mLmm Outline Preview to Chapter 6

Process of Metabolism Within a Cell 158 In this chapter we will:

Role of Enzymes • Study the chemical reactions mediated by enzymes that

Coenzymes and Oxidation-reduction Reactions constitute the metabolism of a cell.

ATP and Cellular Energy • Learn about the diverse strategies of metabolism that

Metabolic Pathways and Carbon Flow enable cells to sustain life functions.

Autotrophic and Heterotrophic Metabolism. Examine how a cell meets its energy needs by

Autotrophic Metabolism generating ATP.

Heterotrophic Metabolism • Compare various forms of autotrophic and

Metabolic Pathways 164 heterotrophic metabolism.

Respiration • See the chemical reactions that occur in various

Glycolysis metabolic pathways, including fermentation,

Krebs Cycle respiration, photosynthesis, and chemolithotrophy.

Electron Transport Chain and Chemiosmotic • Learn the following key terms and names:

Generation of ATP activation energy Embden-Meyerhof

Aerobic Respiration active site pathway

Anaerobic Respiration adenosine triphosphatase enzymes

Highlight: A Microbial Explanation for Ghosts (ATPase) heterolactic fermentation

Lipid and Protein Catabolism aerobic respiration heterotrophic metabolism

Fermentation alcoholic fermentation homolactic fermentation

Ethanolic Fermentation anabolic pathway Krebs cycle

Newsbreak: Intestinal Yeast Infections Cause anaerobic respiration lactic acid fermentation

Tntmiratinn autotrophic metabolism Methyl Red (MR) test

butanediol fermentation microaerophiles

butanol fermentation mixed-acid fermentation

Highlight: Production of Cheese butyric acid fermentation nitrogen fixation

Propionic Acid Fermentation Calvin cycle nitrogenase

Mixed-acid Fermentation capnophiles photoautotrophic

Butanediol Fermentation catabolic pathway metabolism

Butanol Fermentation cellular metabolism propionic acid

Photosynthetic Metabolism chemiosmosis fermentation

Photoautotrophs chemoautotrophic protonmotive force

chemohSiotophic sESvel

Photosystems and ATP Generation metabolism phosphorylation

Calvin Cycle and C0₂ Fixation coenzyme substrates

Chemoautotrophic Metabolism electron transport chain Voges-Proskauer test

Sulfur Oxidation

Nitrification

Nitrogen Fixation

Methanogenesis

Nmbreak: Explosions That Destroy Houses Traced to Methane from Landfill

157

WITHIN A CELL

volves the formation and consumption of ATP. Cellular metabolism transforms the energy stored in light or chemicals into ATP. Cellular metabolism also transforms starting materials into the numerous carbon-containing chemicals that make up the structural i and functional components of the cell.

Energy and materials are transformed within living cells through a complex integrated network of chemical reactions that collectively constitute the metabolism of the cell, or cellular metabolism.

Role of Enzymes ['enzaɪms]

Cellular metabolism is based on chemical reactions catalyzed by enzymes. Enzymes are biological catalysts, which are substances produced by cells that асcelerate the rates of chemical reactions. Almost all biological catalysts are proteins but a very few are RNA. Virtually every step in cell metabolism involves an enzyme. Enzymes increase the rates of a cell's chemical reactions by more than a million times.

Energy is required for a chemical reaction to occur. Enzymes bind to molecules and bonds in such a way that the energy required to initiate a chemical reaction, called the activation energy, is lowered (FIG. 6-1 1). This lowering of the activation energy is critical because it permits reactions to occur at life-support

FIG. 6-1 An input of energy, called the activation energy, is needed to start a chemical re­action. A catalyst lowers the activation energy. In biological systems, enzymes serve as the catalysts to lower the activation energy.

158

ing temperatures. The result is that the reaction oc­curs more rapidly than it otherwise would at those temperatures.

An input of energy—the activation energy — is needed to initiate a chemical reaction.

Enzymes are biological catalysts that lower the acti­vation energy so that chemical reactions can occur within living cells.

Some molecules can bind to a particular enzymes that the enzyme can catalyze a chemical reaction. Such molecules are called the substrates of that enzyme (FIG. 6-2). Enzymes can bind [baɪnd] to substrate molecules because the three-dimensional shape of the enzyme fits the substrate molecule, sort of like a lock fits a key. Enzymes exhibit great specificity in the reactions that they catalyze. When an enzyme binds to a substrate it forms an enzyme-substrate complex. The enzymesubstrate complex then breaks down, releasing the enzyme and the product(s) of the reac­tion. The enzyme is not consumed in the overall re­action and can continue to act as a catalyst.

