Lecture Connections 13 | Bioenergetics and Reactions

Lecture Connections 13 | Bioenergetics and Reactions © 2009 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 NAD+ and 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 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 Free Energy, or the Equilibrium Constant Measure the Direction of Spontaneous Processes Hydrolysis Reactions tend to be Strongly Favorable (Spontaneous) 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 Molecular Basis for Thioester Reactivity • The orbital overlap between the carbonyl group and sulfur is not as good as the resonance overlap between oxygen and the carbonyl group in esters Oxidation-Reduction Reactions • Reduced organic compounds serve as fuels from which electrons can be stripped off during oxidation 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- ) 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 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 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 Chapter 13: Summary In this chapter, we learned that the rules of thermodynamics, and organic chemistry still apply to living systems For example: • Group transfer reactions are favorable when the free energy of products is much lower than the free energy of reactants In biochemical phosphoryl transfer reactions, the good phosphate donors are destabilized by electrostatic repulsion, and the reaction products are often stabilized by resonance • Unfavorable reactions can be made possible by chemically coupling a highly favorable reaction to the unfavorable reaction For example, ATP can be synthesized in the cell using energy in phosphoenolpyruvate • Oxidation-reduction reaction commonly involve transfer of electrons from reduced organic compounds to specialized redox cofactors The reduced cofactors can be used in the biosynthesis, or may serve as a source of energy for ATP synthesis ...CHAPTER 13 Bioenergetics and Reactions Key topics: – Thermodynamics applies to biochemistry, too – Organic chemistry... • Cleavage and formation of C–C bonds • Cleavage and formation of polar bonds • Nucleophilic substitution mechanism • Addition–elimination mechanism • Hydrolysis and condensation reactions •... C-C bonds as shown above Nucleophiles and Electrophiles in Biochemistry Examples of Nucleophilic CarbonCarbon Bond Formation Reactions Addition–Elimination Reactions • Substitution from sp3 carbon