1. Chapter 27 & 28 Metabolic pathway & Energy production Chemistry B11

2. Metabolism Chemical reactions in cells that break down or build molecules. It produces energy and provide substances to cell growth. Catabolic reactions: Anabolic reactions: Complex molecules  Simple molecules + Energy Simple molecules + Energy (in cell)  Complex molecules

3. Metabolism in cell Carbohydrates Polysaccharides Proteins Lipids Glucose Fructose Galactose Amino acids Glycerol Fatty acids Stage 1: Digestion and hydrolysis GlucosePyruvateAcetyl CoA Citric Acid cycle CO 2 & H 2 O Urea NH 4 + Stage 2: Degradation and some oxidation Stage 3: Oxidation to CO 2, H 2 O and energy e e Mitochondria (Formation of Acetyl CoA)

4. Cell Structure Membrane Nucleus Cytoplasm (Cytosol) Mitochondria

5. Nucleus: consists the genes that control DNA replication and protein synthesis of the cell. Cytoplasm: consists all the materials between nucleus and cell membrane. Cytosol: fluid part of the cytoplasm (electrolytes and enzymes). Mitochondria: energy producing factories. Cell Structure Enzymes in matrix catalyze the oxidation of carbohydrates, fats, and amino acids. Produce CO 2, H 2 O, and energy.

6. ATP and Energy - Adenosine triphosphate (ATP) is produced from the oxidation of food. - Has a high energy. - Can be hydrolyzed and produce energy. Ribose 3 Phosphates

7. ATP and Energy PiPi (adenosine triphosphate) (adenosine diphosphate)(inorganic phosphate) - We use this energy for muscle contraction, synthesis an enzyme, send nerve signal, and transport of substances across the cell membrane. - 1-2 million ATP molecules may be hydrolysis in one second (1 gram in our cells). - When we eat food, catabolic reactions provide energy to recreate ATP. ADP + P i + 7.3 kcal/mol  ATP

8. Stage 1: Digestion CarbohydratesLipids (fat)Proteins Convert large molecules to smaller ones that can be absorbed by the body.

9. Digestion: Carbohydrates + + Polysaccharides Dextrins MaltoseGlucose Mouth Salivary amylase Stomach pH = 2 (acidic) Maltose + Maltase Glucose Lactose + Lactase GalactoseGlucose Sucrose + Sucrase FructoseGlucose Small intestine pH = 8 Dextrins Bloodstream Liver (convert all to glucose) α- amylase (pancreas)

10. Digestion: Lipids (fat) Intestinal wall Monoacylglycerols + 2 Fatty acids → Triacylglycerols Small intestine Bloodstream Glycerol + 3 Fatty acids H2CH2C HC H2CH2C Fatty acid + 2H 2 O H2CH2C HC H2CH2C OH Fatty acid OH + 2 Fatty acids lipase (pancreas ) TriacylglycerolMonoacylglycerol Protein Lipoproteins Chylomicrons Lymphatic system Cells Enzymes hydrolyzes liver Glucose

11. Digestion: Proteins Intestinal wall Small intestine Bloodstream Cells Stomach Pepsinogen Pepsin Proteins Polypeptides HCl Polypeptides Amino acids Trypsin Chymotrypsin denaturation + hydrolysis hydrolysis

12. Some important coenzymes 2 H atoms 2H + + 2e - oxidation Coenzyme + Substrate Coenzyme(+2H) + Substrate(-2H) Reduced Oxidized NAD + FAD Coenzyme A Coenzymes

13. NAD + Nicotinamide adenine dinucleotide ADP (vitamin) Ribose (Vitamin B 3 )

14. - Is an oxidizing agent. - Participates in reactions that produce (C=O) such as oxidation of alcohols to aldehydes and ketones. NAD + CH 3 -CH 2 -OH + NAD + CH 3 -C-H + NADH + H + NAD + + 2H + + 2e -  NADH + H + + O

15. FAD Flavin adenine dinucleotide ADP (Vitamin B 2 ) (sugar alcohol)

16. FAD - Is an oxidizing agent. - Participates in reaction that produce (C=C) such as dehydrogenation of alkanes. R-C-C-R + FAD R-C=C-H + FADH 2 H H HH HH

17. Coenzyme A (CoA) Aminoethanethiol ( vitamin B 5 ) Coenzyme A

18. Coenzyme A (CoA) CH 3 -C- + HS-CoA CH 3 -C-S-CoA O O Acetyl group Coenzyme AAcetyl CoA - It activates acyl groups (RC-), particularly the Acetyl group (CH 3 C-). O O

