Lecture 1- Metabolism: Basic Concepts and Design

1. Lecture 1- Metabolism: Basic Concepts and Design • Chem 454: Regulatory Mechanisms in Biochemistry • University of Wisconsin-Eau Claire

2. Introduction • Questions we will focus on this semester: • How does a cell extract energy and reducing power from its environment? • How does a cell synthesize the building blocks of its macromolecules and the then the macromolecules themselves? • How are these processes integrated and regulated?

3. Introduction • Living organisms require an input of free energy to meet various needs: • For mechanical work • For active transport of molecules and ions • For synthesis of biomolecules

4. Introduction • Living organisms require an input of free energy • Phototrophs • Use energy from the sun to convert energy-poor molecules into energy rich molecules • Chemotrophs • Obtain energy by oxidizing the energy-rich molecules made by the phototrophs

5. Introduction • Reduced molecules are energy-rich • Oxidized molecules are energy-poor

6. Introduction • Energy from photosynthesis or the oxidation of fuels can be transformed into an unequal distribution of ions across a biological membrane. • The ion gradient can be used for • Oxidative phosphorylation to make ATP • Active transport across membranes • Nerve transmission

7. Introductions • Ion gradients: See Chapter 2.3.3

8. Metabolism • Metabolism is composed of many coupled interconnecting reactions

9. Metabolism

10. Metabolism • Classes of metabolic pathways: • Catabolic pathways • Those that convert energy into biologically useful forms • Anabolic pathways • Those that require an input of energy

11. Metabolism • Basic concepts of metabolism include: • Thermodynamically unfavorable reactions can be driven by favorable reactions. • ATP is the universal currency of free energy. • ATP hydrolysis drives metabolism by shifting the equilibrium constant of coupled reactions. • There is a structural basis for the high phosphoryl transfer potential of ATP. • The phosphoryl transfer potential is an important form of cellular energy transformation.

12. Thermodynamics • Thermodynamically unfavorable reactions can be driven by favorable reactions. • Free energy change for a reactions:

13. Thermodyamics • Coupling unfavorable reactions with favorable ones

14. ATP • ATP is the universal currency of free energy

15. ATP • Hydrolysis of ATP:

16. ATP Hydrolysis • ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions

17. ATP Hydrolysis • Problem: • Under standard conditions, the free energy for the hydrolysis of L-glycerol phosphate to form glycerol and inorganic phosphate is -2.2 kcal/mol. Calculate the factor by which the equilibrium ratio for the concentration of L-glycerol phosphate to glycerol is increased when ATP is used as the phosphoryl donor for the formation L-glycerol phosphate in place of inorganic phosphate. Do this calculation for liver where the concentrations for ATP, ADP and Pi are 3.5 mM, 1.8 mM and 5.0 mM, respectively.

18. ATP Hydrolysis • Phosphoryl transfer is a common means of energy coupling • Molecular motors • Muscle contraction • Ion pumps

19. Phosphoryl Transfer • Structural basis for high transfer potential • Compare:

20. Phosphoryl Transfer • Phosphate ester vs Phosphate anhydride

21. Phosphoryl Transfer • Stabilization of orthophosphate • resonance stabilization • electrostatic repulsion • hydration

22. Stabilization of Orthophosphate • Resonance stabilization Orthophosphate Pyrophosphate

23. Phosphoryl Transfer and Energy Transfer • There are other molelcules with favorable phosphoryl transferase energies

24. Phosphoryl Transfer • In terms of energy for phosphoryl transfer, ATP is intermediate:

25. Phosphoryl Transfer • Question: • What information do the ∆Go’ data given in Table 14.1 provide about the relative rates of hydrolysis of pyrophospate and acetyl phosphate?

26. Phosphoryl Transfer • Creatine phosphate is used to generate ATP in the short term:

27. Cellular Energy • The oxidation of Carbon fuels is an important source of cellular energy

28. Cellular Energy • The oxidation of Carbon fuels is an important source of cellular energy

29. Cellular Energy • High phosphoryl transfer potential compounds can couple carbon oxidation to ATP synthesis. • Ion gradients across membranes provide an important form of cellular energy • The extraction of energy from foodstuffs occurs in stages.

30. Coupling oxidation to ATP synthesis • High phosphoryl transfer potential compounds can couple carbon oxidation to ATP synthesis. • Example from glycolysis:

31. Coupling oxidation to ATP synthesis • In the next step ATP is harvested from the high energy phosphate intermediate.

32. Ion Gradients • Ion gradients across membranes provide an important form of cellular energy

33. Cellular Energy • Ion gradients across membranes can be used to synthesize ATP

34. Cellular Energy • Extraction of energy from foodstuffs is carried out in stages:

35. Recurring Motifs in Metabolism • Activated carriers exemplify the modular design and economy of metabolism. • Key reactions are reiterated throughout metabolism. • Metabolic processes are regulated in three principle way.

36. Activated Carriers • ATP is an activated carrier of phosphate groups • Other examples include: • Activated carriers of electrons in oxidation reactions • Activated carriers of electrons in reductive biosynthesis • Activated carriers of two-carbon fragments

37. Activated carriers of electrons in catabolism • NAD+ • (Nicotinamide • Adenine • Dinucleotide)

38. Activated carriers of electrons in catabolism • FAD • (Flavin • Adenine • Dinucleotide)

39. Activated carriers of electrons in catabolism • Reduction of isoalloxazine ring of FAD

40. Activated carriers of electrons in biosynthesis • NADPH • (Nicotinamide • Adenine • Dinucleotide • Phosphate)

41. Activated carriers of acyl groups • Coenzyme A is a carrier of Acyl groups

42. Activated Carriers • Other common activated carriers:

43. Key Reactions • There are six basic reactions in metabolism:

44. Key Reactions • Metabolic motifs

45. Metabolic Regulation • Metabolic processes are regulated in different ways: • Enzyme levels • Enzyme activity • Accessiblity of substrates to the enzyme

46. Metabolic Regulation • Degradative and biosynthesis pathways are usually distinct • Compartmentalization • Allosteric control

47. Metabolic Regulation • The energy charge

48. Evolution of Metabolic Pathways • The structures of ATP, CoEnzyme A NADH and FADH2 belie their “RNA world” origin.

49. Problems • The pK of an acid is measure of its proton-group-transfer potential • Derive a relation between ΔGo’ and pK. • What is the ΔGo’ for the ionization of acetic acid, which has a pK of 4.8?

50. Problems • Calculate ΔGo’ for the isomerization of glucose 6-phosphate to glucose 1-phosphate. What is the equilibrium ration of glucose 6-phosphate to glucose 1-phosphate at 25°C?