Biochemistry (BIO 024) Module #7 Past Paper PDF

Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:___...

Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Lesson title: BIOCHEMICAL ENERGY PRODUCTION (KREB’S Materials: CYCLE and ELECTRON TRANSPORT CHAIN (ETC)) Pen, SAS Lesson Objectives: by the end of this module, you should be able to References: 1. Define metabolism and its related terms. ▪ stoker, H. S. 2. Distinguishing anabolic from catabolic metabolism. (2017).Biochemistry (3rd ed.). 3. Identifying the parts of the cell where the metabolic reaction (M. Finch, Ed.) Belmont CA, occurs, and important intermediate compounds involved. USA,page 191-206 ▪ https://www.youtube.com/wat 4. Illustrate the Krebs Cycle and the Electron transport chain ch?v=C8VHyezOJD4 (part1) ▪ https://www.youtube.com/wat ch?v=E_UG3WnsW3o (part2) Productivity Tip: Take a quite tour outside your house. Take a small snack and do short physical exercises. Now, wonder how you provided your energy and how you consumed your energies out from the sources and exertion that you had. This activity will give you the idea to ask how your body able to do such provision and consumption of energy in your daily living. This will give you a hint of the module that you are about to deal with. A. LESSON PREVIEW/REVIEW 1) Introduction (1 min) Metabolism is the sum total of all the biochemical reactions that take place in a living organism. Human metabolism is quite remarkable. An average human adult whose weight remains the same for 40 years processes about 6 tons of solid food and 10,000 gallons of water, during which time the composition of the body is essentially constant. Just as gasoline is put into a car to make it go or a kitchen appliance is plugged in to make it run, the human body needs a source of energy to make it function. Even the simplest living cell is continually carrying on energy-demanding processes such as protein synthesis, DNA replication, RNA transcription, and membrane transport. A metabolic pathway is a series of consecutive biochemical reactions used to convert a starting material into an end product, which is either linear or cyclic. In this module, we will be focused with the common metabolic pathway (sum total of all biochemical reaction of citric acid cycle, the electron transport chain, and oxidative phosphorylation) by which all of the macromolecules will go through. The basic knowledge you got from of all the modules you’ve gone through is essential for your study of metabolism. This document is the property of PHINMA EDUCATION Page |1  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ 2) Activity 1: What I Know Chart, part 1 (3 mins) Instructions: "In this chart, reflect on what you know now. Do not worry if you are sure or not sure of your answers. This activity simply serves to get you started on thinking about our topic. Answer only the first column, "What I know" based on the question of the second column. Leave the third column "What I learned" blank at this time. What I Know Questions: What I Learned (Activity 4) 1. Where does human gets their energy from? 2. How much energy do we get from a cycle of metabolism? 3. Where does metabolism takes place in our cell? B.MAIN LESSON: Activity 2: Content notes (70 min). Instructions: Make your own side notes upon looking at this module. It would help if you also watch videos to get a full recap of the metabolic pathways we are about to discuss. 2 TYPES OF METABOLISM ▪ ANABOLISM is all metabolic reactions in which small biochemical molecules are joined together to form larger ones - Consumes energy. - Ex. Oxidation of glucose ▪ CATABOLISM is all metabolic reactions in which large biochemical molecules are broken down to smaller ones - Releases energy - Ex. Synthesis of proteins : Eukaryotic cell is a cell in which the DNA is found in a membrane-enclosed nucleus. Organelles: ▪ Nucleus – DNA replication and RNA synthesis ▪ Plasma membrane – Cellular boundary ▪ Cytoplasm - the water-based material that lies between the nucleus and the outer membrane of the cell ▪ Mitochondria - generates of most of the energy for a cell ▪ Lysosome - contains hydrolytic enzymes needed for cellular rebuilding, repair, and degradation ▪ Ribosome – site for protein synthesis This document is the property of PHINMA EDUCATION Page |2  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ MITOCHONDRIA: Powerhouse of the cell ▪ Outer membrane: ▪ 50% lipid and 50% protein ▪ freely permeable to small molecules. ▪ Inner membrane ▪ about 20% lipid and 80% protein ▪ Highly impermeable to most substances ▪ Interior region: called matrix ▪ Region between inner & outer membrane: intermembrane space Folds into cristae to increase surface area ATP synthase complexes: small spherical knob attached to cristae o Site for ATP synthesis IMPORTANT NUCLEOTIDE-CONTAINING