Part two krbs cycle


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  • Part two krbs cycle

    1. 1. Part two principle of biochemistryMetabolism and biological energy 2-carbohydrate Metabolism 2-Tri-carboxylic Acid cycle 3-Electron Transport System Course code: HFB324 Credit hours: 3 hours Dr. Siham Gritly Dr. Siham Gritly 1
    2. 2. Tricarboxylic acid cycle Dr. Siham Gritly 2
    3. 3. • lactate: a 3-carbon compound produced from pyruvate during anaerobic metabolism• oxaloacetate: a carbohydrate intermediate of the TCA cycle.Oxidative phosphorylation is the process that conserves the energy of the ETC by phosphorylation of ADP to ATPThe chemiosmotic coupling theory explains how oxidative phosphorylation links the ETC and ATP synthesis Dr. Siham Gritly 3
    4. 4. • Cytochromes are, in general, membrane- bound (i.e. inner mitochondrial memberane) hemoproteins containing heme groups and are primarily responsible for the generation of ATP via electron transport Dr. Siham Gritly 4
    5. 5. 2-Tri-carboxylic Acid cycle Citric Acid Cycle, Krebs Cycle 2nd phase of cellular respiration• *kerbs cycle is a series of reactions in the Mitochondria that bring about the catabolism of acetyl residues, liberating hydrogen equivalent (2H) which on oxidation lead to the release of most of the free energy of tissue fuels.• the acetyl residues are in the form of acetyl Co- enzyme A (active acetate).• *reducing equivalent (electrons) are oxidized by respiratory chain with release of ATP. Dr. Siham Gritly 5
    6. 6. • It is the final pathway for oxidation of glucose, lipids and protein for the generation of ATP.• It catalyzed the combination of their common metabolite----acetyl Co-enzyme A with oxaloacetate to form citrate by series of dehydrogenation and decarboxylation reaction ,• citrate or citric acid is degraded releasing reducing equivalent (energy in the form of H molecules) and 2 carbon dioxide and regenerating oxaloacetate. Dr. Siham Gritly 6
    7. 7. The beginning of the cycle• *lactic acid is oxidized to pyruvate and the pyruvate is oxidized by specific enzyme to acetyl-Co enzyme A.• *acetyl-Co enzyme A (2C) is combined with another acid known as oxaloacetate (4C) to yield citric acid (6C).• *one molecule of acetyl Co-enzyme A is oxidized to CO2 +H2O in each cycle.• *the oxaloacetate regenerated react with another molecule of acetyl Co-enzyme A and the cycle is repeated• *many specific enzymes enter in this reaction mainly Thiamin Pyrophosphatase (TPP) Dr. Siham Gritly 7
    8. 8. Citric acid cycle has two functions• 1-function in anabolism and catabolism of carbohydrates, fatty acids and amino acids• 2-provides intermediates for synthesis of compound required for the body functioning Dr. Siham Gritly 8
    9. 9. Location of citric acid cycle • Located in the mitochondrial matrix • Mitochondrial membrane facilitates the transfer of reducing equivalent H to the adjacent enzymes of respiratory chainMitochondria structure:1) inner membrane2) outer membrane3) cristae4) Matrix Dr. Siham Gritly 9
    10. 10. 3 stages of The Krebs Cycle• 1. Acetyl CoA (2 C) binds a four carbon molecule (oxaloacetate) producing a six carbon molecule (citrate).• 2. Two carbons are removed as carbon dioxide.• 3. The four carbon starting material is regenerated.• The Krebs Cycle generates ATP and many energized electrons (in the form of FADH2 and NADH) for the electron transport chain. Dr. Siham Gritly 10
    11. 11. Reactions of the TCA Cycleref. 1996–2012, LLC | info @ Dr. Siham Gritly 11
    12. 12. 1. Citrate synthase (synthesis of citric acid) The citric acid cycle begins when Coenzyme Atransfers its 2-carbon acetyl group to the 4-carbon compound oxaloacetate to form the 6-carbon molecule citrate Acetyl CoA and oxaloacetic acid condense to form citric acid. The acetyl group CH3COO is transferred from CoA to oxaloacetic acid at the ketone carbon, which is then changed to an alcohol. Dr. Siham Gritly 12
