CHAPTER 13 Bioenergetics and Reactions

1. CHAPTER 13Bioenergetics 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 NAD+ and FAD, which serve as universal electron carriers

2. 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

3. 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

4. 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 the themselves, living systems must be able to extract useable energy from the surrounding, and release useless energy (heat) back to the surrounding

6. Free Energy, or the Equilibrium Constant Measure the Direction of Spontaneous Processes

9. Hydrolysis Reactions tend to be Strongly Favorable (Spontaneous)

11. Complete Oxidation of Reduced Compounds is Strongly Favorable • This is how chemotrophs obtain most of their energy • In biochemistry the oxidation of reduced fuels with O2 is stepwise and controlled • Recall that being thermodynamically favorable is not the same as being kinetically rapid

12. Lesson in Quantum Chemistry • Most organic molecules, including the reduced fuels, are in the singlet spin state • All electrons are paired into electron pairs • Molecular oxygen is in the triplet spin state • Two electrons are unpaired • Direct electron transfer from a singlet reduced species to a triplet oxidizing species is quantum-mechanically forbidden • This is why direct oxidation (spontaneous combustion) of biomolecules does not occur readily • Few cofactors, such as transition metal ions, and flavin adenine dinucleotide are able to catalyze consecutive single-electron transfers needed for utilization of O2

13. Review of Organic Chemistry • Most reactions in biochemistry are thermal heterolytic processes • 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 cofactors

14. Oxidations-reductions (e- transfers) • Group transfers (H+, CH3+, PO32-) • 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) Chemical Reactivity Most reactions fall within few categories:

15. Phosphoryl Transfer from ATP • ATP is frequently the donor of the phosphate in the biosynthesis of phosphate esters

17. Hydrolysis of ATP is Favorable Under Standard Conditions • Better charge separation in products • Better solvation of products • More favorable resonance stabilization of products

19. Actual Gof 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 • G0also Mg++ dependent

22. Actual ATP Concentration Depends on Tissue Type • Cellular ATP concentration is usually far above the equilibrium concentration, making ATP a very potent source of chemical energy

24. Several Phosphorylated Compounds Have Large G’° for Hydrolysis • Again, electrostatic repulsion within the reactant molecule is relieved • The products are stabilized via resonance, or by more favorable solvation • The product undergoes further tautomerization

26. Phosphates: Ranking by the Standard Free Energy of Hydrolysis • Reactions such as PEP + ADP = Pyruvate + ATP are favorable, and can be used to synthesize ATP

28. Hydrolysis of Thioesters • Hydrolysis of thioesters, such as acetyl-CoA is strongly favorable • Acetyl-CoA is an important donor of acyl groups • Feeding two-carbon units into metabolic pathways • Synthesis of fatty acids • In acyl transfers, molecules other than water accept the acyl group

30. Oxidation-Reduction Reactions • Reduced organic compounds serve as fuels from which electrons can be stripped off during oxidation

31. Reversible Oxidation of a Secondary Alcohol to a Ketone • Many biochemical oxidation-reduction reactions involve transfer of two electrons • In order to keep charges in balance, proton transfer often accompanies electron transfer • In many dehydrogenases, the reaction proceeds by a stepwise transfers of proton ( H+ ) and hydride ( :H- )

33. NAD and NADP are Common Redox Cofactors • These are commonly called pyridine nucleotides • They can dissociate from the enzyme after the reaction • In a typical biological oxidation reaction, hydride from an alcohol is transferred to NAD+ giving NADH

35. Formation of NADH can be Monitored by UV-Spectrophotometry • Measure the change of absorbance a 340 nm • Very useful signal when studying the of kinetics of NAD-dependent dehydrogenases

37. Flavin Cofactors allow Single Electron Transfers • Permits the use of molecular oxygen as an ultimate electron acceptor • flavin-dependent oxidases • Flavin cofactors are tightly bound to proteins