AN OVERVIEW OF BIOCHEMICAL PATHWAYS- SOURCE OF ALL METABOLIC FUEL

1. Dr. Tanmay Sanyal (W.B.E.S)
Assistant Professor
Krishnagar Govt. College

2. Metabolism - the sum of all chemical processes carried out by living
cells
Catabolism - the chemical reactions that break larger molecules into
smaller molecules. It is usually an exergonic process.
Anabolism - the chemical reactions that form larger molecules from
smaller molecules. It is usually an endergonic process.
Autotroph - an organism that obtains its energy from sunlight or
inorganic chemicals. Plants, photosynthetic protists, and
photosynthetic prokaryotes are autotrophs.
Heterotroph - an organism that obtains its energy by consuming and
degrading organic molecules. Some eat other organisms, some
parasitize, some degrade the remains of once-living organisms.
Animals, Fungi, many protists and most prokaryotes are
heterotrophs.
Cells harvest chemical energy from foodstuffs in a series of
exergonic reactions. The harvested energy can then be used to power
energy demanding processes including endergonic reactions.

4. Glycolysis
Glykys = Sweet, Lysis = splitting
During this process one molecule of glucose (6 carbon
molecule) is degraded into two molecules of pyruvate (three
carbon molecule).
Free energy released in this process is stored as 2
molecules of ATP, and 2 molecules of NADH.
Glucose + 2NAD+ = 2Pyruvate + 2NADH + 2H+ Go = -146
kJ/mol 2ADP + 2Pi = 2ATP + 2H2O Go = 2X(30.5
kJ/mol) = 61 kJ/mol


Go (overall) = -146+61 = -85 kJ/mol
In standard condition glycolysis is an exergonic reaction
which tends to be irreversible because of negative Go.

5. → It is also called as Embden-Meyerhof Pathway (EMP)
→ it is defined as the sequence of reactions converting
glucose or glycogen to pyruvate or lactate with
production of ATP.
→ Enzymes takes place in cytosomal fraction of the
cell.
→ major pathway in tissues lacking mitochondria like
erythrocytes, cornea, lens etc.
→ it is essential for brain which is dependent in
glucose for energy.
→ under anaerobic condition = glu + 2ADP + 2iP
----- 2 Lactate + 2ATP

6. Fate of glucose in living systems
Glucose + 6O2 = 6CO2 + 6H2O Go= -2840 kJ/mol
Glucose + 2NAD+ = 2Pyruvate + 2NADH + 2H+  Go = -146kJ/mol

7. Historical Perspective
Glycolysis was the very first biochemistry or oldest biochemistry
studied. It is the first metabolic pathway discovered.
Louis Pasture 1854-1864: Fermentation is caused by microorganism.
Pastuer’s effect: Aerobic growth requires less glucose than
anaerobic condition.
Buchner; 1897: Reactions of glycolysis can be carried out in cell-
free yeast extract.
Harden and Young 1905: 1: inorganic phosphate is required for
fermentation. 2: yeast extract could be separated in small molecular
weight essential coenzymes or what they called Co-zymase and
bigger molecules called enzymes or zymase.
1940: with the efforts of many workers, complete pathways for
glycolysis was established.

9. There are 10 enzyme-catalyzed reactions in glycolysis.
There are two stages
Stage 1: (Reactions 1-5) A preparatory stage in which glucose is
phosphorylated, converted to fructose which is again forphorylated
and cleaved into two molecules of glyceraldehyde-3-phosphate. In
this phase there is an investment of two molecules of ATP.
Stage 2: (Reactions 6-10) (Pay off phase): The two molecules of
glyceraldehyde-3- phosphate are converted to pyruvate with
concomitant generation of four ATP molecules and two molecules of
NADH. Thus there is a net gain of two ATP molecules per molecule
of Glucose in glycolysis.
Importance of phosphorylated intermediates:
1. Possession of negative charge which inhibit their diffusion through
membrane.
2. Conservation of free energy in high energy phosphate bond.
3. Facilitation of catalysis.

13. 1. Hexokinase reaction: Phosphorylation of hexoses
(mainly glucose)
I. This enzyme is present in most cells. In liver Glucokinase
is the main hexokinase (both ISOENZYMES) which
prefers glucose as substrate.
II. It requires Mg-ATP complex as substrate. Un-complexed
ATP is a potent competitive inhibitor of this enzyme.
Enzyme catalyses the reaction by proximity effect; bringing
the two substrate in close proximity.

