MIC 205 Microbiology: Microbial Metabolism | PDF

MIC 205 - Microbiology Lecture 5: Chew your food carefully! Ch. 5 Microbial Metabolism Lecturer: Patrick Daydif Office: UCENT 356 Phone: (602) 496-0599 Email: [email protected] Office Hours: Please refer to Canvas (or by appointment) The best way to...

MIC 205 - Microbiology Lecture 5: Chew your food carefully! Ch. 5 Microbial Metabolism Lecturer: Patrick Daydif Office: UCENT 356 Phone: (602) 496-0599 Email: [email protected] Office Hours: Please refer to Canvas (or by appointment) The best way to contact me and answer your questions is Face to Face. 1 Metabolism Sum of all chemical reactions that lead to the energy exchanges required for growth and reproduction – Requires a source of energy and raw materials – Provides the tools necessary for obtaining and/or synthesizing all four classes of organic macromolecules – Minimum requirements: energy source, carbon, nitrogen, water, various ions (esp. iron) Human bodies are a great source of energy and raw materials for many (but not all) microbes Growth requirements and metabolic byproducts often used for classification purposes! 2 2 Metabolism Cells need energy for... – Locomotion – nutrients don’t always come to them – Reproduction – mating partners don’t always come to them – Storage – nutrients are not always readily available – Energy production – nutrients often must be broken down into simple building blocks to convert them into usable forms – Growth – simple building blocks need to be reassembled into macromolecules that can’t be obtained from the environment These principles apply to nearly all living organisms and form the foundation of most metabolic processes So... where do cells get energy? 3 3 1  Energy Storage and ATP Microbes harvest energy and raw materials from the controlled breakdown of organic substrates (lipids, carbohydrates, proteins) Energy is concentrated and stored in the high-energy phosphate bonds of adenosine triphosphate (ATP) Phosphorylation: chemical addition of inorganic phos- phate to ADP – Substrate-level – Oxidative – Photophosphorylation Anabolic pathways use some energy by breaking phosphate bonds 4 4 The Energy Molecules Energy is stored in the form of activated carrier. (ATP/NADH/FADH/NADPH) for only brief periods of time. – The high-energy covalent bond in ATP (CASH) is a common energy “currency” that is recognized by all cells, to do cellular work that is needed for survival Long-term energy storage (Stocks and bonds) is accomplished by polysaccharide and fat (triglycerides) – These molecules can be broken down to generate ATP for immediate use. 5 Cells spend ATP like we spend cash money!!! 5 Energy Generation and Use Is Coupled anabolic reactions simple ATP ADP + Pi complex molecules molecules catabolic reactions 6 6 2  Basic Chemical Reactions of Metabolism Two major classes of metabolic reactions – Catabolic pathways Break larger molecules into smaller products Large to small Exergonic – Anabolic pathways Synthesize large molecules from the products of catabolism Small to large Endergonic 7 Reduction & Oxidation Reactions (REDOX) Cells make ATP by first releasing energy in the form of electrons from organic and inorganic compounds (electron donors) O oxidation I involves L loss of electrons R reduction I involves G gain of electrons These reactions are always coupled/ occur simultaneously Cells use electron carrier molecules to carry electrons 8 8 Electron Carrier Molecules Primary electron carriers for the temporary storage of energy derived from metabolic redox reactions – NAD+ – nicotinamide adenine dinucleotide – NADP+ - nicotinamide adenine dinucleotide phosphate – FAD – flavin adenine dinucleotide Derived from B vitamins oxidized E E E reduced 9 9 3  Electron Carrier Molecules Primary electron carriers for the temporary storage of energy derived from metabolic redox reactions – NAD+ – nicotinamide adenine dinucleotide – NADP+ - nicotinamide adenine dinucleotide phosphate – FAD – flavin adenine dinucleotide Derived from B vitamins oxidized reduced 10 10 Electron Carrier Molecules 11 11 Reduction and Oxidation Reactions How do cells make lots of ATP? O oxidation – Glucose (Snickers bars!!!) Break down food I involves particles to release energy. The L loss of electrons energy comes out of the food as electrons. R reduction I involves G gain of electrons How do cells “move” energy? – Shuttles! Electron carriers, like NADH. Oxidation involves loss of electrons. Reduction involves gain of electrons. Oxidation and reduction (redox) reactions are always coupled. 