chapter 3 essentials of metabolism
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CHAPTER 3 ESSENTIALS OF METABOLISM Photo courtesy of Dr. Brian Oates Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 WHY IS THIS IMPORTANT? It is important to have a basic understanding of metabolism because it governs the survival and growth of microorganisms. The growth of microorganisms can have a direct effect on infectious disease. Good metabolic function makes pathogens more successful at causing disease. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 OVERVIEW Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science BASIC CONCEPTS OF METABOLISM Metabolism is: A series of chemical processes that go on in living organisms. Used to obtain energy. Linked to growth. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 BASIC CONCEPTS OF METABOLISM Carbon and energy are required for growth. The body has two processes by which it can obtain carbon: Autotrophy – carbon is obtained from inorganic substances Heterotrophy – carbon is obtained from other organic molecules Nearly all infectious organisms are chemoheterotrophs. Chemoheterotrophs obtain energy by breaking down other organic molecules and compounds. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 OXIDATION & REDUCTION REACTIONS Metabolism is broken down into two parts: Catabolism – molecules are broken down through metabolic processes to release the energy stored in their chemical bonds. Anabolism – metabolic processes in which the energy derived from catabolism is used to build large organic molecules from smaller ones. Both processes involve electron transfer and oxidation and reduction reactions. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science OXIDATION & REDUCTION REACTIONS An oxidation reaction is a chemical reaction in which an atom, ion or molecule loses one or more electrons. A reduction reaction is a chemical reaction in which an atom, ion or molecule gains one or more electrons. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 OXIDATION & REDUCTION REACTIONS Oxidation and reduction reactions always occur together. The combination of an oxidation reaction and a reduction reaction are jointly referred to as redox reactions. When a substance is oxidized, it loses electrons. When a substance is reduced, it gains electrons. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 RESPIRATION In metabolism, respiration occurs at the cellular level and is not the same as breathing (respiration at the macroscopic level). Cellular respiration describes catabolic processes and is divided into: Aerobic respiration – metabolism that uses oxygen Anaerobic respiration– metabolism that does not use oxygen Facultatively anaerobic respiration – metabolism that can use oxygen but can also occur without it Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science METABOLIC PATHWAYS Metabolic reactions occur in series of chemical reactions called pathways. The following is an example of a pathway. A is the initial substrate and E is the final product of the pathway, with B, C, and D being intermediates. A B C D E Each step in the pathway is mediated or facilitated by a specific enzyme. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ENZYMES Enzymes are proteins that act as catalysts for metabolic reactions, making the reaction go faster. Each enzyme is specific for a reaction. Enzymes are found in all living organisms and most cells contain hundreds of types which are constantly being manufactured and replaced. Enzymes work by lowering the energy of activation. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ENZYMES Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science PROPERTIES OF ENZYMES Enzymes have specific three dimensional shapes: if the shape changes, activity is inhibited. The shape of the molecule provides a distinctive site called the active site. It is here that: The substrate fits into the enzyme and the reaction occurs. The enzyme and substrate interact to form the enzymesubstrate complex. The active site has to have the proper shape for the enzyme to work. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 PROPERTIES OF ENZYMES Enzymes are generally highly specific. A given enzyme catalyzes only one type of reaction. Most enzymes react with only one particular substrate. The shape of an enzyme molecule and the electrical charges found at the active site allow for the reaction to work and are responsible for the enzyme’s specificity. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 PROPERTIES OF ENZYMES Some enzymes work on more than one substrate but in these cases the enzymes always work in a particular type of reaction. A proteolytic enzyme always degrades proteins because it reacts only with peptide bonds. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science COENZYMES AND CO-FACTORS Many enzymes can catalyze a reaction only if other substances are present at the active site. Co-factors are helper substances that are inorganic ions such as magnesium, zinc, or manganese. Coenzymes are helper substances that are non-protein organic molecules. Co-factors or coenzymes bind to the active site and change the shape of the active site so the substrate now fits. These enzymes are referred to as apoenzymes. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 COENZYMES AND CO-FACTORS Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 COENZYMES AND CO-FACTORS Coenzymes and co-factors can also be used as carrier molecules. When a carrier molecule receives either electrons or hydrogen atoms, it becomes reduced. When a carrier molecule releases electrons or hydrogen atoms, it becomes oxidized. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science COENZYMES AND CO-FACTORS Two coenzyme carrier molecules frequently encountered in biological reactions are: NAD+ = nicotinamide adenine dinucleotide FAD = flavin adenine dinucleotide. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ENZYME INHIBITION Enzyme inhibition takes place in three ways: Competitive inhibition Allosteric inhibition Feedback inhibition Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 COMPETITIVE INHIBITION The inhibitor molecule is similar in structure to the substrate and competes with the substrate to bind to the active site. When the inhibitor has bound to the active site, the substrate cannot bind. The binding of the competitor is reversible and dependent upon the relative numbers of inhibitor molecules and substrate molecules present. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science COMPETITIVE INHIBITION Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ALLOSTERIC INHIBITION This activity also involves inhibitor molecules but they do not block the active site. Inhibitor molecules bind to a part of the enzyme away from the active site: the allosteric site. This binding changes the shape of the active site in such a way that it can no longer fit properly with the substrate. The binding of some allosteric inhibitors is reversible. