7/5/2014. Microbial. Metabolism. Basic Chemical Reactions Underlying. Metabolism. Metabolism: Overview
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1 PowerPoint Lecture Presentations prepared by Mindy Miller-Kittrell, North Carolina State University Basic Chemical Reactions Underlying Metabolism Metabolism C H A P T E R 5 Microbial Metabolism Collection of controlled biochemical reactions that take place within a microbe Ultimate function of metabolism is to reproduce the organism Basic Chemical Reactions Underlying Metabolism Metabolic Processes Guided by Eight Statements Every cell acquires nutrients Metabolism requires energy from light or catabolism of nutrients Energy is stored in adenosine triphosphate (ATP) Cells catabolize nutrients to form precursor metabolites Precursor metabolites, energy from ATP, and enzymes are used in anabolic reactions Enzymes plus ATP form macromolecules Cells grow by assembling macromolecules Cells reproduce once they have doubled in size Metabolism: Overview 1
2 Basic Chemical Reactions Underlying Metabolism Catabolism and Anabolism Two major classes of metabolic reactions Catabolic pathways Break larger molecules into smaller products Exergonic (release energy) Anabolic pathways Synthesize large molecules from the smaller products of catabolism Endergonic (require more energy than they release) Figure 5.1 Metabolism is composed of catabolic and anabolic reactions. Basic Chemical Reactions Underlying Metabolism Oxidation and Reduction Reactions Transfer of electrons from an electron donor to an electron acceptor Reactions always occur simultaneously Cells use electron carriers to carry electrons (often in H atoms) Three important electron carriers Nicotinamide adenine dinucleotide (NAD + ) Nicotinamide adenine dinucleotide phosphate (NADP + ) Flavin adenine dinucleotide (FAD) Figure 5.2 Oxidation-reduction, or redox, reactions. 2
3 Oxidation-Reduction Reactions Basic Chemical Reactions Underlying Metabolism ATP Production and Energy Storage Organisms release energy from nutrients Can be concentrated and stored in high-energy phosphate bonds (ATP) Phosphorylation inorganic phosphate is added to substrate Cells phosphorylate ADP to ATP in three ways Substrate-level phosphorylation Oxidative phosphorylation Photophosphorylation Anabolic pathways use some energy of ATP by breaking a phosphate bond Basic Chemical Reactions Underlying Metabolism The Roles of Enzymes in Metabolism Enzymes: Overview Enzymes are organic catalysts Increase likelihood of a reaction 3
4 Basic Chemical Reactions Underlying Metabolism The Roles of Enzymes in Metabolism Naming and classifying enzymes Six categories of enzymes based on mode of action Hydrolases Isomerases Ligases or polymerases Lyases Oxidoreductases Transferases Basic Chemical Reactions Underlying Metabolism The Roles of Enzymes in Metabolism Figure 5.3 Makeup of a holoenzyme. Inorganic cofactor Active site The makeup of enzymes Many protein enzymes are complete in themselves Apoenzymes are inactive if not bound to nonprotein cofactors (inorganic ions or coenzymes) Binding of apoenzyme and its cofactor(s) yields holoenzyme Coenzyme (organic cofactor) Apoenzyme (protein) Some are RNA molecules called ribozymes Holoenzyme 4
5 Figure 5.4 The effect of enzymes on chemical reactions. Reactants Activation energy without enzyme Activation energy with enzyme Products Figure 5.5 Enzymes fitted to substrates. Figure 5.6 The process of enzymatic activity. Substrate (Fructose 1,6-bisphosphate) Active sites similar to substrate's shape Substrate Enzyme (Fructose-1,6- bisphosphate aldolase) Enzymesubstrate complex Enzyme Enzyme-substrate complex; active sites become exact shape of substrate Glyceraldehyde-3P 4 Dihydroxyacetone-P Products 5
