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RESERVE / Biochemistry / BIOC 308 / how are organic molecules broken down by catabolic pathways

how are organic molecules broken down by catabolic pathways

how are organic molecules broken down by catabolic pathways

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School: Case Western Reserve University
Department: Biochemistry
Course: Molecular Biology
Professor: David samols
Term: Spring 2017
Tags:
Cost: 25
Description: CHAPTER (9) CELLULAR RESPIRATION AND FERMINATI ON The catabolic pathways of glycolysis and cellular respiration release the chemical energy in glucose and other fuels and use it to produce ATP
Uploaded: 08/06/2017
6 Pages 975 Views 0 Unlocks
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Where does the protein gradient that powers ATP synthase come from?




How do electrons that are exerted from glucose and other stored potential in NADH finally reach oxygen?




How does NAD+ trap electrons from glucose and other organic molecules in food?



CHAPTER (9) CELLULAR RESPIRATION AND FERMINATION The catabolic pathways of glycolysis and cellular respiration release the chemical energy in glucose and  other fuels and use it to produce ATP.  Glycolysis occurring in the cytosol, produces ATP, pyruvate, and NADH; the latter two may then entre the  mitochondria for respiration. A Mitochondrion consist of a matrix in which the enzymes of the citric acid  cycle are localized and a highly folded inner membrane in which electron transport chains are  embedded. The redox reactions of the electron transport chain pump H into the intermembrane space.  ATP is produced by oxidative phosphospholeration, using a chemiosmotic mechanism in which a proton  motive force drives protons through ATP synthase located in the membrane (9.1) Catabolic Pathways yield energy by oxidizing organic fuel Catabolic pathways and production of ATP  ♦ The breaking down of complex organic molecules in catabolic pathways releases energy that cells  can use to do work. This energy is available from the arrangement of their electrons in the bonds  between their atoms. ♦ With the help of enzymes, the cell breaks down a complex molecule to simpler molecules that  have less energy ( this degradation occurs in steps) . The energy difference is what cause energy to  produce some can be used to do work and other is released as heat.  ♦ Fermentation is a catabolic process that occurs without oxygen and partially degrades sugars or  other fuels to release energy.  ♦ Aerobic Respiration: is the most efficient catabolic pathway uses oxygen in the breakdown of  glucose (or other energy rich organic compounds) to yield carbon dioxide and water and yield energy as  ATP and heat. Aerobic respiration is often referred to as cellular respiration. Aerobic respiration is an  exergonic and spontaneous reaction which indicates that the products have less energy from the  reactants.    ♦ Anaerobic Respiration: of some prokaryotes, does not use oxygen as a reactant but has a similar  process.  Obligate Anaerobe: cannot survive in the presence of O2, use only fermentation and or anaerobic  respiration.  Facultative anaerobe can use either fermentation or aerobic respiration depending on O2 availability.  Redox Reactions: Oxidation and Reduction  Redox-reactions; or oxidation reduction reactions involve the partial or complete transfer of one or more  electrons from one reactant to another. The transfer of energy from one reactant to another.  Oxidation is the loss of electrons from one substance  Reduction is the addition of electrons to another substance.  Reducing Agent: is the substance that becomes oxidized and loses electrons (electron donor).  Oxidizing Agent: is the substance that becomes reduced and gains electrons (electron acceptor). Oxygen strongly attracts electrons and is one of the most powerful oxidizing agents (it becomes  reduced). As electrons shift towards a more electronegative they give up potential energy. Thus, Chemical energy is released in a redox reaction that relocates the electrons closer to the oxygen.  Organic molecules with an abundance of hydrogen are rich in “hilltop” electrons that release their  potential energy when they fall near oxygen. At certain steps in the oxidation of glucose, two hydrogen atoms are removed by enzymes called  dehydrogenase, and the two electrons and one proton are passed to a coenzyme NAD+ (nicotinamide  adenine dinucleotide) reducing it to NADH.  