    13. 13. • The beginning step of the citric acid cycle occurs when;-• a four carbon compound (oxaloacetic acid) condenses with acetyl CoA (2 carbons) to form citric acid (6 carbons)• the starting point for the citric acid cycle. Dr. Siham Gritly 13
    14. 14. Step 2 aconitaseisomerization of the position of the -OH group on citric acid. This first step is a dehydration of an alcohol to make an alkene The citrate is rearranged to form an isomeric form isocitrate The citrate is rearranged into its isomer, isocitrate by the enzyme aconitase. Dr. Siham Gritly 14
    15. 15. 3. Isocitrate DehydrogenaseOxidative decarboxylation of isocitrate to yield a -ketoglutarateThe 6-carbon isocitrate is oxidized and a molecule of carbondioxide is removed producing the 5-carbon molecule alpha- ketoglutarate. During this oxidation, NAD+ is reduced to NADH + H+ First oxidative decarboxylation Dr. Siham Gritly 15
    16. 16. • This is the first step where a carbon group is lost as carbon dioxide in a decarboxylation reaction (oxidation reaction)• The electron reduces NAD+ to NADH,• the proton is released as an H+ ion. Dr. Siham Gritly 16
    17. 17. 4 -Ketoglutarate Dehydrogenase complexAlpha-ketoglutarate is oxidized, carbon dioxide isremoved, and coenzyme A is added to form the 4- carbon compound succinyl-CoA. During this oxidation, NAD+ is reduced to NADH + H+ A second oxidative decarboxylation high energy thioester succinyl-Co-A Dr. Siham Gritly 17
    18. 18. • Second stage where NADH and the second CO2 are formed (A second oxidative decarboxylation) Ketoglutarate Dehydrogenase complex need coenzymes (TPP, NAD, FAD and Co-A)• Result of reaction is a high energy thioester succinyl-Co-A Dr. Siham Gritly 18
    19. 19. 5. succinyl-CoA synthase (succinate thiokinase) CoA is removed from succinyl-CoA to produce succinate. Theenergy released is used to make guanosine triphosphate (GTP) from guanosine diphosphate (GDP) and Pi by substrate-level phosphorylation GTP can then be used to make ATP Succinic acid, a 4 carbon acid, is the product of this reaction(the beginning of the cycle). substrate-level phosphorylation GTP can be used to make ATP Dr. Siham Gritly 19
    20. 20. • The energy conserved from previous step in the succinyl-C A as the thioester bond is released in the form of ATP• This is the only reaction where ATP is released at the substrate level• The hydrolysis of the thioester bond (exothermic) is coupled with the formation of guanosine triphosphate first but is further coupled with the ADP to make ATP). Dr. Siham Gritly 20
    21. 21. 6. Succinate dehydrogenase (flavoprotein) Succinate is oxidized to fumarate. During thisoxidation, two electrons and two protons produced are transferred to FAD, which becomes FADH2. Dr. Siham Gritly 21
    22. 22. • Succinic acid is degraded further to fumarate (4C) by the flavoprotein enzyme succinate dehydrogenase• succinate dehydrogenase the only enzyme bound to inner surface of inner mitochondrial membrane• The reaction produced FADH2 Dr. Siham Gritly 22
    23. 23. 7 Fumarase (fumarate hydratase)Water is added to fumarate to form malate (malic acid) Dr. Siham Gritly 23
    24. 24. • In step 7 by the action of Fumarase water is added to fumarate to form malate (malic acid) this is a Hydration reaction to form an alcohol from alkene functional group• This is a simple hydration reaction of an alkene (C to C=C) fumarate to form an alcohol (-OH is bound to a C atom) malate.• Malate is freely permeable to mitochondrial membrane where then converted to oxaloacetate Dr. Siham Gritly 24
    25. 25. 8 malate dehydrogenase. Malate is oxidized to produce oxaloacetate, thestarting compound of the citric acid cycle. During this oxidation, NAD+ is reduced to NADH + H+ Dr. Siham Gritly 25