6 Enzymes: Steps in a Reaction Basic Chemical Reactions Underlying Metabolism The Roles of Enzymes in Metabolism Enzyme activity Many factors influence the rate of enzymatic reactions Temperature ph Enzyme and substrate concentrations Presence of inhibitors Inhibitors block an enzyme's active site Do not denature enzymes Three types Figure 5.7 Representative effects of temperature, ph, and substrate concentration on enzyme activity. Figure 5.8 Denaturation of protein enzymes. 6
7 Figure 5.9 Competitive inhibition of enzyme activity. Substrate Competitive inhibitor Enzymes: Competitive Inhibition Enzyme Reversible competitive inhibitor Substrate Enzyme Increase in substrate concentration Figure 5.10 Allosteric control of enzyme activity. Active site Enzyme Substrate Distorted active site Enzyme-Substrate Interaction: Noncompetitive Inhibition Allosteric site Allosteric inhibitor Allosteric (noncompetitive) inhibition Distorted, nonfunctional active site Substrate Active site becomes functional Allosteric site Allosteric activation Allosteric activator 7
8 Figure 5.11 Feedback inhibition. Substrate Pathway shuts down Bound end-product (allosteric inhibitor) Enzyme 1 Allosteric site Pathway operates Many organisms oxidize carbohydrates as primary energy source for anabolic reactions Glucose is most common carbohydrate used Feedback inhibition Intermediate A Glucose is catabolized by two processes Cellular respiration Enzyme 2 Fermentation Intermediate B End-product Enzyme 3 Figure 5.12 Summary of glucose catabolism. Respiration G L Y C O L Y S I S Glucose Fermentation Glycolysis 2 Pyruvic acid Acetyl-CoA KREBS CYCLE Pyruvic acid (or derivative) Formation of fermentation end-products Occurs in cytoplasm of most cells Involves splitting of a six-carbon glucose into two threecarbon sugar molecules Substrate-level phosphorylation direct transfer of phosphate between two substrates Net gain of two ATP molecules, two molecules of NADH, and precursor metabolite pyruvic acid Electrons Final electron acceptor 8
9 Glycolysis: Overview Glycolysis Divided into three stages involving 10 total steps Energy-investment stage Lysis stage Energy-conserving stage Figure 5.13 Glycolysis. Glycolysis: Steps 9
10 Figure 5.14 Example of substrate-level phosphorylation. Phosphoenolpyruvate (PEP) Pyruvic acid Cellular Respiration Resultant pyruvic acid is completely oxidized to produce ATP by series of redox reactions Three stages of cellular respiration Holoenzyme Phosphorylation 1. Synthesis of acetyl-coa 2. Krebs cycle 3. Final series of redox reaction (electron transport chain) Figure 5.15 Formation of acetyl-coa. Cellular Respiration Synthesis of acetyl-coa Results in Two molecules of acetyl-coa Two molecules of CO 2 Two molecules of NADH 10
11 Cellular Respiration The Krebs cycle Great amount of energy remains in bonds of acetyl-coa Transfers much of this energy to coenzymes NAD + and FAD Occurs in cytosol of prokaryotes and in matrix of mitochondria in eukaryotes Cellular Respiration The Krebs cycle Six types of reactions in Krebs cycle Anabolism of citric acid Isomerization Redox reactions Decarboxylations Substrate-level phosphorylation Hydration reaction Figure 5.16 The Krebs cycle. Krebs Cycle: Overview 11
12 Krebs Cycle: Steps Cellular Respiration The Krebs cycle Results in Two molecules of ATP Two molecules of FADH 2 Six molecules of NADH Four molecules of CO 2 Figure 5.17 An electron transport chain. Cellular Respiration Path of Respiration Fermentation Electron transport electrons Most significant production of ATP occurs from series of redox reactions known as an electron transport chain (ETC) Series of carrier molecules that pass electrons from one to another to final electron acceptor Energy from electrons is used to pump protons (H + ) across the membrane, establishing a proton gradient Located in cristae of eukaryotes and in cytoplasmic Final electron acceptor membrane of prokaryotes 12
