Metabolism :

1. Metabolism:

2. Key words • Metabolism – definition • Catabolism and anabolism – definition, example • Identify/distinguish structure of coenzymes • Identify structure of ATP

3. The study of the biochemical reactions in an organism, including the coordination, regulation and energy needs What is Metabolism? • Definition: Metabolism is the sum total of the chemical reactions of biomolecules in an organism • Metabolism consists of • catabolism: the breakdown of larger molecules into smaller ones; an oxidative process that releases energy • anabolism: the synthesis of larger molecules from smaller ones; a reductive process that requires energy • Catabolism: the oxidative breakdown of nutrients • Anabolism: the reductive synthesis of biomolecules

4. Terminology in Metabolism light • Eg. 6 CO2(g) + 6 H2O(l) → C6H12O6(aq) + 6 O2(g) • Anabolism • Metabolic pathway: A sequence of reactions, where the product of one reaction becomes the substrate for the next reaction. - either linear pathway or cyclic pathway - metabolic pathways proceed in many stages, allowing for efficient use of energy • Metabolites: intermediates in metabolic pathway photosynthesis C6H12O6 (aq) + 6O2 (g) → 6CO2 (g) + 6H2O Catabolism respiration

5. Metabolic pathway

6. Metabolic pathway: linear or cyclic

7. A Comparison of Catabolism and Anabolism • Metabolism is the sum total of the chemical reactions of biomolecules in an organism

8. Metabolism • Metabolism involves the energy flow in the cell • Photoautotroph via photosynthesis transfers the energy to heterotrophs • Heterotrophs obtain the energy through oxidation/reduction of organic compounds (carbohydrate, lipid and proteins) •  Food supplies the energy • Energy = ATP

9. The Role of Oxidation and Reduction in Metabolism • Oxidation-Reduction (redox) reactions are those in which electrons are transferred from a donor to an acceptor • oxidation: the loss of electrons; the substance that loses the electrons is called a reducing agent • reduction: the gain of electrons; the substance that gains the electrons is called an oxidizing agent • Carbon in most reduced form- alkane • Carbon in most oxidized form- CO2 (final product of catabolism) ReducedOxidized

10. Oxidation and Reduction in Metabolism Reduction – gain e Oxidation – less e Oxidizing agent – eacceptor reducing agent – edonor

11. Metabolism: Features A group of noncovalently associated enzymes that catalyze 2 or more sequential steps in metabolic/biochemical pathway Metabolic pathway: • Enzymes – multienzymes • Coenzymes • ATP – produced or used Regulation of metabolic pathway: • Feedback inhibition or • Feed-forward activation

12. Metabolism: Regulation • Regulation of metabolic pathway: • Feedback inhibition = product (usually ultimate product) of a pathway controls the rate of synthesis through inhibition of an early step (usually the first step) A  B  C  D  E P • Feed-forward activation = metabolite produced early in pathway activates enzyme that catalyzes a reaction further down the pathway A  B  C  D  E P E1 E2 E3 E4 E5 — E1 E2 E3 E4 E5 +

13. Coenzymes Coenzymes in metabolism: • NAD+/NADH • NADP+/NADPH • FAD+/FADH2 • Coenzyme A (CoASH) – activation of metabolites Electron carriers

14. NAD+/NADH: An Important Coenzyme • Nicotinamide adenine dinucleotide (NAD+) is an important coenzyme • Acts as a biological oxidizing agent • The structure of NAD+/NADH is comprised of a nicotinamide portion. • It is a derivative of nicotinic acid • NAD+ is a two-electron oxidizing agent, and is reduced to NADH Reduced form, NADH carries 2 electrons

15. NADP+/NADPH: Also comprised of nicotinamide portion • Nicotinamide adenine dinucleotidephosphate (NADP+) – oxidizing agent • NADPH involves in reductive biosynthesis • Differ with NAD+ at ribose (C2 contain a phosphoryl group, PO32- • As electron carrier in photosythesis and pentose phosphate pathway Reduced form, NADPH carries 2 electrons Anabolism

16. The Structures Flavin Adenine Dinucleotide (FAD) • FAD is also a biological oxidizing agent • FAD – can accept one-electron or two-electron The terminal e acceptor (O2) can accept only unpaired e (e must be transferred to O2 one at a time) FADH carries 1 electron, FADH2 carries 2 electrons

17. FAD/FADH2 • FADH (semiquinone form) carries 1 electron, • FADH2 (fully reduced hydroquinone form) carries 2 electrons * 1 1 Formation of fully reduced hydroquinone form bypass the semiquinone form