    26. 26. • Oxidation reaction of malate by the action of enzyme malate dehydrogenase• This is the final reaction in the citric acid cycle. The reaction is the oxidation of an alcohol to a ketone to make oxaloacetic acid.• The coenzyme NAD+ causes the transfer of two hydrogens and 2 electrons to NADH + H+.• This is a final entry point into the electron transport chain (substrate level). Dr. Siham Gritly 26
    27. 27. Final products of citric acid cycle• 2 acetyl groups + 6 NAD+ + 2 FAD + 2 ADP + 2 Pi• forms;• 4 CO2• + 6 NADH• + 6 H+• + 2 FADH2• + 2 ATP Dr. Siham Gritly 27
    28. 28. 3-Electron transport chain The electron transport chain is third and final common pathway in aerobic cellular respiration to generate ATP.• In this pathway electrons (reducing equivalents H+) are transferred to oxygen• electrons transport between electron donor (NADH) and electron acceptor (O2).• Passage of electrons between donor and acceptor releases energy This result is the formation of electrochemical proton gradient which used to generate ATP Dr. Siham Gritly 28
    29. 29. Mechanism of the chain• Chemiosmotic theory• According to the theory, the transfer of electrons down an electron transport system through a series of oxidation-reduction reactions releases energy.• This energy allows certain carriers in the chain to transport hydrogen ions (H+ or protons) across a membrane Dr. Siham Gritly 29
    30. 30. • electrochemical gradient or potential difference across the membrane demonstrate the concentration of hydrogen ions on one side of the membrane• One side of the membrane is positive (protons accumulate) the other side is negative this lead to held the membrane to its energized state (proton motive force)• The NADH + H+ and FADH2 carry protons and electrons to the electron transport chain to generate additional ATP by oxidative phosphorylation Dr. Siham Gritly 30
    31. 31. • the actions of the chain is carried on by highly organized oxidation-reduction enzymes, coenzymes and electron carrier cytochromes Dr. Siham Gritly 31
    32. 32. The purpose of the electron transport chain• 1) to pass along 2H+ ions and 2e- to react with oxygen; 2) to conserve energy by forming three ATPs; and 3) to regenerate the coenzymes back to their original form as oxidizing agents Dr. Siham Gritly 32
    33. 33. Location of Electron transport chain• This chain is located in the inner mitochondrial membrane of cell, protons are transported from the matrix of the mitochondria across the inner mitochondrial membrane to the intermembrane space located between the inner and outer mitochondrial membranesMitochondria structure:1) inner membrane2) outer membrane3) cristae4) Matrix Dr. Siham Gritly 33
    34. 34. the electron transport chain may be found in the cytoplasmic membrane or the inner membrane of mitochondria Dr. Siham Gritly 34
    35. 35. What are the initial reactants which start the electron transportchain?• During various steps in glycolysis and the citric acid cycle, the oxidation of certain intermediate precursor molecules causes the reduction of NAD+ to NADH + H+ and FAD to FADH2.• NADH and FADH2 then transfer protons and electrons to the electron transport chain to produce additional ATPs from oxidative phosphorylation (is when phosphorylation is coupled with biological oxidation) Dr. Siham Gritly 35
    36. 36. Dr. Siham Gritly 36
    37. 37. Components of ETC• NAD dehydrogenase• FMN, FAD• Ubiquinone or Co-enzyme Q (fat soluble not protein)• Iron containing proteins (iron-sulfur Fe-S protein)• Cytochromes (haemprotein) b, c, c1, aa3• aa3 or cytochrome oxidase Dr. Siham Gritly 37
    38. 38. Components are present in the innermitochondrial membrane as four complexes(cytochromes- electron carrier proteins)• Complex-I NADH- Ubiquinone oxido- reductase• Complex-II Succinate- Ubiquinone oxido- reductase• Complex III Ubiquinol- Cytochrome c oxidoreductase• Complex IV cytochromec (cyt) - Oxygen oxidoreductase Dr. Siham Gritly 38
