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| Extended Lecture Outline |
Chapter 7: Energy And Metabolism |
SECTION A. BASIC CHEMICAL CONCEPTS
7.1 Energy cannot be created or destroyed.
a. Matter and energy are fundamental to science.
1. Matter is defined as anything that has mass, occupies space, and can be perceived in some way.
2. Energy is defined as the capacity to do work (Figure 7.1).
3. Potential energy is energy that could be turned into work.
4. Kinetic energy is the energy of motion (Figure 7.1).
b. Physicists recognize four basic forces, and each of them creates some kind of potential energy, which can manifest itself as movement, as work.
1. Objects have gravitational potential energy due to their position above the ground.
2. Nuclear energy exists because of the strong force that holds the nuclei of atoms together, and the weak force that underlies the most common kind of radioactivity.
3. The electromagnetic force, the force of attraction and repulsion between charged particles, is responsible for electrical energy.
4. All matter has internal energy, which is commonly detected as heat; it is the combined kinetic energy of atoms and molecules in random motion.
c. Thermodynamics deals with the energy of a system; a system is any part of the universe that isolated and studied.
1. A system is only defined by imaginary boundaries, isolated hypothetically from its surroundings.
2. The simplest systems are physically isolated so they cannot exchange either matter or energy with their surroundings.
3. Closed systems can exchange energy but not matter.
4. Open systems are those through which energy and matter constantly flow.
5. Biological systems are examples of open systems.
7.2 Chemical reactions entail changes in energy.
a. The energy that determines whether a reaction can occur at all, involves the bonds between atoms (Figure 7.2).
1. The forces of attraction and repulsion between protons and electrons in atoms create energy in the interaction between the atoms.
2. When atoms are infinitely apart, the energy is zero.
3. As atoms get closer together, the energy falls, but if they are pushed too close, the energy rises again.
4. Every system is most stable at its point of least energy.
5. The energy needed to break bonds, enough to separate atoms, is called the bond energy of the molecule.
b. Just as matter tends to achieve its lowest-energy, most stable state, a chemical reaction tends to go from a higher to a lower energy state.
1. When atoms are bonded they are in a certain energy state, and the total energy of all the bonds involved determines whether the products of a reaction hold more or less energy than do the reactants.
c. Enthalpy (denoted by H) is defined as heat content of a system.
1. During a chemical reaction, the difference in enthalpy between the initial and final states of a system is: DH = Hof all products — Hof all reactants.
2. The Greek letter delta (D) means "change in" or "difference between."
3. When reactions produce heat, energy is coming out of the system so DH is negative. When heat is absorbed in the reaction, DH is positive.
7.3 Some reactions occur spontaneously and others do not.
a. A spontaneous process occurs without any outside help.
1. Spontaneous does not necessarily mean instantaneous. Some spontaneous processes like rusting are very slow processes.
2. A spontaneous process is a change that goes downhill energetically, which is the natural way for things to flow. A non-spontaneous process is an uphill change.
b. Since matter tends toward its lowest-energy state, we expect reactions to naturally run downhill energetically, to a more stable condition.
c. We expect all natural, spontaneous chemical processes to give off heat. There are some exceptions to this rule, as with the melting of ice, which requires heat absorption.
d. Events are not driven only by the tendency to achieve a state of low energy but also by the tendency for things to become disordered.
7.4 Chemical reactions entail changes in entropy as well as in heat content.
a. Things tend to become more disordered (Figure 7.4).
b. It is the natural way of all things to move toward disorder if they are not constantly forced toward order.
c. The drive toward disorder is measured by the entropy (denoted by S) of a system.
1. The second law of thermodynamics states that in all natural processes the entropy of an isolated system tends to increase to a maximum.
2. Figure 7.5 shows how ice has low entropy and is highly ordered, but when it gains heat from the warm water, the molecules in the ice break bonds and return to the liquid state.