14. 2. Phosphoglucose Isomerase or Phosphohexose Isomerase:
Isomerization of G6P to Fructose 6 phosphate.
I. This enzyme catalyzes the reversible isomerization of G6P (an
aldohexose) to F6P (a ketohexose).
II. This enzyme requires Mg ++ for its activity.
III. It is specific for G6P and F6P.

15. 3. Phosphofructokinase-1 Reaction: Transfer of phosphoryl group
from ATP to C-1 of F6P to produce Fructose 1,6 bisphosphate.
III.
I. This step is an important irreversible, regulatory step.
II. The enzyme Phosphofructokinase-1 is one of the most complex
regulatory enzymes, with various allosteric inhibitors and
activators.
ATP is an allosteric inhibitor, and Fructose 2,6 biphosphate is
an activator of this enzyme.
IV. ADP and AMP also activate PFK-1 whereas citrate is an inhibitor.

16. 4. Aldolase Reaction: Cleavage of Fructose 1,6 bisphosphate into
glyceraldehyde 3 phosphate (an aldose) and dihydroxy acetone
phosphate (a ketose).
I. This enzyme catalyses the cleavage of F1,6 biphosphate by aldol
condensation mechanism.
II. As shown below, the standard free energy change is positive in
the forward direction, meaning it requires energy. Since the
product of this reaction are depleted very fast in the cells, this
reaction is driven in forward direction by the later two reactions.

17. 5. Triose phosphate mutase reaction: Conversion of
Dihydroxyacetone phosphate to glyceraldehyde 3 Phosphate.
I. This a reversible reaction catalysed by acid-base
catalysis in which Histidine-95 and Glutamate -165 of the
enzyme are involved.

18. 6. Glyceraldehyde-3-phosphate dehydrogenase reaction (GAPDH):
Conversion of GAP to Bisphosphoglycerate.
III.
I. This is the first reaction of energy yielding step. Oxidation of
aldehyde derives the formation of a high energy acyl phosphate
derivative.
II. An inorganic phosphate is incorporated in this reaction without
any expense of ATP.
NAD+ is the cofactor in this reaction which acts as an oxidizing
agent. The free energy released in the oxidation reaction is used in
the formation of acylphosphate.

19. 7. Phosphoglycerate kinase Reaction: Transfer of phosphoryl
group fron 1,3 bisphosphoglycerate to ADP generating ATP.
III.
I. The name of this enzyme indicates its function for reverse
reaction.
II. It catalyses the formation by proximity effect. ADP-Mg bind on
one domain and 1,3BPG binds on the other and a conformational
change brings them together similar to hexokinase.
This reaction and the 6th step are coupled reaction generating
ATP from the energy released by oxidation of 3-
phosphoglyceraldehyde.
IV. This step generates ATP by SUBSTRATE-LEVEL
PHOSPHORYLATION.

20. 8.Phosphoglycerate Mutase Reaction: Conversion of
3- phosphoglycerate to 2-phosphoglycerate (2-PG).
I. In active form, the phosphoglycerate mutase is phosphorylated
at His-179.
II. There is transfer of the phosphoryl group from enzyme to 3-PG,
generating enzyme bound 2,3-biphosphoglycerate intermediate.
In the last step of reaction the phosphoryl group from the C-3 of
the intermediate is transferred to the enzyme and 2-PG is
released.
III. In most cells 2,3BPG is present in trace amount, but in
erythrocytes it is present in significant amount. There it regulates
oxygen affinity to hemoglobin.