    39. 39. electrons are transported to meet up with oxygen from respirationat the end of the chain. The overall electron chain transportreaction is: 2 H+ + 2 e+ + 1/2 O2 ---> H2O + energy 2 hydrogen ions, 2 electrons, and an oxygen molecule react to form as a product water with energy released in an exothermic reaction Dr. Siham Gritly 39
    40. 40. Reactions of Electron Transport Chain• Electron carriers (NAD, FAD) carry the high energy electrons that produced in the first and second processes of cellular respiration (glycolysis &citric acid cycle) to a group of enzymes in inner membrane of mitochondria• *NAD+ molecule accepts and transfers one hydride ion (H- i.e. one H+ & 2e-)• *FMN or FAD or coenzyme Q accepts and donates 2H2 (2H+ & 2e) a time Dr. Siham Gritly 40
    41. 41. • *cytochrome or iron-sulfer protein molecule accepts and transfers only one electron but no H+• Enzymes move electron along from one molecule to the other• As the electrons (2e) passed, H+ ions are pumped to the outer membrane of mitochondria Dr. Siham Gritly 41
    42. 42. Formation of ATP in oxidative phosphorylation• During the transfer of electrons energy is produced• The energy is coupled to the formation of ATP by phosphorylation of ADP by the action of ATP synthase complex• (ATP synthase complex converts this mechanical work into chemical energy by producing ATP Dr. Siham Gritly 42
    43. 43. • The transport of one pair of electrons from NADH to oxygen through the electron transport chain produces three molecules of ATP• the transport of one pair of electrons from FADH2 to oxygen through the electron transport chain produces two molecules of ATP. Dr. Siham Gritly 43
    44. 44. • The ion gradient is used to run the ATP production by the electron transport phosphorylation (chemiosmosis)• By the end electrons produced energy, electron carriers are back again the process continue• Oxygen is the last electron acceptor• Water is the last product made O2 picks up electron and combines with a H+ ions Dr. Siham Gritly 44
    45. 45. Reduction of oxygen to water• Cytochrome oxidase (cyt aa3) the last cytochrome complex passes electron from cytochrome c to molecular oxygen• O2 molecules must accept 4 electrons to reduce to water• There are only two electrons per turn of ETC ETC must cycle twice to pass along 4 electrons to O2 Dr. Siham Gritly 45
    46. 46. Each oxygen atom with two electrons accepts twoprotons thus a molecule of water resultthe reduction of oxygen to water result in productionof about 300 ml of water/day (metabolic water) molecule of water Dr. Siham Gritly 46
    47. 47. The end products of cellular respiration (glucose oxidation) (glycolysis, citric acid cycle &ETC)• The over all equation of glucose oxidation=• C6H1206 +6O2→6CO2 +6H2O +ATP (36ATP- 2ATP)• Glycolysis =• 2ATP• 2NADH• 2Pyruvate Dr. Siham Gritly 47
    48. 48. • Products of pyruvate oxidation (to acetyl CA)• 2CO2• 2NADH• 2acetyl-CA• Products of Kerb’s cycle• 4CO2• 2FAD• 6NADH• 2ATP• 6 H+ Dr. Siham Gritly 48
    49. 49. What are the final products of the chain• Products of Electron transport chain• H2O• 3 ATP as free energy Dr. Siham Gritly 49
    50. 50. Dr. Siham Gritly 50
    51. 51. Gluconeogenesis (glucose synthesis)• Production of glucose from non carbohydrates• The primary carbon skeletons used for gluconeogenesis are derived from pyruvate, lactate, glycerol, and the amino acids alanine and glutamine.• The liver is the major site of gluconeogenesis, Dr. Siham Gritly 51
    52. 52. Ref. Michael W King, PhD | © 1996–, LLC | info Dr. Siham Gritly 52
    53. 53. Glycogen metabolism• Glycogen is the major storage form of glucose in liver and muscle• Metabolism involved• 1-glycogenesis• 2-glycogenolysis Dr. Siham Gritly 53
