CZ5225: Modeling and Simulation in Biology Lecture 9: Biological Pathways I: Metabolic Pathways...

CZ5225: Modeling and Simulation in BiologyCZ5225: Modeling and Simulation in Biology

Lecture 9: Biological Pathways I: Lecture 9: Biological Pathways I: Metabolic PathwaysMetabolic Pathways

Prof. Chen Yu ZongProf. Chen Yu Zong

Tel: 6874-6877Tel: 6874-6877Email: Email: yzchen@cz3.nus.edu.sgyzchen@cz3.nus.edu.sg

http://xin.cz3.nus.edu.sghttp://xin.cz3.nus.edu.sgRoom 07-24, level 7, SOC1, NUSRoom 07-24, level 7, SOC1, NUS

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All metabolism may be thought of as the coupling of energy production and energy use.

Some key concepts about metabolism

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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 ReactionsEnergy and Chemical Reactions

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• Lower activation E• Specificity• Activation• Cofactors• Modulators

– Acidity– Temperature– Competitive inhibitors– Allosteric– Concentrations

Enzymes speed biochemical reactionsEnzymes speed biochemical reactions

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Enzymes speed biochemical reactionsEnzymes speed biochemical reactions

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• Defined:– Equilibrium– Reversible

Law of Mass ActionLaw of Mass Action

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• Oxidation–reduction• Hydrolysis–dehydration• Addition–subtraction exchange• Ligation

Types of Enzymatic ReactionsTypes of Enzymatic Reactions

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• Pathways– Intermediates– Catabolic - energy– Anabolic - synthesis

Cell MetabolismCell Metabolism

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Metabolic PathwaysCatabolic 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 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

• Catabolic and anabolic pathways differ