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by: Carly Miller
Carly Miller
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Jonas King
Class Notes




Popular in Biochemistry

Popular in Biochemistry

This 31 page Class Notes was uploaded by Carly Miller on Sunday January 31, 2016. The Class Notes belongs to BCH 4613 at Mississippi State University taught by Jonas King in Spring 2016. Since its upload, it has received 17 views. For similar materials see Biochemistry in Biochemistry at Mississippi State University.


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Date Created: 01/31/16
13 | Bioenergetics and Reactions © 2013 W. H. Freeman and Company CHAPTER 13 Bioenergetics and Reactions Key topics : – Thermodynamics applies to biochemistry, too – Organic chemistry principles are still valid – Some biomolecules are “high energy” with respect to their hydrolysis and group transfers – Energy stored in reduced organic compounds can be used to reduce cofactors such as NADand FAD, which serve as universal electron carriers Life needs energy • Recall that living organisms are built of complex structures • Building complex structures that are low in entropy is only possible when energy is spent in the process • The ultimate source of this energy on Earth is the sunlight Metabolism is the sum of all chemical reactions in the cell • Series of related reactions form metabolic pathways • Some pathways are primarily energy-producing – This is catabolism • Some pathways are primarily using energy to build complex structures – This is anabolism or biosynthesis 13 | Bioenergetics and Reactions © 2013 W. H. Freeman and Company Laws of thermodynamics apply to living organisms • Living organisms cannot create energy from nothing • Living organisms cannot destroy energy into nothing • Living organism may transform energy from one form to another • In the process of transforming energy, living organisms must increase the entropy of the universe • In order to maintain organization within themselves, living systems must be able to extract useable energy from their surroundings, and release useless energy (heat) back to their surroundings G = H - TS Free energy, or the equilibrium constant, measures the direction of processes Energetics of Some Chemical Reactions • Hydrolysis reactions tend to be strongly favorable (spontaneous) • Isomerization reactions have smaller free-energy changes – Isomerization between enantiomers: ∆G° = 0 • Complete oxidation of reduced compounds is strongly favorable – This is how chemotrophs obtain most of their energy – In biochemistry, the oxidation of reduced fuels 2ith O is stepwise and controlled – Recall that being thermodynamically favorable is not the same as being kinetically rapid Calculating ΔG′° Calculate the standard free-energy change of the reaction catalyzed by the enzyme phosphoglucomutase Glucose 1-phosphate → glucose 6-phosphate given that, starting with 20 mM glucose 1-phosphate and no glucose 6-phosphate, the final equilibrium mixture at 25°C and pH 7.0 contains 1.0 mM glucose 1-phosphate and 19 mM glucose 6-phosphate. Does the reaction in the direction of glucose 6-phosphate formation proceed with a loss or a gain of free energy? First we calculate the equilibrium constant: We can now calculate the standard free-energy change: Because the standard free-energy change is negative, the conversion of glucose 1-phosphate to glucose 6-phosphate proceeds with a loss (release) of free energy. (For the reverse reaction, ΔG′° has the same magnitude but the opposite sign.) Energetics within the cell are not standard • The actual free-energy change of a reaction in the cell depends on: – The standard change in free energy – Actual concentrations of products and reactants – For the reaction aA + bB cC + dD: c d ∆G = ∆G'°+ RT ln [C] [D] [A] [B]b • Standard free-energy changes are additive: (1) A ▯ B ΔG°’ 1 (2) B ▯ C ΔG°’ 2 Sum: A ▯ C ΔG°’ + ΔG°’ 1 2 Review of Organic Chemistry • Most reactions in biochemistry are thermal heterolytic processes- in which an anion and cation are created and both electrons from the reactant will remain on one of the products. • Nucleophiles react with electrophiles • Heterolytic bond breakage often gives rise to transferable groups, such as protons • Oxidation of reduced fuels often occurs via transfer of electrons and protons to a dedicated redox cofactor Chemical Reactivity Most reactions fall within few categories: •Cleavage and formation of C–C bonds •Cleavage and formation of polar bonds ‒ Nucleophilic substitution mechanism ‒ Addition–elimination mechanism • Hydrolysis and condensation reactions •Internal rearrangements •Eliminations (without cleavage) •Group transfers (H , CH , PO 2–) 3 3 •Oxidations-reductions (e transfers) Chemistry at Carbon • Covalent bonds can be broken in two ways • Homolytic cleavage is very rare • Heterolytic cleavage is common, but the products are highly unstable and this dictates the chemistry that occurs Homolytic vs. Heterolytic Cleavage Nucleophiles and Electrophiles in Biochemistry Nucleophiles – Electrophiles – functional groups electron-deficient rich in and capable functional groups of donating that seek electrons electrons Chemical properties of Carbonyl groups Examples of Nucleophilic Carbon-Carbon Bond Formation Reactions We’ll see in… Glycolysis CAC Fatty acid catabolism Isomerizations and Eliminations: No Change in Oxidation State Addition–Elimination Reactions • Substitution from sp carbon proceeds normally via the nucleophilic substitution (N 1 or N 2) mechanism • Substitution from the sp carbon proceeds normally via the nucleophilic addition–elimination mechanism 2 – Nucleophile adds to the sp center giving a tetrahedral intermediate – Leaving group eliminates from the tetrahedral intermediate – Leaving group may pick up a proton Addition–Elimination Reactions Group Transfer Reactions • Proton transfer, very common • Methyl transfer, various biosyntheses • Acyl transfer, biosynthesis of fatty acids • Glycosyl transfer, attachment of sugars • Phosphoryl transfer, to activate metabolites ‒ also important in signal transduction 13.3 Chemical Reactivity Most reactions fall within few categories: •Cleavage and formation of C–C bonds •Cleavage and formation of polar bonds ‒ Nucleophilic substitution mechanism ‒ Addition–elimination mechanism • Hydrolysis and condensation reactions •Internal rearrangements •Eliminations (without cleavage) •Group transfers (H , CH , PO 2–) 3 3 •Oxidations-reductions (e transfers) Nucleophilic Displacement • Substitution from sp phosphorous proceeds via the nucleophilic substitution (usually associativeN Slike) mechanism – Nucleophile forms a partial bond to the phosphorous center giving a pentacovalent intermediate or a pentacoordinated transition state Nucleophilic Displacement Phosphoryl Transfer from ATP ATP is frequently thenor of the phosphate in the biosynthesis of phosphate esters. Hydrolysis of ATP is highly favorable under standard conditions • Better charge separation in products • Better solvation of products • More favorable resonance stabilization of products Actual ∆G of ATP hydrolysis differs from ∆G°’ • The actual free-energy change in a process depends on: – The standard free energy – The actual concentrations of reactants and products • The free-energy change is more favorable if the reactant’s concentration exceeds its equilibrium concentration • True reactant and the product are Mg-ATP and Mg-ADP, respectively [MgADP ] [P ] – ∆G° also Mg dependent ∆G = ∆G°+R' ln 2− i [MgATP ] ∆G° of ATP hydrolysis is Mg dependent Cellular ATPconcentration is usually far above the equilibrium concentration, making ATP a very potent source of chemical energy.


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