Substrate + Enzyme Enzyme-substrate complex Enzyme + Product

key reactions in metabolic pathways govern whether molecules are degraded as an ATP-generating energy source or converted for use in biosynthesis.

The actual site of the enzyme that is responsible for its catalytic action is called the active site. Because protein shapes are not rigid ['rɪʤɪd], when some enzymes bind to their substrate, there may be a slight [slaɪt] alter­ation in the shape of the enzyme molecule so that there is a good fit between substrate and enzyme. The fit is essential for the enzymatic reaction to occur. If the shape of the enzyme is altered so that it can no longer function as a catalyst, the enzyme is said to be denatured. Heating and certain chemicals can dena­ture enzymes, destroying their catalytic activities.

Enzymes exhibit a high degree of substrate speci­ficity.

The enzymes a particular cell synthesizes will deter­mine which chemical reactions occur in cellular me­tabolism of that cell.

COENZYMES [kō'enˌzīms] AND OxiDATION-REDUCTION [rɪ'dʌkʃ(ə)n] Reactions

Many of the chemical reactions in cellular metabo­lism are oxidation-reduction reactions in which elec­trons and protons are exchanged between molecules. Many of these reactions are used to extract energy from organic compounds. In these reactions, elec­trons and protons often are transferred to a molecule

Process of metabolism within a cell 1 59

160 CHAPTER 6 CELLULAR METABOLISM

called a coenzyme (FIG. 6-3). A coenzyme is an or­ganic molecule that serves as a carrier of electrons and/or protons during metabolism. The coenzyme NAD⁺ (nicotinamide adenine dinucleotide) is the common temporary holder of electrons and protons in many metabolic pathways. An example of such a reaction is:

malate + NAD⁺ > oxaloacetate + NADH + H⁺

The reduced coenzyme NADH formed in this reac­tion can then donate an electron and a proton to an­other molecule so that the coenzyme is reoxidized. Other important coenzymes used in cellular metabo­lism are NADP (nicotinamide adenine dinucleotide phosphate) and FAD (flavin adenine dinucleotide).

ATP and Cellular Energy

A central concern of cellular metabolism is the flow of energy. All of the activities of living organisms use energy. Living systems can neither create nor destroy energy. Rather, living systems transform en­ergy, capturing energy from one source and using that energy to drive the essential chemical reactions that enable cells to carry out the life functions of growth and reproduction. Some cells capture energy directly from sunlight; others obtain energy from the oxidation ("burning") of organic or inorganic chemi­cals. Regardless of the source of energy, all cells employ the same strategy of carrying out metabolic

reactions that transfer energy to molecules of AT Then ATP serves as the molecule for transferring er ergy within the cell. A growing cell of the bacteriur Escherichia coli must synthesize approximately 2. million molecules of ATP per second to support it energy needs.

During metabolism, energy is transferred to and stored within molecules of ATP.

ATP is the universal energy carrier of all living cells.

In particular, the energy from ATP is used to drive the energy-requiring reactions of biosynthesis that are needed for cellular growth and reproduction. ATP contains a phosphate functional group joined to the rest of the molecule by a high-energy bond (FIG. 6-4). Breaking this bond yields an inorganic phos­phate group (Pj) and a molecule of adenosine diphos­phate (ADP) and releases a large amount of energy approximately 7300 calories for every 6.023 X 10²³ molecules (mole) of ATP converted to ADP + p. This energy can be used to drive the cell's energy-requir­ing chemical reactions.

In cellular metabolism, energy-requiring reactions occur because they are coupled with reactions that cleave [kliːv] atp.

