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2. Energy and the Cell
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3. 5.11 Chemical reactions either release or store energy
Exergonic reactions release energy.
Endergonic reactions require energy and yield products rich in potential energy.
Metabolism encompasses all of a cell’s chemical reactions.
Checkpoint Question Response
Some of it is stored in ATP molecules; the rest is released as heat.
Student Misconceptions and Concerns
Students with limited exposure to physics may have never understood the concepts of energy and the conservation of energy. They also may not have distinguished between potential and kinetic energy. Understanding such broad and new abstract concepts requires time and concrete examples. (5.10–5.12)
Too often we hear or read that some thing or reaction creates energy. We might hear or read that a power plant “produces” energy or that mitochondria “make” energy. Even in our classroom conversations, we may occasionally make this error. When discussing the first law of thermodynamics, consider emphasizing the inaccuracy of such statements. (5.11)
Although typically familiar with the concept of dietary calories, students often struggle to think of calories as a source of potential energy. For many students, it is not clear that potential energy is stored in food as calories. (5.11)
Teaching Tips
The same mass of fat stores nearly twice as many calories (about 9 kcal per gram) as an equivalent mass of protein or carbohydrates (about 4.5–5 kcal per gram). Thus, when comparing equal masses of fat, protein, and lipid, the fat has nearly twice the potential energy. Fat is therefore an efficient way to store energy in animals and many plants. To store an equivalent amount of energy in the form of carbohydrates or proteins would require about twice the mass, adding a significant burden to the organism’s structure. (For example, if you were 20 pounds overweight, you would be nearly 40 pounds overweight if the same energy were stored as carbohydrates or proteins instead of fat.) (5.11)
The amount of energy each adult human needs to generate the ATP required in a day is tremendous. Here is a calculation that has impressed many students. Depending on the size and activity of a person, a human might burn 2,000 dietary calories (kilocalories) a day. This is enough energy to raise the temperature of 20 liters of liquid water from 0º to 100ºC. This is something to think about the next time you heat water on the stove! If you can bring in 10 2-liter bottles, you can help students visualize how much liquid water can be raised from 0º to 100ºC. (Note: 100 dietary calories raises about 1 liter of water 100ºC, but it takes much more energy to melt ice or to convert boiling water into steam.) (5.11–5.12)
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4. Reactants Potential energy Energy of molecules Products Amount of
Figure 5.11a
Reactants
Amount of
energy released
Potential energy
of molecules
Energy
Products
Figure 5.11a Exergonic reaction, energy released
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5. Products Potential energy Energy of molecules Reactants Amount of
Figure 5.11b
Products
Potential energy
of molecules
Energy
Amount of
energy required
Reactants
Figure 5.11b Endergonic reaction, energy released
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6. Triphosphate Adenosine P P P ATP Figure 5.12a_1
Figure 5.12a_1 The hydrolysis of ATP yielding ADP, a phosphate group, and energy (step 1)
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7. Triphosphate H2O Diphosphate Adenosine P P P Adenosine P P + P +
Figure 5.12a_2
Triphosphate
H2O
Diphosphate
Adenosine P P P
Adenosine P P + P +
Energy
ATP
ADP
Phosphate
Figure 5.12a_2 The hydrolysis of ATP yielding ADP, a phosphate group, and energy (step 2)
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8. Protein filament moved
Figure 5.12b
Chemical work P
ATP P +
ADP + P
Reactants
Product formed
Transport work
ATP
ADP + P P P
Transport protein
Solute transported
Figure 5.12b How ATP powers cellular work
Mechanical work
ADP
ATP
ADP + P P
Motor protein
Protein filament moved
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9. ATP synthesis requires energy ATP ATP hydrolysis releases energy
Figure 5.12c
ATP synthesis
requires energy
ATP
ATP hydrolysis
releases energy
Energy from
cellular respiration
Energy for
cellular work
Figure 5.12c The ATP cycle
ADP + P
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10. How Enzymes Function
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11. 5.13 Enzymes speed up the cell’s chemical reactions by lowering energy barriers
Enzymes are protein catalysts that decrease the activation energy needed to begin a reaction.
