Citric Acid Cycle

Describe the role of the citric acid cycle as a central metabolic mechanism. Explain what happens to the cells’ abilities to oxidize acetyl CoA when intermediates of the cycle are drained off for amino acid biosynthesis. Glucose is a source of energy that is metabolized into glycolysis to pyruvate yielding ATP. To become more efficient, pyruvate must be oxidized into carbon dioxide and water. This combustion of carbon dioxide and water to generate ATP is called cellular respiration (Tymoczko, Berg & Stryer, 2013, p. 315). In eukaryotic cells, this aerobic process is used because of the efficiency.Cellular respiration is divided into parts: carbon fuels are completely oxidized with a concomitant generation of high transfer potential electrons in a series of reactions called citric acid cycle, tricarboxylic acid cycle, or Krebs cycle (Tymoczko, p. 318); the acetyl groups are fed into the citric cycle which are oxidized to CO2 and the energy released in conserved reduced electron carriers- NADH and FADH; the high transfer potential electrons transferred to oxygen to form water in a series of oxidation-reduction reactions called oxidative phosphorylation (Tymoczko, p.  318).The citric acid cycle takes place in the mitochondria and is the central metabolic hub in the cell; the gateway to aerobic metabolism of all fuel molecules (Tymoczko, p. 318). This cycle is important source for the building blocks of molecules such as amino acids, nucleotide bases, and porphyrin. Pyruvate can convert into different molecules depending on the aerobic (acetyl coenzyme A) or anaerobic condition (lactic acid or ethanol). In the presence of oxygen, acetyl CoA is able to enter the citric acid cycle because this is the most acceptable fuel input into the cell.The path that the pyruvate takes depends on the energy needs of the cell and the oxygen availability (Tymoczko, p. 318). Pyruvate dehydrogenase complex consist of three distinct enzymes each with its own active site: Pyru vate dehydrogenase catalyzes the decarboxylation of pyruvate and the formation of acetyllipoamide, dihydrolipoyl transacetylase forms acetyl CoA, and dihydrolipoly dehydrogenase regenerates the active transacetylase (Tymoczko, p. 319).These three enzymes participate with five coenzymes: thiamine pyrophosphate, lipoic acid, coenzyme A, NAD+, and FAD. Acetyl CoA undergoes oxidation by donating the acetyl group to the four-carbon compound oxaloacetate to form the six-carbon citrate. Citrate is transformed to isocitrate (six-carbon molecule), that is dehydrogenated with the loss of CO2 (twice) to yield a five-carbon compound a-ketoglutarate (oxoglutarate). A-ketoglutarate undergoes loss of CO2 yielding a four-carbon succinate and second molecule of CO2.Succinate is enzymatically converted into a three step four-carbon oxaloacetate. Citric acid cycle removes electrons from citrate and uses these electrons to form NADH and FADH2. These electrons carriers yield nine molecules of ATP when o xidized by O2 in oxidative phosphorylation. Electrons released in the reoxidations of NADH and FADH2 flow through a series of membrane proteins (electron-transport chain) generating a proton gradient across the membrane. This proton gradient is used to generate ATP from ADP and inorganic phosphate (Tymoczko, p. 330).The citric acid is comprised of two stages: Each turn of the cycle, one acetyl group (two-carbon) enters the acetyl-CoA and two molecules of CO2 leave-one molecule of oxaloacetate is used to form citrate then metabolized to a four carbon molecule; the remaining four carbon molecule is metabolized after many reactions- oxaloacetate is regenerated. The citric acid cycle has eight steps: 1. The formation of citrate is the condensation of acetyl-CoA with oxaloacetate to form citrate and is catalyzed by citrate synthase. This occurs by the condensation of four-carbon unit, oxaloacetate, and a two-carbon unit, the acetyl group of acetyl CoA.Oxaloacetate reacts with acetyl CoA and water to yield citrate and CoA (Tymoczko, p. 330). 