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CZ5225: Modeling and Simulation in BiologyCZ5225: Modeling and Simulation in Biology
• Examples: degradation, pathways by which nutrients and cellular components are broken down for reuse or to generate energy
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Metabolic PathwaysAnabolic Pathways:
• Those that require inputs of energy to proceed are called anabolic pathways
• 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
*******************************************A C + D G0’ = - 3 kcal mol-1
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• Feedback inhibition• Enzyme modulators• No enzyme• Enzyme isolation• Energy availability - ATP
Control of Metabolic PathwaysControl of Metabolic Pathways
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ATP is the Universal Currency of Free EnergyMetabolism is facilitated by the use of a common energy currency
Part of the free energy derived from the oxidation of foodstuffsand 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 thesehydrolyses is approximately -12 kcal mol-1
ATP hydrolysis drives metabolism by shifting the equilibrium ofcoupled 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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• Glycolysis– Phosphorylation– Pyruvate
• Anaerobic respiration• Lactate production• 2 ATPs produced
ATP ProductionATP Production
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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
Pyruvate MetabolismPyruvate Metabolism
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Pyruvate Metabolism
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• High energy electrons• Energy transfer
– ATP synthesized from ADP
– H2O is a byproduct
Electron TransportElectron Transport
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Electron Transport
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• Complex Carbohydrates• Glycogen catabolism
– Liver storage– Muscle storage
• Glucose produced
Biomolecules Catabolized to Make ATPBiomolecules Catabolized to Make ATP
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Protein Catabolism• Deamination• Conversion
– Glucose– Acetyl CoA
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• Higher energy content• Triglycerides to glycerol
– Glycerol– Fatty acids– Ketone bodies - liver
Lipid CatabolismLipid Catabolism
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Lipid Catabolism
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Stages of Catabolism from Foodstuffs
Extraction of energyfrom foodstuffs canbe divided intothree stages
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• Glycogen synthesis– Liver storage – Glucose to
glycogen• Gluconeogenesis
– Amino acids– Glycerol– Lactate
Synthetic (Anabolic) pathways
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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 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
pyruvate Glyceraldehyde-3-P
The top half of the molecule of glucose
Both the EM and the ED pathway convert a glucose molecule to two molecules of pyruvate.
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 multi-cellular 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 cellsby 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 theDesired 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 relativeconcentrations of reactants and productsEnzymes act to restore equilibrium
Reactions far from equilibrium —
IrreversibleEnzymes act as dams — have insufficient activity toallow reaction to approach equilibrium; reactants build up; changes in activity of enzyme change flux
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Thermodynamics of Metabolic PathwaysThree 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