CZ5225: Modeling and Simulation in Biology
Lecture 9: Biological Pathways I:
Metabolic Pathways
Prof. Chen Yu Zong
Tel: 6874-6877
Email: yzchen@cz3.nus.edu.sg
http://xin.cz3.nus.edu.sg
Room 07-24, level 7, SOC1, NUS
Some key concepts about metabolism
All metabolism may be thought of as the coupling of energy
production and energy use.
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Some key concepts about metabolism
Certain biochemical reactions occur spontaneously
Net release of energy
Others must be “forced” to occur
coupling
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Energy and Chemical Reactions
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Enzymes speed biochemical reactions
•
•
•
•
•
Lower activation E
Specificity
Activation
Cofactors
Modulators
– Acidity
– Temperature
– Competitive inhibitors
– Allosteric
– Concentrations
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Enzymes speed biochemical reactions
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Law of Mass Action
• Defined:
– Equilibrium
– Reversible
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Types of Enzymatic Reactions
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•
•
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Oxidation–reduction
Hydrolysis–dehydration
Addition–subtraction exchange
Ligation
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Cell Metabolism
• Pathways
– Intermediates
– Catabolic - energy
– Anabolic - synthesis
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Metabolic Pathways
Catabolic Pathways:
•
Those that convert energy into biologically useful forms are
called catabolic pathways
•
Fuels (carbs & fats)  CO2 + H2O + useful energy:
catabolism
•
Examples: degradation, pathways by which nutrients
and cellular components are broken down for reuse or
to generate energy
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Metabolic Pathways
Anabolic Pathways:
•
•
Those that require inputs of energy to proceed are called
anabolic pathways
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Useful energy + small molecules  complex
molecules: anabolism
•
Biosynthesis, building up of biomolecules from simpler
components
Pathways that can be either anabolic or catabolic are
referred to as amphibolic pathways
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Coupling favorable & unfavorable reactions
A pathway must satisfy minimally two criteria:
1. Reaction must be specific, yielding only one particular product or set
of products. Enzymes provide specificity
2. Whole set of reactions in a pathway must be thermodynamically
favored. A reaction can occur spontaneously only if G, the change
in free energy, is negative
3. An important thermodynamic fact: the overall free energy change for
a chemically coupled series of reactions is equal to the sum of the
free-energy changes of the individual steps
AB+C
G0’ = + 5 kcal mol-1
BD
G0’ = - 8 kcal mol-1
*******************************************
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AC+D
G0’ = - 3 kcal mol-1
Control of Metabolic Pathways
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•
•
•
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Feedback inhibition
Enzyme modulators
No enzyme
Enzyme isolation
Energy availability - ATP
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ATP is the Universal Currency of Free Energy
Metabolism is facilitated by the use of a common energy currency
Part of the free energy derived from the oxidation of foodstuffs
and from light is transformed into ATP - the energy currency
A large amount of free energy is liberated when ATP is
hydrolyzed to ADP & Pi, or ATP to AMP & PPi
ATP + H2O  ADP + Pi
G0’ = -7.3 kcal mol-1
ATP + H2O  AMP + PPi
G0’ = -10.9 kcal mol-1
Under typical cellular conditions, the actual G for these
hydrolyses is approximately -12 kcal mol-1
ATP hydrolysis drives metabolism by shifting the equilibrium of
coupled reactions: by a factor of approximately 108
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Structures of ATP, ADP,& AMP
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Structures of ATP, ADP,& AMP
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Coupled Reactions Involving ATP
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Coupled Reactions Involving ATP
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Coupled Reactions Involving ATP
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ATP Production
• Glycolysis
– Phosphorylation
– Pyruvate
• Anaerobic respiration
• Lactate production
• 2 ATPs produced
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Pyruvate Metabolism
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•
•
•
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Aerobic respiration
In mitochondria
Acetyl CoA and CO2
Citric Acid Cycle
Energy Produced
– 1 ATP
– 3 NADH
– 1 FADH
• Waste–2 CO2s
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Pyruvate Metabolism
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Electron Transport
• High energy electrons
• Energy transfer
– ATP synthesized from ADP
– H2O is a byproduct
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Electron Transport
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Biomolecules Catabolized to Make ATP
• Complex Carbohydrates
• Glycogen catabolism
– Liver storage
– Muscle storage
• Glucose produced
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Protein Catabolism
• Deamination
• Conversion
– Glucose
– Acetyl CoA
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Lipid Catabolism
• Higher energy content
• Triglycerides to glycerol
– Glycerol
– Fatty acids
– Ketone bodies - liver
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Lipid Catabolism
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Stages of Catabolism from Foodstuffs
Extraction of energy
from foodstuffs can
be divided into
three stages
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Synthetic (Anabolic) pathways
• Glycogen synthesis
– Liver storage
– Glucose to
glycogen
• Gluconeogenesis
– Amino acids
– Glycerol
– Lactate
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Lipogenesis
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•
•
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Acetyl Co A
Glycerol
Fatty acids
Triglycerides
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Protein Synthesis
• 20 Amino
acids
• DNA code
sequence
• mRNA
transcription
processing
• Translation by
ribosomes
• Chain
(polymer) of
amino acids
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Embden-Meyerhof Pathway
(EM, glycolysis)
Major pathway for the conversion of hexose sugars into
pyruvate.
