Metabolism: Study of Cellular Biochemical Reactions PDF

Metabolism: Study of Cellular Presented by: Joselito R. Tumulak Jr., RCh Biochemical Reactions Professor of Biochemistry OVERVIEW OF METABOLISM METABOLISM - sum total of all Amphibolic Pathways chemical reactions in...

Metabolism: Study of Cellular Presented by: Joselito R. Tumulak Jr., RCh Biochemical Reactions Professor of Biochemistry OVERVIEW OF METABOLISM METABOLISM - sum total of all Amphibolic Pathways chemical reactions in the cell OVERVIEW OF METABOLISM Anabolism and catabolism occur simultaneously. - The cell manages this conflicting processes by regulating them separately and localizing in different cellular compartments. METABOLIC PATHWAYS Metabolic pathways can be linear, cyclic, or branch. SPECIFIC LOCATION OF METABOLIC REACTIONS INSIDE THE CELL KEY INTERMEDIATES OF METABOLISM 1. Adenosine Phosphates KEY INTERMEDIATES OF METABOLISM 2. Flavin Adenine Dinucleotide (FAD) KEY INTERMEDIATES OF METABOLISM Oxidation-reduction reaction of FAD KEY INTERMEDIATES OF METABOLISM 3. Nicotinamide Adenine Dinucleotide + (NAD ) KEY INTERMEDIATES OF METABOLISM Oxidation-reduction reaction of NAD+ KEY INTERMEDIATES OF METABOLISM 3. Coenzyme A (coA) Acetyl coA BIOCHEMICAL ENERGY PRODUCTION CITRIC ACID CYCLE The citric acid cycle is a series of biochemical reaction in which the acetyl of acetyl coA is oxidized to CO2 and the reduced NADH and FADH2 are produced. REACTIONS OF THE CITRIC ACID CYCLE Step 1: Formation of Citrate The enzyme citrate synthase is allosterically inhibited by NADH and succinyl coA. REACTIONS OF THE CITRIC ACID CYCLE Step 2: Isomerization of Citrate Aconitase is inhibited by fluroacetate, a Trojan horse inhibitor. REACTIONS OF THE CITRIC ACID CYCLE Step 3: Oxidative Decarboxylation of Isocitrate NADH and ATP are allosteric inhibitor of the enzyme, ADP is an allosteric activator. REACTIONS OF THE CITRIC ACID CYCLE Step 4: Oxidative Decarboxylation of α-ketoglutarate REACTIONS OF THE CITRIC ACID CYCLE Step 5: Thioester Cleavage of Succinyl coA and Phosphorylation of GDP REACTIONS OF THE CITRIC ACID CYCLE Step 6: Oxidation of Succinate Succinate dehydrogenase is the only enzyme of the TCA that is bound to the inner mitochondrial membrane. REACTIONS OF THE CITRIC ACID CYCLE Step 7: Hydration of Fumarate REACTIONS OF THE CITRIC ACID CYCLE Step 8: Oxidation of L-Malate SUMMARY OF THE REACTIONS OF THE CITRIC ACID CYCLE CITRIC ACID CYCLE IS AN AMPHIBOLIC PATHWAY ELECTRON TRANSPORT CHAIN The electron transport chain is an elaborate and highly organized chain of proteins and coenzymes where the electrons of the reduced NADH and FADH2 are transported until it reaching O2 (molecular oxygen) producing water..  ELECTRON TRANSPORT CHAIN NADH-Coenzyme Succinate-Coenzyme Coenzyme Q- Cytochrome c Q reductase Q reductase cytochrome reductase oxidase All these complexes are integrated in the inner membrane of the mitochondrion. COMPLEX I: NADH-CoQ Reductase 1 2 The final product of this complex is the reduced CoQH2 which shuttles electrons into Complex III. The energy produced by electron transfer in Complex I can be used to pump protons + (H ) across inner membrane, COMPLEX II: Succinate-CoQ Reductase The final product of this complex is also CoQH2 which shuttles electrons into Complex III. The energy produced by electron transfer in Complex II is lesser than in Complex I, so this cannot pump protons (H ) + across inner membrane. COMPLEX III: CoQ-Cytochrome Reductase Cytochromes contain heme. The electron transfer proceeds from CoQH2 to an FeSP, then to cyt b, then to another FeSP, then to cyt c1, and finally to cyt c. Cyt c delivers its electrons to complex IV. COMPLEX IV: CoQ-Cytochrome Reductase The electron movement flows from cyt c to cyt a then to cyt a3. In addition to iron center, cyt a and cyt a3 also have copper ions. O2 + 4 H + +4 e-  2 H2O  INHIBITORS OF ELECTRON TRANSPORT CHAIN Complex I is inhibited by Complex IV is inhibited by rotenone, a common insecticide. cyanide and carbon monoxide. OXIDATIVE PHOSPHORYLATION Oxidative phosphorylation is the biochemical process by which ATP is synthesized from ADP as a result of the transfer of electrons and