and on the x-axis, and beat frequency or percent of cells active each responding as dependent variables). Labels and units are important for accurate depiction and full credit. Line graphs are most appropriate for indicating rates of change and correlations between the variable in this situation. 100 Mader, Biology, 12 th Edition, Chapter 6

14 2. This data supports the claim that ATP concentration does impact cell motility in that with a greater concentration of ATP, more flagella became active, and not only that, but their beat frequency increased (and therefore how active they were increased). This would indicate that ATP does play a role in providing energy for cells. It is particularly obvious that nothing else was providing energy when it is noted that in the absence of ATP, no movement at all was observed. ATP needed to reach a particular concentration for the cells to become motile, and then an increase in ATP meant increases in cell motility. 3. This follow-up question woud discern if the nucleotide ATP is the only energy unit for the cell or if other nucleotides could also give the cell energy. A similar lab set up to the first would suffice in answering this prompt, although students may select a more creative way to assess cell motility. Cells would need to be in a solution void of nucleotides, including ATP. Then another nucleotide could be added, slowly increasing the concentration from 0 µm until about 100% of the cells in the sample are motile. Beat frequency of flagella may, again, also be measured. It should be noted that only one nucleotide should be tested for at a time, in order to control variables. If cells do not show increased motility with increasing concentration of the new nucleotide, then results would further support the idea that ATP is the energy unit of the cell with regard to motility. Mader, Biology, 12 th Edition Chapter 6 101

15 Additional Questions for AP Practice 1. Select the best justification for the claim that many shared core processes that evolved are preserved and exist is a wide variety of organisms. A) All heterotrophs depend on autotrophs for the carbohydrates that they need to convert into ATP. B) All autotrophs convert solar energy into chemical energy with a loss of heat energy. C) All organisms use ATP as their principal energy molecule for metabolism and growth. D) Both multi-cellular heterotrophs and autotrophs require the conversion of chemical molecules into ATP. 2. Use the model below to explain how enzymes function. 3. According to the second law of thermodynamics, whenever energy is transformed, there is always an increase in the A) free energy of the system. B) free energy of the universe. C) entropy of the system. D) entropy of the universe. 102 Mader, Biology, 12 th Edition, Chapter 6

16 4. A 15% solution of starch and water at room temperature does not readily decompose to form a solution of simple sugars because A) the starch solution has less free energy than the sugar solution. B) the activation energy barrier for this reaction cannot be surmounted. C) the hydrolysis of starch to sugar is endergonic. D) starch cannot be hydrolyzed in the presence of so much water. 5. Analyze the data below and describe how temperature can affect the activity of this enzyme. Justify this explanation with information about the structure and function of the enzyme. Mader, Biology, 12 th Edition Chapter 6 103

17 Grid-In Questions 1. Pepsin is the enzyme in the stomach responsible for degrading protein from food into peptides. If a person takes an antacid and raises their stomach ph to 3.5, by how many ph units is the stomach off the optimal conditions for pepsin to degrade proteins? 2. The gut of many herbivores host symbiotic bacteria which produce an enzyme called cellulase which breaks cellulose down into monosaccharides. This graph shows the amount of monosaccharides produced as cellulase breaks down 1 mg of cellulose. Calculate the rate of change in monosaccharide production between hours 1.5 and Mader, Biology, 12 th Edition, Chapter 6

18 Answers to Additional Questions for AP Practice 1. C is the correct answer. While all answers are true, the best justification for the wide distribution of the core process of energy use is described in C. 2. An enzyme binds to its substrate and puts the substrate in the correct position through the enzyme s induced fit change. This allows the reaction to occur with a smaller amount of energy input, known as energy of activation. 3. C is the correct. Entropy, or disorganized energy, increases during energy transformations because some energy will be lost as heat. 4. B is the correct answer. Without an enzyme, the activation energy is too great for the reaction to occur. 5. As temperature increases, the activity of the enzyme increases up to a point. The increase in activity is due to an increase in molecular motion that enables the enzyme and substrate to interact with increase speed. At a certain point, the temperature causes the amino acids that are the structure of the protein start to break apart. The enzyme denatures and loses function. Answers to Grid-In Questions 1. Chapter: 6 Metabolism: Energy and Enzymes ph= = Chapter: 6 Metabolism: Energy and Enzymes Answer: 20% Rate of change between hour 1.5 and 2 = ((40%-30%)/(2 hr-1.5 hr))= (10%/0.5 hr) = +20%/hr Mader, Biology, 12 th Edition Chapter 6 105