COMPOUNDS in METABOLIC PATHWAYS CoA (Coenzyme A) ATP (Adenosine Triphosphate) Active portion is –SH (sulfhydryl group) or as CoA-SH the net energy produced used for Derivative of Vit. B5 cellular reactions FAD (Flavin Adenine Dinucleotide) Coenzyme required for redox reactions NAD (Nicotinamide adenine dinucleotide) FAD+- oxidized form, FADH2-reduced form Coenzyme required for redox reactions Derivative of Vit. B2 NAD+- oxidized form, NADH-reduced form Derivatove of Vit. B3 This document is the property of PHINMA EDUCATION Page |3  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Classification of metabolic Intermediate: REDOX REACTION: Oxidation – hydrogen atom loss Reduction- hydrogen atom gain. An Overview of Biochemical Energy Production Common metabolic pathway is the sum total of the biochemical reactions of the citric acid cycle, the electron transport chain, and oxidative phosphorylation. This document is the property of PHINMA EDUCATION Page |4  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Stage 1:DIGESTION ▪ is the biochemical process by which food molecules, through hydrolysis, are broken down into simpler chemical units that can be used by cells for their metabolic need ▪ begins in the mouth (saliva contains starch digesting enzymes), continues in the stomach (gastric juices), and is completed in the small intestine (the majority of digestive enzymes and bile salts). ▪ end products of digestion o carbohydrates -glucose and other monosaccharides o proteins- amino acids o fats and oils- fatty acids and glycerol ▪ products pass across intestinal membranes and into the blood, where they are transported to the body’s cells. Stage 2: acetyl group formation, ▪ reaction in: o cytosol: glucose metabolism o mitochondria: fatty acid metab ▪ End product: Acetyl CoA ▪ Primary products: 2-carbon acetyl units (which become attached to coenzyme A to give acetyl CoA) and the reduced coenzyme NADH. Stage 3: the citric acid cycle, ▪ Occurs:mitochondria. ▪ Acetyl groups are oxidized to produce CO2 (which we exhale during breathing) and energy. ▪ Some of the energy released by these reactions is lost as heat, and some is carried by the reduced coenzymes NADH and FADH2 to the fourth stage. Stage 4: the electron transport chain and oxidative phosphorylation ▪ Occurs: mitochondria. ▪ NADH and FADH2 are oxidized to release H+ and electrons ▪ H+ is transported to the inter-membrane space in mitochondria ▪ Electrons are transferred to molecular O2, inhaled via breathing, O2 is reduced to H2O ▪ H+ reenter the mitochondrial matrix and drive ATP synthase reaction to produce ATP ▪ ATP molecules, the primary energy carriers in metabolic pathways. This document is the property of PHINMA EDUCATION Page |5  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ THE CITRIC ACID CYCLE The citric acid cycle is the series of biochemical reactions in which the acetyl portion of acetyl CoA is oxidized to carbon dioxide and the reduced coenzymes FADH2 and NADH are produced. This document is the property of PHINMA EDUCATION Page |6  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ ▪ This cycle stage 3 of biochemical energy production gets its name from the first intermediate product in the cycle, citric acid. ▪ Aka Krebs cycle, after its discoverer Hans Adolf Krebs, and as the tricarboxylic acid cycle, in reference to the three carboxylate groups present in citric acid ▪ take place in the mitochondrial matrix for eukaryotes and cytosol for the prokaryotes. ▪ Oxidation (produces NADH or FADH2), and decarboxylation, (carbon chain is shortened by the removal of a carbon atom as a CO2 molecule), are steps involved. Summary of the Citric Acid Cycle An overall summary equation for the citric acid cycle is obtained by adding together 1 mol. Glucose glycolysis 2 mol.pyruvate the individual reactions of the cycle: Note: Since there are 2 molecules of pyruvate, the cycle will be repeated twice. Hence, Important features of the cycle include the following: product will be 1. The “fuel” for the cycle is acetyl CoA, obtained from the doubled also. breakdown of carbohydrates, fats, and proteins. 2. Four of the cycle reactions involve oxidation and reduction. The oxidizing agent is either NAD1 (three times) or FAD (once). The operation of the cycle depends on the availability of these oxidizing agents. 3. In redox reactions, NAD1 is the oxidizing agent when a carbon–oxygen double bond is formed; FAD is the oxidizing agent when a carbon–carbon double bond is formed. 4. The three NADH and one FADH2 that are formed during the cycle carry electrons and H1 to the electron transport chain (Section 23.8) through which ATP is synthesized. 5. Two carbon atoms enter the cycle as the acetyl unit of acetyl CoA, and two carbon atoms leave the cycle as two molecules of CO2. The carbon atoms that enter and leave are not the same ones. The carbon atoms that leave during one turn of the cycle are carbon atoms that entered during the previous turn of the cycle. 