3. Entropy introduces direction to a process, direction in time and sometimes direction in space. Ice melts, but water does not spontaneously turn to ice.
d. The first and second laws of thermodynamics come together through another quantity, free energy.
1. Free energy is denoted by G: G = H — TS; where H = enthalpy, T = temperature (0ūK = — 273.16ūC), and S = entropy.
2. When a process occurs at a constant temperature, the change in free energy is DG = DH — T DS.
e. Some processes are driven mostly by increasing entropy and others mostly by decreasing enthalpy (Figure 7.6).
f. The change in free energy, DG, determines whether a process is going uphill or downhill, because it takes account of both the tendency toward minimum energy and the tendency toward maximum disorder.
1. When a real system is at equilibrium, its free energy is a minimum.
2. In exergonic reactions, like the formation of water, the components lose free energy. These reactions occur naturally and spontaneously.
3. Endergonic reactions, like the separation of hydrogen and oxygen gas from water, can only happen if energy is put into the system.
SECTION B. APPLICATIONS TO METABOLISM
7.5 The need to decrease entropy is a central problem of biology.
a. Organisms are organized, orderly beings. They have low entropy.
1. Organisms have lower entropy and more free energy than the materials from which they are made.
2. As an organism grows, it builds up free energy within itself and seems to violate the second law of thermodynamics.
b. Since organisms are not exempt from the laws of physics, it is only an illusion that they are violating the second law.
1. This law says that an isolated system achieves minimum free energy, but an organism is not an isolated system.
2. Organisms are constantly exchanging energy and matter with the environment. Organisms extract free energy from the surroundings and leave wastes with less energy behind (Figure 7.8).
3. If one were to view an organism along with its environment, one would see that entropy increases and free energy decreases in accordance with the laws of physics.
7.6 Organisms construct and maintain themselves through enzyme-catalyzed pathways.
a. Metabolism is organized into streams of chemical activity known as metabolic pathways, which are analogous to the assembly lines of a factory (Figure 7.9).
1. In an organism, the materials moving through a metabolic pathway are known as metabolites–or intermediary metabolites–because they are in an intermediate stage of assembly or breakdown.
2. A pathway is a sequence of chemical reactions, each catalyzed by one enzyme, each making a small change in the metabolite.
3. Some pathways break down molecules step by step and others synthesize the monomers of cell structure and then polymerize these monomers into macromolecules.
4. Some pathways consume energy and others provide the energy needed to do all this work.
b. In an organism, some enzymes are built into enzyme complexes or membranes, where they apparently operate like assembly lines, but many enzymes float about freely, neither organized nor attached to a solid foundation.
c. All the molecules of any metabolite form a pool in a cell (Figure 7.11).These pools are just abstractions, not physically separated collections of molecules, since all the molecules are actually mixed together in the cytosol.
d. Compartmentalization in eucaryotes confines some materials and raises their concentrations so substrates can more easily encounter the enzymes that operate on them.
e. Metabolism consists of metabolic pathways in which a series of enzymes transform compounds (metabolites) step by small step.
f. Metabolism has two distinct aspects (Figure 7.12).
1. Catabolism is the process where cells break down incoming food molecules into smaller molecules and save some of their energy for use elsewhere.
2. Anabolism or biosynthesis is the process where cells build up smaller molecules into monomeric molecules such as amino acids and then polymerize these monomers into macromolecules.
7.7 Energy-consuming processes can be driven by coupling them to energy-yielding processes.
a. The downhill reactions of catabolism drive the uphill reactions of anabolism (biosynthesis).
b. One reaction can only drive another if the two are linked or coupled to each other by sharing a chemical component and this can occur in two general ways (Figure 7.13).
1. The first way depends on the fact that the actual free energy change in a reaction decreases as the concentrations of the products decreases.
2. As long as the second reaction releases more energy than the first one consumes, the sum of the reactions has a negative free energy and so together they will take place spontaneously.
3. A second kind of coupling uses a group transfer reaction in which some atom or group of atoms is transferred from one molecule to another.
