Metabolic pathway & Energy production Chemistry 20 Chapter 19 & 20 Metabolic pathway & Energy production

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

Metabolism in cell Mitochondria e e Urea NH4+ CO2 & H2O Step 3: Proteins Amino acids e Citric Acid cycle Glucose Fructose Galactose Carbohydrates Polysaccharides Glucose Pyruvate Acetyl CoA e CO2 & H2O Glycerol Lipids Fatty acids Step 3: Oxidation to CO2, H2O and energy Step 1: Digestion and hydrolysis Step 2: Degradation and some oxidation

Cell Structure Nucleus Membrane Mitochondria Cytoplasm (Cytosol)

Enzymes in matrix catalyze the oxidation of carbohydrates, fats , Cell Structure 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. Enzymes in matrix catalyze the oxidation of carbohydrates, fats , and amino acids. Produce CO2, H2O, and energy.

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

ATP and Energy Pi ADP + Pi + 7.3 kcal/mol  ATP (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 + Pi + 7.3 kcal/mol  ATP

Step 1: Digestion Convert large molecules to smaller ones that can be absorbed by the body. Carbohydrates Lipids (fat) Proteins

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

Digestion: Lipids (fat) H2C Fatty acid lipase (pancreas) H2C OH Small intestine HC Fatty acid + 2H2O HC Fatty acid + 2 Fatty acids H2C Fatty acid H2C OH Triacylglycerol Monoacylglycerol Intestinal wall Monoacylglycerols + 2 Fatty acids → Triacylglycerols Protein Lipoproteins Chylomicrons Lymphatic system Bloodstream Enzymes hydrolyzes Glycerol + 3 Fatty acids Cells liver Glucose

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

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

NAD+ Nicotinamide adenine dinucleotide ADP (vitamin) Ribose

NAD+ Is a oxidizing agent. Participates in reactions that produce (C=O) such as oxidation of alcohols to aldehydes and ketones. O CH3-CH2-OH + NAD+ CH3-C-H + NADH + H+ NAD+ + 2H+ + 2e-  NADH + H+ +

FAD Flavin adenine dinucleotide (Vitamin B2) (sugar alcohol) ADP

FAD Is a oxidizing agent. Participates in reaction that produce (C=C) such as dehydrogenation of alkanes. R-C-C-R + FAD R-C=C-H + FADH2 H

Coenzyme A (CoA) HS-CoA Coenzyme A Aminoethanethiol ( vitamin B5)

- It activates acyl groups, particularly the acetyl group. Coenzyme A (CoA) - It activates acyl groups, particularly the acetyl group. O O CH3-C- + HS-CoA CH3-C-S-CoA Acetyl group Coenzyme A Acetyl CoA

Metabolism in cell Mitochondria e e Urea NH4+ CO2 & H2O Step 3: Proteins Amino acids e Citric Acid cycle Glucose Fructose Galactose Carbohydrates Polysaccharides Glucose Pyruvate Acetyl CoA e CO2 & H2O Glycerol Lipids Fatty acids Step 3: Oxidation to CO2, H2O and energy Step 1: Digestion and hydrolysis Step 2: Degradation and some oxidation

Step 2: Glycolysis 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). 2 ADP + 2Pi 2 ATP O C6H12O6 + 2 NAD+ 2CH3-C-COO- + 2 NADH + 4H+ Glucose Pyruvate Inside of cell

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

Important intermediate product Aerobic conditions Pyruvate is oxidized and a C atom remove (CO2). Acetyl is attached to coenzyme A (CoA). Coenzyme NAD+ is required for oxidation. O O O CH3-C-C-O- + HS-CoA + NAD+ CH3-C-S-CoA + CO2 + NADH pyruvate Coenzyme A Acetyl CoA Important intermediate product in metabolism.

Anaerobic conditions When we exercise, the O2 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 O2. Most lactate is transported to liver to convert back into pyruvate. CH3-C-C-O- O pyruvate Lactate HO H Reduced NADH + H+ NAD+

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.