12 12 4  Proteins Chains of unique sequences of amino acid monomers – composed of carbon, hydrogen, oxygen, nitrogen, and sulfur Cellular workhorses that perform a variety of essential functions... – Maintain cell and its structure – Catalyze enzymatic reactions – Regulate cellular processes – Transport metabolites, ions, etc. – Defend against pathogens Peptide bond – covalent bond formed between amino acids 13 13 Protein Structure 14 14 Protein Structure 15 15 5  Enzymes in Metabolism Enzymes are proteins! Function as catalysts that lower activation energy of chemical reactions Active site complementary to the shape of the substrate Enzyme-substrate specificity Most are composed entirely of protein; some require non- protein cofactors; such as Zn+ or Mg+ and coenzymes; such as NAD+ 16 16 Enzyme Activity 17 17 Enzyme Activity Factors influence the rate of enzymatic reactions – Temperature – pH 18 18 6  Enzyme Activity Factors influence the rate of enzymatic reactions – Temperature – pH – Enzyme and substrate concentrations – Presence of inhibitors MIC 205 – Chapter 5) 19 19 Enzyme Activity (Inhibitors) Inhibitors are substances that completely alter or block an enzyme’s activity on its substrate. Ways to inhibit enzymes. Feedback inhibition of amino acid synthesis 20 Carbohydrate Catabolism Carbohydrate Catabolism – Many organisms oxidize carbohydrates as a primary energy source for anabolic reactions – Glucose is the most common carbohydrate used Pyruvate oxidation – Two processes can catabolize–Glucose: Cellular Respiration Fermentation 21 7  Respiration Complete breakdown of organic energy sources into CO2 and water Glucose is the most common energy source; various catabolic pathways allow for the breakdown of complex carbohydrates, lipids, and proteins Stages – Pyruvate oxidation – Krebs (citric acid) cycle – Electron transport chain Respiration Aerobic: Process yields about 38ish ATP units per glucose and oxygen is the terminal electron acceptor. Anaerobic: Process yields about 28ish ATP units per glucose and oxygen is NOT terminal electron acceptor. Fermentation: Only uses glycolysis and a final step. Process yields about 2 ATP units per glucose 22 Carbohydrate Catabolism Embden-Meyerhof-Parnas (EMP) Pathway (glycolysis) – First step of glucose catabolism via both respiration and fermentation – Splits six-carbon glucose into two three-carbon pyruvates – Includes substrate-level production of ATP! – Contains 3 stages Energy-investment, Lysis, Energy-conserving Pentose Phosphate Pathway – Forms phosphorylated pentoses (ribulose, xylulose, ribose) – Creates precursor metabolites for synthesis of the nucleotides and some amino acids – Creates unique sugars ( Such as 3,4,5,6,7 Carbon molecules) Entner-Doudoroff Pathway – Utilizes a unique set of enzymes to form pyruvate 23 – Uncommon, but used by P. aeruginosa, E. faecalis 23 EMP Pathway (Glycolysis) Process requires the use of two ATP molecules!!! “Gotta add energy to extract energy!” 24 24 8  EMP Pathway (Glycolysis) Substrate level phosphorylation High energy phosphate bond is directly transferred from one substrate to another 25 25 EMP Pathway (Glycolysis) E Substrate level phosphorylation High energy phosphate bond is directly transferred from one substrate to another 26 26 Aerobic/ Anaerobic Respiration Pyruvate oxidation 34 34 9  Aerobic/ Anaerobic Respiration Pyruvate oxidation TCA (Krebs, Citric acid) cycle – Harnesses a large amount of energy that remains in the bonds of acetyl-CoA molecules – Main goal: transfer energy to NAD+ and FAD electron carriers for use in oxidative phosphorylation or to provide carbon skeletons for anabolism. – Key entry/exit point for amino acid and lipid catabolism and anabolism 35 35 Aerobic/ Anaerobic Respiration Electron transport chain (ETC) – Series of membrane-bound electron carrier molecules that perform a highly coordinated series of redox reactions – Oxidation of ETC leads to proton gradient across membrane; gradient drives ATP synthesis via oxidative phosphorylation – Located in the cell membrane of bacteria 43 43 Electron Transport Chain (ETC) e- Oxygen is the only terminal electron acceptor of aerobic respiration!!!!, But how is electron transport coupled to ATP MIC 205 – Chapter 5 synthesis? 