4. This kind of reaction yields so much free energy that it can drive the first one.
7.8 In biological reactions, free energy is carried primarily in ATP.
a. A potential is a measure of a system's ability to do work, and organisms make use of several kinds of potentials.
1. A cell can acquire a chemical potential by concentrating some molecule or ion in a compartment (Figure 7.14).
2. Since this orderly arrangement has low entropy, the concentrated molecules or ions tend to go to a high-entropy state by escaping from the compartment, moving out into regions of lower concentration, and they can be made to do work as they move.
3. An electrical potential, or voltage, is created by building up a high concentration of electrons or ions in one place. This system can do work as the charged particles escape, perhaps in an electric current.
4. Work is also done when a chemical group is transferred in a coupled reaction, and the potential for doing work is measured by a group transfer potential.
b. Metabolic reactions can be driven by the transfer of many chemical groups, but nature has selected one group for use as a kind of universal energy currency: the phosphoryl group.
c. The ability of a compound to transfer this group is measured by its phosphoryl-group transfer potential which is just the free energy of removing the phosphoryl through hydrolysis.
1. Some molecules have a low phosphoryl-group transfer potential with little ability to donate a phosphoryl group to something else.
2. Other compounds can donate the group quite readily and have a high potential. Cells use these compounds to carry free energy.
d. Adenosine triphosphate (ATP) is the universal energy carrier in all organisms.
e. Depending on the actual concentrations of ATP and phosphoric acid inside a cell, the transfer of a phosphoryl group from ATP provides about 11—13 kcal of energy per mole, and this is enough to drive many endergonic reactions.
f. ATP or a similar nucleotide is used in phosphorylation reactions, where it transfers its terminal phosphoryl group to some other molecule, thereby effectively energizing, or activating, the second molecule (Figure 7.15).
1. ATP is the major source of free energy in cells, with similar nucleotides playing secondary roles, and its energy is used for three kinds of work (Figures 7.16, 7.17).
2. TP drives biosynthetic pathways.
3. ATP supplies energy for transporting ions and molecules across cell membranes.
4. By activating certain motor proteins, ATP supplies the energy for motion, including small movements of cellular components, locomotion of single cells and muscle contraction in animals.
7.9 Ecosystems operate on a flow of energy that comes from the sun.
a. The ultimate source of energy for life on earth is the sun.
b. Plants, algae, and some kinds of bacteria are phototrophic organisms, or phototrophs;they capture light energy in the process of photosynthesis.
1. Phototrophs synthesize the organic molecules of their own structure from carbon dioxide and other simple inorganic materials.
2. Energy, which is derived from light in this case, is needed to drive the synthesis.
3. As phototrophs grow, they store energy in their structures.
4. Most phototrophs ultimately serve as food for chemotrophic organisms, or chemotrophs; organisms such as animals whose energy source is chemical rather than
c. Energy that sustains life has to come from the organism's environment, often from other organisms (Figure 7.18).
d. Organisms are related energetically as members of a food chain, which is a series of organisms that eat one another (Figure 7.19).
e. An ecosystem is best described as a complicated, tangled food web (Figure 7.20).
f. In a food web, energy is brought into the system by phototrophs that act as producers. Producers store energy in their structure and are eaten by primary consumers, or herbivores which use some of that stored energy for their own growth and reproduction.
g. Primary consumers and herbivores are often eaten by secondary consumers or carnivores, which use some of the energy in the herbivore's structure.
h. Some members of the ecosystem are omnivores, which are organisms that eat a mixture of plant and animal materials.
i. Decomposers are organisms like molds and bacteria that decay biomolecules as they grow and take their share of energy.
j. Dividing the biological world into various kinds of "-trophs" (different trophic levels) to show distinctive metabolisms is a hallmark of modern biological thought.
1. Organisms can be distinguished by their source of carbon, the major constituent of organic molecules.
2. Autotrophic organisms, or autotrophs, can make their own organic compounds from CO2, water and other inorganic materials.