6. Four B vitamins are necessary for the proper functioning of the cycle: riboflavin (in both FAD and the a-ketoglutarate dehydrogenase complex), nicotinamide (in NAD+), pantothenic acid (in CoA—SH), and thiamine (in the a- ketoglutarate dehydrogenase complex). 7. One high-energy GTP molecule is produced by phosphorylation. 1 CYLCE OF CITRIC ACID CYCLE This document is the property of PHINMA EDUCATION Page |7  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Reactions of the Citric Acid Cycle Step 1: Formation of Citrate. Acetyl CoA, which carries the two-carbon degradation product of carbohydrates, fats, and proteins, enters the cycle by combining with the four- carbon keto dicarboxylate species oxaloacetate. This results in the transfer of the acetyl group from coenzyme A to oxaloacetate, producing the C6 citrate species and free coenzyme A. There are two parts to the reaction: (1) the condensation of acetyl CoA and oxaloacetate to form citryl CoA, a process catalyzed by the enzyme citrate synthase and (2) hydrolysis of the thioester bond in citryl CoA to produce CoA-SH and citrate, also catalyzed by the enzyme citrate synthase. Step 2: Formation of Isocitrate. Citrate is converted to its less symmetrical isomer isocitrate in an isomerization process that involves a dehydration followed by a hydration, both catalyzed by the enzyme aconitase. The net result of these reactions is that the - OH group from citrate is moved to a different carbon atom. Citrate is a tertiary alcohol and isocitrate a secondary alcohol.Tertiary alcohols are not readily oxidized; secondary alcohols are easier to oxidize. The next step in the cycle involves oxidation. Step 3: Oxidation of Isocitrate and Formation of CO 2. This step involves oxidation–reduction (the first of four redox reactions in the citric acid cycle) and decarboxylation. The reactants are a NAD+ molecule and isocitrate. The reaction, catalyzed by isocitrate dehydrogenase, is complex: (1) Isocitrate is oxidized to a ketone (oxalosuccinate) by NAD+, releasing two hydrogens. (2) One hydrogen and two electrons are transferred to NAD+ to form NADH; the remaining hydrogen ion (H+) is released. (3) The oxalosuccinate remains bound to the enzyme and undergoes decarboxylation (loses CO2), which produces the C5 a-ketoglutarate (a keto dicarboxylate species). This step yields the first molecules of CO2 and NADH in the cycle. Step 4: Oxidation of a-Ketoglutarate and Formation of CO 2. This second redox reaction of the cycle involves one molecule each of NAD+, CoA-SH, and a-ketoglutarate. The catalyst is a three-enzyme system called the a- ketoglutarate dehydrogenase complex. The B vitamin thiamin, in the form of TPP, is part of the enzyme complex, as is Mg2+ ion. As in Step 3, both oxidation and decarboxylation occur. There are three products: CO 2, NADH, and the C4 species succinyl CoA. Step 5: Thioester Bond Cleavage in Succinyl CoA and Phosphorylation of GDP. Two reactant molecules are involved in this step—a Pi (HPO4-2) and a GDP (similar to ADP). The entire reaction is catalyzed by the enzyme succinyl-CoA This document is the property of PHINMA EDUCATION Page |8  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ synthetase. For purposes of understanding the structural changes that occur, the reaction can be considered to occur in two steps. In the first step, succinyl CoA is converted to succinyl phosphate (a high-energy phosphate compound); CoA– SH is a product of this change. The phosphoryl group present in succinyl phosphate is then transferred to GDP; the products of this change are GTP and succinate. Thinking of the two steps as occurring concurrently gives the following energy analysis: When broken, the high-energy thioester bond in succinyl CoA releases energy, which is trapped by formation of GTP. The function of the GTP produced is similar to that of ATP, which is to store energy in the form of a high-energy phosphate bond. Steps 6 through 8 of the citric acid cycle involve a sequence of functional group changes that have been encountered several times in the organic sections of the text. The reaction sequence is. Step 6: Oxidation of Succinate. This is the third redox reaction of the cycle. The enzyme involved is succinate dehydrogenase, and the oxidizing agent is FAD rather than NAD+. Two hydrogen atoms are removed from the succinate to produce fumarate, a C4 species with a trans double bond. FAD is reduced to FADH2 in the process. Step 7: Hydration of Fumarate. The enzyme fumarase catalyzes the addition of water to the double bond of fumarate. The enzyme is stereospecific, so only the L isomer of the product malate is produced. Step 8: Oxidation of L-Malate to Regenerate