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Chapter 6: An introduction to metabolism Metabolism Energy and Life 1. The chemistry of life is organized into metabolic pathways i. Metabolism is all the chemical reactions in an organism 1. All about managing materials and energy resources in the cell 2. Catabolic pathways are about degradation a. Major pathway is respiration 3. Anabolic pathways are about synthesis a. Example is synthesis of proteins form amino acids ii. Energy coupling 1. Energy produced in catabolism is used to drive anabolism 2. Organisms transform energy i. Chemical energy is a form of potential energy stored in molecules as a result of the arrangement of the atoms in those molecules 3. The energy transformations of life are subject to two laws of thermodynamics i. First Law: principle of conservation of energy 1. Organisms are energy transformers ii. Second Law: every energy transformation makes the universe more disordered 1. Energy flows to living systems in the from of light and leaves in the form of heat 4. Organisms live at the expense of free energy i. Exergonic reaction proceed with a net release of free energy ii. Endergonic reactions adsorb free energy for the environment iii. ATP is responsible for most energy coupling in cells 5. ATP powers cellular work i. Cells do three types of work 1. Mechanical work (moving parts of the cell) 2. Transport work (moving molecules across membrane against concentration gradients) 3. Chemical work (synthesis activities) ii. The 3 P tail of ATP is unstable due to all the negative charges close to each other 1. ATP readily gives up a P to reduce the instability 2. The recipient of the P is phosphorylated which is also less stable than the original molecule, unstable molecules are more reactive 3. Regeneration of ATP from ADP requires coupling to an exergonic reaction Enzymes 1. Enzymes speed up metabolic reactions by lowering energy barriers i. An enzyme is a catalytic protein ii. Starting a reaction involves activation energy so the reactants can reach the transition state, which is unstable (nice graphs on page 97) iii. Enzymes lower the activation energy of a specific reaction 2. Enzymes are substrate specific i. The substrate fits the active site 1. Induced fit means the substrate can make the active site fit the substrate closely 3. The active site is the catalytic center of the enzyme i. The induced fit can apply stress to the substrate molecule, stretching or bending critical chemical bonds ii. The active site can provide a micro-environment conductive to particular reactions iii. The active site can temporarily participate in the reaction 4. A cells physical and chemical environment affects enzyme activity i. 3 D structure of a protein is sensitive to temperature and pH ii. Reaction velocity increases with increasing temperature up to a point iii. Enzymes also have an optimal pH The control of metabolism 1. Metabolic control often depends on allosteric regulation i. Competitive inhibitor mimics the substrate and blocks the active site ii. Noncompetitive inhibitor binds to a location (allosteric site) away from the active site but changes the conformation so that the active site does not function iii. Allosteric enzymes are usually made of multiple polypeptides and fluctuate between active forms and inactive forms iv. Allosteric activators can stabilize the active form v. Allosteric inhibitors can stabilize the inactive form vi. Feedback inhibition happens when the product of a multiple step process inhibits the enzyme at the beginning of the process vii. An enzyme made of subunits can show cooperativity when the binding of a substrate to one active site can change the conformation of the other active sites to amplify the enzyme 2. The localization of enzymes in a cell helps order metabolism i. Enzymes for several steps in a pathway are assembled into multienzyme complex ii. Enzymes can be located together in fixed locations in the cell or in the membrane Example is enzymes for respiration are in the mitochondria