hydrogen ions ATP Synthase from NADH or FADH2 to O2 through the electron carriers involved in the electron transport chain. OXIDATIVE PHOSPHORYLATION The oxidative phosphorylation is a coupled reaction and is based on the chemiosmotic theory. - Transfer of electrons from NADH pumps a total + of 10 H , while FADH2 pumps a total of 6 H. + OXIDATIVE PHOSPHORYLATION The pumping of H + ions across inner membrane produces a proton gradient. The protons are propelled back to the matrix through a complex known as proton-translocating ATP synthase which synthesizes ATP in the matrix. ATP SYNTHASE The F0 sector contains the proton channel and rotates every time a proton passes. The F1 sector is known as rotor comprising γ and ε subunits. It is surrounded by the catalytic α and β subunits that synthesizes the ATP. -The last unit, the “stator,” containing the δ subunit, stabilizes the whole complex.  TRANSFER OF ATP INTO OUTSIDE OF MATRIX The ATP produced through oxidative phosphorylation is moved from the matrix to the intermembrane space by a transport protein known as ATP-ADP translocase embedded in the inner mitochondrial membrane. P/O RATIO FOR OXIDATIVE PHOSPHORYLATION The P/O ratio is the number of molecules ATP formed per two electrons flowing through ETC, and this is dependent on the H + that is transported by the electron transfer. Recent study elucidated that there is 1 ATP molecule produced in every 4 H+ ions. Thus: ATP PRODUCTION OF THE COMMON METABOLIC PATHWAY For every acetyl coA that enters the citric acid cycle, 10 ATP are produced after ETC and oxidative phosphorylation. METABOLISM OF CARBOHYDRATES Carbohydrates DIGESTION AND ABSORPTION OF CARBOHYDRATES GLYCOLYSIS: MAIN CATABOLIC PATHWAY OF CARBOHYDRATES Glucose (6 Cs) Pyruvate Pyruvate (3 Cs) (3 Cs) FATES OF PYRUVATE Pyruvate is a versatile metabolite and can be used in different ways. REACTIONS OF GLYCOLYSIS Reaction 1: Phosphorylation of Glucose Phosphorylation keeps glucose substrate in the cells. This reaction keeps the intracellular concentration of glucose low REACTIONS OF GLYCOLYSIS Phosphorylation of glucose is achieved by the isoenzymes hexokinase and glucokinase. HEXOKINASE GLUCOKINASE - Present in most tissues of the body - Present only in the liver - Relatively non-specific - Highly specific only for glucose - Works efficiently at normal blood glucose level - Works only at high glucose levels in the liver - Primarily responsible for phosphorylating - Regulates blood sugar level glucose in glycolysis REACTIONS OF GLYCOLYSIS Reaction 1: Phosphorylation of Glucose This is the first regulated reaction in glycolysis, wherein hexokinase is allosterically inhibited by glucose-6-phosphate. REACTIONS OF GLYCOLYSIS Reaction 2: Isomerization of Glucose-6-Phosphate Converts the hemiacetal –OH o to 1 alcohol which can easily be phosphorylated. Activates C3 which facilitates C-C cleavage in the next steps. REACTIONS OF GLYCOLYSIS Reaction 3: Phosphorylation of Fructose-6-Phosphate at C1 This reaction commits the cell in metabolizing glucose rather than converting it to another sugar or storing it. After this reaction, no other pathways are available. REACTIONS OF GLYCOLYSIS Reaction 3: Phosphorylation of Fructose-6-Phosphate at C1 This is the second regulated reaction of glycolysis. The enzyme is regulated by ATP. High levels of ATP decreases the activity of this enzyme, and low levels of ATP stimulates the reaction. Citrate is also an allosteric inhibitor of phosphofructokinase. REACTIONS OF GLYCOLYSIS Reaction 4: Cleavage of Fructose-1,6-Bisphosphate Fructose bisphosphate aldolase cleaves fructose-1,6- bisphosphate to yield dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3- phosphate REACTIONS OF GLYCOLYSIS Reaction 5: Isomerization of Glyceraldehyde-3-Phosphate to DHAP Only glyceraldehyde-3-phosphate can proceed to the glycolytic pathway. The enzyme triose phosphate isomerase is one of the enzymes that have evolved to a state of catalytic perfection. REACTIONS OF GLYCOLYSIS Reaction 6: Oxidation and Phosphorylation of Glyceraldehyde-3- Phosphate Overall, the reaction results in the oxidation of an aldehyde to a carboxylic acid, formation of carboxylic