Oxaloacetate. In the fourth oxidation–reduction reaction of the cycle, a molecule of NAD+ reacts with malate, picking up two hydrogen atoms with their associated energy to form NADH+ H+. The needed enzyme is malate dehydrogenase. The product of this reaction is regenerated oxaloacetate, which can combine with another molecule of acetyl CoA (Step 1), and the cycle can begin again. The Electron Transport Chain The electron transport chain is a series of biochemical reactions in which electrons and hydrogen ions from NADH and FADH2 are passed to intermediate carriers and then ultimately react with molecular oxygen to produce water. NADH and FADH2 are oxidized in this process. Water is formed when the electrons and hydrogen ions that originate from these reactions react with molecular oxygen. The electrons that pass through the various steps of the electron transport chain (ETC) lose some energy with each transfer along the chain. Some of this “lost” energy is used to make ATP from ADP (oxidative phosphorylation), This document is the property of PHINMA EDUCATION Page |9  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ (If you have data, please click the link in the sources provided and watch the video ) This document is the property of PHINMA EDUCATION P a g e | 10  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ The enzymes and electron carriers needed for the ETC are located along the inner mitochondrial membrane. Within this membrane are four distinct protein complexes, each containing some of the molecules needed for the ETC process to occur. These four protein complexes, which are tightly bound to the membrane, are NADH–coenzyme Q reductase COMPLEX I NADH dehydrogenase complex NADH oxido-reductase Succinate–coenzyme Q reductase COMPLEX II Succinate dehydrogenase complex Coenzyme Q–cytochrome c reductase COMPLEX III Cytochrome reductase Q-cytochrome oxidoreductase Cytochrome c oxidase COMPLEX IV A heme and copper containing complex COMPLEX V ATP SYNTHASE COMPLEX (for Oxidation phosphorylation) Two electron carriers, coenzyme Q and cytochrome c, which are not tightly associated with any of the four complexes, serve as mobile electron carriers that shuttle electrons between the various complexes. The discussion of the individual reactions that occur in the ETC is divided into four parts, each part dealing with the reactions associated with one of the four protein complexes. Complex I: NADH–Coenzyme Q Reductase NADH, from the citric acid cycle, is the source for the electrons that are processed through complex I, the largest of the four protein complexes. Complex I contains more than 40 subunits, including the B vitamin-containing fl avin mononucleotide (FMN) and several iron–sulfur proteins (FeSP). The net result of electron movement through complex I is the transfer of electrons from NADH to coenzyme Q (CoQ), a result implied by the name of complex I: NADH–coenzyme Q reductase. The actual electron transfer process is not, however, a single-step direct transfer of electrons from NADH to CoQ; several intermediate carriers are involved. The fi rst electron transfer step that occurs in complex I involves the interaction of NADH with flavin mononucleotide (FMN). The NADH is oxidized to NAD+ (which can again participate in the citric acid cycle) as it passes two hydrogen ions and two electrons to FMN, which is reduced to FMNH2. NADH supplies both electrons and one of the H+ ions that are transferred; the other H+ ion comes from the matrix solution. The next steps involve transfer of electrons from the reduced FMNH 2 through a series of iron/sulfur proteins (FeSPs). The iron present in these FeSPs is Fe3+, which is reduced to Fe2+. The two H atoms of FMNH2 are released to solution as two H+ ions. Two FeSP molecules are needed to accommodate the two electrons released by FMNH2 because an Fe3+/Fe2+ reduction involves only one electron. This document is the property of PHINMA EDUCATION P a g e | 11  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ In the final complex I reaction, Fe(II)SP is reconverted into Fe(III)SP as each of two Fe(II)SP units passes an electron to CoQ, changing it from its oxidized form (CoQ) to its reduced form (CoQH 2). Coenzyme Q, in both its oxidized and reduced forms, is lipid soluble and can move laterally within the mitochondrial membrane. Its function is to shuttle its newly acquired electrons to complex III, where it becomes the initial substrate for reactions at this complex. The Q in the designation coenzyme Q comes from the name quinone. Structurally, coenzyme Q is a quinone derivative. In its most common form, coenzyme Q has a long carbon chain containing 10 isoprene units attached to its quinone unit. The actual changes that occur within the structure of CoQ as it accepts the two electrons and the two H+ ions involve the quinone part of its