13 e e e e 7/5/2014 Electron Transport Chain: Overview Cellular Respiration Electron transport Four categories of carrier molecules Flavoproteins Ubiquinones Metal-containing proteins Cytochromes Aerobic respiration: oxygen serves as final electron acceptor Anaerobic respiration: molecule other than oxygen serves as final electron acceptor Figure 5.18 One possible arrangement of an electron transport chain. Bacterium Mitochondrion Electron Transport Chain: The Process Intermembrane space Matrix Exterior Cytoplasmic membrane Cytoplasm FMN H + H + Exterior of prokaryote or intermembrane space of mitochondrion Phospholipid membrane 1 2 Ubiquinone e e Cyt b H + H+ Cyt c Cyt a Cyt a 3 H + H + H + H + e e NADH + H + FADH 2 e e 4 NADH NAD + Cyt c 1 FAD + from glycolysis, H + FADH 2 Krebs cycle, H + from pentose phosphate Krebs cycle pathway, and Entner-Doudoroff pathway H + H + e e H + H + ATP synthase Cytoplasm of prokaryote or matrix of mitochondrion 1 / 2 O 2 ADP + P 3 H 2O ATP 13
14 Electron Transport Chain: Factors Affecting ATP Yield Cellular Respiration Chemiosmosis Use of ion gradients to generate ATP Cells use energy released in redox reactions of ETC to create proton gradient Protons flow down electrochemical gradient through ATP synthases that phosphorylate ADP to ATP Called oxidative phosphorylation because proton gradient is created by oxidation of components of ETC Total of ~34 ATP molecules formed from one molecule of glucose Alternatives to Glycolysis Yield fewer molecules of ATP than does glycolysis Reduce coenzymes and yield different metabolites needed in anabolic pathways Two pathways Pentose phosphate pathway Entner-Doudoroff pathway 14
15 Figure 5.19 The pentose phosphate pathway. Figure 5.20 Entner-Doudoroff pathway. Glucose Glucose 6-phosphate 6-Phosphogluconic acid 2-Keto-3-deoxy- 6-phosphogluconic acid Glyceraldehyde 3-phosphate (G3P) Steps 6 10 of glycolysis Pyruvic acid Pyruvic acid To Krebs cycle or fermentation Figure 5.21 Fermentation. Fermentation Sometimes cells cannot completely oxidize glucose by cellular respiration Cells require constant source of NAD + Cannot be obtained simply by using glycolysis and Krebs cycle Fermentation pathways provide cells with alternative source of NAD + Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as final electron acceptor 15
16 Figure 5.22 Representative fermentation products and the organisms that produce them. Fermentation Other Catabolic Pathways Lipids and proteins contain energy in their chemical bonds Can be converted into precursor metabolites Serve as substrates in glycolysis and the Krebs cycle 16
17 Figure 5.23 Catabolism of a fat molecule. Figure 5.24 Protein catabolism. Glycerol Fatty acid chains Polypeptide Protease s 3 Lipase Extracellular fluid Fatty acid Glycerol + Fatty acids DHAP To step 5 glycolysis To electron transport chain Amino acids Shorter fatty acid Acetyl-CoA Cytoplasmic membrane Deamination Hydrolysis Beta-oxidation To Krebs cycle Cytoplasm To Krebs cycle Photosynthesis Photosynthesis: Overview Many organisms synthesize their own organic molecules from inorganic carbon dioxide Most of these organisms capture light energy and use it to synthesize carbohydrates from CO 2 and H 2 O by a process called photosynthesis 17
18 Metabolism Photosynthesis Chemicals and Structures Chlorophylls Type of pigment molecule that photosynthetic organisms use to capture light energy Composed of hydrocarbon tail attached to light-absorbing active site centered on magnesium ion Active sites are structurally similar to cytochrome molecules in ETC Structural differences cause absorption at different wavelengths Photosynthesis Figure 5.25 Photosynthetic structures in a prokaryote. Chemicals and Structures Photosystems Arrangement of molecules of chlorophyll and other pigments to form light-harvesting matrices Photosystem embedded in membrane (sectioned) Chlorophyll Thylakoid membrane Active site Thylakoid Embedded in cellular membranes called thylakoids In prokaryotes invagination of cytoplasmic membrane Tail (carbon chain) In eukaryotes formed from inner membrane of chloroplasts Arranged in stacks called grana Stroma is space between outer membrane of granum and thylakoid membrane 18