44 44 10  Electron transport coupled to ATP synthesis Proton (H+) gradient created during electron transport in the ECT Protons flow down the gradient through the ATPase ATP Synthase powered by proton gradient to create ATP ADP + pi →ATP 45 45 Key Principles of ETC Cells use the energy released in redox reactions of ETC to pump protons (H+) across the membrane Proton pumping establishes an electrochemical gradient known as a proton gradient; proton gradient possesses potential energy called proton motive force H+ ions, propelled by proton motive force, flow down their electrochemical gradient through ATP synthases (protein channels) that phosphorylate ADP +Pi → ATP Called oxidative phosphorylation because proton gradient created by oxidation of components of ETC A total of 38 ATP molecules are formed from one molecule of glucose! What happens if oxygen is not available for aerobic respiration? 46 46 Anaerobic Respiration The process is more efficient than fermentation but less compared to aerobic respiration. O2 is not the terminal electron acceptor; alternative final electron acceptors (e.g., NO3- → NO2- ,SO4-2, CO3-2) MIC 205 – Chapter 5 47 47 11  Comparing Respiration & Fermentation Why does anaerobic respiration produce fewer ATP units compared to aerobic respiration? 2 ATP What happens if oxygen or respiratory chain is not available for aerobic or anaerobic respiration? 28 ATP 38 ATP Remember !! The process is efficient than fermentation but less so than aerobic respiration with respect to ATP produced. 48 48 Carbohydrate Catabolism Carbohydrate Catabolism – Many organisms oxidize carbohydrates as a primary energy source for anabolic reactions – Glucose is the most common carbohydrate used Pyruvate oxidation – Two processes can catabolize glucose: Cellular Respiration Fermentation 49 Fermentation Sometimes cells cannot completely oxidize glucose by cellular respiration Cells require a constant source of NAD+ that cannot be obtained by simply using glycolysis and the Krebs cycle – In respiration, electron transport regenerates NAD+ from NADH Fermentation pathways provide cells with alternate sources of NAD+ – Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule as an electron acceptor rather than ETC (NADH oxidized to NAD+ while organic molecule reduced) 51 51 12  Fermentation Partial oxidation of sugar to release Glycolysis energy using an organic molecule as an electron acceptor ATP Main goal: regenerate NAD+ for NADH glycolysis to support substrate-level production of ATP NAD+ Not as efficient as respiration – most of the potential energy remains in the bonds of fermentation products A net total of only 2 ATP molecules are formed from one molecule of glucose! 52 52 The Big Picture Glycolysis and the TCA (citric acid) cycle are central to metabolic pathways Different types of mole- cules (lipids, amino acids, carbohydrates) enter the process at different steps Different types of mole- cules can be interconverted; pathways are both catabolic and anabolic 58 58 Pentose Phosphate Pathway Creates unique carbon skeletons 4 carbon (Erythrose), 5 carbon (ribulose, xylulose, ribose), 7 carbon (sedoheptulose) Creates precursor nucleotides metabolites for the synthesis of nucleotides and some amino acids NADP→ NADPH Needed for Calvin cycle 59 59 13  Other Catabolic Reactions NO GLUCOSE!!! 60 60 Regulation of Metabolic Functions Cells often synthesize the enzymes needed to break down a particular substrate only when that substrate is readily available If two energy sources are available, cells catabolize the more energy efficient of the two first – Glucose (I) vs. Lactose (II) – Controlled at the genetic level Glucose MIC 205 – Chapter 5 61 61 Regulation of Metabolic Functions Cells synthesize the metabolites they need but typically cease synthesis if the metabolite is available Cells use inhibitors to control the activity of enzymes Eukaryotic cells keep metabolic processes from interfering with each other by isolating particular enzymes within membrane-bound organelles 62 62 14  Anabolic Pathways Carbohydrate Biosynthesis – Calvin-Benson cycle and Gluconeogenesis Lipid Biosynthesis Amino Acid Biosynthesis Nucleotide Biosynthesis Photosynthesis 63 63 Gluconeogenesis Inputs : Energy= ATP, NADH, 2 molecules of pyrvrate Output: Glucose!!!! Similar to running Glycolysis but backward! 64 64 Calvin-Benson Cycle This cycle is used to make glucose as part of photosynthesis's dark reactions. Inputs : Rubisco Energy= ATP, NADPH, 3 CO2 Output: Glucose!!!! 65 65 15  Lipid Biosynthesis A variety of routes synthesizes Lipids. Lipids are synthesized from glycerol and three molecules of fatty 66 66 Amino Acid Biosynthesis 67 67 Nucleotide Biosynthesis Nucleotides produced from precursor metabolites derived from glycolysis and the Krebs cycle: – Ribose and deoxyribose formed from ribose-5 phosphate, phosphate – Purines and pyrimidines formed from the amino acids glutamine and aspartic acid. 68 68 16