Energy from respiration is slowly released in a series of redox reactions as electrons are passed from  NADH down an electron transport chain, a group of carrier molecules located in the inner mitochondrial  membrane (or in the plasma membrane of aerobic prokaryotes), to a stable location close to a highly  electronegative oxygen atom, forming water.  Stepwise Energy Harvest via NAD+ and Electron Transport Chain Cellular respiration dose not oxidize glucose in one step but it breaks it down in several steps each  broken down by an enzyme.  Electrons are taken from the glucose, and each electron travels with a proton which makes up a  hydrogen. The hydrogen first is stopped by an electron carrier or a coenzyme called NAD+.  NAD+ is a good electron carrier because it can cycle easily between the oxidized (NAD+) and reduced  (NADH) states. NAD+ is an oxidizing agent in respiration.  How does NAD+ trap electrons from glucose and other organic molecules in food?  (1) Enzymes called dehydrogenase removes a pair of hydrogen atoms ( 2 electrons and 2 protons)  from the substrate (Glucose for example) thereby oxidizing it.  (2) The dehydrogenase delivers the 2 electrons and one proton to  the coenzyme NAD+. The other  hydrogen is released to the surrounding. The NAD+ now becomes neutralized and reduced to NADH.  NAD+ is one of the most versatile electron acceptors  (3) lose very little potential energy when they are transferred to them.  (4) NADH is an energy storage house that can be used after they fall down from the energy gradient to  oxygen. ATP can then use this energy.  How do electrons that are exerted from glucose and other stored potential in NADH finally reach  oxygen?  Respiration uses an electron transport chain to break the fall of electrons to oxygen into several  energies- releasing steps.   Electron Transport chain a sequence of electron carrier moelcules (membrane proteins) that shuttle  electrons down a series of redox reactions that release energy used to make ATP. When electron transfers from NADH to oxygen is an exergonic reaction  Energy is not released in one step , electrons cascade down from one carrier molecule to another in a  series of redox reactions losing some energy in every step intel it reaches the terminal acceptor that has a strong affinity for electrons. Every carrier is more electronegative than the previous.  Electrons transferred from glucose to NAD+  , that is reduced to NADH falls down an energy  gradient in an  electron transport chain to a more stable location with the electronegative oxygen.   The Stages of Cellular Respiration a Preview Obtain energy from Glucose by cellular respiration has three metabolic processes: stage (1) Glycolysis,  Stage (2) (Pyruvate oxidation and citric acid cycle), Stage(3) (oxidative Phospholeration: electron  transport and chemiosmosis). Stage (1) Glycolysis:  Glycolysis, which occurs in the cytosol, it breaks down glucose into two molecules of pyruvate. When the  Glucose is broken down to two pyruvate energy is released and is used and is used to change 2ADP to  2ATP, and 2NAD is reduced to 2NADH that can be used later in cellular respiration to produce more ATP.   Within the mitochondrion matrix or in the cytosol of prokaryotes, pyruvate is oxidized to acetyl CoA.  Stage (2) Pyruvate Oxidation and the Citric Acid Cycle:  The citric acid cycle then oxidizes acetyl CoA to CO2 in the mitochondrion. (In prokaryotes, this occurs in  the cytosol) In some steps Event in Stage (1)(2) have redox reaction in which electrons are transferred to NAD+( to  produce NADH) or FAD (to produce FADH2)  remember this occurs by the enzyme dehydrogenases.  NADH passes electrons to the electron transport chain, at the bottom of which they combine with H+ and  Oxygen to form water.  Stage (3) Oxidative Phospholeration : Electron Transport and Chemiosmosis: The electron transport chain then accepts electrons carried by NADH and FADH2 and passes the  electrons from one molecule to another. At the end of the chain the electrons are combined with  molecular oxygen and Hydrogen ions forming water. The energy released at each step is stored in the  mitochondrion (or prokaryotic cell) and is used to make ATP from ADP this is called phospholeration.  Oxidative Phospholeration: The production of ATP using energy derived from redox reactions of an  electron transport chain this occurs in the mitochondrion; the third major stage of cellular  respiration.Oxydative phospoleration includes both the electron transport chain and chemiosmosis .