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ALLOSTERIC INHIBITION Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science FEEDBACK INHIBITION Feedback inhibition is used in many of the metabolic pathways found in the cell. The final product in a pathway accumulates and begins to bind to and inactivate the enzyme that catalyzes the first reaction of the pathway. It is reversible and, when the level of end product decreases, the inhibition stops and the pathway begins to function again. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 FEEDBACK INHIBITION Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 FACTORS THAT AFFECT ENZYME REACTIONS Three major factors affect enzyme activity: Temperature – Can break hydrogen bonds and change shape pH – Can break hydrogen bonds and change shape Concentration of substrate, product & enzyme – Lower numbers of substrate, product, and enzyme molecules means a lower level of activity. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science CATABOLIC PROCESSES IN METABOLISM Catabolic processes in metabolism cause the breakdown of large organic molecules into smaller ones. These are called fueling reactions because they cause a release of energy. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 CATABOLIC PROCESSES IN METABOLISM There are three important pathways by which most organisms release energy from nutrient molecules: Glycolysis Krebs cycle Electron transport chain Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 GLYCOLYSIS The catabolic pathway is used by most organisms. The best example of this pathway is glucose breakdown. The process itself is a series of chemical reactions. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science GLYCOLYSIS The reactions occur in the cytoplasm and do not require oxygen. Four ATP molecules are produced in glycolysis The first steps of the pathway consume two ATP molecules. The net gain is two ATP molecules. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 GLYCOLYSIS Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 GLYCOLYSIS During glycolysis: Phosphates are transferred to substrates by phosphorylation. Phosphorylation makes the substrates more energetic. After a series of steps, the 6-carbon glucose molecule is broken into two 3-carbon pyruvate molecules. NAD+ carries electrons to the electron transport chain. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science GLYCOLYSIS Glycolysis can lead to further pathways. Krebs cycle and cellular respiration (aerobic) Fermentation (anaerobic) Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 GLYCOLYSIS Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 THE KREBS CYCLE The Krebs cycle is also known as the TCA cycle or the citric acid cycle. It is an aerobic catabolic pathway seen in aerobic cellular respiration. Pyruvate is further metabolized in this process. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science THE KREBS CYCLE Pyruvate is first modified with coenzyme A The Krebs cycle is a series of reactions in which chemical changes occur. This produces the Acetyl-CoA complex. Within these reactions, hydrogen atoms are removed and their electrons are transferred to coenzyme carrier molecules. The hydrogen atoms are carried by NAD+ and FAD to the electron transport system. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 THE KREBS CYCLE Three important things happen in the Krebs cycle: Carbon is oxidized as CO2. Electrons are transferred to coenzyme carrier molecules that take the electrons to the electron transport chain. Energy is captured and stored when ADP is converted to ATP. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 THE KREBS CYCLE Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science ELECTRON TRANSPORT CHAIN The electron transport chain is a sequence of molecules. In eukaryotes, they are found in the inner mitochondrial membrane. In prokaryotes, they are organized in the plasma membrane. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ELECTRON TRANSPORT CHAIN Electrons are transferred to a final electron acceptor. In aerobic respiration, the final acceptor is oxygen. In anaerobic respiration, the final acceptor is an inorganic oxygen-containing molecule. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ELECTRON TRANSPORT CHAIN Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science ELECTRON TRANSPORT CHAIN Electron transport differs from organism to organism and some organisms use more than one type. As electrons move from one molecule to another in the chain, energy is released via a process called chemiosmosis. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 CHEMIOSMOSIS As electrons are transferred along the electron transport chain, protons are pumped out of the cell. This causes the proton concentration outside the cell to be higher than inside the cell, causing a concentration gradient to form. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 CHEMIOSMOSIS Specialized membrane proteins allow protons to re-enter the cell. Energy is released as protons re-enter the cell. This energy is used to bind phosphate to ADP, making the high-energy molecule ATP. The difference in proton concentration in this process is called the proton motive force. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science CHEMIOSMOSIS Cells using anaerobic respiration generate two molecules of ATP from one glucose molecule. Cell using aerobic respiration generate thirty eight total molecules of ATP from one glucose molecule. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 FERMENTATION Fermentation is the enzymatic breakdown of carbohydrates in which the final electron acceptor is an organic molecule. ATP is synthesized by substrate-level phosphorylation but is not linked to electron transport. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 FERMENTATION No oxygen is required for ATP to be synthesized. Fermentation yields two molecules of ATP per glucose molecule. Different microorganisms use different fermentation pathways. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science FERMENTATION Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ANABOLISM Anabolic reactions are classified as biosynthetic reactions because they are used to synthesize all the biological molecules needed by the cells of living organisms. Biosynthetic reactions form the network of pathways that produce the components required by the cell for growth and survival. These reactions are fueled by the energy stored in high-energy bonds in ATP. Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 ANABOLISM Microbiology: A Clinical Approach Approach, © byGarland Tony Srelkauskas Science © Garland Science ISBN: 978-0-8153-6514-3 Microbiology: A Clinical Approach [9780815365143] © Garland Science