structure, as is shown in Figure 23.12b. The two H+ ions that CoQ picks up in forming CoQH2 come from solution. Complex II: Succinate–Coenzyme Q Reductase Complex II, which is much smaller than complex I, contains only four subunits, including two FeSPs. This complex is used to process the FADH2 that is generated in the citric acid cycle when succinate is converted to fumarate. (Thus the use of the term succinate in the name of complex II.) CoQ is associated with the operations in complex II in a manner similar to its actions in complex I. It is the fi nal recipient of the electrons from FADH 2, with iron–sulfur proteins serving as intermediaries. Thus complexes I and II produce a common product, the reduced form of coenzyme Q (CoQH 2). As was the case with complex I, the reduced CoQH2 shuttles electrons to complex III. This document is the property of PHINMA EDUCATION P a g e | 12  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Figure 23.13 summarizes the electron transport chain reactions associated with complexes I and II. In Figure 23.13a the net process is shown with only starting and end products shown. In Figure 23.13b individual reaction detail is shown. Note the general pattern that is developing for the electron carriers. They are reduced (accept electrons) in one step and then regenerated (oxidized; lose electrons) in the next step so that they can again participate in electron transport chain reactions. Complex III: Coenzyme Q–Cytochrome c Reductase Complex III contains 11 different subunits. Electron carriers present include several iron–sulfur proteins as well as several cytochromes. A cytochrome is a hemecontaining protein in which reversible oxidation and reduction of an iron atom occur. This document is the property of PHINMA EDUCATION P a g e | 13  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Heme, a compound also present in hemoglobin and myoglobin. Heme-containing proteins function similarly to FeSP; iron changes back and forth between the 13 and 12 oxidation states. Various cytochromes, abbreviated cyt a, cyt b, cyt c, and so on, differ from each other in (1) their protein constituents (2) the manner in which the heme is bound to the protein and (3) attachments to the heme ring. Again, because the Fe3+/Fe2+ system involves only a one-electron change, two cytochrome molecules are needed to move two electrons along the chain. The initial substrate for complex III is CoQH 2 molecules carrying the electrons that have been processed through complex I (from NADH) and also those processed through complex II (from FADH 2). The electron transfer process proceeds from HEME CoQH2 to an FeSP, then to cyt b, then to another FeSP, then to cyt c1, and finally to cyt c. Cyt c can move laterally in the intermembrane space; it delivers its electrons to complex IV. Cyt c is the only one of the cytochromes that is water soluble. The initial oxidation–reduction reaction at complex III is between CoQH2 and an iron–sulfur protein (FeSP). The H+ ions produced from the oxidation of CoQH2 go into cellular solution. All further redox reactions at complex III involve only electrons, which are conveyed further down the enzyme complex chain. Figure 23.14 shows diagrammatically the electron transfer steps associated with complex III. Complex IV: Cytochrome c Oxidase Complex IV contains 13 subunits, including two cytochromes. The electron movement flows from cyt c (carrying electrons from complex III) to cyt a to cyt a3. In the final step of electron transfer, the electrons from cyt a3 and hydrogen ions from cellular solution combine with oxygen (O2) to form water. It is estimated that 95% of the oxygen used by cells serves as the final electron acceptor for the ETC. The two cytochromes present in cytochrome c oxidase (a and a3) differ from previously encountered cytochromes in that each has a copper atom associated with it in addition to its iron center. The copper atom sites participate in the electron transfer process as do the iron atom sites, with the copper atoms going back and forth between the reduced Cu1 state and the oxidized Cu21 state. Figure 23.15 shows the electron transfer sequence through these copper and iron sites. Schematic diagram summarizing the flow of electrons through the four complexes of the electron transport chain. This document is the property of PHINMA EDUCATION P a g e | 14  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ 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 from NADH or FADH2 to O2 through the electron carriers involved in the electron transport chain. Oxidative phosphorylation is conceptually simple but mechanistically complex. Determining the details of oxidative phosphorylation has been—and still is—one of the most challenging research areas in biochemistry. Coupled reactions are pairs of biochemical reactions that