21. 9. Enolase Reaction: Dehydration of 2-phosphoglycerate (2-PG)
to phosphoenolpyruvate (PEP).
I. Dehydration of 2-PG by this reaction increases the standard
free enrgy change of hydrolysis of phosphoanhydride bond.
II. Mechanism: Rapid extraction of proton from C-2 position by a
general base on enzyme, generating a carbanion. The abstracted
proton is readily exchanges with solvent.
III. The second rate limiting step involves elimination of OH group
generating PEP

22. 10. Pyruvate Kinase Reaction: Transfer of phosphoryl group
from PEP to ADP generating ATP and Pyruvate.
I. This is the second substrate level phosphorylation reaction of
glycolysis.
II. This enzyme couple the free energy of PEP hydrolysis to
the synthesis of ATP
III. This enzyme requires Mg++ and K+

24. Energetics and products of Glycolysis:

25. 1. Gly-3-PO4--- 1,3 Bisphosphoglycerate = 6 ATP
2. 1,3 Bisphosphoglycerate-3-Phosphoglycerate = 2 ATP
3. Phosphoenolpyruvate-- Enol pyruvate = 2 ATP
ATP CONSUMED:
4. Glucose---- Glucose-6-PO4 = 1 ATP
5. Fru-6-PO4---- Fru-1,6 bisphosphate = 1ATP
------------------------------------
Net ATPsynthesized 10 – 2 = 8 ATP
Energetics of Glycolysis Pathway
ATP FORMED:

26. Homolactic Fermentation
In an anaerobic condition or in the need of
sudden need of high amount of ATP,
glycolysis is the main source for generation
of ATP.
NAD+ is one of the crucial cofactor required
for GAPDH reaction. In order to regenerate
NAD+ from the reduced form (NADH), this
reaction takes place in muscle cells.
Lactate dehydrogenase (LDH) reduces
pyruvate to lactate using NADH and thereby
oxidizing it to NAD+
Other than regenerating NAD+ for running
GAPDH reaction, LDH reaction is a waste of
energy, and its product lactic acid brings the
pH lower and causes fatigue.

27. INHIBITORS
1. Iodoacetate inhibit Gly-3-PO4 dehydrogenase
involved in gly-3-PO4 to
1,3-bisphosphoglycerate
2. Arsenate inhibit synthesis of ATP in the
conversion of 1,3 bisphosphoglycerate to
3-phosphoglycerate.
3. Fluoride inhibit enolase in conversion of
2-Phosphoglycerate to phosphoglycerate
4. Bromohydroxyacetonephosphate- Inhibitor
of dihydroxy acetone phosphate (DHAP)
5. Oxamate- Inhibitor of Lactate dehydrogenase

28. Effect of hormones in glycolysis
1. Insulin stimulate Hexokinase & Glucokinase
by converting glucose to glu-6-PO4
2. Insulin stimulate Phosphofructokinase converting
fru-6-PO4 to Fru-1,6 bisphosphate
3. Glucagon stimulate liver glu-6-PO4 by
converting glu-6-PO4 to glucose & fru-1,6-
bisphosphate.
4. Fru-1,6- bisphosphate is converted to fru-6-PO4

29. Regulation of Glycolysis:
There are three steps in glycolysis that have
enzymes which regulate the flux of
glycolysis.
I. The hexokinase (HK)
II.The phoshofructokinase (PFK)
III.The pyruvate kinase

34. GLUCONEOGENESIS
GLYCOGENESIS
GLYCOGENOLYSIS

35. Gluconeogenesis
Gluconeogenesis is the process whereby precursors
such as lactate, pyruvate, glycerol, and amino acids
are converted to glucose.
Fasting requires all the glucose to be synthesized
from these non-carbohydrate precursors.
Most precursors must enter the Krebs cycle at some
point to be converted to oxaloacetate.
Oxaloacetate is the starting material for
gluconeogenesis

39. Pyruvate is converted to oxaloacetate before
being changed to Phosphoenolpyruvate
1. Pyruvate carboxylase catalyses the ATP-driven
formation of oxaloacetate from pyruvate and CO2
2. PEP carboxykinase (PEPCK) concerts oxaloacetate
to PEP that uses GTP as a phosphorylating agent.

40. Gluconeogenesis is not just the reverse
of glycolysis
Several steps are different so that control of one
pathway does not inactivate the other. However
many steps are the same. Three steps are different
from glycolysis.
1 Pyruvate to PEP
2 Fructose 1,6- bisphosphate to Fructose-6-
phosphate
3 Glucose-6-Phosphate to Glucose

41. Regulators of gluconeogenic enzyme activity
Enzyme Allosteric Allosteric Enzyme Protein
Inhibitors Activators Phosphorylation Synthesis
PFK ATP, citrate AMP, F2-6P
FBPase AMP, F2-6P
PK Alanine F1-6P Inactivates
Pyr. Carb. AcetylCoA
PEPCK Glucogon
PFK-2 Citrate AMP, F6P, Pi Inactivates
FBPase-2 F6P Glycerol-3-P Activates

