Chap 3 Metabolism and Growth I. Metabolism Definitions: Metabolism includes two parts: anabolism and catabolism Catabolism: Anabolism: Aerobic metabolism: catabolism anabolis m catabolis anabolis m Anaerobic metabolism: Ex: yeast can exist either aerobically or anaerobically (called facultative anaerobe), the growth rate is lower under anaerobic conditions. Energy Currency 1
ATP (adenosine triphosphate) that possesses high-energy phosphoanhydride bonds. The Phosphoanhydride adenin energy released by the bond breaking of ATP is supplied to the bond-forming processes. General representations: adenosine II. Catabolic Pathways Purposes of breaking down a substrate: Catabolism provides the following: building units for the synthesis of new cells energy, mainly in the form of ATP, to drive the synthesis of other intermediates and products 2
A central pathway: Glycolysis Major form of degradation of glucose, also called EMP pathway. 10 steps are involved, and the overall reaction is 3
4
5
Tricarboxylic acid cycle (citric acid cycle, Krebs Cycle) The end product of the glycolysis, pyruvate, can be converted to acetyl coenzyme A (acetyl-coa). Acetyl-Co A can generate a large number of intermediates, but one of its major roles is to go through TCA cycle under aerobic conditions. pyruvate dehydrogenase The main purposes of TCA cycle: 1. Provides key intermediates for biosynthetic reactions (Fig. 2.5). 2. Produce The overall reaction is: FAD: flavin adenine dinucleotide, analogue of NAD +, an essential redox cofactor FADH: a half-reduced form FADH 2: fully reduced form, analogous to NADH GDP: guanosine diphosphate, an analogue of ADP The initial oxaloacetate needed as the priming reactant can be synthesized by: 6
pyruvateccarboxylas e If an organism grows on a C2 compound, or on a fatty acid, hydrocarbon or any substrate that is degraded into C2 units, the TCA cycle is not sufficient, then alternative pathway can be utilized, e.g. glyoxylate by-pass (Fig. 2-12, skip the details). Many other carbon sources can be utilized by specific enzyme systems in the microorganisms. Thus special microorganisms can be applied as waste disposal units, forming the basis of environmental biotechnology. Ex: microbial degradation of oils and fatty acids. The oils, when consumed by the microorganism, are initially hydrolyzed by lipase, into fatty acids and glycerol. Glycerol glyceraldehyde 3-phosphate (Fig. 2-6). Fatty acids fatty acly-coa oxidation shorter acetyl-coa units (Fig. 2-13) Energy production in aerobic organisms by electron transport chain The reducing power of cofactors (NADH, FADH2) is released by the Electron transport is conducted by carriers Oxidative phosphorylation occurs on either the During electron transport, the flow of electrons creates a proton gradient (high [H+] on the outside of the membrane), so H + tends to flow back 7
Direction of e - transport (CoQ) G=-69.5 kj/mol G=-36.7 kj/mol G=-112 kj/mol Voet, D., Voet, J., (2004) Biochemistry. 3 rd Ed. (Vol.1) John Wiley & Sons. New York. 8
For each co-factor, the overall reactions may be written as: Overall ATP yields for glucose metabolism C6H12O6 +38 Pi+38 ADP+6O2 6H2O +6 CO2 + 38 ATP Anaerobic Metabolism Oxidative phosphorylation cannot occur substrate-level phosphorylation (energy provided by degrading the original substrate) is an alternative route, but the efficiency of energy production is typically 8% of aerobic metabolism. Anaerobic metabolism can occur in bacteria, yeast and even higher animals (e.g. lactate accumulation in the muscles during hyper-activity of an athlete). Several products of anaerobic metabolism stemming from glucose: Ethanol: produced by yeast (e.g. S. cerevisiae), bacteria and by many fungi Glycerol: by yeast when conversion of pyruvate to ethanol is blocked. Lactate: formed by lactic bacteria 9
III. Anabolic Pathways (Biosynthesis) The provision of energy (ATP), reducing power (NADH and NADPH) and various precursors from the breakdown of substrates provide the cell with the necessary means of regenerating itself. The cell undertakes the biosynthesis of the macromolecules (e.g. nucleic acids, proteins, lipids (for membranes) and polysaccharides) from these simple building blocks. Other pathways: pentose (C5) and tetrose (C4) phosphate pathways to provide C5 and C4 units, and NADPH for biosynthesis. Two types of metabolisms: primary metabolism and secondary metabolism. Primary metabolism Occurs during 10
During this phase, the cells grow at an exponential rate and the cell components-dna, RNA, proteins, lipids, etc- are rapidly synthesized. Eventually, the cells must run out of certain nutrient (even if this is only O2) growth rate slows and eventually ceases.. Secondary metabolism When active multiplication ceases, some primary metabolism continues to maintain vital components: e.g. key proteins must be replaced (proteins under turnover) But the cell mainly diverts its metabolism to the secondary metabolism to arise sometimes as storage products (e.g. poly- -hydroxybutyrate or triacylglycerol), or other products not present during exponential phase (see Fig. 2-19). Secondary metabolites are of considerable biotechnological importance (e.g. antibiotics). References: 1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P. (2002) Molecular Biology of the Cell, 4th Ed. Garland Science, New York. 2. Voet, D., Voet, J., (2004) Biochemistry. 3 rd Ed. (Vol.1) John Wiley & Sons. New York. IV. Appendix 11
A simplified schematic illustration of metabolic pathways (http://www.usuhs.edu/pat/deinococcus/metabolicpathways.html) 12