18. Coenzyme A in Activation of Metabolic Pathways • A step frequently encountered in metabolism is activation • activation: the formation of a more reactive substance • A metabolite is bonded to some other molecule and the free-energy change for breaking the new bond is negative. • Causes next reaction to be exergonic

19. Coenzyme A (CoASH) • Coenzyme A – functions as a carrier of acetyl and other acyl groups • Has sulfhydryl/thiol group Thioester bond CoASH Acetyl-CoA: is a “high-energy” compound because of the presence of thioester bond – hydrolysis will release energy

20. ATP- high energy compound • ATP is essential high energy bond-containing compound • Phosphorylation of ADP to ATP requires energy • Hydrolysis of ATP to ADP releases energy nucleotide Phosphorylation: the addition of phosphoryl (PO32-) group/Pi (inorganic phosphate)

21. Metabolism: (2)

22. ATP- high energy compound • ATP is essential high energy bond-containing compound • Phosphorylation of ADP to ATP requires energy • Hydrolysis of ATP to ADP releases energy nucleotide Phosphorylation: the addition of phosphoryl (PO32-) group/Pi (inorganic phosphate)

23. The Phosphoric Anhydride Bonds in ATP are “High Energy” Bonds Phosphoanhydride / • “High Energy” bonds- bonds that require or release convenient amounts of energy, depending on the direction of the reaction • Couple reactions: the energy released by one reaction, such as ATP hydrolysis, provides energy for another reactions to completion – in metabolic pathway

24. Couple reaction: example

25. Role of ATP as Energy Currency Phosphorylation of ADP requires energy from breakdown of nutrients (catabolism) The energy from hydrolysis of ATP will be used in the formation of products (anabolism)

26. Metabolism of Carbohydrate Catabolism Anabolism

27. Major pathways of carbohydrate metabolism. Fig 8.1 3rd ed

28. Key words • Glycolysis, the fate for pyruvate • Substrate-level phosphorylation and oxidative phosphorylation

29. Glycolysis • Glycolysis is the first stage of glucose metabolism • Glycolysis converts 1 molecule of glucose to 2 units of pyruvate (three C units) and the process involves the synthesis of ATP and reduction of NAD+ (to NADH) • The pathway has 10 steps/reactions • Glycolysis are divided into 2 stages/phases, • Phase 1=1st 5 reactions • Phase 2=2nd 5 reactions Linear pathway

30. Glycolysis • Glycolysis are divided into 2 stages/phases, • Phase 1=1st 5 reactions • Energy investment – • A hexose sugar (glucose) is split into 2 molecules of three-C metabolite (glyceraldehyde-3-phosphate = GAP). The process consume 2 ATP • Phase 2=2nd 5 reactions • Energy recovery – • The two molecules of GAP are converted to 2 molecules of pyruvate with the generation of 4 ATP and 2 NADH. • Overall equation – Glucose + 2 NAD+ + 2 ADP + 2Pi  2 pyruvate + 2 NADH + 2 ATP + 2 H2O + 4H+ Glycolysis has a net “profit” of 2 ATP per glucose

31. The Reactions of Glycolysis glucokinase 1 Use ATP • Phosphorylationof glucose to give glucose-6-phosphate • Isomerization of glucose-6-phosphate to give fructose-6-phosphate • Phosphorylationof fructose-6-phosphate to yield fructose-1,6-bisphosphate • Cleavageof fructose-1,6,-bisphosphate to give glyceraldehyde-3-phosphate and dihydroxyacetone phosphate • Isomerization of dihydroxyacetone phosphate to give glyceraldehyde-3-phosphate – isomerase enzyme 2 Use ATP 3 phosphofructokinase 4 5

32. The Reactions of Glycolysis (Cont’d) Glyceraldehyde-3-P dehydrogenase oxidation 6 Electron acceptor – NAD+ • Oxidation of glyceraldehyde-3-phosphate to give 1,3-bisphosphoglycerate • Transfer of a phosphate groupfrom 1,3-bisphosphoglycerate to ADP to give 3-phosphoglycerate • Isomerizationof 3-phosphoglycerate to give 2-phosphoglycerate • Dehydration of 2-phosphoglycerate to give phosphoenolpyruvate • Transfer of a phosphate groupfrom phosphoenolpyruvate to ADP to give pyruvate transfer 7 Phosphorylation of ADP to ATP 8 isomerization dehydration 9 transfer 10 Phosphorylation of ADP to ATP