Student Misconceptions and Concerns
For students not previously familiar with activation energy, analogies can make all the difference. Activation energy can be thought of as a small input that is needed to trigger a larger output. This is like (a) an irritated person who needs only a bit more frustration to explode in anger, (b) small waves that lift debris over a dam, or (c) lighting a match around lighter fluid. In each situation, the output is much greater than the input. (5.13)
Teaching Tips
The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder why DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. (5.13–5.15)
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12. Reaction without enzyme Reaction with enzyme
Figure 5.13_1
Activation
energy
barrier
Enzyme
Activation
energy
barrier
reduced by
enzyme
Reactant
Reactant
Energy
Energy
Figure 5.13_1 The effect of an enzyme in lowering the activation energy (part 1)
Products
Products
Reaction without enzyme
Reaction with enzyme
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13. 5.14 A specific enzyme catalyzes each cellular reaction
An enzyme’s substrate fits specifically in its active site. 1
The enzyme is available
with an empty active site
Substrate
(sucrose)
Active site 2
The substrate
enters the active
site, which enfolds
the substrate with
an induced fit
Student Misconceptions and Concerns
The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support. (5.14–5.15)
Teaching Tips
The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder why DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. (5.13–5.15)
The text notes that the relationship between an enzyme and its substrate is like a handshake, with each hand generally conforming to the shape of the other. This induced fit is also like the change in shape of a glove when a hand is inserted. The glove’s general shape matches the hand, but the final “fit” requires some additional adjustments. (5.14)
Active Lecture Tips
See the Activity “Students, Design Your Own Enzyme-Catalyzed Reaction” on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. (5.14)
Enzyme
(sucrase)
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14. The enzyme is available with an empty active site
Figure 5.14_1 1
The enzyme is available
with an empty active site
Active site
Enzyme
(sucrase)
Figure 5.14_1 The catalytic cycle of an enzyme (step 1)
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15. The enzyme is available with an empty active site
Figure 5.14_2 1
The enzyme is available
with an empty active site
Substrate
(sucrose)
Active site 2
The substrate
enters the active
site, which enfolds
the substrate with
an induced fit
Enzyme
(sucrase)
Figure 5.14_2 The catalytic cycle of an enzyme (step 2)
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16. The enzyme is available with an empty active site
Figure 5.14_3 1
The enzyme is available
with an empty active site
Substrate
(sucrose)
Active site 2
The substrate
enters the active
site, which enfolds
the substrate with
an induced fit
Enzyme
(sucrase)
H2O
Figure 5.14_3 The catalytic cycle of an enzyme (step 3) 3
The substrate
is converted
to products
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17. The enzyme is available with an empty active site
Figure 5.14_4 1
The enzyme is available
with an empty active site
Substrate
(sucrose)
Active site 2
The substrate
enters the active
site, which enfolds
the substrate with
an induced fit
Enzyme
(sucrase)
Glucose
Fructose
H2O
Figure 5.14_4 The catalytic cycle of an enzyme (step 4) 4
The products
are released 3
The substrate
is converted
to products
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18. 5.14 A specific enzyme catalyzes each cellular reaction
Checkpoint question Explain how an enzyme speeds up a specific reaction.
Checkpoint Question Response
An enzyme lowers the activation energy needed for a reaction when its specific substrate enters its active site. With an induced fit, the enzyme strains bonds that need to break or positions substrates in an orientation that aids the conversion of reactants to products.
Student Misconceptions and Concerns
The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support. (5.14–5.15)
Teaching Tips
The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder why DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. (5.13–5.15)
The text notes that the relationship between an enzyme and its substrate is like a handshake, with each hand generally conforming to the shape of the other. This induced fit is also like the change in shape of a glove when a hand is inserted. The glove’s general shape matches the hand, but the final “fit” requires some additional adjustments. (5.14)
Active Lecture Tips
See the Activity “Students, Design Your Own Enzyme-Catalyzed Reaction” on the Instructor Exchange. Visit the Instructor Exchange in the MasteringBiology instructor resource area for a description of this activity. (5.14)
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19. 5.15 Enzyme inhibition can regulate enzyme activity in a cell
A competitive inhibitor competes with the substrate for the active site.
A noncompetitive inhibitor alters an enzyme’s function by changing its shape.
Feedback inhibition helps regulate metabolism.