3. Heterotrophic organisms, or heterotrophs, can only live on the organic compounds already made by some other organism.
4. Most of the ecosystem's producers are photoautotrophs, like plants, which use light for energy and CO2 as their carbon source (Figure 7.21).
5. Some unusual bacteria are chemoautotrophs, which grow on CO2 by extracting energy from inorganic materials.
6. Most consumers are chemoheterotrophs, which extract energy from the organic molecules they consume as they transform these molecules into their own structure.
7. Other bacteria are photoheterotrophs, which use organic molecules as the source of their material but get their energy from light.
7.10 Useful energy can be obtained from oxidative reactions.
a. Energy is extracted from compounds in the environment through processes of oxidation and reduction, the primary energy-yielding reactions of life.
1. A substance is oxidized when it gives up electrons (or hydrogen atoms).
2. A substance is reduced when it gains electrons (or hydrogen atoms).
3. The combined processes, called redox or oxidoreduction, must occur together since electrons have to come from somewhere and go somewhere.
4. The substance that gives an electron is the reducing agent.
5. The substance that gains an electron is the oxidizing agent (Figure 7.22).
6. The strength of any substance as a reducing agent is given by its reduction potential, which is measured relative to a standard reaction in which hydrogen ions are converted into hydrogen gas.
b. More reduced compounds have more energy.
1. In order to show whether a substance is being oxidized or reduced in a reaction, each element in a compound is assigned an oxidation state, a formal number that shows how many positive or negative charges it must carry to account for the charge of the whole molecule.
2. Reduction literally means a reduction in oxidation state while oxidation means an increase in oxidation state.
c. Redox reactions are central to the storage of energy in ATP as they occur in certain cellular structures like mitochondria and chloroplasts in eucaryotes, and in special cell membranes in procaryotes (Figure 7.23).
1. The process depends on creating minute electric currents in the membranes of these structures and using some of their energy to make ATP.
2. In mitochondria, electrons are carried from reduced organic compounds to the final oxidizing agent, oxygen.
3. In chloroplasts, electric currents originate from compounds that have become energized by absorbing light.
7.11 Two kinds of nucleotides are used as oxidizing and reducing agents.
a. In addition to energy-carrying molecules like ATP, cells need oxidizing and reducing agents for many steps in metabolism.
b. Metabolic oxidations called dehydrogenations occur when a pair of hydrogen atoms is removed.
c. Metabolic reductions called hydrogenations occur when a pair of hydrogen atoms is added.
d. The enzymes that participate in dehydrogenations and hydrogenations are called dehydrogenases and reductases.
e. These enzymes use two kinds of coenzymes, which are also nucleotides.
f. Nicotinamide adenine dinucleotide or NAD+ (Figure 7.24) is one of the coenzymes, and it is a double nucleotide.
g. Nicotinamide is a base that has a special capacity for oxidation and reduction.
h. The other important coenzyme of oxidoreduction is flavin adenine dinucleotide (FAD), whose flavin ring is an oxidizing agent.
i. FAD is usually attached as a prosthetic group on certain proteins, called flavoproteins, which are built into the cellular systems that oxidize organic molecules and synthesize ATP.
7.12 ATP and NADPH provide the energy and reducing power needed for biosynthesis.
a. Metabolism provides energy for biosynthesis and growth, for movement, and for transporting materials in and out of cells.
b. The chemical reactions of biosynthesis are organized into metabolic pathways, each step catalyzed by a different enzyme.
c. The endergonic (uphill) reactions of biosynthesis are driven by compounds such as ATP that have high group-transfer potentials.
d. All organisms must have supplies of both ATP for energy and NADPH for reducing power.
e. A heterotroph lives on reduced monomers, such as sugars. During catabolism, it breaks these molecules down to smaller molecules while oxidizing them to release some of their energy, which is stored as ATP and NAD(P)H (Figure 7.26).
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