33. Glycolysis By kinase enzyme at step1, 3,7 and 10 • Dephosphorylation of ATP • Phosphorylation of ADP • Oxidation of intermediates and reduction of NAD+ to NADH by dehydrogenase reactions - step 6 - glyceraldehyde-3-phosphate dehydrogenase

34. ATP production • ATP is produced by phosphorylation of ADP - is through substrate-level phosphorylation • Substrate-level phosphorylation – the process of forming ATP by phosphoryl group transfer from reactive intermediates to ADP • 1,3-bisphosphoglycerate and phosphoenolpyruvate – “high-energy” intermediates/compounds • Oxidative phosphorylation – the process of forming ATP via the pH gradient as a result of the electron transport chain. Glycolysis - Step 7 and 10

35. Fates of Pyruvate From Glycolysis • Once pyruvate is formed, it has one of several fates • In aerobic metabolism-pyruvate will enter the citric acid cycle, end product in aerobic metabolism CO2 and H2O • In anaerobic metabolism- the pyruvate loses CO2 • produce ethanol = alcoholic fermentation • produce lactate = anaerobic glycolysis

36. Anaerobic Metabolism of Pyruvate • Under anaerobic conditions, the most important pathway for the regeneration of NAD+ is reduction of pyruvate to lactate • Lactate dehydrogenase (LDH) is a tetrameric isoenzyme consisting of H and M subunits; H4 predominates in heart muscle, and M4 in skeletal muscle In muscle, during vigorous exercise – demand of ATP  but O2 is in short supply  is largely synthesized via anaerobic glycolysis which rapidly generates ATP rather than through slower oxidative phosphorylation

37. Alcoholic Fermentation In anaerobic bacteria • Two reactions lead to the production of ethanol: • Decarboxylation of pyruvate to acetaldehyde • Reduction of acetaldehyde to ethanol • • Pyruvatedecarboxylase is the enzyme that catalyzes the first reaction • This enzyme require Mg2+ and the cofactor, thiamine pyrophosphate (TPP) • • Alcohol dehydrogenase catalyzes the conversion of acetaldehyde to ethanol

38. NAD+ Needs to be Recycled to Prevent Decrease in Oxidation Reactions

39. Structure of cell Cytoplasm/ Cytosol

41. Where does the Glycolysis Take Place? Cytosol Glycolysis is universal!

42. Citric Acid Cycle = Krebs Cycle, Tricarboxylic acid Cycle (TCA)

43. Metabolism: Features A group of noncovalently associated enzymes that catalyze 2 or more sequential steps in metabolic/biochemical pathway Metabolic pathway: • Enzymes – multienzymes • Coenzymes • ATP – produced or used

44. Couple reaction: example

45. Coenzymes Coenzymes in metabolism: • NAD+/NADH • NADP+/NADPH • FAD+/FADH2 • Coenzyme A (CoASH) – activation of metabolites Electron carriers

46. Glycolysis • Glycolysis are divided into 2 stages/phases, • Phase 1=1st 5 reactions • Energy investment – • A hexose sugar (glucose) is split into 2 molecules of three-C metabolite (glyceraldehyde-3-phosphate = GAP). The process consume 2 ATP • Phase 2=2nd 5 reactions • Energy recovery – • The two molecules of GAP are converted to 2 molecules of pyruvate with the generation of 4 ATP and 2 NADH. • Overall equation – Glucose + 2 NAD+ + 2 ADP + 2Pi  2 pyruvate + 2 NADH + 2 ATP+ 2 H2O + 4H+ Glycolysis has a net “profit” of 2 ATP per glucose

47. Fates of Pyruvate From Glycolysis • Once pyruvate is formed, it has one of several fates • In aerobic metabolism-pyruvate will enter the citric acid cycle, end product in aerobic metabolism CO2 and H2O • In anaerobic metabolism- the pyruvate loses CO2 • produce ethanol = alcoholic fermentation • produce lactate = anaerobic glycolysis Glycolysis – in cytoplasm

48. Key words • Definition – citric acid cycle • Explain the citric acid cycle • Distinguish between glycolysis and citric acid cycle • Understand -oxidation – catabolism of lipid

49. Citric acid cycle • Requires aerobic condition • Amphibolic (both catabolic & anabolic) • Serves 2 purposes: • Oxidize Acetyl-CoA to CO2 to produce energy (ATP & reducing power of NADH & FADH2)-involved in the aerobic catabolism of carbohydrates, lipids and amino acids • Supply precursors for biosynthesis of carbohydrates, lipids, amino acids, nucleotides and porphyrins

50. Citric Acid Cycle = Krebs Cycle = Tricarboxylic acid Cycle (TCA)