Metabolism in cell Mitochondria e e Urea NH4+ CO2 & H2O Step 3: Proteins Amino acids e Citric Acid cycle Glucose Fructose Galactose Carbohydrates Polysaccharides Glucose Pyruvate Acetyl CoA e CO2 & H2O Glycerol Lipids Fatty acids Step 3: Oxidation to CO2, H2O and energy Step 1: Digestion and hydrolysis Step 2: Degradation and some oxidation

Step 3: Citric Acid Cycle Is a central pathway in metabolism. Uses acetyl CoA from the degradation of carbohydrates, lipids, and proteins. Two CO2 are given off. There are four oxidation steps in the cycle provide H+ and electrons to reduce FAD and NAD+ (FADH2 and NADH). 8 reactions

Reaction 1 Formation of Citrate O CH3-C-S-CoA + COO- CH2 COO- HO C Acetyl CoA CH3-C-S-CoA + COO- CH2 COO- H2O HO C COO- + CoA-SH C=O Oxaloacetate CH2 CH2 COO- COO- Citrate Coenzyme A

Isomerisation to Isocitrate Reaction 2 Isomerisation to Isocitrate Because the tertiary –OH cannot be oxidized. (convert to secondary –OH) COO- COO- CH2 CH2 Isomerisation HO C COO- H C COO- CH2 HO C H COO- COO- Citrate Isocitrate

First oxidative decarboxylation (CO2) Reaction 3 First oxidative decarboxylation (CO2) Oxidation (-OH converts to C=O). NAD+ is reduced to NADH. A carboxylate group (-COO-) is removed (CO2). COO- COO- COO- CH2 CH2 CH2 H C COO- H C COO- CH2 CO2 HO C H O C O C COO- COO- COO- Isocitrate α-Ketoglutrate

Second oxidative decarboxylation (CO2) Reaction 4 Second oxidative decarboxylation (CO2) Coenzyme A convert to succinyl CoA. NAD+ is reduced to NADH. A second carboxylate group (-COO-) is removed (CO2). COO- COO- CH2 CH2 CH2 CH2 O C O C + CO2 COO- S-CoA α-Ketoglutrate Succinyl CoA

Hydrolysis of Succinyl CoA Reaction 5 Hydrolysis of Succinyl CoA Energy from hydrolysis of succinyl CoA is used to add a phosphate group (Pi) to GDP (guanosine diphosphate). Phosphate group (Pi) add to ADP to produce ATP. COO- COO- CH2 CH2 ADP + Pi ATP + H2O + GDP + Pi + GTP + CoA-SH CH2 CH2 O C COO- S-CoA Succinate Succinyl CoA

Dehydrogenation of Succinate Reaction 6 Dehydrogenation of Succinate H is removed from two carbon atoms. Double bond is produced. FAD is reduced to FADH2. COO- COO- CH2 CH CH2 CH COO- COO- Succinate Fumarate

Reaction 7 Hydration Water adds to double bond of fumarate to produce malate. COO- COO- H2O CH HO C H CH CH2 COO- COO- Fumarate Malate

Dehydrogenation forms oxaloacetate Reaction 8 Dehydrogenation forms oxaloacetate -OH group in malate is oxidized to oxaloacetate. Coenzyme NAD+ is reduced to NADH + H+. COO- COO- + H+ HO C H C=O CH2 CH2 COO- COO- Malate Oxaloacetate

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

Summary 12 ATP produced from each acetyl-CoA

until they combine with oxygen to form H2O. Electron Transport H+ and electrons from NADH and FADH2 are carried by an electron carrier until they combine with oxygen to form H2O. FMN (Flavin Mononucleotide) Fe-S clusters Electron carriers Coenzyme Q (CoQ) Cytochrome (cyt)

FMN (Flavin Mononucleotide) H (Vitamin B2) (sugar alcohol) - 2H+ + 2e- H - FMN + 2H+ + 2e- → FMNH2 Reduced

Fe-S Clusters Fe3+ + 1e- Fe2+ Reduced S S S S Fe3+ Fe2+ S S S S Cys

Coenzyme Q (CoQ) Q + 2H+ + 2e- → QH2 Reduced Reduced Coenzyme Q (QH2) OH 2H+ + 2e- OH Coenzyme Q Reduced Coenzyme Q (QH2) Q + 2H+ + 2e- → QH2 Reduced

They contain an iron ion (Fe3+) in a heme group. Cytochromes (cyt) They contain an iron ion (Fe3+) in a heme group. They accept an electron and reduce to (Fe2+). They pass the electron to the next cytochrome and they are oxidized back to Fe3+. Fe3+ + 1e- Fe2+ Oxidized Reduced cyt b, cyt c1, cyt c, cyt a, cyt a3