43. Fructose-6-phosphate
PFK-2 PFK-2 F2,6Pase F2,6Pase
Fructose-2,6-bisPhosphate
Fructose-1,6-bisPhosphate
P
P
PFK-1 FBPase
(+) (-)
cAMP-dependent protein kinase
AMP (+)
ATP (-)
Citrate (-)
AMP (-)
AMP (+)
F-6-P (+)
citrate (-)
F-6-P (-)
Hormonal control of glycolysis and gluconeogenesis

48. Glycogen Storage
• Glycogen is a D-glucose polymer
• a(14) linkages
• a(16) linked branches every 8-14 residues

49. Glycogen Syntheisis

51. UDP-glucose Pyrophorylase

52. Glycogen Synthase

53. Glycogen Breakdown or Glycogenolysis
•Three steps
• Glycogen phosphorylase
Glycogen + Pi <-> glycogen + G1P
(n residues) (n-1 residues)
• Glycogen debranching
• Phosphofructomutase

55. Glycogen Phosphorylase

56. Glycogen Debranching Enzyme

57. Coordinate control of glycogen metabolism

58. Regulation of glycogen synthesis by protein phosphatase 1. Protein
phosphatase 1 stimulates glycogen synthesis while inhibiting glycogen
breakdown. Active enzymes are shown in green and inactive enzymes in red.

59. Regulation of protein phosphatase 1 (PP1) in muscle takes place in two
steps. Phosphorylation of GM by protein kinase A dissociates the catalytic subunit
from its substrates in the glycogen particle. Phosphorylation of the inhibitor
subunit by protein kinase A inactivates the catalytic unit of PP1.

60. Insulin inactivates
glycogen synthase
kinase. Insulin
triggers a cascade that
leads to the
phosphorylation and
inactivation of
glycogen synthase
kinase and prevents
the phosphorylation
of glycogen synthase.
Protein phosphatase 1
(PP1) removes the
phosphates from
glycogen synthase,
thereby activating the
enzyme and allowing
glycogen synthesis.
IRS, insulin-receptor
substrate.

61. Glycogen Storage Disease

63. THE CITRIC ACID CYCLE
It is called the Krebs cycle or the tricarboxylic and is
the “hub” of the metabolic system. It accounts for
the majority of carbohydrate, fatty acid and amino
acid oxidation. It also accounts for a majority of the
generation of these compounds and others as well.
Amphibolic - acts both catabolically and
anabolically
3NAD+ + FAD + GDP + Pi + acetyl-CoA
3NADH + FADH + GTP + CoA + 2CO2

64. History
By 1930 it was established that the addition of lactate,
acetate succinate, malate, a-ketoglutaric acid
(dicarboxylic acids) and citrate and isocitrate
(tricarboxylic acids) when added to muscle mince that
they stimulated oxygen consumption and release of CO2
1935Albert Szent-Gyorgyi showed that
Succinate Fumarate Malate Oxaloacetate
Carl Martius and Franz Knoop showed
Citrate cis-aconitate isocitrate a ketoglutarate
succinate fumarate malate oxaloacetate

65. Martius and Knoop showed that pyruvate and
oxaloacetate could form citrate non-enzymatically by
the addition of peroxide under basic conditions.
Krebs showed that succinate is formed from fumarate,
malate or oxaloacetate. This is interesting since it was
shown that the other way worked as well!!
Pyruvate can form citrate enzymatically
Pyruvate + oxaloacetate citrate + CO2
The interconversion rates of the intermediates was fast
enough to support respiration rates.

66. Overview

68. The citric acid cycle enzymes are found
in the matrix of the mitochondria
Substrates have to flow across the outer and inner
parts of the mitochondria

70. Pyruvate to Acetyl CoA

73. Regulation
of
TCA Cycle

77. AMPHIBOLIC PATHWAY
1. Cells are constantly carrying out thousands of
chemical reactions needed to keep the cell, and your
body as a whole, alive and healthy. These chemical
reactions are often linked together in chains, or
pathways. All of the chemical reactions that take place
inside of a cell are collectively called the cell’s
metabolism. Overview of metabolism
2. Contains both catabolic and anabolic reactions.
Catabolic – Energy from oxidation of acetyl CoA is
stored in reduced coenzymes.
Anabolic – Several intermediates are precursors in
biosynthetic pathways Krebs Cycle is Amphibolic.

