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Engineering of Biological Processes Lecture 1: Metabolic pathways Mark Riley, Associate Professor Department of Ag and Biosystems Engineering The University of Arizona, Tucson, AZ 2007 Objectives: Lecture 1 Develop basic metabolic processes Carbon flow Energy production Cell as a black box Inputs Outputs Cell Sugars Amino acids Small molecules Oxygen CO2, NH4, H2S, H2O Energy Protein Large molecules Metabolic processes • Catabolic = Breakdown: • generation of energy and reducing power from complex molecules • produces small molecules (CO2, NH3) for use and as waste products • Anabolic = Biosynthesis: • construction of large molecules to serve as cellular components such as • amino acids for proteins, nucleic acids, fats and cholesterol • usually consumes energy Concentration of components in a cell Component u moles per g dry cell Weight (mg) per g dry cell Approx MW u moles / L Proteins 5081 643 50,000 12.9 Nucleotides RNA DNA 630 100 216 33 100,000 2,000,000 2.2 0.000016 Lipo-polysaccharides 218 40 1,000 40 Peptidoglycan 166 28.4 10,000 2.8 Polyamines 41 2.2 1,000 2.2 6236 962.6 NA NA TOTAL Mosier and Ladisch, 2006 Cell composition Dry weight vs. wet weight 70% of the composition is water CHxOyNz Dry weight consists of: Element E. coli Yeast C O N H P S K Na Others 50% 20% 14% 8% 3% 1% 1% 1% <1% 50% 34% 8% 6% 1% <1% <1% <1% <1% Inputs (cellular nutrients) • Carbon source – sugars • glucose, sucrose, fructose, maltose • polymers of glucose: cellulose, cellobiose • Nitrogen – amino acids and ammonia • Energy extraction: – oxidized input → reduced product – reduced input → oxidized product Other inputs to metabolism Compounds General reaction Example of a species carbonate CO2 → CH4 fumarate fumarate → succinate iron Fe3+ → Fe2+ Shewanella putrefaciens nitrate NO3- → NO2- Thiobacillus denitrificans sulfate SO42+ → HS- Desulfovibrio desulfuricans Methanosarcina barkeri Proteus rettgeri Energy currency ATP NADH FADH2 Adenosine triphosphate Nicotinamide adenine dinucleotide Flavin adenine dinucleotide The basic reactions for formation of each are: ADP + Pi → ATP AMP + Pi → ADP NAD+ + H+ → NADH FADH + H+ → FADH2 Redox reactions of NAD+ / NADH Nicotinamide adenine dinucleotide O H O H H CNH2 + H+ CNH2 + 2 e- N+ N R R NAD+ NADH NAD+ is the electron acceptor in many reactions Glycolysis Glucose Glucose 6-Phosphate Fructose 6-Phosphate Fructose 1,6-Bisphosphate Dihydroxyacetone phosphate Glyceraldehyde 3-Phosphate 2-Phosphoglycerate Phosphoenolpyruvate Pyruvate TCA cycle NADH Acetate Acetyl CoA Citrate Oxaloacetate NADH Isocitrate Malate CO2+NADH a-Ketoglutarate Fumarate GTP Succinate FADH2 GDP+Pi CO2+NADH Glycolysis Also called the EMP pathway (Embden-Meyerhoff-Parnas). Glucose + 2 Pi + 2 NAD+ + 2 ADP → 2 Pyruvate + 2 ATP + 2 NADH + 2H+ + 2 H2O 9 step process with 8 intermediate molecules 2 ATP produced / 1 Glucose consumed Anaerobic Pyruvate dehydrogenase pyruvate + NAD+ + CoA-SH → acetyl CoA + CO2 + NADH + H+ Occurs in the cytoplasm Acetyl CoA is transferred into the mitochondria of eukaryotes Co-enzyme A, carries acetyl groups (2 Carbon) Citric Acid Cycle The overall reaction is: Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O → 3 NADH + 3H+ + FADH2 + CoA-SH + GTP + 2 CO2 2 ATP (GTP) produced / 1 Glucose consumed Anaerobic Oxidative phosphorylation – (respiration) Electrons from NAD and FADH2 are used to power the formation of ATP. NADH + ½ O2 + H+ → H2O + NAD+ ADP + Pi + H+ → ATP + H2O 32 ATP produced / 1 Glucose consumed Aerobic Overall reaction Complete aerobic conversion of glucose Glucose + 36Pi + 36 ADP + 36 H+ + 6O2→ 6 CO2 + 36 ATP + 42 H2O Products of anaerobic metabolism of pyruvate Succinate Malate Lactate Oxaloacetate Pyruvate Acetyl CoA Acetate Ethanol Acetaldehyde Acetoacetyl CoA Acetolactate Acetoin Butanol Butyrate Butylene glycol Formate CO2 H2 Fermentation No electron transport chain (no ox phos). Anaerobic process Glucose (or other sugars) converted to lactate, pyruvate, ethanol, many others Energy yields are low. Typical energy yields are 1-4 ATP per substrate molecule fermented. In the absence of oxygen, the available NAD+ is often limiting. The primary purpose is to regenerate NAD+ from NADH allowing glycolysis to continue. Glycolysis Glucose Glucose 6-Phosphate Fructose 6-Phosphate Fructose 1,6-Bisphosphate Dihydroxyacetone phosphate Glyceraldehyde 3-Phosphate 2-Phosphoglycerate Phosphoenolpyruvate Lactate Pyruvate TCA cycle NADH Acetate Acetyl CoA Ethanol Citrate Oxaloacetate NADH Fermentation Isocitrate Malate CO2+NADH a-Ketoglutarate Fumarate GTP Succinate FADH2 GDP+Pi CO2+NADH NAD+ NADH Glycolysis Glucose C6H12O6 Lactate CH3CHOHCOO Pyruvate CH3CCOO O CO2 + H2O O2 H+ CO2 Ethanol CH3CH2OH + NAD Acetaldehyde CHOCH3 NADH Types of fermentation • Lactic acid fermentation (produce lactate) – Performed by: • Lactococci, Leuconostoc, Lactobacilli, Streptococci, Bifidobacterium • Lack enzymes to perform the TCA cycle. Often use lactose as the input sugar (found in milk) • Alcoholic fermentation (produce ethanol) Alcoholic fermentation Operates in yeast and in several microorganisms Pyruvate + H+ ↔ acetaldehyde + CO2 Acetaldehyde + NADH + H+ ↔ ethanol + NAD+ Reversible reactions Acetaldehyde is an important component in many industrial fermentations, particularly for food and alcohol. Yeasts Only a few species are associated with fermentation of food and alcohol products, leavening bread, and to flavor soups Saccharomyces species Cells are round, oval, or elongated Multiply by budding Cell metabolism If no oxygen is available Glucose C6H12O6 → lactic acid + energy 2 C3H6O3 Anaerobic metabolism Lactic acid fermentation Alcoholic fermentation 2 ATP Cell metabolism Glucose + oxygen → carbon dioxide + water + energy C6H12O6 6 O2 6 CO2 If plenty of oxygen is available Aerobic metabolism 6H2O 36 ATP Summary of metabolism Pathway NADH FADH2 ATP Glycolysis PDH TCA 2 2 6 0 0 2 2 0 2 Total ATP (+ ox phos) 6 6 24 Total 10 2 4 36 or, Fermentation 1-2 0 0-2 1-4