Student Misconceptions and Concerns
The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support. (5.14–5.15)
Teaching Tips
The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder why DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. (5.13–5.15)
Enzyme inhibitors that block the active site are like (a) a person sitting in your assigned theater seat or (b) a car parked in your parking space. Analogies for inhibitors that change the shape of the active site are more difficult to imagine. Consider challenging your students to think of such analogies. (Perhaps someone who adjusted the position of the driver’s seat of your car, leaving you unable to reach the gas pedal.) (5.15)
Feedback inhibition relies on the negative feedback of the accumulation of a product. Ask students in class to suggest other products of reactions that inhibit the process that made them when the product reaches high enough levels. (Gas station pumps routinely shut off when a high level of gasoline is detected. Furnaces typically turn off when enough heat has been produced.) (5.15)
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20. Normal binding of substrate
Figure 5.15a
Substrate
Active site
Enzyme
Normal binding of substrate
Competitive
inhibitor
Noncompetitive
inhibitor
Figure 5.15a How inhibitors interfere with substrate binding
Enzyme inhibition
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21. Intermediate molecules
Figure 5.15b D –
Feedback inhibition
Enzyme 1
Enzyme 2
Enzyme 3
Figure 5.15b Feedback inhibition of a metabolic pathway in which product D acts as an inhibitor of enzyme 1 A B C D
Reaction 1
Reaction 2
Reaction 3
Starting
molecule
Product
Intermediate molecules
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22. 5.15 Enzyme inhibition can regulate enzyme activity in a cell
Checkpoint question Explain an advantage of feedback inhibition to a cell.
Checkpoint Question Response
It prevents the cell from wasting valuable resources by synthesizing more of a particular product than is needed.
Student Misconceptions and Concerns
The specific interactions of enzymes and substrates can be illustrated with simple physical models. Many students new to these concepts will benefit from several forms of explanation, including diagrams such as those in the textbook, physical models, and the opportunity to manipulate or create their own examples. Just like pitching a tent, new concepts are best constructed with many lines of support. (5.14–5.15)
Teaching Tips
The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder why DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. (5.13–5.15)
Enzyme inhibitors that block the active site are like (a) a person sitting in your assigned theater seat or (b) a car parked in your parking space. Analogies for inhibitors that change the shape of the active site are more difficult to imagine. Consider challenging your students to think of such analogies. (Perhaps someone who adjusted the position of the driver’s seat of your car, leaving you unable to reach the gas pedal.) (5.15)
Feedback inhibition relies on the negative feedback of the accumulation of a product. Ask students in class to suggest other products of reactions that inhibit the process that made them when the product reaches high enough levels. (Gas station pumps routinely shut off when a high level of gasoline is detected. Furnaces typically turn off when enough heat has been produced.) (5.15)
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23. 5.16 CONNECTION: Many drugs, pesticides, and poisons are enzyme inhibitors
Many beneficial drugs act as enzyme inhibitors.
Teaching Tips
Challenge your class to identify advantages of specific enzyme inhibitors for pest control. These advantages include (a) the ability to target chemical reactions of only certain types of pest organisms and (b) the ability to target chemical reactions that are found in insects but not in humans. (5.16)
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24. 5.16 CONNECTION: Many drugs, pesticides, and poisons are enzyme inhibitors
Enzyme inhibitors have also been developed as
pesticides and
deadly poisons for chemical warfare.
Checkpoint question What determines whether enzyme inhibition is reversible or irreversible?
Checkpoint Question Response
If the inhibitor binds to the enzyme with covalent bonds, the inhibition is usually irreversible. When weak chemical interactions bind inhibitor and enzyme, the inhibition is reversible.
Teaching Tips
Challenge your class to identify advantages of specific enzyme inhibitors for pest control. These advantages include (a) the ability to target chemical reactions of only certain types of pest organisms and (b) the ability to target chemical reactions that are found in insects but not in humans. (5.16)
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25. You should now be able to
Describe the fluid mosaic structure of cell membranes.
Describe the diverse functions of membrane proteins.
Relate the structure of phospholipid molecules to the structure and properties of cell membranes.
Define diffusion and describe the process of passive transport.
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26. You should now be able to
Explain how osmosis can be defined as the diffusion of water across a membrane.
Distinguish between hypertonic, hypotonic, and isotonic solutions.
Explain how transport proteins facilitate diffusion.
Distinguish between exocytosis, endocytosis, phagocytosis, and receptor-mediated endocytosis.
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27. You should now be able to
Define and compare endergonic and exergonic reactions.
Explain how ATP functions as an energy shuttle.
Explain how enzymes speed up chemical reactions.
Explain how competitive and noncompetitive inhibitors alter an enzyme’s activity.
Explain how certain drugs, pesticides, and poisons can affect enzymes.
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