84. Pentose Phosphate Pathway
One fate of G6P is the pentose
phosphate pathway.

85. The pentose pathway is a shunt
• The pathway begins with the glycolytic intermediate
glucose 6-P.
• It reconnects with glycolysis because two of the end
products of the pentose pathway are glyceraldehyde
3-P and fructose 6-P; two intermediates further down
in the glycolytic pathway.
• It is for this reason that the pentose pathway is often
referred to as a shunt.

86. It’s a shunt

87. The pentose
pathway can
be divided
into two
phases.
Non-oxidative
interconversion of sugars

88. NADPH + H+ is formed
from two separate
reactions.
The glucose 6-phosphate
DH (G6PD) reaction is
the rate limiting step and
is essentially irreversible.
There is a medical story
for this enzyme.
Cells have a greater need
for NADPH than ribose 5-
phosphate.

90. Regulation of the Pentose Pathway
• Glucose 6-phosphate DH is the regulatory enzyme.
• NADPH is a potent competitive inhibitor of the enzyme.
• Usually the ratio NADPH/NADP+ is high so the enzyme
is inhibited.
• But, with increased demand for NADPH, the ratio
decreases and enzyme activity is stimulated.
• The reactions of the non-oxidative portion of the pentose
pathway are readily reversible.
• The concentrations of the products and reactants can shift
depending on the metabolic needs of a particular cell or
tissue.

92. Where do all the NADH’s and FADH2’s Go

93. What flows from the TCA cycle to ETS is the NADH.
It is the oxidation of NADH drives the production of ATP.
The TCA intermediates function in other pathways, the product
of this oxidative pathway, NADH is the substrate for the ETS.

94. ATP accounting so far…
• Glycolysis: 2 ATP
• Kreb’s cycle: 2 ATP
• Life takes a lot of energy to run, need to
extract more energy than 4 ATP!
What’s the
point?
A working muscle recycles over
10 million ATPs per second
There’s got to be a better way!

95. There is a better way!
• Electron Transport Chain
– series of molecules built into inner
mitochondrial membrane
• along cristae
• transport proteins & enzymes
– transport of electrons down ETC linked to
pumping of H+ to create H+ gradient
– yields ~34 ATP from 1 glucose!
– only in presence of O2 (aerobic respiration)

96. Mitochondria
• Double membrane
–outer membrane
–inner membrane
• highly folded cristae
• enzymes & transport
proteins
–intermembrane space
• fluid-filled space
between membranes

97. Glycolsis Krebs cycle
8 NADH
2 FADH2
Remember the Electron Carriers?
4 NADH
Glucose
G3P
Time to
break open
the bank!

98. Electron Transport Chain

99. Electron Transport Chain
intermembrane
space
inner
mitochondrial
membrane
NAD
+
Q
C
NAD
H
H2
O
H+
e–
2H+
+
2
H+
H+
e–
FADH2
1 O
2
NADH
dehydrogenase
cytochrome
bc complex
cytochrome c
oxidase complex
mitochondrial
matrix
e–
H
H  e- + H+
NADH  NAD+ +H
H
FAD
p
e
Building proton gradient!
What powers the proton (H+) pumps?…

100. Electrons flow downhill
• Electrons move in steps from carrier
to carrier downhill to O2
– each carrier more electronegative
– controlled oxidation
– controlled release of energy
make ATP
instead of
fire!

101. H+
ADP + Pi
H+
H+
H+
H+ H+
H+ H+
H+
We did it!
ATP
• Set up a H+ gradient
• Allow the protons
to flow through
ATP synthase
• Synthesizes ATP
ADP + Pi →ATP
Are we
there yet?
“proton-motive” force

102. Composition of the Electron Transport Chain
• Four large protein complexes.
• Complex I - NADH-Coenzyme Q reductase
• Complex II - Succinate-Coenzyme Q reductase
• Complex III - Cytochrome c reductase
• Complex IV - Cytochrome c oxidase
• Many of the components are proteins with
prosthetic groups to move electrons.

