Chapter 8: An Introduction to Metabolism

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Chapter 8: An Introduction to Metabolism Concept 8.1 An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics 1.

Define metabolism. The totality of an organism’s chemical reactions, consisting of catabolic and anabolic pathways, which manage the material and energy resources of the organism.

2.

There are two types of reactions in metabolic pathways: anabolic and catabolic. a. Which reactions release energy? catabolic b. Which reactions consume energy? anabolic c. Which reactions build up larger molecules? catabolic d. Which reactions break down molecules? catabolic e. Which reactions are considered “uphill”? anabolic f. What type of reaction is photosynthesis? catabolic g. What type of reaction is cellular respiration? catabolic h. Which reactions require enzymes to catalyze reactions? catabolic, anabolic

3.

Contrast kinetic energy with potential energy. Kinetic energy is associated with the relative motion of objects, whereas potential energy refers to an object not presently moving; it is the energy that matter possesses because of its location or structure.

4.

Which type of energy does water behind a dam have? A mole of glucose? Water behind a dam has potential energy. A mole of glucose also has potential energy, though more specifically, glucose has chemical energy, a term used by biologists to refer to the potential energy available for release in a chemical reaction.

5.

What is meant by a spontaneous process? A process that occurs without an overall input of energy; a process that is energetically favorable.

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Concept 8.2 The free-energy change of a reaction tells us whether the reaction occurs spontaneously 6.

What is free energy? What is its symbol? Free energy is the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. Free energy is symbolized by the letter G, after Professor Willard Gibbs.

7.

For an exergonic reaction, is ∆G negative or positive? An exergonic reaction proceeds with a net release of free energy. Because the chemical mixture loses free energy, ∆G is negative for an exergonic reaction.

8.

Is cellular respiration an endergonic or an exergonic reaction? What is ∆G for this reaction? Cellular respiration is an exergonic reaction. The ∆G for this reaction is: ∆G = –686 kcal/mol (–2,870 kJ/mol)

9.

Is photosynthesis endergonic or exergonic? What is the energy source that drives it? Photosynthesis is an endergonic reaction. Plants get the required energy—686 kcal to make a mole of glucose—from the environment by capturing light and converting its energy into chemical energy.

10.

To summarize, if energy is released, ∆G must be what? ∆G must be negative.

Concept 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions 11.

List the three main kinds of work that a cell does. Give an example of each. a. Chemical work, the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers b. Transport work, the pumping of substances across membranes against the direction of spontaneous movement; possible examples include the sodium-potassium pump and proton pump c. Mechanical work, such as the beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction

12.

Here is a molecule of ATP. Label it. Use an arrow to show which bond is likely to break. See page 149 of your text for the labeled figure. a. By what process will that bond break? Hydrolysis

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b. Explain the name ATP by listing all the molecules that make it up. ATP contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups bonded to it, forming adenosine triphosphate. 13.

When the terminal phosphate bond is broken, a molecule of inorganic phosphate Pi is formed, and energy is released. For this reaction: ATP  ADP + Pi, ∆G = –7.3 kcal/mol (–30.5 kJ/mol) Is this reaction endergonic or exergonic? Exergonic

FYI: An essay question on the 2009 AP Biology exam asked students to identify the molecules that make up ATP. What are they again? Sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups 14.

What is energy coupling? In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction.

15.

In many cellular reactions, a phosphate group is transferred from ATP to some other molecule in order to make the second molecule less stable. The second molecule is said to be phosphorylated intermediate.

16.

Look for this amazing bit of trivia on page 151: If you could not regenerate ATP by phosphorylating ADP, how much ATP would you need to consume each day? If ATP could not be regenerated by the phosphorylation of ADP, humans would use up nearly their body weight in ATP each day.

Concept 8.4 Enzymes speed up metabolic reactions by lowering energy barriers 17.

What is a catalyst? A chemical agent that selectively increases the rate of a reaction without being consumed by the reaction.

18.

What is activation energy (EA)? The amount of energy that reactants must absorb before a chemical reaction will start; also called free energy of activation.

19.

Label the x-axis of this graph “Progress of the Reaction” and the y-axis “Free Energy.” Label EA on this sketch, both with and without an enzyme. See page 152 of your text for the labeled figure.

