Microbial Metabolism - Enzymes, Reactions, and Pathways PDF

Microbial 5 Metabolis m Glucose Glucose Microbial Metabolism Learning Objectives 5-1 Explain the term metabolism, enzyme, and oxidation- reduction and the function of enzyme. 5-2 List and provide examples of three types of phosphorylation reactions that generate...

Microbial 5 Metabolis m Glucose Glucose Microbial Metabolism Learning Objectives 5-1 Explain the term metabolism, enzyme, and oxidation- reduction and the function of enzyme. 5-2 List and provide examples of three types of phosphorylation reactions that generate ATP. 5-3 Explain the overall function of metabolic pathways. 5-4 Describe the chemical reactions of glycolysis. 5-5 Explain the products of the Krebs cycle. 5-6 Identify the functions of the pentose phosphate and Entner-Doudoroff pathways. 5-7 Compare and contrast aerobic, anaerobic respiration and fermentation. Figure 5.11 An Overview of Respiration and Fermentation. Big Picture: Metabolism Metabolism is the buildup and breakdown of nutrients within a cell These chemical reactions provide energy and create substances that sustain life Catabolism: breaks down complex molecules; provides energy and building blocks for anabolism; exergonic Anabolism: uses energy and building blocks to build complex molecules; endergonic Metabolic pathways are sequences of enzymatically catalyzed chemical reactions in a cell Metabolic pathways are determined by enzymes Enzymes accelerate, or catalyze, chemical reactions. The molecules at the beginning of the process are called substrates and the enzyme converts these into different molecules, called products Figure 5.1 The role of ATP in coupling anabolic and catabolic reactions. Catabolic and Anabolic Reactions The collision theory states that chemical reactions occur when atoms, ions, and molecules collide Activation energy is the collision energy required for a chemical reaction to occur Reaction rate is the frequency of collisions containing enough energy to bring about a reaction Reaction rate can be increased by enzymes or by increasing temperature, pressure, or concentration Enzymes and Chemical Reactions Catalysts speed up chemical reactions without being altered Enzymes are biological catalysts Enzymes act on a specific substrate and lower the activation energy Figure 5.2 Energy requirements of a chemical reaction. Reaction Activation without enzyme energy without enzyme Reaction Activation with enzyme energy with Reactant enzyme Initial energy level Final energy level Products Enzymes and Chemical Reactions Substrate contacts the enzyme's active site to form an enzyme-substrate complex Substrate is transformed and rearranged into products, which are released from the enzyme Enzyme is unchanged and can react with other substrates Enzyme Components Apoenzyme: protein portion Cofactor: nonprotein component Coenzyme: organic cofactor Holoenzyme: apoenzyme plus cofactor Figure 5.4 Components of a holoenzyme. Coenzyme Substrate Apoenzyme Cofactor Holoenzyme (protein portion), (nonprotein portion), (whole enzyme), inactive activator active Factors Influencing Enzyme Activity Temperature High temperature and pH extreme pH denature Substrate proteins If the concentration of concentration Inhibitors substrate is high (saturation), the enzyme catalyzes at its maximum rate Figure 5.5a Factors that influence enzymatic activity, plotted for a hypothetical enzyme. Inhibitors Competitive inhibitors fill the active site of an enzyme and compete with the substrate Figure 5.7a-b Enzyme inhibitors. Similar molecular structure Normal Binding Action of Enzyme of Substrate Inhibitors Competitive Substrate inhibitor Active site Enzyme (A potent (para- anti-bacterial aminobenzoic drug) acid, a folic acid precursor, an essential nutrient in the synthesis of folic acid) Inhibitors Noncompetitive inhibitors interact with another part of the enzyme (allosteric site) rather than the active site in a process called allosteric inhibition Figure 5.7a-c Enzyme inhibitors. Normal Binding of Substrate Action of Enzyme Inhibitors Substrate Altered Active site active site Enzyme Non- competitive Allosteric inhibitor site Feedback Inhibition Figure 5.8 Substrate Feedback inhibition. Pathway End-product of a Operates reaction allosterically Pathway Shuts Down inhibits enzymes Enzyme 1 from earlier in the Allosteric Bound pathway site end-product Intermediate A Enzyme 2 Feedback Inhibition Intermediate B Enzyme 3 End-product Enzymes Often Team Up in Metabolic Pathways A metabolic pathway is a sequence of chemical reactions. – Starts with a substrate, has intermediates