phosphoric anhydride, and reduction of NAD+ to NADH. The newly added phosphate group is a high-energy phosphate group REACTIONS OF GLYCOLYSIS Reaction 6: Oxidation and Phosphorylation of Glyceraldehyde-3- Phosphate The enzyme involved in this reaction can be inactivated by iodoacetate, which reacts with and blocks the essential cysteine residue in the active site. The enzyme is also the site of action of 3+ arsenate (AsO4 ), an anion analogous to phosphate REACTIONS OF GLYCOLYSIS Reaction 7: Formation of 3- Phosphoglycerate and First 2 ATP Molecules The break-even reaction of glycolysis in terms of ATP production ATP production in this step involves substrate-level phosphorylation. REACTIONS OF GLYCOLYSIS Reaction 8: Isomerization of 3- Phosphoglycerate to 2- Phosphoglycerate REACTIONS OF GLYCOLYSIS Reaction 9: Dehydration of 2- Phosphoglycerate Forming Phosphoenolpyruvate (PEP) The dehydration reaction form a new C-C double bond which converts the phosphate group of PEP into a high-energy phosphate group. REACTIONS OF GLYCOLYSIS Reaction 10: Formation of Pyruvate and Final 2 ATP Molecules Because each glucose molecule sends two molecules of glyceraldehyde-3-phosphate into the second phase of glycolysis, 2 ATP molecules are produced in this step (same as reaction 7). REACTIONS OF GLYCOLYSIS Reaction 10: Formation of Pyruvate and Final 2 ATP Molecules This is the last regulated reaction of glycolysis. It is activated by AMP and fructose-1,6-bisphosphate and inhibited by ATP, acetyl coA, and alanine. When this enzyme is inhibited, the PEP will be used as a substrate for glucose synthesis in the process known as gluconeogenesis. SUMMARY OF THE REACTIONS OF GLYCOLYSIS REGULATIONS OF GLYCOLYSIS ENTRY OF OTHER MONOSACCHARIDES TO GLYCOLYSIS  ENTRY OF PYRUVATE TO THE CITRIC ACID CYCLE The oxidative decarboxylation of pyruvate to acetyl-CoA is the link between glycolysis and the citric acid cycle. The reaction is catalyzed by pyruvate dehydrogenase, a multienzyme complex. GLYCEROL-3-PHOSPHATE SHUTTLE Via the glycerol-3-phosphate shuttle, cytosolic NADH can be used to produce mitochondrial FADH2. As a result, cytosolic NADH oxidized via this shuttle route yields only 1.5 molecules of ATP. This shuttle operates in the muscles and nerve cells. MALATE-ASPARTATE SHUTTLE Via the Malate-asprate shuttle, cytosolic NADH can be used to produce mitochondrial NADH. As a result, cytosolic NADH oxidized via this shuttle route yields only 2.5 molecules of ATP. This shuttle operates in the heart cells. NET YIELD OF ATP PER GLUCOSE MOLECULES GLUCONEOGENESIS Gluconeogenesis is the metabolic pathway by which glucose is synthesized from non-carbohydrate materials. Pyruvate Lactate Glycerol Amino Acids GLUCONEOGENESIS Glycolysis and gluconeogenesis are not exact opposites. 12 compounds are involved in gluconeogenesis and only 11 in glycolysis. THE REACTIONS OF GLUCONEOGENESIS CORI CYCLE OTHER METABOLIC PATHWAYS OF CARBOHYDRATES MOBILIZATION OF FATS CATABOLISM OF GLYCEROL The glycerol travels to the liver or kidneys, where it is converted to dihydroxyacetone phosphate, a glycolysis intermediate. CATABOLISM OF GLYCEROL ATP YIELD OF CATABOLISM OF GLYCEROL  CATABOLISM OF FATTY ACIDS There are three parts to the process by which fatty acids are broken down to obtain energy: 1. The fatty acid must be activated by bonding to coenzyme A. 2. The fatty acid must be transported into the mitochondrial matrix by a shuttle mechanism. 3. The fatty acid must be repeatedly oxidized, cycling through a series of four reactions, to produce acetyl CoA, FADH2, and NADH. ACTIVATION OF FATTY ACIDS The fatty acid is first converted to a high-energy derivative of coenzyme A. This reaction is concomitant to hydrolysis of ATP to AMP which is equivalent to using 2 ATP. TRANSPORT OF FATTY ACIDS BETA-OXIDATION OF FATTY ACIDS ATP YIELD OF CATABOLISM OF FATTY ACIDS KETONE BODIES There should be an adequate balance between carbohydrate and lipid metabolism to ensure that all acetyl coA produced from fat catabolism goes into the Krebs Cycle. KETONE BODIES Excess acetyl CoA is diverted to the formation of ketone bodies, specifically acetoacetate, β- hydroxybutyrate, and acetone.