    54. 54. glycogenesis• Is a pathway for formation of glycogen from glucose• This process required energy in the form of ATP and UTP (uridine triphosphate)• It occur in muscle and in liver when insulin/glucagonratio Dr. Siham Gritly 54
    55. 55. Dr. Siham Gritly 55
    56. 56. Reactions of glycogenesis• 1-Phosphorylated of glucos to glucose 6-phosphate (hexokinase in muscles and glucokinase in liver• 2-glucose 6-phosphate is converted to glucose 1- phosphate (phosphoglucomutase)• 3-glucose 1-phosphate react with uridine triphosphate to form active nucleotide uridine diphosphate glucose (UDP-GLc) by the action of UDP-glucose pyrophosphorylase.• Pyrophosphate (PiPi)is the second product of the reaction, is hydrolyzed to two inorganic phosphate by the action of pyrophosphatase Dr. Siham Gritly 56
    57. 57. • 4-pre-existing glycogen molecule must be present to start reaction 4• By the action of enzyme glycogen synthase the C1 of the glucose of UDP-GLc forms a glycosidic bond with C4 of glucose residue of the re-existing glycogen (glycogen primer) liberating uridine diphosphate (UDP)• 5-a new alfa-1-4 linkage is formed between carbon 1 of incoming glucose and carbon 4 of the terminal glucose of the glycogen primer Dr. Siham Gritly 57
    58. 58. • 6-when the chain lengthened to a minimum of 11 residues a second enzyme (branching enzyme) amylo-1,4 to 1,6-transglucosidase transfers a part of the 1,4-chain minimum length of glucose residues to a neighboring chain to form alpha 1,6-linkage (branching point of the molecule) Dr. Siham Gritly 58
    59. 59. Glycogenolysis• Glycogenolysis is the process of degradation of glycogen to glucose 6-phosphate (muscle) and glucose (liver) Dr. Siham Gritly 59
    60. 60. Dr. Siham Gritly 60
    61. 61. Reactions of glycogenolysis• 1-phosphorolysis of alpha 1,4-glycosidic bonds of glycogen to yield glucose 1-phosphate and residual glycogen molecule• This reaction is catalyzed by glycogen phosphrylase• 2-by the action of phosphorylase, glucan transferase and de-branching enzyme leads to complete breakdown of glycogen with the formation of glucose 1-phosphate and free glucose Dr. Siham Gritly 61
    62. 62. • 3-glucose 1-phosphate is converted to glucose 6-phosphate by phosphoglucomutase• This is a reversible reaction• 4-in the liver specific enzyme glucose 6- phosphatase removes phosphate from glucose 6-phosphate and free glucose which in turn diffuses from the cell to the blood Dr. Siham Gritly 62
    63. 63. Pentose phosphate pathway• Known as hexose monophosphate shunt, phosphgluconate pathway• It is the pathway for formation of pentose (5C) sugar from hexose sugar (6C)• It is a multi-cyclic process in which three molecules of glucose 6-phosphate yeilds;• -3 molecules of CO2• -3 molecules of 5-carbon sugar Dr. Siham Gritly 63
    64. 64. The primary functions of Pentose phosphate Ref. 1996–2012 pathway themedicalbiochemistryp, LLC | info @ themedicalbiochemistryp• The primary functions of this pathway are:• 1. To generate reducing equivalents, in the form of NADPH, for reductive biosynthesis reactions within cells.• 2. To provide the cell with ribose-5-phosphate (R5P) for the synthesis of the nucleotides and nucleic acids.• 3. metabolize dietary pentose sugars derived from the digestion of nucleic acids as well as to rearrange the carbon skeletons of dietary carbohydrates into glycolytic/gluconeogenic intermediates. Dr. Siham Gritly 64
    65. 65. Location of pentose phosphate pathway• Main site of Pentose phosphate pathway in cytosol due to the presence of the enzymes Dr. Siham Gritly 65
    66. 66. Reaction of pentose phosphate pathway• Two phases for the reaction;• 1-oxidative irreversible phase• 2-non-oxidative reversible phase Dr. Siham Gritly 66
    67. 67. Ref. Michael W King, PhD | © 1996–2012, LLC | info@ Dr. Siham Gritly 67