occur concurrently in which energy released by one reaction is used in the other reaction. Oxidative phosphorylation and the oxidation reactions of the electron transport chain are coupled systems. The interdependence (coupling) of ATP synthesis with the reactions of the ETC is related to the movement of protons (H+ ions) across the inner mitochondrial membrane. Three of the four protein complexes involved in the ETC chain (I, III, and IV) have a second function besides electron transfer down the chain. They also serve as “proton pumps,” transferring protons from the matrix side of the inner mitochondrial membrane to the intermembrane space. Some of the H+ ions crossing the inner mitochondrial membrane come from the reduced electron carriers, and some come from the matrix; the details of how the H+ ions cross the inner mitochondrial membrane are not fully understood. For every two electrons passed through the ETC, four protons cross the inner mitochondrial membrane through complex I, four through complex III, and two more through complex IV. This proton flow causes a build up of H+ ions (protons) in the intermembrane space; this high concentration of protons becomes the basis for ATP synthesis. The “proton flow” explanation for ATP–ETC coupling is formally called chemiosmotic coupling. Chemiosmotic coupling is an explanation for the coupling of ATP synthesis with electron transport chain reactions that requires a proton gradient across the inner mitochondrial membrane. The main concepts in this explanation for coupling follow. 1. The result of the pumping of protons from the mitochondrial matrix across the inner mitochondrial membrane is a higher concentration of protons in the intermembrane space than in the matrix. This concentration difference constitutes an electrochemical (proton) gradient. A chemical gradient exists whenever a substance has a higher concentration in one region than in another. Because the proton has an electrical charge (H+ ion), an electrical gradient also exists. Potential energy is always associated with an electrochemical gradient. 2. A spontaneous flow of protons from the region of high concentration to the region of low concentration occurs because of the electrochemical gradient. This proton flow is not through the membrane itself (it is not permeable to H+ ions) but rather through enzyme complexes called ATP synthases located on the inner mitochondrial membrane This document is the property of PHINMA EDUCATION P a g e | 15  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ (Section 23.2). This proton flow through the ATP synthases “powers” the synthesis of ATP. ATP synthases are thus the coupling factors that link the processes of oxidative phosphorylation and the electron transport chain. 3. ATP synthase has two subunits, the F0 and F1 subunits. The F0 part of the synthase is the channel for proton flow, whereas the formation of ATP takes place in the F1 subunit. As protons return to the mitochondrial matrix through the F0 subunit, the potential energy associated with the electrochemical gradient is released and used in the F1 subunit for the synthesis of ATP. 4. The ATP produced trhough oxidative phosphorylation must be moved from the matrix back to the intermembrane space before it can be used in the metabolic reactions. For each ATP molecule transferred from the matrix to the intermembrane space an ADP , a Pi, and an H+ ion move in the opposite direction. COMPUTATION OF ATP: This document is the property of PHINMA EDUCATION P a g e | 16  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ This document is the property of PHINMA EDUCATION P a g e | 17  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Activity 3: Skill-building Activities (with answer key) (25 mins + 5 mins checking) MATCHING TYPE: Match the following with the correct answer. Write the answer before the number. Column A Column B A. Metabolism ________1. the net energy produced used for cellular reactions B. Catabolism ________2. A Derivative of Vit. B5 C. Anabolism ________3. Coenzyme required for redox reactions D. NAD ________4. is the sum total of all the biochemical reactions that take place in a living organism E. CoA ________5. is all metabolic reactions in which small F. FAD biochemical molecules are joined together to form larger ones G. ATP MATCHING TYPE: Write A-for anabolic and B-catabolic before the number 1. Synthesis of proteins from amino acids 2. Formation of a triacylglycerol from glycerol and fatty acids 3. Hydrolysis of a polysaccharide to produce monosaccharides 4. Formation of a polynucleotide from nucleotides FILL IN THE DIAGRAM: FILL IN THE BLANK. Fill in the missing information to the blank provided. Ex. Pyruvate Oxidation Pyruvate enters the mitochondrion from the cytoplasm. One carbon atom is removed via decarboxylation and hydrogen is removed using NAD+. Coenzyme A becomes attached to the remaining carbon atoms, creating acetyl–CoA , which then enters the Krebs cycle. This document is the property of PHINMA EDUCATION P a g e | 18  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Krebs Cycle 1. _______ enters the cycle and then combines with 2. _____________ to make the six-carbon compound 3.