19. Metabolism in cell Carbohydrates Polysaccharides Proteins Lipids Glucose Fructose Galactose Amino acids Glycerol Fatty acids Stage 1: Digestion and hydrolysis GlucosePyruvateAcetyl CoA Citric Acid cycle CO 2 & H 2 O Urea NH 4 + Stage 2: Degradation and some oxidation Stage 3: Oxidation to CO 2, H 2 O and energy e e Mitochondria (Formation of Acetyl CoA)

20. - We obtain most of our energy from glucose. - Glucose is produced when we digest the carbohydrates in our food. - We do not need oxygen in glycolysis (anaerobic process). C 6 H 12 O 6 + 2 NAD + 2CH 3 -C-COO - + 2 NADH + 4H + O PyruvateGlucose 2 ADP + 2Pi 2 ATP Inside of cell (Cytoplasm) Glycolysis: Oxidation of glucose Stage 2: Formation of Acetyl CoA

21. Pathways for pyruvate Aerobic conditions: if we have enough oxygen. Anaerobic conditions: if we do not have enough oxygen. - Pyruvate can produce more energy.

22. Aerobic conditions - Pyruvate is oxidized and a C atom remove (CO 2 ). - Acetyl is attached to coenzyme A (CoA). - Coenzyme NAD + is required for oxidation. CH 3 -C-C-O - + HS-CoA + NAD + CH 3 -C-S-CoA + CO 2 + NADH O O pyruvate Coenzyme A Acetyl CoA O Important intermediate product in metabolism.

23. Anaerobic conditions - When we exercise, the O 2 stored in our muscle cells is used. - Pyruvate is reduced to lactate. - Accumulation of lactate causes the muscles to tire and sore. - Then we breathe rapidly to repay the O 2. - Most lactate is transported to liver to convert back into pyruvate. CH 3 -C-C-O - O O pyruvate Lactate O HO H Reduced NADH + H + NAD +

24. Glycogen - If we get excess glucose (from our diet), glucose convert to glycogen. - It is stored in muscle and liver. - We can use it later to convert into glucose and then energy. - When glycogen stores are full, glucose is converted to triacylglycerols and stored as body fat.

25. Metabolism in cell Carbohydrates Polysaccharides Proteins Lipids Glucose Fructose Galactose Amino acids Glycerol Fatty acids Stage 1: Digestion and hydrolysis GlucosePyruvateAcetyl CoA Citric Acid cycle CO 2 & H 2 O Urea NH 4 + Stage 2: Degradation and some oxidation Stage 3: Oxidation to CO 2, H 2 O and energy e e Mitochondria (Formation of Acetyl CoA)

26. Step 3: Citric Acid Cycle - Is a central pathway in metabolism. - Uses acetyl CoA from the degradation of carbohydrates, lipids, and proteins. - Two CO 2 are given off. - There are four oxidation steps in the cycle provide H + and electrons to reduce FAD and NAD + (FADH 2 and NADH). 8 reactions

27. Reaction 1 Formation of Citrate CH 3 -C-S-CoA O Acetyl CoA COO - C=O CH 2 COO - Oxaloacetate COO - CH 2 COO - C HO COO - Citrate + CoA-SH Coenzyme A + H2OH2O

28. Reaction 2 Isomerisation to Isocitrate COO - CH 2 COO - C HO COO - Citrate Isocitrate COO - CH 2 C COO - C H HO H Isomerisation - Because the tertiary –OH cannot be oxidized. (convert to secondary –OH)

29. Reaction 3 First oxidative decarboxylation (CO 2 ) Isocitrate COO - CH 2 C COO - C H HO H - Oxidation (-OH converts to C=O). - NAD + is reduced to NADH. - A carboxylate group (-COO - ) is removed (CO 2 ). COO - CH 2 C COO - C H O α- Ketoglutrate COO - CH 2 C COO - CH 2 O CO 2

30. Reaction 4 Second oxidative decarboxylation (CO 2 ) α- Ketoglutrate COO - CH 2 C COO - CH 2 O Succinyl CoA COO - CH 2 C S-CoA CH 2 O + CO 2 - Coenzyme A convert to succinyl CoA. - NAD + is reduced to NADH. - A second carboxylate group (-COO - ) is removed (CO 2 ).