( In  prokaryotes this process occur in the plasma membrane) The energy released in this chain of redox reactions is used to synthesize ATP by oxidative  phosphorylation, a process that includes electron transport and chemiosmosis.  Up to 32 molecules of ATP may be generated for each glucose molecule oxidized to CO2 . About 10% of  this ATP is produced by substrate-level phospholeration, in which an enzyme transfers a phosphate  group from a substrate molecule to ADP.  90% of ATP is produced by oxidative phospholeration in  respiration.  (9.2) Glycolysis Harvests Chemical Energy by Oxidizing Glucose to Pyruvate  Glycolysis, a 10-step process occurring in the cytosol, has an energy investment phase and an energy  payoff phase.  Two molecules of ATP are consumed as glucose is split into two molecules of a three-carbon sugar  (glyceraldehyde-3-phosphate). The oxidation of these molecules and the production of pyruvet  yields  2NADH and 4ATP by substrate level phospholeration. For each molecule of glucose, glycolysis yields two  molecules of pyruvate, 2NADH, and a net gain of 2ATP.  Note: No glucose is changed to CO2 during glycolysis. Glycolysis occurs whether Oxygen is present or not  Enzymes catalyze each steps-in glycolysis. Kinases transfer phosphate groups from ATP ; other enzymes  leave the six-carbon sugars and rearrange atoms in substrate molecules; and a dehydrogenase oxidizes  glyceraldehyde-3-phosphate and reduces NAD+.(9.3) After a Pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation  of organic molecules Oxidation of Pyruvate to Acetyl CoA  The Pyruvate produced in glycolysis is actively transported into the mitochondrion. In a series of steps  within multi-enzyme complex:  A carboxyl group is removed from the three carbon pyruvate and released as CO2 The remaining two group is oxidized to form acetate, with the accompanying reeducation of NAD+ to NADH ; and a  coenzyme A is attached by its sulfur atom to acetate, forming Acetyl CoA.  Citric Acid Cycle In the Citric Acid Cycle, the acetyl group of acetyl CoA is added to oxaloacetate to form citrate, which is  progressively decomposed to oxaloacetate. For each turn of the citric acid cycle,  ♦ 2 carbons enter from Acetyl CoA; 2 carbons leave completely oxidyed as CO2 ♦ 3 NADH and one FADH2 are formed  ♦ 1 ATP (GTP in most animal cells) is made by substrate level phospholeration.  It takes two turns of the citric acid cycle to oxidize the two acetyl groups derived from a single glucose  molecule.  (9.4) During Oxidative Phospholeration, Chemiosmosis Couples Electron transport to synthesis ATP The first two stages of respiration have produced only 4 ATP molecules per glucose. A  much more impressive yield of ATP is achieved through oxidative phosphoseration.  The Pathway of Electron Transport  Thousands of electron transport chains are embedded in the cristae (infoldings) of the inner  mitochondrial membrane (or in the plasma membrane of prokaryotes). The components of the electron  transport chain are organized into four complexes, and most are proteins to which non protein  prosthetic groups are tightly bound.  The electron carriers shift between reduced and oxidized states as they donate and accept  electrons, with the free energy of electrons decreasing step by step.  (1) The transfer of electrons proceeds from NADH to a  flavoprotein to an iron-sulfur protein  (complex 1)  to a mobile hydrophobic molecule called ubiquinone (CoQ or Coenzyme Q).  (2) Next, electrons are passed down a series of molecules called cytochrome, which are proteins  with iron containing heme groups.  (3) The last cytochrome (cyta 3) passes two electron oxygen which picks up tw hydrogen forming  water (4) FADH2 adds its electrons to a chain at a lower energy level (within complex II); Thus less  energy is provided by FADH2 as compared to NADH Chemiosmosis: The Energy Coupling Mechanism ATP  Synthase, a protein complex embedded in the inner mitochondrial membrane or in the  prokaryotic plasma membrane, uses the energy in the energy in the proton (H+) gradient to make ATP( it  makes ATP from ADP) . An example of this is the process of chemiosmosis.  The flow of H+ down their gradient through the stator and rotor part of the ATP synthase  complex causes the rotor and the attached rod to rotate, activating catalytic sites in the knob protein,  Where ADP and inorganic phosphate join to make ATP. Where does the protein gradient that powers ATP synthase come from?  