It results in the formation of:
-two NADH
- two ATP
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(from Glyceraldehide-3-P to
Pyruvate)
Gain of 4 ATP
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The Hexose Monophosphate (HM)
Pathway (also known as oxidative pentose,
OM, or pentose phosphate pathway)
It provides all the key intermediates not provided by the EM
pathway.
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The Entner-Doudoroff Pathway
It may be considered an alternate hexose monophsphate pathway.
It provides a minimum of five of the critical biosynthetic
intermediates:
- glucose-6-P
- triose phosphate
- 3-phosphoglycerate
- phosphoenol pyruvate (PEP)
- pyruvate
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The Entner-Doudoroff Pathway
It begins the same as the HM pathway up to phosphogluconic acid.
Then, instead of being converted to pentose and carbon dioxide, it
is dehydrated yielding 2-keto-3, dehydro, 6 phosphogluconic acid.
pyruvate
Glyceraldehyde-3-P
The top half of the
molecule of glucose
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The Entner-Doudoroff Pathway
Both the EM and the ED pathway convert a glucose molecule
to two molecules of pyruvate.
pyruvate
Glyceraldehyde-3-P
The top half of the molecule of glucose
In the EM pathway, pyruvate arises by the intermediate
formation of glyceraldehyde-3-P. In the ED pathway, from the
top half of the molecule of glucose.
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Cyclic Metabolic Pathway
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Multiple Metabolic Pathways
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Multiple Metabolic Pathways
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Multiple Metabolic Pathways
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Post –Translational Protein Modification
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Metabolic Engineering
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Cells developed optimal use of their resources for their
survival.
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Metabolic pathways are networks, regulated to optimally
distribute their fluxes for best use of resources
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Metabolic engineering is to overcome the cellular
regulation to produce product of our interest; or to create
a new product that the host cells normally don’t need to
produce.
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Scope of Metabolic Engineering
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Modify host cells, host multi-cellular organisms, or product
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Improved production, in selectivity or in quantity, of
chemicals already produced by the host organism
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Extended substrate range for growth and product
formation
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Addition of new catabolic activities for degradation of
toxic chemicals
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Production of chemicals new to the host organism
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Modification of cell properties
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Methods of Metabolic Engineering
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Repeated mutations
were necessary to
create strains of the
mold Penicillium
chrysogenum which
produce high titers of
penicillin; that became
the foundation of a
commercial process
and changed human
health care.
•
Radiation and chemical
agents were employed
by investigators to
induce mutations in the
microorganism.
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Methods of Metabolic Engineering
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Identify the target phenotype or trait
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Increase the frequency of occurrence of gene(s) that may confer
the phenotype
– Increase the mutation frequency in producing cells
by Mutagen treatment (UV, X-ray, chemical mutagen) (Classical method)
– Introduce additional gene(s) (that may already exist or absent in the host
cell) known to give cells the desired properties (Genetic Engineering)
– Introduce genetic element to inactivate or activate the gene by random
insertion of extra sequence
•
Identify the mutants (clones) that have the
Desired trait.
Two general means
• Screening
• Selection
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Methods of Metabolic Engineering
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Methods of Metabolic Engineering
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Methods of Metabolic Engineering
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Metabolic Engineering
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Metabolic Engineering
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Thermodynamics of Metabolic Pathways
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Thermodynamics of Metabolic Pathways
Thermodynamics, as Related to Metabolism
Reactions near equilibrium —
Easily switch direction depending on relative
concentrations of reactants and products
Enzymes act to restore equilibrium
Reactions far from equilibrium —
Irreversible
Enzymes act as dams — have insufficient activity to
allow reaction to approach equilibrium; reactants
build up; changes in activity of enzyme change flux
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Thermodynamics of Metabolic Pathways
Three Major Implications of Thermodynamics for Metabolism
•Metabolic pathways are irreversible.
Biological systems are governed by thermodynamics!
For a process to be spontaneous ∆G must be negative
• Every metabolic pathway has a committed step.
Usually the first irreversible step unique to a pathway.
Usually an important site of regulation
• Catabolic and anabolic pathways differ
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