Download Biological Pathways II: Metabolic Pathways

CZ5211 Topics in Computational Biology
Lecture 7: Biological Pathways II:
Metabolic Pathways
Prof. Chen Yu Zong
Tel: 6874-6877
Email: [email protected]
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
Other must be “forced” to occur
coupling
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Energy and Chemical Reactions
Figure 4-5: Energy transfer and storage in biological 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:
– Equlibrium
– Reversible
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Types of Enzymatic Reactions
•
•
•
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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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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
•
•
•
•
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 Embden-Meyerhof Pathway
(EM, glycolysis)
It results in the formation of six of the critical biosynthetic
intermediates
Which ones? (look at the table provided)
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*
*
*
(from Glyceraldehide-3-P to
Pyruvate)
Gain of 4 ATP
*
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*
*
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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
Cells developed optimal use of their resources for their
survival.
Metabolic pathways are networks, regulated to optimally
distribute their fluxes for best use of resources
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
Modify host cells, host multicellular organisms, or product
Improved production, in selectivity or in quantity, of chemicals
already produced by the host organism
Extended substrate range for growth and product
formation
Addition of new catabolic activities for degradation of
toxic chemicals
Production of chemicals new to the host organism
Modification of cell properties
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Methods of Metabolic Engineering
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
Identify the target phenotype or trait
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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