When some members of the electron transport chains pass electrons, they also accept and  release protons, which are deposited in the intermembrane space. The Proton Motive Force is the  potential energy of the proton gradient  Examples of Chemiosmosis—The use of H+ gradient across a membrane to drive cellular work:  (1) In mitochondria, Exergonic redox reactions produce the proton gradient that drives the production of  ATP. (2)  Chloroplasts use light energy to create the proton motive force used to make ATP. (3)  Prokaryotes use Proton gradients generated across the plasma membrane to transport molecules,  make ATP and rotate flagella. An Accounting of ATP production by cellular respiration  About 30 to 32 ATPs may be produced per glucose molecule oxidized. These numbers are only estimates  for the three reactions; The ratio of NADH to ATP is not a hole number – experimental data indicate that  production of 2.5 ATPs/NADH and 1.5 ATPs/FADH2;  The electron produced from NADH in glycolysis may be passed across the mitochondrial membrane to  NAD+ or FAD depending on the type of shuttle used in the cell; and the proton motive force generated by  the electron transport chain is also used to power other work in the mitochondrion.  The efficiency of energy conversion in respiration is about 34%. The remaining 66% is lost as heat. In the  brown fat cells of some mammals, an uncoupling protein allows protons to flow back across the inner  mitochondrial membrane. Without the generation of ATP ( which would inhabit cellular respiration), Fats  continue to be oxidized and heat is generated during hibernation.  (9.5) Fermentation and Anabolic respiration enable cells to produce ATP without Oxygen Some organisms can oxidize organic substances without oxygen by either fermentation  or anaerobic respiration ;;;;;;;;;;;;;;;;;;;;;;;;;;; Anaerobic respiration involves an organism that generates ATP through an electron transport chain that  does not use oxygen as the final electron acceptor. Some bacteria use sulfate ions to accept electrons  generating H2S rather than H2O.  Fermentations is the oxidation of glucose in glycolysis produces a net 2 ATP by substrate-level  phospholeration, and NADH is recycled to NAD+ by the transfer of electrons by the transfer of electrons  to pyruvates or derivatives of pyruvate.  Types Of Fermentation  Pyruvate is converted to acetaldehyde, and CO2 Fermentation involves glycolysis and reactions that regenerate NAD+ by transferring the electrons from  NADH to pyruvates or its derivatives  The NAD+ can be used to oxidize sugar by glycolysis  We have two main Types Of Fermentation:  (1) Alcohol fermentation: pyruvate is converted to ethanol in 2 steps. Step (1) releases CO2 From  Pyruvate which is then converted to acetaldehyde. Step (2) acetaldehyde is reduced by NADH to  become ethanol. This continuous supply of NAD+ is needed for glycolysis. (2) Lactic Acid Fermentation: Pyruvate is directly reduced by NADH to form lactate there is  no CO2 involved.  (9.6) Glycolysis and the citric acid cycle connect to many other metabolic pathways  The Versatility of Catabolism Fats, proteins, and carbohydrates can all be used in cellular respiration. Proteins are  digested into the amino acids, which are then delaminated ( the amino group is removed) and  can enter glycolysis or the citric acid cycle at several points.  The Digestion of Fats yields glycerol, which is fed into glycolysis and fatty acids which  are then broken down by beta oxidation to two carbon fragments that enter the citric acid  cycle as acetyl CoA.  Biosynthesis (anabolic pathways) The organic molecules of food also provide carbon skeletons for biosynthesis.  Some  monomers such as amino acids can be directly incorporated into the cells macromolecule.  Intermediate compounds of glycolysis and citric acid cycles serve as prerecusors for anabolic  pathways. Carbohydrates, Fats, and Proteins can be interconverted to provide for a cell’s needs.  Regulation of Cellular respiration via Feedback Mechanism Though feedback inhibition, the end-product of an anabolic pathway inhibits an enzyme early  in the pathway, thus preventing a cell from producing an excess of a substance.  The Supply of ATP in the Cell regulates respiration. The allosteric enzyme that catalyzes the  third step glycolysis, phosphofructokinase, is inhabited by ATP and activated by AMP (derived  from ADP). Phosphofructokinase is also inhabited by citrate released from the mitochondria,  thereby synchronizing the rates of glycolysis and the citric acid cycle. Other enzymes located at  key intersections help to maintain metabolic pathways.

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