________. During the eight steps of the Krebs cycle,4. _______ undergoes a number of reactions, releasing 5._______ and 6.______ in a number of steps. 7._______ is eventually converted into 8._________ (final and first molecule) so it can be used again during the Krebs cycle. Products of the Krebs Cycle 9._______ is released as waste. 10.______ (coenzyme) and 11.______ (coenzyme)move to the next stage of cellular respiration. Energy is released in the form of 12._______. A glucose molecule produces 13.______ (how many) molecules of 14.______(product) because two molecules of 15._______ are created from each molecule of 16._________. This document is the property of PHINMA EDUCATION P a g e | 19  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ FILL IN THE DIAGRAM: Activity 4: What I Know Chart, part 2 (2 mins) Instruction: To review what was learned from this session, please go back to Activity 1 and answer the “What I Learned” column. Notice and reflect on any changes in your answers. Activity 5: Check for Understanding (10 mins) Instruction: Now it’s time for you to figure this one out on your own! Take time to read, analyze, and understand the following questions. For this instance, you will not have the chance to check if you have the correct answers since there are no more keys to correction. MULTIPLE CHOICE: WRITE the letter of your choice before each number. Good luck! LESSON WRAP-UP This document is the property of PHINMA EDUCATION P a g e | 20  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ ELECTRON TRANSPORT CHAIN: Fill in the missing pieces of information with the process. CHOICES: MATCHING TYPE: Write the letter of the correct answer. A. Oxygen _______1. Where does ETC occur? B. Mitochondria _______2.Final oxygen acceptor? C. H2O _______3. Electron + final electron acceptor and hydrogen ion combine to form what product. D. ATP synthase _______4.The complex involved on oxidative phosphorylation E. Cytochrome c oxidase F. Cytosol G. ATP This document is the property of PHINMA EDUCATION P a g e | 21  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Activity 4: What I Know Chart, part 2 (2 mins) Instruction: To review what was learned from this session, please go back to Activity 1 and answer the “What I Learned” column. Notice and reflect on any changes in your answers. Activity 5: Check for understanding (15 mins) Instruction: Now it’s time for you to figure this one out on your own! Take time to read, analyze, and understand the following questions. For this instance, you will not have the chance to check if you have the correct answers since there are no more keys to correction. WRITE the letter of your choice before each number Good luck! 1. Which of the following statements about mitochondria is 6. ATP synthesis via oxidative phosphorylation correct? depends on the passage of which of the a. The outer membrane of mitochondria is not permeable following species through membrane-bound ATP to any molecules. synthase? b. The interior region of a mitochondrion is the a. NADH intermembrane space. b. FADH2 c. The folds of the outer membrane are called cristae. c. H+ d. Mitochondria are located within the cellular cytosol. d. NAD+ 2. In which of the following listings of citric acid cycle 7. Which of the following is a correct letter designation intermediates are the compounds listed for the reduced form of a coenzyme? in the order in which they are encountered in a turn of the a. NAD+ cycle? b. FADH2 a. citrate, oxaloacetate, fumarate c. NADH2 b. isocitrate, succinyl CoA, oxaloacetate d. both A and C c. fumarate, malate, alpha-ketoglutarate d. oxaloacetate, succinate, citrate 8. In which of the following citric acid cycle reactions 3. At which step in the electron transport chain does O2 does the coenzyme FAD participate? participate? a. citrate → isocitrate a. first step b. succinate → fumarate b. second step c. malate → oxaloacetate c. next to last step d. both A and B d. last step 9. Which of the following carry electrons from the citric 4. The “fuel” for the citric acid cycle is: acid cycle to the electron carriers of the a. acetyl CoA electron transport chain? b. citric acid a. CoA c. citrate ion b. NAD+ d. oxaloacetate ion c. FADH2 d. both B and C 5. Which of the following sets of electron carriers is associated with the electron transport chain reactions that occur at 10. Precursor for Krebs cycle production of acetyl CoA protein complex I? a.Glucose c. Oxaloacetate a. CoQ b.Pyruvate d. Citrate b. NADH c. cyt c d. FADH2 This document is the property of PHINMA EDUCATION P a g e | 22  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ 1) Activity 6: Thinking about Learning (5 mins) A. Work Tracker: You are done with this session! Let’s track your progress. Shade the session number you just completed. P1 P2 1 2 3 4 5 6 7 8 9 10 B. Think about your Learning: Tell me about your thoughts! Today’s topic is all about the Metabolism. 