31. Reaction 5 Hydrolysis of Succinyl CoA Succinyl CoA COO - CH 2 C S-CoA CH 2 O - Energy from hydrolysis of succinyl CoA is used to add a phosphate group (P i ) to GDP (guanosine diphosphate). - The hydrolysis of GTP is used to add a P i to ADP to produce ATP. + H 2 O + GDP + P i COO - CH 2 COO - Succinate + GTP + CoA-SH GTP + ADP → GDP+ ATP

32. Reaction 6 Dehydrogenation of Succinate - H is removed from two carbon atoms. - Double bond is produced. - FAD is reduced to FADH 2. COO - CH 2 COO - Succinate COO - CH COO - Fumarate

33. Reaction 7 Hydration - Water adds to double bond of fumarate to produce malate. COO - C CH 2 COO - HO H Malate H2OH2O COO - CH COO - Fumarate

34. Reaction 8 Dehydrogenation forms oxaloacetate - -OH group in malate is oxidized to oxaloacetate. - Coenzyme NAD + is reduced to NADH + H +. COO - C CH 2 COO - HO H Malate COO - C=O CH 2 COO - Oxaloacetate + H +

35. Summary The catabolism of proteins, carbohydrates, and fatty acids all feed into the citric acid cycle at one or more points: Citric Acid Cycle

36. Summary

38. The main function of the citric acid cycle is to produce reduced coenzymes (NADH and FADH 2 ). Summary These molecules enter the electron transport chain (Stage 4) and ultimately produce ATP. Feedback Mechanism The rate of the citric acid cycle depends on the body’s need for energy. When energy demands are high and ATP is low → the cycle is activated. When energy demands are low and NADH is high → the cycle is inhibited.

39. Stage 4: Electron Transport & Oxidative Phosphorylation -Most of energy generated during this stage. -It is an aerobic respiration (O 2 is required). 1. Electron Transport Chain (Respiratory Chain) 2. Oxidative Phosphorylation

40. Electron Transport H + and electrons from NADH and FADH 2 are carried by an electron carrier until they combine with oxygen to form H 2 O. FMN (Flavin Mononucleotide) Fe-S clusters Coenzyme Q (CoQ) Cytochrome (cyt) Electron carriers

41. FMN (Flavin Mononucleotide) (Vitamin B 2 ) (sugar alcohol) - 2H + + 2e - - H H FMN + 2H + + 2e - → FMNH 2 Reduced

42. Fe-S Clusters Fe 3+ S S S S Cys Fe 2+ S S S S Cys + 1 e - Fe 3+ + 1e - Fe 2+ Reduced

43. Coenzyme Q (CoQ) OHOH OHOH 2H + + 2e - Reduced Coenzyme Q (QH 2 ) Coenzyme Q Q + 2H + + 2e - → QH 2 Reduced

44. Cytochromes (cyt) - They contain an iron ion (Fe 3+ ) in a heme group. - They accept an electron and reduce to (Fe 2+ ). - They pass the electron to the next cytochrome and they are oxidized back to Fe 3+. Fe 3+ + 1e - Fe 2+ Reduced Oxidized cyt b, cyt c 1, cyt c, cyt a, cyt a 3

45. Electron Transfer Mitochondria

46. Electron Transfer Complex I NADH + H + + FMN → NAD + + FMNH 2 FMNH 2 + Q → QH 2 + FMN NADH + H + + Q → QH 2 + NAD + Complex II FADH 2 + Q → FAD + QH 2

47. Electron Transfer Complex III QH 2 + 2 cyt b (Fe 3+ ) → Q + 2 cyt b (Fe 2+ ) + 2H + Complex IV 4H + + 4e - + O 2 → 2H 2 O Aerobic From the electron transport chain From inhaled air From reduced coenzymes or the matrix

48. Oxidative Phosphorylation Transport of electrons produce energy to convert ADP to ATP. ADP + P i + energy → ATP + H 2 O

49. Chemiosmotic model - H + make inner mitochondria acidic. - Produces different proton gradient. - H + pass through ATP synthase (a protein complex). ATP synthase

50. Total ATP Glycolysis: 7 ATP Oxidation of Pyruvate:5 ATP Citric acid cycle:20 ATP 32 ATPOxidation of glucose C 6 H 12 O 6 + 6O 2 + 32 ADP + 32 P i → 6CO 2 + 6H 2 O + 32 ATP

51. Metabolism in cell Carbohydrates Polysaccharides Proteins Lipids Glucose Fructose Galactose Amino acids Glycerol Fatty acids Step 1: Digestion and hydrolysis GlucosePyruvateAcetyl CoA Citric Acid cycle CO 2 & H 2 O Urea NH 4 + Step 2: Degradation and some oxidation Step 3: Oxidation to CO 2, H 2 O and energy e e Mitochondria

52. Oxidation of fatty acids CH 3 -(CH 2 ) 14 -CH 2 -CH 2 -C-OH O  α  oxidation - Oxidation happens in step 2 and 3. - Each beta oxidation produces acetyl CoA and a shorter fatty acid. - Oxidation continues until fatty acid is completely break down to acytel CoA.