103. Flow of electrons
cyt c
Q
Complex I
Complex II Complex III
Complex IV
-0.4
-0.2
0.0
0.2
0.4
0.6
0.8
1.0
NADH
NAD+
1/2 O2
Path of
Electrons
succinate
(FADH2)
fumarate
+ 2 H+
H2O
Energy is not released at once, but in incremental
amounts at each step.

104. Inner mitochondrial membrane
Outer mitochondrial membrane
H+ H+
H+
H+
H+
H+
H+
H+
H+
H+
H+
H+ H+
H+
H+
ADP + P
i ATP
Electron
Transport
Chain
ATP
synthase
complex

105. Oxidative phosphorylation
• The electron-transport chain moves electrons from
NADH and FADH2 to O2.
• In the mean time, ADP is phosphorylated to ATP.
• The two processes are dependent on each other.
ATP cannot be synthesized unless there is energy
from electron transport.
• Electrons do not flow to O2, unless there is need for
ATP.

106. 3 ATP are generated when two
electrons are transported from
NADH to O2.
The oxidation of FADH2 only
produces 2 ATP.

108. Thylakoid
space
Photophosphorylation
Stroma
ADP + Pi 2H+
2H+
2H+
2H+ +
1/2O2
H2O
ATP
ATP
synthetase
2H+
1/2O2
2e-
2H+
2e-
2H+
NADP+
NADPH+
+ H+
Thylakoid
membrane
2e-

111. Amino acid oxidation and the production of urea
Waste or reuse
Oxidation

112. Ammonia has to be eliminated
• Ammonia originates in the catabolism of amino
acids that are primarily produced by the
degradation of proteins – dietary as well as
existing within the cell:
digestive enzymes
proteins released by digestion of cells sloughed-off
the walls of the GIT
muscle proteins
haemoglobin
intracellular proteins (damaged, unnecessary)

113. • Ammonia is toxic, especially for the CNS,
because it reacts with -ketoglutarate, thus
making it limiting for the TCA cycle 
decrease in the ATP level
• Liver damage or metabolic disorders
associated with elevated ammonia can lead to
tremor, slurred speech, blurred vision, coma,
and death
• Normal conc. of ammonia in blood: 30-60 µM
Ammonia has to be eliminated

114. Overview of amino acid catabolism in mammals
2 CHOICES
1.Reuse
2.Urea cycle
Fumarate
Oxaloacetate

115. Nitrogen removal from amino acids
Transamination
Oxidative
deamination
Urea cycle
Aminotransferase
PLP

116. Step 1: Remove amino group
Step 2: Take amino group to liver for
nitrogen excretion
Step 3: Entry into mitochondria
Step 4: Prepare nitrogen to enter urea cycle
Step 5: Urea cycle
Nitrogen removal from amino acids

117. Excretory forms of nitrogen
a) Excess NH4
+ is excreted as ammonia (microbes, aquatic
vertebrates or larvae of amphibia),
b) Urea (many terrestrial vertebrates)
c) or uric acid (birds and terrestrial reptiles)

118. Step 1. Remove amino group
• Transfer of the amino group of an amino acid to an -keto
acid  the original AA is converted to the corresponding -
keto acid and vice versa:
Type of hydrolysis
H2O + NH4+

119. • Transamination is catalyzed by
transaminases (aminotransferases) that
require participation of
pyridoxalphosphate:
amino acid
pyridoxalphosphate Schiff base
+H2O
Schiff base=
Amine +
aldehyde
coupling
product

120. Step 2: Take amino group to liver for
nitrogen excretion
Glutamate
dehydrogenase
The glutamate dehydrogenase of mammalian
liver has the unusual capacity to use either
NAD+ or NADP+ as cofactor
Glutamate releases its amino group
as ammonia in the liver.
The amino groups from many of the
a-amino acids are collected in the
liver in the form of the amino group
of L-glutamate molecules.

121. 1. Glutamate
transferres one amino group WITHIN cells:
Aminotransferase → makes glutamate from a-ketogluta-rate
Glutamate dehydrogenase → opposite
2. Glutamine
transferres two amino group BETWEEN cells → releases its
amino group in the liver
3. Alanine
transferres amino group from tissue (muscle) into the liver
Nitrogen carriers

122. Move within cells
SynthAtase = ATP
In liver
Move between cells

123. Glucose-alanine cycle
Ala is the carrier of ammonia and of the carbon
skeleton of pyruvate from muscle to liver.
The ammonia is excreted and the pyruvate is used
to produce glucose, which is returned to the muscle.
Alanine plays a special role in transporting
amino groups to liver.

