Lecture 5: Metabolic Organization and Regulation Dr. AKM Shafiqul Islam 03/03/08

Metabolic Organization and Regulation The cell must have control on its complex array of chemical reactions so that supply and demand for materials, energy, and electrons are balanced and the resources are used efficiently. The reaction system must be organized or structured in a way consist with effective control The modulation of the activities of key enzimes control through the cell’s many branched and looped metabolic reaction pathway

We can gain an appreciation for the importance and efficacy of these controls and structures by examining metabolic pathway of E. coli bacterium

The cells divide every 20 minutes, and they conduct an amazing array of chemical functions with great precision, productivity and balance proteins are synthesized per second in the cell Proteins are large biopolymer with average 300 covalent bonds. So, total 420,000 peptide bond formed per second Living cell is able to achieve such prodigious rates of protein synthesis at the expense of a substantial portion of its metabolically derived energy Almost 2½ million ATP molecules are involved in biosynthesis

Key Crossroad and Branch Points in Metabolism A straight sequence of metabolic reactions is encountered in committed conversions along a particular pathway The first and last of the either starting nutrient, final cellular or excreted product, or branch point from which several alternative reactions are emanate Typically first irreversible reaction leading from a branch is an allosterically controlled step Then by regulating entry into the subsequent reaction sequence, the cell determine the allocation of metabolites which has several alternative uses by the cell

Key Crossroad and Branch Points in Metabolism We shall first examine the importance of branching reaction structures in a global perspective All metabolic activities in the cell depend on the flow of reactions through three primary crossroads –glucose-6-phosphate –pyruvate –acetyl CoA The relative magnitudes of these follows are regulated by the cell in response to metabolic requirements and cell’s current composition

Key Crossroad of Carbon Metabolism

End Product Metabolism Cell release a variety of chemicals into their environment. These products are the result of energy-yielding metabolism e.g., alcohol and organic acids are example of catabolic metabolism of end product Other metabolic products are –antibiotics –toxins –alkaloids the metabolic products and growth factors serve special functions for the cell

Anaerobic Metabolism (Fermentation) Products Many organisms proceed from glucose via the EMP, HMP and/or ED pathways to pyruvate. The metabolic route from pyruvate to alcohol can vary significantly. Economically most important pathway from pyruvate to ethanol by the following sequences Pyruvate Acetaldehyde + NADH + H + ethanol + NAD + acetaldehyde + CO 2 pyruvate deccarboxylase alcohol dehydrogenase

Another carbohydrate fermentation, NADH formed in the pathways to pyruvate is oxidized. The utilization of NADH in fermentation product formation is the lactic acid or homolactic fermentation, which proceed pyruvate to lactate in single step Acetaldehyde + NADH + H + lactate + NAD + lactate dehydrogenase

Other carbohydrate fermentation

Partial Oxidation and End Products Normally water and CO 2 are the metabolic end products of respiration for most aerobic microorganisms Under abnormal conditions or with a few aerobic microbes, the oxidation of organic nutrient is not completed and end products are accumulated Some of the partial oxidation are economic importance

The production of citric acid by the mold A. niger, the sugar concentration very high and the concentration of iron low, the yield of citric acid can be increased greatly

Secondary Metabolic Synthesis Microoganisms and other cells synthesis secondary metabolites when the cell and their environment are appropriate conditions. These are not synthesized substantial amount during cell growth Secondary metabolites are very tremendously in their chemical structure and biological activity For example 600 different antibiotics have been identified Both Bacillus subtilis and Streptomyces griseus produce more than 50 different antibiotics

Overall Growth Stoichometry: Medium Formulation and Yield Factors Cell growth involves consumption of substrate which provide energy and raw materials required for the synthesis of additional cell mass Alternately, this process require that the cell environment contains elements needed to form additional cell mass and that the free energy of substrates consumed should exceed free energy of cell and metabolic products

Medium formulation is complicated for the following reasons –some substrate elements are released in products, not assimilated into cell material –rate limitations as well as stoichiometric limitations must be considered –specific nutrients my be limiting or specific products may be inhibitory due to the metabolic properties of a particular cell strain

The number of nutrient components in the medium is typically large and we cannot include all of them in either of process stoichiometry or of process control. Therefore we seek a rational simplification of the description of the system based upon identification of certain limiting compounds or elements. Limiting compound – if the cell growth are to continue which substrate would be completely exhausted first

Another type of limiting component can be identified based on medium composition effect on cells growth rate. The growth-rate limiting medium component may be identified for a particular strain and environment in the following way.

The total amount of cell mass formed by cell growth is proportional to the mass of substrate utilized. The yield factor Y x/s is the corresponding defined as –The yield factor has a dimensional unit implied by the units used for cell amount and substrate amount –The yield factor is constant for a particular cell cultivation system. –The relationship it provide is extremely useful for knowledge either of the substrate or cell mass cell mass concentration change suffices to determine the other quantity based on stoichiometry alone