Biochemistry II - Chem 473

1. II BIOENERGETICS AND METABOLISM • 13 Bioenergetics and Biochemical Reaction Types • 14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway • 15 Principles of Metabolic Regulation • 16 The Citric Acid Cycle • 17 Fatty Acid Catabolism • 18 Amino Acid Oxidation and the Production of Urea • 19 Oxidative Phosphorylation and Photophosphorylation • 21 Lipid Biosynthesis • 22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules • 23 Hormonal Regulation and Integration of Mammalian Metabolism • III INFORMATION PATHWAYS • 24 Genes and Chromosomes • 25 DNA Metabolism • 26 RNA Metabolism • 27 Protein Metabolism • 28 Regulation of Gene Expression Biochemistry II - Chem 473

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. O2, CO2 and Nitrogen Cycles

4. Energy Flows through ATP and redox carriers to couple Catabolic and Anabolic Pathways

5. Nonlinear Metabolic Pathways

6. microbiome

7. Glycan metabolism

8. Metabolism Is the Sum of All Chemical Reactions in the Cell • Series of related reactions form metabolic pathways • Some pathways are primarily energy-producing • Catabolism • Some pathways are primarily using energy to build complex structures • Anabolism or biosynthesis

9. 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

10. Laws of Thermodynamics Apply to Living Organisms • Living organisms cannot create energy • Living organisms cannot destroy energy • 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

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

13. Hydrolysis Reactions tend to be Strongly Favorable (Spontaneous)Isomerization Reactions Have Smaller Free Energy ChangesComplete Oxidation of Reduced Compounds is Strongly Favorable

14. 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

15. 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:

16. 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

17. Chemistry at Carbon Homolytic cleavage is very rare, heterolytic cleavage is common but does not occur for C-C bonds Covalent bonds can be broken in two ways

18. Nucleophiles and Electrophiles in Biochemistry

19. Examples of Nucleophilic Carbon-Carbon Bond Formation Reactions

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

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

22. 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

23. 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

25. 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

26. 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

27. 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

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

29. 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- )

30. 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

31. 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

32. 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.