The formation of ATP from ADP + Pj is an energy requiring reaction. This reaction cannot occur spontaneously. When coupled to a spontaneously occur

FIG. 6-4 Adenosine triphosphate (ATP) is a compound with high-energy phosphate bonds. When ATP is converted to adenosine diphosphate (ADP) a high-energy phosphate bond is cleaved, releasing about 7.5 kcal/mole that can be used to drive other chemical re­actions.

pumped out of prokaryotic cells across the plasma membrane or the membrane-bound organelles (mito­chondria and chloroplasts) of eukaryotic cells as a re­sult of oxidation-reduction reactions that transport electrons and protons through membrane-embedded carriers. As the proton concentration across the mem­brane becomes higher on one side than the other, the protons on that side of the membrane are driven back across the membrane. The force exerted by these pro­tons to drive them back across the membrane is called the protonmotive force. The passage of these protons through specific channels in the membrane provides the energy for the formation of ATP from ADP + Pi.

Metabolic Pathways and Carbon Flow

The chemical reactions of metabolism occur in se­quences. In each sequence the product of one chemi­cal reaction becomes the substrate for the enzyme that catalyzes the next reaction. The overall ordered sequences of enzymecatalyzed chemical reactions are called biochemical pathways or metabolic path­ways. The sequential steps between the starting sub­strate molecule(s) and the end product(s) constitute the intermediary metabolism of the cell.

The enzymatically mediated metabolic reactions of

a cell proceed via a series of small discrete steps

that establish a metabolic pathway.

Metabolic pathways that involve the breakdown (degradation) of organic molecules are said to be

FIG. 6-5 In substrate-level phosphorylation an energy yield reaction directly provides the energy for the generation of ATP; this occurs via a coupled reaction.

ring, energy-releasing reaction, however, the syntheisis of ATP from ADP + P_: does take place, because energy is now available to drive the synthesis of ATP.

The generation of ATP by coupling energetically favorable reactions to the synthesis of ATP from ADP plus either an organic or inorganic phosphate source is called substrate-level phosphorylation (FIG. 6-5).

In other cellular reactions the chemical formation of ATP is driven by a diffusion force in a process known as chemiosmosis (FIG. 6-6). Protons are

FIG. 6-6 In chemiosmosis the metabolic reactions of the cell are used to establish a proton gradient across a membrane. This proton gradient exerts a force called the protonmotive force that is used to generate ATP.

catabolic (meaning to break down). A catabolic path­way is one in which larger molecules are split into smaller ones. Such pathways can be used to obtain energy from organic chemicals, for example. The processes that expend energy to synthesize organic molecules are said to be anabolic (meaning to build up). The catabolic and anabolic pathways of a cell are interconnected so that the substrates used to feed the cell can be changed into the molecules that make up a living cell.

Catabolism means degradative process and anabo­lism means biosynthetic process.

Cells must be able to process matter from available starting material into their own structural and func­tional components. As with energy, the chemical re­actions of living systems can neither create nor de­stroy matter. Cells obtain matter from their sur­roundings and the chemical reactions the cells perform can change the combinations of atoms within that matter to form new molecules. Thus the various available starting substrate molecules are transformed by cellular metabolism into the many different macromolecules of the cell. These macro­molecules include, among others, proteins for en­zymes, lipids for membranes, carbohydrates for var­ious structures such as cell walls, and nucleic acids for the storage and expression of genetic information.

Carbon is the backbone atom of all organic chemi­cals. In terms of carbon flow, the basic strategy of the cell is to form relatively small molecules that can act as the basis for the carbon skeletons of larger macro­molecules (FIG. 6-7). When a microorganism uses an organic substrate, like glucose, to generate ATP, it fol­lows a catabolic pathway to break that molecule down into smaller compounds; these smaller com­pounds then act as building blocks—called precur­sors—for the biosynthesis of macromolecules. Then the microorganism uses an anabolic pathway to transform small molecules into larger molecules.

FIG. 6-7 The metabolic strategy of a cell is to break down substances into smaller compounds via catabolic path­ways. The small compounds that are formed are used as the substrates for biosynthetic reactions in anabolic path­ways.

Autotrophic and Heterotrophic Metabolism

Microorganisms exhibit differing strategies of metab­olism for meeting their common needs. These needs include synthesizing ATP and transforming carbon- containing molecules into the macromolecules that constitute the cells of the microorganism. Two dis­tinct modes of microbial metabolism have evolved for accomplishing these tasks: autotrophy (meaning self-feeding) and heterotrophy (meaning other-feeding).

