Kuliah 3 (Metabolic_pathways).ppt
- 1. 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
- 2. Objectives: Lecture 1 Develop basic metabolic processes Carbon flow Energy production
- 3. Cell as a black box Cell Inputs Outputs Sugars Amino acids Small molecules Oxygen CO2, NH4, H2S, H2O Energy Protein Large molecules
- 4. 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
- 5. 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 TOTAL 6236 962.6 NA NA Mosier and Ladisch, 2006
- 6. Cell composition Dry weight vs. wet weight 70% of the composition is water 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% CHxOyNz
- 7. 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
- 8. Other inputs to metabolism Compounds General reaction Example of a species carbonate CO2 → CH4 Methanosarcina barkeri fumarate fumarate → succinate Proteus rettgeri iron Fe3+ → Fe2+ Shewanella putrefaciens nitrate NO3- → NO2- Thiobacillus denitrificans sulfate SO4 2+ → HS- Desulfovibrio desulfuricans
- 9. Energy currency ATP Adenosine triphosphate NADH Nicotinamide adenine dinucleotide FADH2 Flavin adenine dinucleotide The basic reactions for formation of each are: ADP + Pi → ATP AMP + Pi → ADP NAD+ + H+ → NADH FADH + H+ → FADH2
- 10. Redox reactions of NAD+ / NADH Nicotinamide adenine dinucleotide N+ R H CNH2 O N R H CNH2 O H + H+ NAD+ NADH + 2 e- NAD+ is the electron acceptor in many reactions
- 11. Glucose Glucose 6-Phosphate Fructose 6-Phosphate Fructose 1,6-Bisphosphate Glyceraldehyde 3-Phosphate Pyruvate Acetate Acetyl CoA Citrate a-Ketoglutarate Succinate Fumarate Oxaloacetate Malate Isocitrate CO2+NADH FADH2 CO2+NADH NADH NADH GTP GDP+Pi Phosphoenolpyruvate Dihydroxyacetone phosphate 2-Phosphoglycerate Glycolysis TCA cycle
- 12. 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
- 13. 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)
- 14. 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
- 15. 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
- 16. Overall reaction Complete aerobic conversion of glucose Glucose + 36Pi + 36 ADP + 36 H+ + 6O2→ 6 CO2 + 36 ATP + 42 H2O
- 17. Products of anaerobic metabolism of pyruvate Pyruvate Lactate Acetate Acetaldehyde Ethanol Formate Acetolactate Acetoin Butylene glycol Acetoacetyl CoA Butanol Butyrate Oxaloacetate Malate Succinate Acetyl CoA CO2 H2
- 18. 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.
- 19. Glucose Glucose 6-Phosphate Fructose 6-Phosphate Fructose 1,6-Bisphosphate Glyceraldehyde 3-Phosphate Pyruvate Acetate Acetyl CoA Citrate a-Ketoglutarate Succinate Fumarate Oxaloacetate Malate Isocitrate CO2+NADH FADH2 CO2+NADH NADH NADH GTP GDP+Pi Phosphoenolpyruvate Dihydroxyacetone phosphate 2-Phosphoglycerate Glycolysis TCA cycle Lactate Ethanol Fermentation
- 21. 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)
- 22. 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.
- 23. 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
- 24. Cell metabolism If no oxygen is available Glucose → lactic acid + energy C6H12O6 2 C3H6O3 2 ATP Anaerobic metabolism Lactic acid fermentation Alcoholic fermentation
- 25. Cell metabolism Glucose + oxygen → carbon dioxide + water + energy C6H12O6 6 O2 6 CO2 6H2O 36 ATP If plenty of oxygen is available Aerobic metabolism
- 26. Summary of metabolism Pathway NADH FADH2 ATP Total ATP (+ ox phos) Glycolysis 2 0 2 6 PDH 2 0 0 6 TCA 6 2 2 24 Total 10 2 4 36 or, Fermentation 1-2 0 0-2 1-4