19 Photosynthesis Photosynthesis Chemicals and Structures Two types of photosystems Photosystem I (PS I) Photosystem II (PS II) Photosystems absorb light energy and use redox reactions to store energy in the form of ATP and NADPH Light-dependent reactions depend on light energy Light-independent reactions synthesize glucose from carbon dioxide and water Light-Dependent Reactions As electrons move down the chain, their energy is used to pump protons across the membrane Photophosphorylation uses proton motive force to generate ATP Photophosphorylation can be cyclic or noncyclic Figure 5.26 Reaction center of a photosystem. Light Acceptor Reaction center chlorophyll Figure 5.27 The light-dependent reactions of photosynthesis: Cyclic and noncyclic photophosphorylation. ATP synthase Light Cytoplasm of prokaryote Membrane of or stroma of prokaryote or chloroplast Cytochromes Fe of thylakoid in Reaction center chloroplast Cu Photosystem I Exterior of prokaryote or thylakoid space of chloroplast Cyclic photophosphorylation Cytoplasm of prokaryote or stroma of chloroplast Light Reaction center Cytochromes Photosystem II Quinone To Calvin-Benson cycle Light Reaction center Fe ATP synthase Membrane of prokaryote or of thylakoid in chloroplast Possible path of energy transfer Photosystem: reaction center Photosystem I Cu Exterior of prokaryote or thylakoid space of chloroplast Noncyclic photophosphorylation NADPase 19
20 Photosynthesis: Light Reaction: Cyclic Photophosphorylation Photosynthesis: Light Reaction: Noncyclic Photophosphorylation Photosynthesis Light-Independent Reactions Do not require light directly Use ATP and NADPH generated by light-dependent reactions Key reaction is carbon fixation by Calvin-Benson cycle Three steps Fixation of CO 2 Reduction Regeneration of RuBP 20
21 Figure 5.28 Simplified diagram of the Calvin-Benson cycle. Photosynthesis: Light-Independent Reaction Other Anabolic Pathways Anabolic reactions are synthesis reactions requiring energy and a source of precursor metabolites Energy derived from ATP from catabolic reactions Many anabolic pathways are the reverse of catabolic pathways Reactions that can proceed in either direction are amphibolic 21
22 Figure 5.29 The role of gluconeogenesis in the biosynthesis of complex carbohydrates. Figure 5.30 Biosynthesis of fat, a lipid. Figure 5.31 Examples of the synthesis of amino acids via amination and transamination. Figure 5.32 The biosynthesis of nucleotides. 22
23 Integration and Regulation of Metabolic Function Cells synthesize or degrade channel and transport proteins Cells often synthesize enzymes only when substrate is available Cells catabolize the more energy-efficient choice if two energy sources are available Cells synthesize metabolites they need, cease synthesis if metabolite is available Integration and Regulation of Metabolic Function Eukaryotic cells isolate enzymes of different metabolic pathways within membrane-bounded organelles Cells use allosteric sites on enzymes to control activity of enzymes Feedback inhibition slows/stops anabolic pathways when product is in abundance Cells regulate amphibolic pathways by requiring different coenzymes for each pathway Integration and Regulation of Metabolic Function Two types of regulatory mechanisms Figure 5.33 Integration of cellular metabolism (shown in an aerobic organism). Control of gene expression Cells control amount and timing of protein (enzyme) production Control of metabolic expression Cells control activity of proteins (enzymes) once produced 23
24 Metabolism: The Big Picture 24
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