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Introduction to Metabolism.docx

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Xudong Zhu

Introduction to Metabolism metabolism - sum total of all chemical reactions in living cells catabolic reactions - degrade macromolecules and other molecules to release energy anabolic reactions - used to synthesize macromolecules for cell growth, repair, and reproduction Can divide metabolism into 4 groups: carbohydrates, lipids, amino acids, nucleotides.  within each group are a set of pathways  arbitrarily set start and end points for ease of learning and reference  pathways can take different forms: 1) linear - product of one reaction is substrate for another e.g. glycolysis 2) cyclic - regeneration of intermediates e.g. Krebs cycle 3) spiral - same set of enzymes is used repeatedly e.g. fatty acid synthesis, b-oxidation  each pathway may have branch points for metabolites to enter or leave Why have metabolic reactions with so many steps? 1) energy input and output can be controlled - energy transfer occurs in discrete steps as it it transferred to acceptors a little at a time 2) enzymes can catalyze only a single step of a pathway 3) provides opportunities to establish control points, which are essential for cell function Methods of Metabolic Pathway Regulation 1) feedback inhibition  product of pathway controls its own rate of synthesis  occurs in the first committed step E E E 1 2 3 A -----> B -----> C -----> D  advantage is obvious --> prevention of intermediate accumulation 2) feed forward activation (positive feedback)  metabolite produced early in pathway activates an enzyme later in pathway  also prevents accumulation of intermediates E E E E 1 2 3 4 A -----> B -----> C -----> D -----> E 3) allosteric activators and inhibitors 4) covalent modification  addition of phosphoryl groups via protein kinases  removal of phosphoryl groups via phosphatases Major Catabolic Pathways  begins with extracellular digestion of polymers (exogenous) 2  amylase in mouth and intestine work on starch  protein digestion starts in stomach and finished via pancreatic proteases and intestinal peptidases  lipid digestion - triacylglycerols hydrolyzed to fatty acids by phospholipases  absorption occurs in intestine ---> blood ---> body  can also have endogenous sources, such as glycogen and triacylglycerols  catabolism yields 3 possible compounds: 1) acetyl CoA 2) nucleoside triphosphates 3) reduced coenzymes  starts with glycolysis (glucose catabolism), citric acid cycle, polysaccharide mobilization, oxidative phosphorylation  nucleotides are metabolized for excretion, not energy production Thermodynamics and Metabolism  used to understand equilibrium and flux (flow of material through a metabolic pathway) in metabolism  metabolic pathways are not at equilibrium, but at steady state (e.g. leaky bucket)  free energy change (ΔG) is a measure of energy available to proceed in a chemical reaction ΔG = G products Greactants  at equilibrium, ΔG = 0, no free energy available  would like ΔG to be as small as possible (i.e. negative)  Free energy change of a chemical reaction is expressed in terms of changes in heat content (enthalpy) and randomness (entropy) G = H - TS o H = change in enthalpy T = temperature in Kelvin S = change in entropy  when G = -, reaction is spontaneous, and no energy input is needed  when G = +, must supply energy from outside o  when G = 0, reaction is at equilibrium o G ’ = standard free energy change of a biochemical reaction at standard conditions (pH 7.0; 25 C; 1M concentration of solute)  G ’ of a reaction is related to K (equilibrium constant of a reaction) eq A + B ---> C + D G rxn= (GC+ G D -(G AG )B Keq = [C][D] [A][B] o o G ’ = -2.303 RTlog K eq -1 -1 or G ’ = -RT ln Keq R = gas constant 8.315 JK mol  under ideal conditions (standard conditions): o  if Keq > 1, Go’ is negative and reaction will proceed to equilibrium  if Keq = 1, G ’ =0 and reaction is at equilibrium 2 3 o  if Keq <1, G ’ is positive o  G and G ’ are related by the follo
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