CHAPTER 04 (Notes)

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Chapter 4:

Chapter 4 Introduction to Metabolism

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Definitions Metabolism is the entire network of chemical reactions carried out by living cells. Metabolites are molecules formed intermediately in the degradation or biosynthesis of biopolymers. Anabolic reactions are those responsible for the synthesis of the compounds needed for the cell. Catabolic reactions degrade large molecules to liberate smaller molecules and energy. A metabolic pathway is a series of reactions where the product of one reaction becomes the substrate for the next reaction.

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Metabolism

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Metabolism Pathways

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The Discrete Nature of Metabolism, Why? Enzymes are specific, Control of energy input and output.

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Regulation of Metabolic Pathways A B C D E E 1 E 2 E 3 E 4 Pathways proceed in a single direction. If the concentration of the initial substrate decreases or the product concentration rises the flux through a pathway will decrease. Flux I.

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Feedback mechanism Feed-forward activation II. III.

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Allosteric activators and inhibitors phosphoenolpyruvate IV.

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Posttranslational modifications Regulation at the translation level A particular step in a pathway can be modulated if the synthesis of the enzyme is affected V. VI.

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Compartmentalization of Metabolism 1. Simultaneous operation of opposing metabolic pathways. Separate pools of metabolites can be found within a cell (Compartmentalization at cell level). 2. High local concentrations of metabolites and coordinated regulation of enzymes. 3. Formation of multi-enzyme complexes to avoid dilution of the metabolites (Compartmentalization at the molecule level). 4. Site-specific regulation of metabolic processes (tissue specialization). Significance

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Thermodynamics of Metabolic Pathways Gibbs free energy change ( D G ) is a measure of the energy available from a reaction. D G reaction = D G ’ + RT*ln([P]/[R]) D G = D H + T D S Reaction is spontaneous if D G < 0 Reaction is not spontaneous if D G > 0 Many metabolic pathways have a positive D G ’ , however they are spontaneous. It is the ratio of substrates and products that can affect the outcome of the metabolic reaction. A + B ↔ C + D D G reaction = D G ’ + RT*ln([C]*[D]/[A]*[B]) At equilibrium the D G = 0 Q = mass action ratio

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The change between Q and the ratio of product to substrate at equilibrium determines the actual Gibbs free energy for a reaction. When Q is close to Keq the reaction is called near-equilibrium reaction. In this case D G is small, so the reaction is readily reversible. When Q is far from Keq the reaction is known as metabolically irreversible reaction. Most enzymes in a pathway catalyze near-equilibrium reactions. Metabolically irreversible reactions are generally the control points of pathways , and the enzymes that catalyze these reactions are regulated in someway.

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ATP: the Energy source of metabolic pathways

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Hydrolysis of the phosphoanhydrate linkages of ATP is exothermic 1. The hydrolysis decreases electrostatic repulsion among oxygen atoms; ADP and Pi or AMP and PPi are better solvated. Hydrolysis products are more stable then ATP.

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The Metabolic roles of ATP X + Y ↔ X-Y ATP + H 2 O ↔ ADP + P i + H + X + ATP ↔ X-P + ADP X-P + Y + H 2 O ↔ X-Y + P i + H + Glutamate + NH 4 + ↔ glutamine + H 2 O D H = +14 kJmol -1 The ability of ATP to transfer its phosphoryl group is referred to as phosphoryl-group transfer potential 1. Phosphoryl-group transfer

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Why ATP is so commonly used in metabolic pathways? It is a medium energy compound It is kinetically more stable, it can carry chemical potential energy from one enzyme to the other Found in muscles

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2. Nucleotidyl-group transfer

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