1. What interests you about the lesson today? 2. Do you have questions in mind that you are interested to be discussed? Please write it down. ___________________________________________________________ ___________________________________________________________ ___________________________________________________________ ________________________________________________________ ___________________________________________________________ __________________________________________________________ This document is the property of PHINMA EDUCATION P a g e | 23  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: _____________________________________________________________ Class number: _______ Section: ____________ Schedule:_____________________________________ Date:________________ Clinical correlation This document is the property of PHINMA EDUCATION P a g e | 24  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: ____________________________________________________________ Class number: _______ Section: ____________ Schedule: ____________________________________ Date: _______________ B VITAMINS IMPORTANCE IN THE COMMON METABOLIC PATHWAYS: Structurally modified B vitamins function as coenzymes in metabolic pathways. Now that the reactions of the common metabolic pathway have been considered, it is useful to formalize, in a summary fashion, B vitamin involvement in the citric acid cycle and the electron transport chain. As is shown in Figure 23.20, four vitamins have involvement in these metabolic reactions. 1. Niacin—as NAD+ and NADH 2. Ribofl avin—as FAD, FADH2, and FMN 3. Thiamin—as TPP 4. Pantothenic acid—as CoA Without these B vitamins, the human body would be unable to utilize carbohydrates, fats, and proteins as sources of energy. Additionally, the fuel for the citric acid cycle, acetyl CoA, would be unavailable since it contains a B vitamin (pantothenic acid). This document is the property of PHINMA EDUCATION P a g e | 25  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: ____________________________________________________________ Class number: _______ Section: ____________ Schedule: ____________________________________ Date: _______________ KEY TO CORRECTION FOR ACTIVITY 3 Activity 3: Skill-building Activities MATCHING TYPE: Write A-for anabolic and B-catabolic 1. A 2. A 3. B 4. B FILL IN THE DIAGRAM FILL IN THE BLANK. Fill in the missing information to the blank provided. Krebs Cycle Products of the Krebs Cycle 1.Acetyl-CoA 9.CO2. 2.oxaloacetate 10.NADH 3.citrate 11.FADH2 4.citrate 12.ATP. 5.CO2 13.two 6.ATP 14.ATP 7.Citrate 15.pyruvate 8.oxaloacetate 16.glucose. This document is the property of PHINMA EDUCATION P a g e | 26  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: ____________________________________________________________ Class number: _______ Section: ____________ Schedule: ____________________________________ Date: _______________ MATCHING TYPE: 1. B 2. D 3.A 4.C SUGGESTED VIDEOS: Anabolism and catabolism: https://www.youtube.com/watch?v=70O7Cic3J5s How mitochondria produces energy: https://www.youtube.com/watch?v=39HTpUG1MwQ Cellular respiration: https://www.youtube.com/watch?v=4Eo7JtRA7lg KREB’S CYCLE: https://www.youtube.com/watch?v=ubzw64PQPqM Electron transport chain (ETC) Part 1: https://www.youtube.com/watch?reload=9&v=C8VHyezOJD4 Electron transport chain (ETC) Part 2: https://www.youtube.com/watch?v=E_UG3WnsW3o ATP and Respiration: https://www.youtube.com/watch?v=00jbG_cfGuQ ETC Animated: https://www.youtube.com/watch?v=LQmTKxI4Wn4 ATP synthase animated: https://www.youtube.com/watch?v=kXpzp4RDGJI This document is the property of PHINMA EDUCATION P a g e | 27  Course Code: BIO 024 (Biochemistry/Biomolecules) Student Activity Sheet Module #7 Name: ____________________________________________________________ Class number: _______ Section: ____________ Schedule: ____________________________________ Date: _______________ Isomerization Oxidation & decarboxylation Citrate Acotinase Isocitrate dehydrogenase Isocitrate a-ketoglutarate CO2 Oxaloacetate NADH + H 3 1 1 NADH + H Oxidation & 2 decarboxylation Oxidation NADH + H a-ketoglutarate 2O CO2 Malate dehydrogenase dehydrogenase complex GTP FADH2 CoA-SH Succinyl CoA Malate Phosphorylation Fumarate Succinate Hydration Succinyl CoA Oxidation synthetase Fumarase Succinate dehydrogenase This document is the property of PHINMA EDUCATION P a g e | 28