124. Sources of ammonia for the urea cycle:
• Oxidative deamination of Glu, accumulated in the liver by the action of transaminases
and glutaminase
• Glutaminase reaction releases NH3 that enters the urea cycle in the liver (in the
kidney, it is excreted into the urine)
• Catabolism of Ser, Thr, and His (nonoxidative deamination) also releases ammonia:
Serine - threonine dehydratase
Serine →→ pyruvate + NH4
+
Threonine →→ a-ketobutyrate + NH4
+
• Bacteria in the gut also produce ammonia.

125. Review:
• Nitrogen carriers  glutamate, glutamine, alanine
• 2 enzymes outside liver, 2 enzymes inside liver:
• Aminotransferase (PLP) → a-ketoglutarate → glutamate
• Glutamate dehydrogenase (no PLP) → glutamate → a-
ketoglutarate (in liver)
• Glutamine synthase → glutamate → glutamine
• Glutaminase → glutamine → glutamate (in liver)

126. Step 3: entry of nitrogen to mitochondria

127. Step 4: prepare nitrogen to enter urea cycle
Regulation

128. Step 5: Urea cycle aspartate
Ornithine
transcarbamoylase
Argininosuccinate
synthase
Argininosuccinate
lyase
Arginase 1

129. OOA
Oxaloacetate → aspartate

130. Urea cycle – review
(Sequence of reactions)
• Carbamoyl phosphate formation in mitochondria is a prerequisite
for the urea cycle
• (Carbamoyl phosphate synthetase)
• Citrulline formation from carbamoyl phosphate and ornithine
• (Ornithine transcarbamoylase)
• Aspartate provides the additional nitrogen to form
argininosuccinate in cytosol
• (Argininosuccinate synthase)
• Arginine and fumarate formation
• (Argininosuccinate lyase)
• Hydrolysis of arginine to urea and ornithine
• (Arginase)

131. The overall chemical balance of the
biosynthesis of urea
NH3 + CO2 + 2ATP → carbamoyl phosphate + 2ADP + Pi
Carbamoyl phosphate + ornithine → citrulline + Pi
Citrulline + ATP + aspartate → argininosuccinate + AMP + PPi
Argininosuccinate → arginine + fumarate
Arginine → urea + ornithine
Sum: 2NH3 + CO2 + 3ATP  urea + 2ADP + AMP + PPi + 2Pi

132. Regulation of urea cycle
N-acetylglutamic acid – allosteric
activator of CPS-I
• High concentration of Arg →
stimulation of N-acetylation of
glutamate by acetyl-CoA

134. Inborn errors of amino acid metabolism

135. The Cori Cycle
Lactate from active muscle is converted to glucose in liver.

136. Carl and Gerty Cori
Nobel Prize in Physiology and medicine
1947
“for their discovery of the course of the catalytic conversion of glycogen”

137. Lactate and alanine are glucogenic
• In muscle alanine is produced from pyruvate by
transamination.
pyruvate + glutamate  alanine + α-ketoglutarate
• In the liver alanine is converted back to pyruvate.
• In active muscle lactate builds up, passes through the
blood and is converted to pyruvate in the liver.
• Thus, part of the metabolic burden of active muscle is
shifted to the liver.

139. Why is ATP used as the most preferable source of energy?
ATP is the main source of energy for most cellular
processes. ... Because of the presence of unstable,
high-energy bonds in ATP, it is readily hydrolyzed
in reactions to release a large amount of energy.
It is much more energy efficient to add and
remove those phosphate groups than to add and
subtract elements from a glucose molecule, as
there is no way to effectively break it down
without significantly changing its structure, which
makes it harder to build back up.

144. Reference
1. Principles of Biochemistry: Lehninger; 6th edition
2. Principles of Biochemistry: Voet & Voet; 4th edition
3. Biochemistry: Stryer & Berg; 9th edition
4. Biochemistry: Campbell; 8th edition
5. Biochemistry: Satyanarayan; 5th edition
6. Biochemistry: Harper; 31st edition
7. Slideshare.com