Metabolism Intro 2 Rev 1

METABOLISM INTRO 2 Based on Essential Physiological Biochemistry Stephen Reed Prepared by G.A. Diopenes, PhD AY 2224 CHT 413C CONCEPTS IN METABOLISM  Chemical reactions  Substitution  Cleavage  Condensati...

METABOLISM INTRO 2 Based on Essential Physiological Biochemistry Stephen Reed Prepared by G.A. Diopenes, PhD AY 2224 CHT 413C CONCEPTS IN METABOLISM  Chemical reactions  Substitution  Cleavage  Condensation  Addition  Transfer  Chemical equilibrium and steady state  Enzyme kinetics  Bioenergetics  Enzyme-mediated control of metabolic pathways ATOMIC AND MOLECULAR REARRANGEMENTS Isomerization involving (a) a change in functional group or (b) the repositioning of atoms within the same molecule. SUBSTITUTION Replacement of one atom or group with another, for example, a hydrogen atom is replaced by a methyl group. REDOX REACTIONS Oxidation and reduction reactions always occur together and are usually easily spotted because of the involvement of a coenzyme. CLEAVAGE Breaking into parts. CONDENSATION Two molecules join together with the elimination of a H2O. Condensation reactions are used when macromolecules are being formed. Amino acids are joined via peptide bonds and monosaccharides via glycosidic bonds, both of which are condensation reactions. ADDITION a) Two molecules are joined together but water is not eliminated. b) Addition across a double bond TRANSFER a) A phosphate group may be transferred from ATP to a substrate b) A functional group may be ‘swapped’ between two molecules c) Quite complex chemical groupings may be transferred  Equilibrium reactions The majority of biochemical reactions are reversible under typical cellular conditions; in metabolism, we are therefore dealing with chemical equilibria. The word equilibrium (singular) signifies a balance, which in chemical terms implies that the rate of a forward reaction is balanced (i.e. the same as) the rate of the corresponding reverse reaction. For a given reaction, under defined conditions, the point of equilibrium is a constant and given the symbol Keq. CHEMICAL EQUILIBRIUM AND STEADY- STATE  cells are not closed systems  fuel (e.g. a source of carbon and, in aerobic cells, oxygen) and other resources (e.g. a source of nitrogen and phosphorus) are continually being added and waste products removed, but their relative concentrations within the cell are fairly constant being subject to only moderate fluctuation.  no biochemical reaction exists in isolation, but each is part of the overall flow of substrate through the pathway as a whole.  Biochemical reactions never reach a true equilibrium because the product of one reaction is the substrate for the next and so the reaction is ‘pulled’ towards completion achieving net formation of product. STEADY-STATE  If reactions inside a cell were true equilibria, there would be no net flow of substrate, no formation of end products and therefore no metabolic pathway.  In the cell, there is net flow of matter but the instantaneous concentrations of intermediates fluctuate relatively little, unless a ‘stress’ for example the need to respond to a physiological challenge, is placed on the system. DYNAMIC AND QUANTITATIVE ASPECTS OF METABOLISM: BIOENERGETICS  The study of energy changes occurring in cells  Knowledge of the change in free energy of a reaction allows biochemists to make predictions about that reaction and its significance in a metabolic pathway.  A measure of the overall energy change which occurs during a reaction is given by the enthalpy, symbol H which is a function of the entropy (S) and free energy (G) of that reaction. Measure of the overall energy change  Enthalpy, symbol H  function of the entropy (S) and free energy (G) of that reaction.  Entropy is ‘wasted’ energy, associated with disorder and randomness.  Free energy is that energy which can be utilized to perform useful biological work.  Useful biological work  driving metabolism in the right direction  transporting molecules across membranes  causing muscles to contract.  Knowledge of the change in free energy of a reaction allows biochemists to make predictions about that reaction and its significance in a metabolic pathway. DYNAMIC AND QUANTITATIVE ASPECTS OF METABOLISM: BIOENERGETICS For reactions inside cells, the symbol ΔG’ is adopted to indicate ‘actual free energy change under physiological conditions’ (37 o C, pH = 7). STANDARD FREE ENERGY  Comparisons of values for different reactions are meaningless unless they have been determined under identical and standardized experimental conditions. The term standard free energy (symbol ΔGO) is used to specify just such conditions.  ΔGO = the value obtained when the reactants and products (including H+) are at molar concentration and gasses (if present) are at 1 atmosphere of pressure.  1 molar H+ concentration gives a pH 0; biochemical reactions occur at a pH of between 5 and 8, mostly ACTUAL STANDARD FREE ENERGY  Biochemical reactions occur at a pH of between 5 and 8, mostly around pH 7.  ΔG0’ is introduced to indicate that the reaction is occurring at pH 7.  If the reaction conditions are fixed (and standard), the value for ΔG0’, must be a constant for any given biochemical reaction. The value for ΔG0’, may be seen as a ‘benchmark’; the further away ΔG’, is from ΔG0’, the further away the real reaction is from standard conditions. REACTION COUPLING  A physiologically irreversible reaction as described above with a positive ΔG would effectively stall the pathway because the reactants would not have enough energy to form product. This undesirable situation can be overcome by putting energy into the reaction to drive it forward. The energy is provided by another reaction occurring within the cell.  Energy Transfer A Crucial Biological Need Energy acquired from sunlight or food must be used to drive endergonic (energy-requiring) processes in the organism Two classes of biomolecules do this: – Reduced coenzymes (NADH, FADH2) – High-energy phosphate compounds - free energy of hydrolysis larger than -25 kJ/mol) Standard free energies of hydrolysis of high-energy compounds Note difference between overall free energy change and the energy of activation for phosphoryl-group transfer!  ATP An Intermediate Energy Shuttle Device PEP and 1,3-BPG are created in the course of glucose breakdown Their energy (and phosphates) are transferred to ADP to form ATP But ATP is only a transient energy carrier - it quickly passes its energy to a host of energy-requiring processes  Phosphoric Acid Anhydrides Why ATP does what it does! ADP and ATP are examples of phosphoric acid anhydrides Note the similarity to acyl anhydrides Large negative free energy change on hydrolysis is due to: – electrostatic repulsion – stabilization of products by ionization and resonance – entropy factors  Phosphoric-Carboxylic Anhydrides These mixed anhydrides - also called acyl phosphates - are very energy-rich Acetyl-phosphate: G°´ = - 43.3 kJ/mol 1,3-BPG: G°´ = -49.6 kJ/mol Bond strain, electrostatics, and resonance are responsible  Enol Phosphates Phosphoenolpyruvate (PEP) has the largest free energy of hydrolysis of any biomolecule Formed by dehydration of 2-phospho- glycerate Hydrolysis of PEP yields the enol form of pyruvate - and tautomerization to the keto form is very favorable ENZYMES may be separate may be a multienzyme complex Factors affecting rate of reaction [S] [E] presence of activators or inhibitors [coenzyme] pH temperature ENZYME KINETICS - the study of enzyme reaction rates and the conditions which affect them. Zero order First order Effect of Inhibitors Energy generating metabolic processes INTERMEDIARY METABOLISM  describes all reactions concerned with the storage and generation of metabolic energy required for the biosynthesis of low-molecular weight compounds and energy storage compounds (Mathews and Van Holde , 1996).  the structure of each enzyme plays a crucial role in determining the specific properties of each reaction.  metabolic processes occur via a series of individual chemical reactions.  the substrates and products are General overview of the major conserved pathways of intermediary metabolism in C. elegans.