and a final end product – Each reaction is catalyzed by a different enzyme or sometimes by the same ones. – The product of one reaction serves as the substrate for the next. Metabolic pathways and enzyme inhibition. Oxidation-Reduction Reactions Oxidation: removal of electrons Reduction: gain of electrons Redox reaction: an oxidation reaction paired with a reduction reaction Figure 5.9 Oxidation-reduction. Reduction A B A oxidized B reduced Oxidation Oxidation-Reduction Reactions In biological systems, electrons and protons are removed at the same time; equivalent to a hydrogen atom Biological oxidations are often dehydrogenations Figure 5.10 Representative biological oxidation. Containing more energy than NAD+ and used to generate ATP Reduction H+ H (proton) Organic molecule NAD+ coenzyme Oxidized organic NADH + H+ (proton) that includes two (electron carrier) molecule (reduced electron carrier) hydrogen atoms (H) Oxidation The Generation of ATP ATP is generated by the phosphorylation of ADP with the input of energy 1) Substrate-Level Phosphorylation ATP generated when high-energy PO4– is transferred from a phosphorylated compound to ADP 2) Oxidative Phosphorylation Electrons are transferred from one electron carrier to another along an electron transport chain (system) on a membrane that releases energy to generate ATP Figure 5.14 An electron transport chain (system). Enzyme Components Assist enzymes; electron carriers Nicotinamide adenine dinucleotide (NAD+) Nicotinamide adenine dinucleotide phosphate (NADP+) Flavin adenine dinucleotide (FAD) Coenzyme A Each NADH can be oxidized in the electron transport chain to produce 3 molecules of ATP Each FADH2 can produce 2 molecules of ATP 3) Photophosphorylation Occurs only in light- trapping photosynthetic cells Light energy is converted to ATP when the transfer of electrons (oxidation) from chlorophyll pass through a system of carrier molecules Figure 5.25 Cyclic Photophosphorylation. Metabolic Pathways of Energy Production Series of enzymatically catalyzed chemical reactions Extracts energy from organic compounds and stores it in chemical form (ATP) Carbohydrate Catabolism The breakdown of carbohydrates to release energy Glycolysis Krebs cycle Electron transport chain (system) Figure 5.12 An outline of the reactions of glycolysis (Embden-Meyerhof pathway). Glycolysis The oxidation of glucose to pyruvic acid produces ATP and NADH Preparatory stage Energy-conserving stage 2 ATP are used The two glyceraldehyde 3- Glucose is split to form phosphate molecules are two molecules of oxidized to 2 pyruvic acid glyceraldehyde 3- molecules phosphate 4 ATP are produced 2 NADH are produced Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+ 2 pyruvic acid + 4 ATP + 2 NADH + 2H+ Overall net gain of two molecules of ATP for each molecule of glucose oxidized Additional Pathways to Glycolysis Pentose phosphate pathway Uses pentoses and produces NADPH Operates simultaneously with glycolysis Produces important intermediate pentose used in the synthesis of nucleic acids, glucose from CO2 in the photoshythesis and certain amino acids Entner-Doudoroff pathway Produces NADPH and ATP Does not involve glycolysis Occurs in Pseudomonas, Rhizobium, and Agrobacterium Cellular Respiration Oxidation of molecules liberates electrons to operate an electron transport chain Final electron acceptor comes from outside the cell and is inorganic ATP is generated by oxidative phosphorylation Aerobic Respiration Krebs cycle Pyruvic acid (from glycolysis) is oxidized and decarboxylation (loss of CO2) occurs The resulting two-carbon compound attaches to coenzyme A, forming acetyl CoA and NADH Oxidation of acetyl CoA produces NADH, FADH2, and ATP, and liberates CO2 as waste Figure 5.13 The Krebs cycle. Aerobic Respiration Electron transport chain (system) Occurs in the plasma membrane of prokaryotes; inner mitochondrial membrane of eukaryotes Series of carrier molecules (flavoproteins, cytochromes, and ubiquinones) are oxidized and reduced as electrons are passed down the chain Energy released is used to produce ATP by chemiosmosis Figure 5.14 An electron transport chain (system). Aerobic Respiration Chemiosmosis Electrons (from NADH) pass down the electron transport chain while protons are pumped across the membrane Establishes proton gradient (proton motive force) Protons in higher concentration on one side of the membrane diffuse through ATP synthase Releases energy to synthesize ATP The final electron acceptor in the electron transport chain is molecular oxygen (O2) Figure 5.16 Electron transport and the chemiosmotic generation of ATP.