2. The formation of isocitrate via cis-Aconitate. The enzyme aconitase catalyzes the reversible transformation of citrate to isocitrate through formation of tricarboxylic acid cis-aconitate. Citrate is isomerized into isocitrate to enable the six carbon unit to undergo oxidative decarboxylation allowing a dehydration and hydration step of citrate (Tymoczko, p. 332). Aconitase can promote the reversible addition of H2O to double bond of enzyme-bound cis-anonitate in two ways: one leading to citrate and the other to isocitrate.3. Oxidation of isocitrate to a-ketoglutarate and CO2. Isocitrate dehydrogenase catalyzes oxidative decarboxylation of isocitrate to form a-ketoglutarate. The two forms of isocitrate dehydrogenase require NAD+ as electron acceptor and NADP+. This intermediate reaction is oxalosuccinate (unstable alpha-ketoacid). The enzyme loses CO2 to form alpha-ketoglutarate which generates the first high-transfer potentia l electron carrier in the cycle NADH through oxidation (Tymoczko, p. 332). 4. Oxidation of a-ketoglutarate to succinyl-CoA and CO2.Oxidative decarboxylation of a-ketoglutarate is converted to succinyl-CoA and CO2 by the a-ketoglutarate dehydrogenase complex. During this portion of citric acid cycle, the two carbon atoms have entered the cycle and two carbon atoms have been oxidized to CO2. The electrons from oxidations are captured in two molecules of NADH (Tymoczko, p. 333). 5. Conversion of Succinyl-CoA to succinate. Succinyl-CoA has a thioester bond with a strong negative standard free energy of hydrolysis (six-carbon citrate from the four-carbon oxaloacetate and the two-carbon fragment).The energy released in the breakage of the bond is used to drive the synthesis of a phosphoanhydride bond in either GTP or ATP. The enzyme that catalyzes the reaction is succinyl-CoA synthetase. In tissues that require large amount of cellular respirations, ADP predominates whereas anabolic react ions require GDP/GTP (Tymoczko, p. 334). The methylene group (CH2) is converted into a carbonyl group (C=O) in three steps: an oxidation, hydration, and a second oxidation reaction (Tymoczko, p. 335). The energy produced and extracted in the forms of FADH2 and NADH. 6.Oxidation of succinate to fumarate. Succinate formed from succinyl-CoA is oxidized to fumarate by flavoprotein succinate dehydrogenase. FAD is the hydrogen acceptor in the reaction. Succinate dehydrogenase is directly associated with the electron-transport chain transferring two electrons directly from FADH2 to coenzyme CoQ; CoQ passes electrons to the oxygen acceptor (Tymoczko, p. 334). Succinate is oxidized to fumarate; starting the next step of hydration of fumarate to form L-malate. 7. Hydration of fumarate to malate. The hydration of fumarate to L-malate is catalyzed by fumarase.Malate is oxidized to form oxaloacetate and NAD+ is the hydrogen acceptor (Tymoczko, p. 335). 8. Oxidation of Malate to oxaloacetate. Thi s is the last reaction of the citric acid cycle. NAD-linked L-malate dehydrogenase is the oxidation of L-malate to oxaloacetate. The citric acid is considered important in the central metabolic mechanism because: it is the starting points for synthesis of a variety of intermediate compounds such as the metabolism of sugars and amino acids; the metabolism of amino acids and lipids; and it links anaerobic metabolism to aerobic metabolism.The pathway of the citric acid cycle is the intermediate hub of metabolism that serves to fuel many types of compounds. The intermediates are drawn out of the cycle to be used as precursors in many varieties of biological pathways. The citric acid cycle is amphibolic pathway serving as catabolic and anabolic processes. The oxidative catabolism of carbohydrates, fatty acids, and amino acids through reactions serve as precursors. For example, amino acids such as aspartate and glutamate, the carbons of oxaloacetate and a-ketoglutarate build other amino a cids like purine and pyrimidine nucleotides.Oxaloacetate is converted to glucose in gluconeogenesis. Succinyl-CoA is an intermediate in the synthesis of the prophyrin ring of heme groups serving as oxygen carriers (blood) and electron carriers such as cytochromes (Retrieved from Foundations of biochemistry). The mechanisms of the citric acid cycle complement each other by reducing the rate of the formation of acetyl CoA when the energy of the cell is high and biosynthetic intermediates are abundant. This energy is abundant and the cycle can provide a source of building blocks for biomolecules such as nucleotide bases, proteins, and heme groups.This depletes the intermediates and when the cycle needs replenishment of the intermediates, anaplerotic reactions occur (Tymoczko, p. 343). Describe the 3 steps in photosynthesis, detailing the interrelationships among them. (Discussion in the online classroom. ) The three steps part of photosynthesis process involves capturing energy