Autotrophic Metabolism

Microorganisms with autotrophic metabolism are called autotrophs (Table 6-1). The cellular metabo-

TYPE OF METABOLISM DESCRIPTION

Oxygenic photosynthesis Uses two connected photosystems and results in evolution of oxygen, as well as gen­

eration of ATP; carried out by algae and cyanobacteria, which gain reducing power (H⁺) from photolysis of water

Anoxygenic photosynthesis Uses one photosystem and does not result in evolution of oxygen; carried out by

anaerobic photosynthetic bacteria, e.g., green and purple sulfur bacteria, and un­der some conditions by cyanobacteria, which gain reducing power (H⁺) from H₂S or organic compounds

Chemoautotrophic Uses oxidation of inorganic compounds such as sulfur, nitrite, nitrate, and hydrogen

(chemolithotrophic) to establish a protonmotive force across a membrane that results in generation of

ATP by chemiosmosis

lism of autotrophic organisms uses inorganic carbon dioxide as a source of carbon for the biosynthesis of the molecules of the cell. Also, autotrophic metabo­lism almost always generates ATP from the oxidation of inorganic compounds or through the conversion of light energy to chemical energy—not from organic compounds. Photoautotrophic (photosynthetic) mi­croorganisms use light energy and chemoautotrophic (chemolithotrophic) microorganisms use the energy derived from oxidation of inorganic compounds to supply energy needed for synthesis of ATP.

Carbon for the macromolecules of autotrophic mi­croorganisms originates from inorganic carbon dioxide.

Autotrophic metabolism does not use organic com­pounds for the generation of ATP but rather cap­tures light energy or energy from the oxidation of inorganic chemicals; the cellular carbon of au­totrophs comes from carbon dioxide.

Heterotrophic Metabolism

In heterotrophic metabolism the generation of ATP is based on the use of an organic substrate molecule (Table 6-2). The conversion of the organic substrate to end products occurs via a metabolic pathway that releases sufficient energy to be coupled with the synthesis of ATP. The catabolic pathway involves reac- I tions that break down an organic molecule into smaller molecules. Besides using organic compounds I to provide energy for ATP generation, heterotrophs I obtain their cellular carbon from organic substrates.

In heterotrophic metabolism, organic compounds are broken down into smaller molecules, called interme­diary metabolites, that subsequently are used for biosynthesis.

Heterotrophic metabolism uses organic chemicals to supply the energy for ATP generation; the cellular carbon of heterotrophs also comes from organic compounds.

Heterotrophic metabolism occurs by either of two processes: respiration or fermentation. Respiration links the metabolism of an organic substrate with the utilization of an inorganic compound. Respiration is defined as a type of metabolism involving oxidation-reduction reactions where the final electron acceptor that completes the metabolism is an inorganic mole­cule. Often the inorganic compound is molecular oxygen (0₂) so that the process is dependent on air (aerobic respiration) but, in some cases, respiration occurs in the absence of air (anaerobic respiration). ATP is formed during respiration both by substrate- level phosphorylation and by chemiosmosis.

Fermentation is an anaerobic catabolic process that releases energy from sugars or other organic compounds. During fermentation the final electron acceptor is an organic molecule. Only substrate-level phosphorylation is used to generate ATP in a fer­mentation pathway During fermentation, hydrogen ions and electrons are transferred from NADH to pyruvic acid, which is turned into various end prod­ucts. Various microorganisms are able to ferment dif­ferent substrates; the end products depend on the particular microorganism, the substrate, and the ac­tivity of the enzymes that are present (Table 6-3, p. 164).

Respiration requires an inorganic substance, often molecular oxygen, to complete the metabolism of an organic substrate; ATP is generated by both sub­strate level phosphorylation and chemiosmosis dur­ing respiration.

TYPE OF METABOLISM DESCRIPTION

Respiration Uses complete oxidation of organic compounds, requiring an external electron accep­

tor to balance oxidation-reduction reactions used to generate ATP; much of the ATP is formed as a result of chemiosmosis based on the establishment of a proton gradient across a membrane

Aerobic respiration Uses oxygen as the terminal electron acceptor in the membrane-bound pathway that

establishes the proton gradient for chemiosmotic ATP generation

Anaerobic respiration Uses compounds other than oxygen, e.g., nitrate or sulfate, as the terminal electron

acceptor in the membrane-bound pathway that establishes the proton gradient for chemiosmotic ATP generation

Fermentation Does not require an external electron acceptor, achieving a balance of oxidation-re­

duction reactions using the organic substrate molecule; various fermentation path­ways produce different end products