Electron Transfer Mitochondria

Electron Transfer Complex I NADH + H+ + FMN → NAD+ + FMNH2 FMNH2 + Q → QH2 + FMN NADH + H+ + Q → QH2 + NAD+ Complex II FADH2 + Q → FAD + QH2

Electron Transfer Complex III QH2 + 2 cyt b (Fe3+) → Q + 2 cyt b (Fe2+) + 2H+ Complex IV 4H+ + 4e- + O2 → 2H2O

Oxidative Phosphorylation Transport of electrons produce energy to convert ADP to ATP. ADP + Pi + energy → ATP

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

Total ATP Glycolysis: 6 ATP Pyruvate: 6 ATP Citric acid cycle: 24 ATP Oxidation of glucose 36 ATP C6H12O6 + 6O2 + 36 ADP + 36 Pi → 6CO2 + 6H2O + 36 ATP

Metabolism in cell Mitochondria e e Urea NH4+ CO2 & H2O Step 3: Proteins Amino acids e Citric Acid cycle Glucose Fructose Galactose Carbohydrates Polysaccharides Glucose Pyruvate Acetyl CoA e CO2 & H2O Glycerol Lipids Fatty acids Step 3: Oxidation to CO2, H2O and energy Step 1: Digestion and hydrolysis Step 2: Degradation and some oxidation

Oxidation of fatty acids CH3-(CH2)14-CH2-CH2-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.

Oxidation of fatty acids Fatty acid activation - Before oxidation, they activate in cytosol. O O R-CH2-C-OH + ATP + HS-CoA R-CH2-C-S-CoA + H2O + AMP + 2Pi Fatty acid Fatty acyl CoA -Oxidation: 4 reactions

Reaction 1: Oxidation (dehydrogenation) R-CH2-C-C-C-S-CoA + FAD R-CH2-C=C-C-S-CoA + FADH2 H H H Fatty acyl CoA Reaction 2: Hydration H O HO H O R-CH2-C=C-C-S-CoA + H2O R-CH2-C-C-C-S-CoA H H H

Reaction 3: Oxidation (dehydrogenation) HO H O O O R-CH2-C-C-C-S-CoA + NAD+ R-CH2-C-CH2-C-S-CoA + NADH+ H+ H H Reaction 4: Cleavage of Acetyl CoA O O O O R-CH2-C-CH2-C-S-CoA + CoA-SH R-CH2-C-S-CoA + CH3-C-S-CoA Fatty acyl CoA Acetyl CoA

Oxidation of fatty acids One cycle of -oxidation O R-CH2-CH2-C-S-CoA + NAD+ + FAD + H2O + CoA-SH O O R-C-S-CoA + CH3-C-S-CoA + NADH + H+ + FADH2 Fatty acyl CoA Acetyl CoA # of fatty acid carbon # of Acetyl CoA = = 1 +  oxidation cycles 2

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). O Acetone O CH3-C-S-CoA O O CH3-C-CH3 + CO2 + energy CH3-C-CH2-C-O- O OH O CH3-C-S-CoA Acetoacetate CH3-CH-CH2-C-O- Acetyl CoA -Hydroxybutyrate

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.

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)

Metabolism in cell Mitochondria e e Urea NH4+ CO2 & H2O Step 3: Proteins Amino acids e Citric Acid cycle Glucose Fructose Galactose Carbohydrates Polysaccharides Glucose Pyruvate Acetyl CoA e CO2 & H2O Glycerol Lipids Fatty acids Step 3: Oxidation to CO2, H2O and energy Step 1: Digestion and hydrolysis Step 2: Degradation and some oxidation

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. + NH3 O CH3-CH-COO- + -OOC-C-CH2-CH2-COO- alanine α-ketoglutarate NH3 + O CH3-C-COO- + -OOC-CH-CH2-CH2-COO- pyruvate glutamate

Degradation of amino acids Oxidative Deamination NH3 + glutamate dehydrogenase -OOC-CH-CH2-CH2-COO- + H2O + NAD+ glutamate O -OOC-C-CH2-CH2-COO- + NH4+ + NADH + H+ α-ketoglutarate

Urea cycle Ammonium ion (NH4+) is highly toxic. Combines with CO2 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. O 2NH4+ + CO2 H2N-C-NH2 + 2H+ + H2O urea

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.