from th e sunlight; using energy to make ATP and reducing power in the form of NADPH; and using ATP and NADPH to power the synthesis of organic molecules (carbohydrates) from CO2 in the air (carbon fixation).There are two types of reactions that take place to ensure the process of photosynthesis: the light-dependent reactions and the light-independent reactions (Calvin cycle). Light-dependent reactions provide raw materials such as ATP serving as a source of energy and NADPH provides the reducing power (taftcollege. edu). Light reactions result in the creation of reducing power for the production of NADPH, the generation of a transmembrane proton gradient for the formation of ATP, and the production of O2 (Tymoczko, p.  404).The Calvin cycle (C3 photosynthesis) is the pathway that assembles the new molecules which takes place in the stroma of the chloroplasts (Retrieved from Taft College website). Chloroplasts are organelles in which photosynthesis takes place. The main role of chloroplas t is to capture light energy and convert the electromagnetic radiation into chemical energy for the essence and is the key to life on planet earth. Chloroplasts have an inner and outer membrane.The inner membrane surrounds a space called the stroma that contains soluble enzymes (rubisco-important in the Calvin cycle) that reduce power and ATP converting CO2 into sugar (Tymoczko, p. 390). In the stroma, membranous discs called thylakoid are aligned in stacks which are impermeable to most molecules and ions whereas the outer membrane of chloroplast has a permeable membrane to small molecules and ions (Tymoczko, p. 390). Thylakoids have a large surface area for light absorption and the space within them allows rapid accumulation of protons (Retrieved from Taft College website).Chloroplasts contain chlorophyll, a green pigment found inside the thylakoid membranes. Hundreds of chlorophyll molecules function together like an antenna system for the capture of light photons resulting in che mical electron excitement (Gu, 2013). The region of chemical excitation, called an exciton, migrates through the chlorophyll antenna until it reaches a point in the array where it can be funneled into a chemical system (Gu, 2013). Chlorophyll has two types: chlorophyll a, primarily in green plants has less absorption than chlorophyll b.Chlorophyll b has accessory pigments such as carotenoids which give the colors of yellows and reds in plants. The accessory pigments are arranged in numerous light-harvesting complexes that completely surround the reaction center; these pigments absorb light and deliver the energy to the reaction center by resonance energy transfer for conversion into chemical forms (Tymoczko, p. 394). The chlorophyll molecules are arranged in groups called photosystems. There are two types of photosystems are Photosystem I and Photosystem II.When chlorophyll molecule absorbs light, energy from the light raises chlorophyll electron molecules to a higher energy state k nown as being photoactivated (Retrieved from Taft College website). Excited electrons anywhere within the photosystem are then passed on from one chlorophyll molecule to the next until they reach a special chlorophyll molecule at the reaction center of the photosystem leading to a chain of electron carriers (Retrieved from Taft College website). The light-dependent reactions start within Photosystem II.Photosystem II responds to wavelengths shorter than 680 nm sending electrons through a membrane-bound proton pump called cytochrome bf and then to photosystem I to replace the electrons that are donated to photosystem I to NADP+. The electrons in the reaction center of photosystem II are replaced when two molecules of water are oxidized to generate a molecule of oxygen (Tymoczko, p. 395). When excited electrons reach the special chlorophyll molecule at the reaction center of PS II, this chain of electron carriers found within the thylakoid membrane releases energy.The energy is used t o pump protons (hydrogen ions) across the thylakoid membrane into the space within the thylakoid forming a proton gradient. The protons can travel back across the membrane, down the concentration gradient, passing through ATP synthase. ATP synthase is located in the thylakoid membrane and it uses the energy released from the movement of protons down their concentration gradient to synthesize ATP from ADP and inorganic phosphate (Retrieved from Taft College website). This proton gradient is the