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a. What effect does an enzyme have on EA? An enzyme catalyzes a reaction by lowering EA barrier. b. Label ∆G. Is it positive or negative? Negative c. How is ∆G affected by the enzyme? It cannot make an endergonic reaction exergonic. 20.

Label this figure while you define each of the following terms: See page 155 of your text for the labeled figure. enzyme: A macromolecule serving as a catalyst, a chemical agent that increases the rate of a reaction without being consumed by the reaction. Most enzymes are proteins. substrate: The reactant on which an enzyme works. active site: The specific region of an enzyme that binds the substrate and that forms the pocket in which catalysis occurs. products: A material resulting from a chemical reaction.

21.

What is meant by induced fit? How is it shown in the figure in question 20? Caused by entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate. In Figure 8.14 on page 154, when the substrate enters the active site, it forms weak bonds with the enzyme, inducing a change in the shape of the protein. This change allows additional weak bonds to form, causing the active site to enfold the substrate and hold it in place.

22.

Explain how protein structure is involved in enzyme specificity. Enzymes are proteins, and proteins are macromolecules with unique three-dimensioal configuration. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence. The specificity of an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate.

23.

Enzymes use a variety of mechanisms to lower activation energy. Describe four of these mechanisms. a. In reactions involving two or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them.

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b. As the active site of an enzyme clutches the bound substrate, the enzyme may stretch the substrate molecules toward their transition-state form, stressing and bending critical chemical bonds that must be broken during the reaction. c. The active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be without the enzyme. d. Direct participation of the active site in the chemical reaction is another mechanism of catalysis. 24.

Many factors can affect the rate of enzyme action. Explain each factor listed here. a. initial concentration of substrate: The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules. b. pH: With some exceptions, the optimal pH values for most enzymes fall in the range of pH 6–8. c. temperature: Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when molecules move rapidly. Above that temperature, however, the speed of the enzymatic reaction drops sharply.

25.

Recall that enzymes are globular proteins. Why can extremes of pH or very high temperatures affect enzyme activity? Three-dimensional structures of proteins are sensitive to their environment. As a consequence, each enzyme works better under some conditions than other conditions, because these optimal conditions favor the most active shape for their enzyme molecule.

26.

Name a human enzyme that functions well in pH 2. Where is it found? Pepsin, found in the human stomach

27.

Distinguish between cofactors and coenzymes. Give examples of each. A cofactor is any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely and reversibly, along with the substrate, during catalysis. A coenzyme is an organic molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.

28.

Compare and contrast competitive inhibitors and noncompetitive inhibitors. Label each type of inhibitor in this figure. See page 156 of your text for the labeled figure. Competitive inhibitors are substances that reduce the activity of an enzyme by entering the active site in place of the substrate, whose structure it mimics.

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Noncompetitive inhibitors are substances that reduce the activity of an enzyme by binding to a location remote from the active site, changing the enzyme’s shape so that the active site no longer effectively catalyzes the conversion of substrate to product. Concept 8.5 Regulation of enzyme activity helps control metabolism 29.

What is allosteric regulation? Allosteric regulation is the binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.

30.

How is allosteric regulation somewhat like noncompetitive inhibition? How might it be different? It is like noncompetitive inhibition in that it may inhibit enzyme activity, but different in that it may also stimulate enzyme activity.

31.

Explain the difference between an allosteric activator and an allosteric inhibitor. The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme.

32.

Although it is not an enzyme, hemoglobin shows cooperativity in binding O2. Explain how hemoglobin works at the gills of a fish. Hemoglobin is made up of four subunits, each of which has an oxygen-binding site. The binding of an oxygen molecule to one binding site increases the affinity for oxygen of the remaining binding sites. Thus, where oxygen is at high levels, such as in the lungs or gills, hemoglobin’s affinity for oxygen increases as more binding sites are filled.

33.

Study this figure from your book (Figure 8.21) and answer the questions that follow. See page 160 of your text for the labeled figured. a. What is the substrate molecule to initiate this metabolic pathway? Threonine b. What is the inhibitor molecule? Isoleucine c. What type of inhibitor is it? Noncompetitive inhibitor d. When does it have the most significant regulatory effect? When it binds to an allosteric site

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e. What is this type of metabolic control called? Feedback inhibition Test Your Understanding Answers Now you should be ready to test your knowledge. Place your answers here: 1. b

2. c

3. b

4. a

5.c

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6. e

7. e

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