1. Fundamentals of Biochemistry Third Edition Fundamentals of Biochemistry Third Edition Chapter 14 Introduction to Metabolism Chapter 14 Introduction to Metabolism Copyright © 2008 by John Wiley & Sons, Inc. Donald Voet Judith G. Voet Charlotte W. Pratt

2. An example of the complexity of metabolic pathways Metabolic pathways are highly branched, interconnected, and vary substantially between organisms. In class, we’ll cover a couple of pathways in central metabolism that are well conserved.

3. An example of the complexity of metabolic pathways Metabolic pathways are highly branched, interconnected, and vary substantially between organisms. In class, we’ll cover a couple of pathways in central metabolism that are well conserved.

4. Many metabolic reactions require cofactors derived from the diet (vitamins)

5. High energy compounds, coupled reactions, and the logic of metabolism Much of metabolism can be understood as a coupling between favorable and unfavorable reactions, mediated by the production of special high-energy compounds in the cell ATP NADH or NADPH

6. High energy compounds, coupled reactions, and the logic of metabolism Respiration (animals) overall: reduced carbon compounds (e.g. carbohydrates) from the diet are oxidized by O 2 and the energy released is used to carry out endergonic (i.e. energy-requiring) cellular processes. Coupling in respiration: a little ATP is produced directly during the chemical conversions, and the ATP is used to drive subsequent reactions carbohydrate is not oxidized by O 2 directly, but by NAD+, to make NADH some of the NADH is used to drive biosynthetic reactions that are reductive most of the NADH is reoxidized by O 2 by way of an electron transfer chain, in a way that is coupled to formation of a proton gradient, which is then coupled to ATP synthesis (this is called oxidative phophorylation)

7. High energy compounds, coupled reactions, and the logic of metabolism a summary of the overall flow of respiration and the coupling via high energy compounds

8. The cell uses organelles to partition different metabolic pathways allows the cell to have different environments carrying out reactions that might otherwise conflict (e.g. oxidation, reduction)

9. ATP: the cell’s ‘energy currency’ ATP is a key high- energy intermediate in the cell its hydrolysis can be coupled to endergonic reactions, often by ‘group transfer’ of P, though there are other more complex coupling mechanisms involving protein conformational changes.

10. ATP: the cell’s ‘energy currency’ example of coupling via group transfer: glutamate + NH3 (+ATP) -> glutamine (+ADP +Pi)

11. A measure of the phosphate group transfer potential A few compounds have even higher phosphate transfer potentials than ATP these can be used to make ATP when they are produced as intermediates during metabolism

12. A measure of the phosphate group transfer potential A few compounds have even higher phosphate transfer potentials than ATP these can be used to make ATP when they are produced as intermediates during metabolism

13. Standard free energies of reactions coupled to ATP

14. Another very common form of group transfer involves Acetyl-CoA, which carries a 2-carbon acetyl group activated by way of a thioester

15. The oxidation state of carbon is an important concept In respiration, highly reduced carbon (sugar and fat) are converted to the most oxidized form of carbon (CO 2 )

16. A significant fraction of metabolism concerns the flow of electrons (redox reactions) respiration in general, for example NAD + /NADH (and its phosphorylated variant (NADP + /NADPH) is the major carrier of reducing equivalents also useful to think of it as a 2e - (+H + ) transfer hydride transfer

17. Besides NAD(P) + /NAD(P)H, FAD/FADH2 is the second most common carrier of reducing equivalents FAD

18. The potential to transfer reducing equivalents is described by the standard redox potential, E 0 a high positive redox potential means that the half-reaction involving the given redox pair tends to occur as a reduction (i.e. it is a good oxidizing compound; see O 2 ). A low redox potential means the reaction involving the redox pair tends to occur as an oxidation. What matters of course is the relative values.

19. The potential to transfer reducing equivalents is described by the standard redox potential, E 0 to evaluate the standard free energy (  G 0 ) of a full redox reaction (involving electron transfer between two redox pairs): take the E 0 for the pair occuring as a reduction as the reaction is written, and subtract the E 0 for the pair written as an oxidation then,  G 0 =-n F  E 0 (F = 96,500 C/mol)

20. As always, concentrations are critical in understanding the spontaneity (i.e. whether a reaction can go in the forward direction)

21. Studying metabolic enzymes and pathways tracing radioactive elements through pathways (classical methods) genetics (studying effects of gene deletions, for example) enzyme characterization measuring the amounts of mRNA for all the transcripts in the cell (‘transcriptomics’), DNA microarrays or ‘high-throughput sequencing’ measuring the amounts of all the proteins/enzymes in the cell (e.g. by as spectrometry) (‘proteomics’) measuring concentrations of all the metabolic intermediates in the cell (e.g. by mass spectrometry) (‘metabolomics’) modern high-throughput methods

22. Examples of figures for PyMol projects Figure 1 Figure 2 Figure 3