driving force for ATP production (Tymoczko, p.395). The synthesis of ATP in this manner is called non-cyclic photophosphorylation (uses the energy of excited electrons from photosystem II). The electrons from the chain of electron carriers are then accepted by Photosystem I. Photosystem I responds to light within wavelengths shorter than 700 nm and responsible for providing electrons to reduce NADP+ to NADPH, requiring a reduction in power of the electrons (Tymoczko, p. 395). Electrons are rep laced from previous electrons lost from Photosystem I.Photosystem I absorbs light and becomes photoactivated leading to excited electrons that are raised to a higher energy state. These electrons are passed along a short chain of electron carriers and used to reduce NADP+ in the stroma (Retrieved from Taft College website). The powerful reductant ferredoxin reacts with NADP+ forming NADPH. When there is a shortage of NADP+ this inhibits the normal flow of electrons. When this occurs, the alternative pathway for ATP production (cyclic photophosphorylation) begins with Photosystem I absorbing light and becoming photoactivated.The excited electrons from Photosystem I are passed to a chain of electron carriers between Photosystem I and II. These electrons travel along the chain of carriers back to Photosystem I causing the pumping of protons across the thylakoid membrane creating a proton gradient (Retrieved from Taft College website). The protons move back across the thylakoid membrane through ATP synthase producing ATP. The light dependent reactions produce oxygen as a waste product. The special chlorophyll molecules at the reaction center pass electrons to the chain of electron carriers, becoming positively charged.Within the thylakoid space, water molecules are split due to the enzyme at the reaction center known as photolysis (Retrieved from Taft College website). Oxygen and H+ ions are formed, leading to the waste product of oxygen which most living organisms need on earth. The dark phase of photosynthesis starts with the reaction of CO2 and ribulose 1, 5-bisphosphate to form two molecules of 3-phosphoglycerate (Tymoczko, p. 418). The light-independent reactions of photosynthesis occur in the stroma of the chloroplast and involve the conversion of carbon dioxide and other compounds into glucose.The light-independent reactions can be split into three stages; these are carbon fixation, the reduction reactions and finally the regeneration of ribulose bisphospha te – collectively these stages are known as the Calvin Cycle (Retrieved from Taft College website). During carbon fixation, carbon dioxide in the stroma (which enters the chloroplast by diffusion) reacts with a five-carbon sugar called ribulose bisphosphate (RuBP) to form a six-carbon compound which is catalyzed by an enzyme called ribulose bisphosphate carboxylase (large amounts present within the stroma), known as rubisco (Retrieved from Taft College website).Rubisco is the most abundant enzyme in plants and most abundant protein in the biosphere (Tymoczko, p. 409). As soon as the six-carbon compound is formed, it splits to form two molecules of 3-phosphoglycerate. 3-phosphoglycerate is then used in the reduction reactions (Retrieved from Taft College website). 3-phosphoglycerate is reduced during the reduction reactions to a three-carbon sugar called hexose phosphate that consist of 3 types of isomeric forms: glucose 1-phosphate, glucose 6- phosphate, and fructose 6-phosph ate known as hexose monophosphate pool (Tymoczko, p.  409).Energy and hydrogen is needed for the reduction that are supplied by ATP and NADPH and H+ (both produced during light-dependent reactions). The condensation of many molecules of glucose phosphate forms starch in the form of carbohydrates which is stored in plants. The hexose phosphates produced during the reduction reactions, only use one to synthesize glucose phosphate, the other phosphates will be used to regenerate RuBP (Retrieved from Taft College website).The regeneration of RuBP is essential for carbon fixation to continue. Five hexose phosphate molecules will undergo a series of reactions requiring energy from ATP, to form three molecules of RuBP which are consumed and produced during light-independent reactions forming the Calvin cycle. The actual operation of photosynthesis reactions, called the carbon reduction or Calvin cycle, may be summarized as follows: 6 CO2 + 6 RudP —-> 6 RudP + 1 Hexose # of carbons 6 + 30 —-> 30 + 6