1. Part two
principle of biochemistry
Metabolism 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. Tricarboxylic acid cycle
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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 ATP
The chemiosmotic coupling theory explains how
oxidative phosphorylation links the ETC and ATP
synthesis
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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
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5. 2-Tri-carboxylic Acid cycle
Citric Acid Cycle, Krebs Cycle
2nd phase of cellular respiration
• *kerb's 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.
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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.
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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)
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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
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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 chain
Mitochondria structure:
1) inner membrane
2) outer membrane
3) cristae
4) Matrix
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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.
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11. Reactions of the TCA Cycle
ref. 1996–2012 themedicalbiochemistrypage.org, LLC | info @
themedicalbiochemistrypage.org
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12. 1. Citrate synthase (synthesis of citric acid)
The citric acid cycle begins when Coenzyme A
transfers 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.
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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.
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14. Step 2 aconitase
isomerization 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.
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15. 3. Isocitrate Dehydrogenase
Oxidative decarboxylation of isocitrate to yield a -ketoglutarate
The 6-carbon isocitrate is oxidized and a molecule of carbon
dioxide is removed producing the 5-carbon molecule alpha-
ketoglutarate. During this oxidation, NAD+ is reduced to
NADH + H+
First oxidative
decarboxylation
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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.
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17. 4 -Ketoglutarate Dehydrogenase complex
Alpha-ketoglutarate is oxidized, carbon dioxide is
removed, 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
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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
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19. 5. succinyl-CoA synthase (succinate thiokinase)
CoA is removed from succinyl-CoA to produce succinate. The
energy 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
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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).
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21. 6. Succinate dehydrogenase (flavoprotein)
Succinate is oxidized to fumarate. During this
oxidation, two electrons and two protons produced are
transferred to FAD, which becomes FADH2.
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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
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23. 7 Fumarase (fumarate hydratase)
Water is added to fumarate to form malate (malic
acid)
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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
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25. 8 malate dehydrogenase.
Malate is oxidized to produce oxaloacetate, the
starting compound of the citric acid cycle. During
this oxidation, NAD+ is reduced to NADH + H+
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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).
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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
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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
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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
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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
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31. • the actions of the chain is carried on by highly
organized oxidation-reduction
enzymes, coenzymes and electron carrier
cytochromes
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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 ATP's;
and
3) to regenerate the coenzymes back to their
original form as oxidizing agents
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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
membranes
Mitochondria structure:
1) inner membrane
2) outer membrane
3) cristae
4) Matrix
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34. the electron transport chain may be found in the cytoplasmic
membrane or the inner membrane of mitochondria
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35. What are the initial reactants which start the electron transport
chain?
• 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)
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36. Dr. Siham Gritly 36

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
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38. Components are present in the inner
mitochondrial 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
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39. electrons are transported to meet up with oxygen from respiration
at the end of the chain. The overall electron chain transport
reaction 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
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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
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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
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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
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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.
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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
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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
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46. Each oxygen atom with two electrons accepts two
protons thus a molecule of water result
the reduction of oxygen to water result in production
of about 300 ml of water/day (metabolic water)
molecule of water
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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
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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. What are the final products of the chain
• Products of Electron transport chain
• H2O
• 3 ATP as free energy
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50. Dr. Siham Gritly 50

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,
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52. Ref. Michael W King, PhD | © 1996–2012
themedicalbiochemistrypage.org, LLC | info @
themedicalbiochemistrypage.org
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53. Glycogen metabolism
• Glycogen is the major storage form of glucose
in liver and muscle
• Metabolism involved
• 1-glycogenesis
• 2-glycogenolysis
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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
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55. Dr. Siham Gritly 55

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
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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
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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)
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59. Glycogenolysis
• Glycogenolysis is the process of degradation
of glycogen to glucose 6-phosphate (muscle)
and glucose (liver)
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60. Dr. Siham Gritly 60

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
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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
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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
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64. The primary functions of Pentose phosphate
Ref. 1996–2012
pathway themedicalbiochemistryp
age.org, LLC | info @
themedicalbiochemistryp
• The primary functions of this pathway are: age.org
• 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.
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65. Location of pentose phosphate pathway
• Main site of Pentose phosphate pathway
in cytosol due to the presence of the
enzymes
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66. Reaction of pentose phosphate pathway
• Two phases for the reaction;
• 1-oxidative irreversible phase
• 2-non-oxidative reversible phase
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67. Ref. Michael W King, PhD | © 1996–2012 themedicalbiochemistrypage.org, LLC | info
@ themedicalbiochemistrypage.org
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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
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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
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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
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71. Ref, Michael W King, PhD | © 1996–2012 hemedicalbiochemistrypage.org, LLC | info @
themedicalbiochemistrypage.org The primary enzymes involved in the non-oxidative
steps of are transaldolase and transketolase:
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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. • 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.
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74. Final products of pentose phosphat shunt
Dr. Siham Gritly 74

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 themedicalbiochemistrypage.org, LLC | info
@ themedicalbiochemistrypage.org
• 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). Nature's 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. • Koppenol, W. H. (2002). "Naming of New Elements (IUPAC Recommendations 2002)" (PDF). Pure
and Applied Chemistry 74 (5): 787–791. doi:10.1351/pac200274050787.
http://media.iupac.org/publications/pac/2002/pdf/7405x0787.pdf.
• 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.
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W. H. Freeman and Company.
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Cummings.
• http://wiki.answers.com/Q/What_is_dehydration_synthesis#ixzz2BuiK645
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