All metabolism may be thought of as the coupling of energy production and energy use.

1. CZ5211 Topics in Computational BiologyLecture 7: Biological Pathways II: Metabolic PathwaysProf. Chen Yu ZongTel: 6874-6877Email: yzchen@cz3.nus.edu.sghttp://xin.cz3.nus.edu.sgRoom 07-24, level 7, SOC1, NUS

2. Some key concepts about metabolism All metabolism may be thought of as the coupling of energy production and energy use.

3. Some key concepts about metabolism Certain biochemical reactions occur spontaneously Net release of energy Other must be “forced” to occur coupling

4. Energy and Chemical Reactions Figure 4-5: Energy transfer and storage in biological reactions

5. Enzymes speed biochemical reactions • Lower activation E • Specificity • Activation • Cofactors • Modulators • Acidity • Temperature • Competitive inhibitors • Allosteric • Concentrations

6. Enzymes speed biochemical reactions

7. Law of Mass Action • Defined: • Equlibrium • Reversible

8. Types of Enzymatic Reactions • Oxidation–reduction • Hydrolysis–dehydration • Addition–subtraction exchange • Ligation

9. Cell Metabolism • Pathways • Intermediates • Catabolic - energy • Anabolic - synthesis

10. Metabolic Pathways • Catabolic Pathways: • Those that convert energy into biologically useful forms are called catabolic pathways • Fuels (carbs & fats)  CO2 + H2O + useful energy: catabolism • Examples: degradation, pathways by which nutrients and cellular components are broken down for reuse or to generate energy

11. Metabolic Pathways • Anabolic Pathways: • Those that require inputs of energy to proceed are called, anabolic pathways • Useful energy + small molecules  complex molecules: anabolism • Biosynthesis, building up of biomolecules from simpler components • Pathways that can be either anabolic or catabolic are referred to as amphibolic pathways

12. Coupling favorable & unfavorable reactions A pathway must satisfy minimally two criteria: Reaction must be specific, yielding only one particular product or set of products. Enzymes provide specificity Whole set of reactions in a pathway must be thermodynamically favored. A reaction can occur spontaneously only if G, the change in free energy, is negative 3. An important thermodynamic fact: the overall free energy change for a chemically coupled series of reactions is equal to the sum of the free-energy changes of the individual steps A  B + C G0’ = + 5 kcal mol-1 B  D G0’ = - 8 kcal mol-1 ******************************************* A  C + D G0’ = - 3 kcal mol-1

13. Control of Metabolic Pathways • Feedback inhibition • Enzyme modulators • No enzyme • Enzyme isolation • Energy availability - ATP

14. ATP is the Universal Currency of Free Energy Metabolism is facilitated by the use of a common energy currency Part of the free energy derived from the oxidation of foodstuffs and from light is transformed into ATP - the energy currency A large amount of free energy is liberated when ATP is hydrolyzed to ADP & Pi, or ATP to AMP & PPi ATP + H2O  ADP + Pi G0’ = -7.3 kcal mol-1 ATP + H2O  AMP + PPi G0’ = -10.9 kcal mol-1 Under typical cellular conditions, the actual G for these hydrolyses is approximately -12 kcal mol-1 ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions: by a factor of approximately 108

15. Structures of ATP, ADP,& AMP

16. Structures of ATP, ADP,& AMP

17. Coupled Reactions Involving ATP

18. Coupled Reactions Involving ATP

19. Coupled Reactions Involving ATP

20. ATP Production • Glycolysis • Phosphorylation • Pyruvate • Anaerobic respiration • Lactate production • 2 ATPs produced

21. Pyruvate Metabolism • Aerobic respiration • In mitochondria • Acetyl CoA and CO2 • Citric Acid Cycle • Energy Produced • 1 ATP • 3 NADH • 1 FADH • Waste–2 CO2s

22. Pyruvate Metabolism

23. Electron Transport • High energy electrons • Energy transfer • ATP synthesized from ADP • H2O is a byproduct

24. Electron Transport

25. Biomolecules Catabolized to make ATP • Complex Carbohydrates • Glycogen catabolism • Liver storage • Muscle storage • Glucose produced

26. Protein Catabolism • Deamination • Conversion • Glucose • Acetyl CoA

27. Lipid Catabolism • Higher energy content • Triglycerides to glycerol • Glycerol • Fatty acids • Ketone bodies - liver

28. Lipid Catabolism

29. Stages of Catabolism from Foodstuffs Extraction of energy from foodstuffs can be divided into three stages

30. Synthetic (Anabolic) pathways • Glycogen synthesis • Liver storage • Glucose to glycogen • Gluconeogenesis • Amino acids • Glycerol • Lactate

31. Lipogenesis • Acetyl Co A • Glycerol • Fatty acids • Triglycerides

32. Protein Synthesis • 20 Amino acids • DNA code sequence • mRNA transcription processing • Translation by ribosomes • Chain (polymer) of amino acids

33. Embden-Meyerhof Pathway (EM, glycolysis) Major pathway for the conversion of hexose sugars into pyruvate. • It results in the formation of: • two NADH • two ATP

34. (from Glyceraldehide-3-P to Pyruvate) Gain of 4 ATP

36. The Embden-Meyerhof Pathway (EM, glycolysis) It results in the formation of six of the critical biosynthetic intermediates Which ones? (look at the table provided)

37. * * * (from Glyceraldehide-3-P to Pyruvate) Gain of 4 ATP *

38. * *

39. The Hexose Monophosphate (HM) Pathway (also known as oxidative pentose, OM, or pentose phosphate pathway) It provides all the key intermediates not provided by the EM pathway.

41. The Entner-Doudoroff Pathway It may be considered an alternate hexose monophsphate pathway. • It provides a minimum of five of the critical biosynthetic intermediates: • glucose-6-P • triose phosphate • 3-phosphoglycerate • phosphoenol pyruvate (PEP) • pyruvate

42. The Entner-Doudoroff Pathway It begins the same as the HM pathway up to phosphogluconic acid. Then, instead of being converted to pentose and carbon dioxide, it is dehydrated yielding 2-keto-3, dehydro, 6 phosphogluconic acid. pyruvate Glyceraldehyde-3-P The top half of the molecule of glucose

43. pyruvate Glyceraldehyde-3-P The top half of the molecule of glucose The Entner-Doudoroff Pathway Both the EM and the ED pathway convert a glucose molecule to two molecules of pyruvate. In the EM pathway, pyruvate arises by the intermediate formation of glyceraldehyde-3-P. In the ED pathway, from the top half of the molecule of glucose.

45. Cyclic Metabolic Pathway

46. Multiple Metabolic Pathways

47. Multiple Metabolic Pathways

48. Multiple Metabolic Pathways

49. Post –Translational Protein Modification

50. Metabolic Engineering Cells developed optimal use of their resources for their survival. Metabolic pathways are networks, regulated to optimally distribute their fluxes for best use of resources Metabolic engineering is to overcome the cellular regulation to produce product of our interest; or to create a new product that the host cells normally don’t need to produce.