    68. 68. reaction 1-oxidative irreversible phase of Pentose phosphate pathway• 1-dehydrogenation of glucose 6-phosphate to 6-phospho-glucono-lactone• Enzyme glucose 6-phosphate dehydrogenase (NADP dependent enzyme)• 2- 6-phospho-glucono-lactone is hydrolyzed by 6-phospho-gluconolactone hydrolase to 6- phosphogluconat Dr. Siham Gritly 68
    69. 69. • 3- 6-phosphogluconat undergo oxidative decarboxylation by the action of 6-phosph- gluconate dehydrogenase (NADP is needed)• The final product are of the oxidative irreversible phase;• -ribulose 5-phosphate• -CO2• -second molecule of NADPH Dr. Siham Gritly 69
    70. 70. reaction 2-non-oxidative reversible phase of Pentose phosphate pathway• ribulose 5-phosphate is converted back to glucose 6-phosphate by sequence reactions• stage 4 involved two enzymes;• 1-ribulose 5-phosphate 3-epimerase; alter configuration of C3 forming epimer xylulose 5-phosphate (ketopentose)• 2-ribose 5-phosphate ketoisomerase; convert ribulose 5-phosphate to aldopentose, ribose 5- phosphate Dr. Siham Gritly 70
    71. 71. Ref, Michael W King, PhD | © 1996–2012, LLC | info The primary enzymes involved in the non-oxidative steps of are transaldolase and transketolase: Dr. Siham Gritly 71
    72. 72. • 5-transketolase which transfers the two carbon 1,2 of keto to aldehyde carbon of aldose sugar• This reaction converts an aldose to ketose TPP are required as co-enzyme additional to Mg2+ Dr. Siham Gritly 72
    73. 73. • 6-transaldolase transfer three carbon dihydroxyacetone• Transaldolase transfers 3 carbon groups and thus is also involved in a rearrangement of the carbon skeletons of the substrates of the PPP. The transaldolase reaction involves Schiff base formation between the substrate and a lysine residue in the enzyme. Dr. Siham Gritly 73
    74. 74. Final products of pentose phosphat shunt Dr. Siham Gritly 74
    75. 75. References• National Center for Biotechnology Information, U.S. National Library of Medicine8600 Rockville Pike, BethesdaMD, 20894USA• Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) Enzyme Nomenclature• Michael W King, PhD | © 1996–2012, LLC | info @• D. Voet, J. G. Voet, Biochemistry, second edition ed., John Wiley &• Sons, New York, 1995• National Center for Biotechnology Information, U.S. National Library of Medicine8600 Rockville Pike, BethesdaMD, 20894USA• Sareen Gropper, Jack Smith and James Groff, Advanced Nutrition and Human Metabolism, fifth ed. WADSWORTH• Lehninger. Principles of bochemistry. by Nelson and Cox, 5th Edition; W.H. Freeman and Company• Naik Pankaja (2010). Biochemistry. 3ed edition, JAYPEE• Emsley, John (2011). Natures Building Blocks: An A-Z Guide to the Elements (New ed.). New York, NY: Oxford University Press. ISBN 978-0-19-960563-7. Dr. Siham Gritly 75
    76. 76. • Koppenol, W. H. (2002). "Naming of New Elements (IUPAC Recommendations 2002)" (PDF). Pure and Applied Chemistry 74 (5): 787–791. doi:10.1351/pac200274050787.• Guyton, C. Arthur. 1985. Textbook of Medical Physiology. 6th edition, W.B. Company• Murry K. Robert, Granner K. daryl, Mayes A. peter, Rodwell W. Victor (1999). Harpers Biochemistry. Appleton and Lange , twent fifth edition• Cooper GM 2000. The Central Role of Enzymes as Biological CatalystsThe Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000• Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life. Boston, Massachusetts: Pearson Prentice Hall• A. Burtis, Edward R. Ashwood, Norbert W. Tietz (2000), Tietz fundamentals of clinical chemistry• Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. pp. 52–59• Maitland, Jr Jones (1998). Organic Chemistry. W W Norton & Co Inc (Np). p. 139. ISBN 0-393- 97378-6.• Nelson DL, Cox MM (2005). Lehningers Principles of Biochemistry (4th ed.). New York, New York: W. H. Freeman and Company.• Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999) Biochemistry. 3rd edition. Benjamin Cummings.• Dr. Siham Gritly 76