53. Oxidation of fatty acids Fatty acid activation - Before oxidation, they activate in cytosol. R-CH 2 -C-OH O + ATP + HS-CoA R-CH 2 -C-S-CoA O + H 2 O + AMP + 2P i Fatty acyl CoAFatty acid  -Oxidation: 4 reactions

54. Reaction 1: Oxidation (dehydrogenation) R-CH 2 -C-C-C-S-CoA O Fatty acyl CoA HH H H + FAD R-CH 2 -C=C-C-S-CoA + FADH 2 O H H Reaction 2: Hydration R-CH 2 -C=C-C-S-CoA + H 2 O O HH R-CH 2 -C-C-C-S-CoA O H H H HO

55. Reaction 3: Oxidation (dehydrogenation) Reaction 4: Cleavage of Acetyl CoA R-CH 2 -C-C-C-S-CoA + NAD + O H H H HOHO R-CH 2 -C-CH 2 -C-S-CoA + NADH+ H + OO R-CH 2 -C-CH 2 -C-S-CoA + CoA-SH OO R-CH 2 -C-S-CoA O CH 3 -C-S-CoA O + Acetyl CoAFatty acyl CoA

56. Oxidation of fatty acids One cycle of  -oxidation R-CH 2 -CH 2 -C-S-CoA + NAD + + FAD + H 2 O + CoA-SH O R-C-S-CoA O CH 3 -C-S-CoA + NADH + H + + FADH 2 O + Acetyl CoAFatty acyl CoA # of Acetyl CoA = # of fatty acid carbon 2 = 1 +  oxidation cycles

57. Ketone bodies - If carbohydrates are not available to produce energy. - Body breaks down body fat to fatty acids and then Acetyl CoA. - Acetyl CoA combine together to produce ketone bodies. - They are produced in liver. - They are transported to cells (heart, brain, or muscle). CH 3 -C-S-CoA O Acetyl CoA CH 3 -C-S-CoA O CH 3 -C-CH 2 -C-O - O O CH 3 -C-CH 3 + CO 2 + energy O Acetoacetate Acetone  -Hydroxybutyrate CH 3 -CH-CH 2 -C-O - OH O

58. Ketosis (disease) - When ketone bodies accumulate and they cannot be metabolized. - Found in diabetes and in high diet in fat and low in carbohydrates. - They can lower the blood pH (acidosis). - Blood cannot carry oxygen and cause breathing difficulties.

59. Fatty acid synthesis - When glycogen store is full (no more energy need). - Excess acetyl CoA convert to 16-C fatty acid (palmitic acid) in cytosol. - New fatty acids are attached to glycerol to make triacylglycerols. (are stored as body fat)

60. Metabolism in cell Carbohydrates Polysaccharides Proteins Lipids Glucose Fructose Galactose Amino acids Glycerol Fatty acids Stage 1: Digestion and hydrolysis GlucosePyruvateAcetyl CoA Citric Acid cycle CO 2 & H 2 O Urea NH 4 + Stage 2: Degradation and some oxidation Stage 3: Oxidation to CO 2, H 2 O and energy e e Mitochondria (Formation of Acetyl CoA)

61. Degradation of amino acids - They are degraded in liver. Transamination: - They react with α- keto acids and produce a new amino acid and a new α- keto acid. - OOC-C-CH 2 -CH 2 -COO - O alanine CH 3 -CH-COO - NH 3 + + α- ketoglutarate - OOC-CH-CH 2 -CH 2 -COO - O pyruvate CH 3 -C-COO - NH 3 + + glutamate

62. Degradation of amino acids Oxidative Deamination - OOC-CH-CH 2 -CH 2 -COO - NH 3 + glutamate + H 2 O + NAD + - OOC-C-CH 2 -CH 2 -COO - O α- ketoglutarate glutamate dehydrogenase + NH 4 + + NADH + H +

63. Urea cycle - Ammonium ion (NH 4 + ) is highly toxic. - Combines with CO 2 to produce urea (excreted in urine). - If urea is not properly excreted, BUN (Blood Urea Nitrogen) level in blood becomes high and it build up a toxic level (renal disease). - Protein intake must be reduced and hemodialysis may be needed. H 2 N-C-NH 2 + 2H + + H 2 O O urea 2NH 4 + + CO 2

64. Energy from amino acids - C from transamination are used as intermediates of the citric acid cycle. - amino acid with 3C: pyruvate - amino acid with 4C: oxaloacetate - amino acid with 5C: α- ketoglutarate - 10% of our energy comes from amino acids. - But, if carbohydrates and fat stores are finished, we take energy from them.