Lecture 1- : Basic Concepts and Design

Chem 454: Regulatory Mechanisms in University of Wisconsin-Eau Claire

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Introduction Questions we will focus on this semester: How does a cell extract energy and reducing power from its environment? How does a cell synthesize the building blocks of its macromolecules and the then the macromolecules themselves? How are these processes integrated and regulated?

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Introduction Living organisms require an input of free energy to meet various needs:

For mechanical work For of molecules and For synthesis of biomolecules

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Introduction Living organisms require an input of free energy Phototrophs

Use energy from the sun to convert energy-poor molecules into energy rich molecules Chemotrophs

Obtain energy by oxidizing the energy-rich molecules made by the phototrophs

4 4 Introduction Reduced molecules are energy-rich Oxidized molecules are energy-poor

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Introduction Energy from photosynthesis or the oxidation of fuels can be transformed into an unequal distribution of ions across a biological membrane.

The gradient can be used for

Oxidative phosphorylation to make ATP

Active transport across membranes

Nerve transmission

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Introductions Ion gradients:

See Chapter 2.3.3 7 7

Metabolism Metabolism is composed of many coupled interconnecting reactions

8 8 Metabolism

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Metabolism Classes of metabolic pathways: Catabolic pathways Those that convert energy into biologically useful forms

Fuels (, fats) CO2 + H2O + useful energy

Anabolic pathways Those that require an input of energy

Useful energy + small molecules complex molecules

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Metabolism

Basic concepts of metabolism include:

Thermodynamically unfavorable reactions can be driven by favorable reactions. ATP is the universal currency of free energy. ATP hydrolysis drives metabolism by shifting the of coupled reactions. There is a structural basis for the high phosphoryl transfer potential of ATP. The phosphoryl transfer potential is an important form of cellular energy transformation.

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Thermodynamics Thermodynamically unfavorable reactions can be driven by favorable reactions. Free energy change for a reactions:

A + B Æ C + D Ê ˆ 0' [C][D] DG = DG + RT lnÁ ˜ † Ë [A][B]¯

12 12 † Thermodyamics Coupling unfavorable reactions with favorable ones

A ¨ B + C DGo' = +5 kcal mol-1 B Æ D DGo' = -8 kcal mol-1 A Æ C + D DGo' = -3 kcal mol-1

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ATP ATP is the universal currency of free energy

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ATP Hydrolysis of ATP:

o -1 ATP + H2O ADP + Pi DG ' = -7.3 kcal mol

o -1 ATP + H2O AMP + PPi DG ' = -10.9 kcal mol

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ATP Hydrolysis ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions

16 16 ATP Hydrolysis Problem: Under standard conditions, the free energy for the hydrolysis of L- to form glycerol and inorganic phosphate is -2.2 kcal/ mol. Calculate the factor by which the equilibrium ratio for the concentration of L- glycerol phosphate to glycerol is increased when ATP is used as the phosphoryl donor for the formation L-glycerol phosphate in place of inorganic phosphate. Do this calculation for liver where the

concentrations for ATP, ADP and Pi are 3.5 mM, 1.8 mM and 5.0 mM, respectively. 17 17

ATP Hydrolysis Phosphoryl transfer is a common means of energy coupling

Molecular motors

Muscle contraction

Ion pumps

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Phosphoryl Transfer Structural basis for high transfer potential Compare:

o -1 ATP + H2O ADP + Pi DG ' = -7.3 kcal mol

o -1 Glycerol 3-phosphate + H2O Glycerol + Pi DG ' = -2.2 kcal mol

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Phosphoryl Transfer Phosphate vs Phosphate anhydride

CH2 OH O O O CH OH Adenosine O P O P O P O O O O O CH2 O P O O Glycerol 3-phosphate (ATP

O O O Y O

CH2 O P O O P O P O X O P O O O O O

Phosphate ester Phosphate anhydryde 20 20 Phosphoryl Transfer Stabilization of orthophosphate

resonance stabilization

electrostatic repulsion

hydration

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Stabilization of Orthophosphate Resonance stabilization

Orthophosphate

Pyrophosphate

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Phosphoryl Transfer and Energy Transfer There are other molelcules with favorable phosphoryl transferase energies

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Phosphoryl Transfer In terms of energy for phosphoryl transfer, ATP is intermediate:

24 24 Phosphoryl Transfer Question: What information do the ∆Go’ data given in Table 14.1 provide about the relative rates of hydrolysis of pyrophospate and acetyl phosphate?

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Phosphoryl Transfer Creatine phosphate is used to generate ATP in the short term:

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Cellular Energy The oxidation of Carbon fuels is an important source of cellular energy

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Cellular Energy The oxidation of Carbon fuels is an important source of cellular energy

28 28 Cellular Energy High phosphoryl transfer potential compounds can couple carbon oxidation to ATP synthesis. Ion gradients across membranes provide an important form of cellular energy The extraction of energy from foodstuffs occurs in stages.

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Coupling oxidation to ATP synthesis

High phosphoryl transfer potential compounds can couple carbon oxidation to ATP synthesis. Example from :

O O O C H C O P O O O + CH OH + NAD + HO P O CH OH + NADH + H+ O O O

CH2 O P O CH2 O P O O O Glyceraldehyde 3-phosphate 1,3-Bisphosphoglycerate

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Coupling oxidation to ATP synthesis In the next step ATP is harvested from the high energy phosphate intermediate.

O O O C O P O C O H O CH OH + ADP CH OH + ATP O O

CH2 O P O CH2 O P O O O 1,3-Bisphosphoglycerate 3-Phosphoglycerate

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Ion Gradients Ion gradients across membranes provide an important form of cellular energy

32 32 Cellular Energy Ion gradients across membranes can be used to synthesize ATP

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Cellular Energy Extraction of energy from foodstuffs is carried out in stages:

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Recurring Motifs in Metabolism Activated carriers exemplify the modular design and economy of metabolism. Key reactions are reiterated throughout metabolism. Metabolic processes are regulated in three principle way.

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Activated Carriers ATP is an activated carrier of phosphate groups Other examples include:

Activated carriers of electrons in oxidation reactions

Activated carriers of electrons in reductive

Activated carriers of two-carbon fragments

36 36 Activated carriers of electrons in NAD+ (Nicotinamide Adenine Dinucleotide)

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Activated carriers of electrons in catabolism FAD (Flavin Adenine Dinucleotide)

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Activated carriers of electrons in catabolism Reduction of isoalloxazine ring of FAD

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Activated carriers of electrons in biosynthesis NADPH (Nicotinamide Adenine Dinucleotide)

40 40 Activated carriers of acyl groups Coenzyme A is a carrier of Acyl groups

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Activated Carriers Other common activated carriers:

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Key Reactions There are six basic reactions in metabolism:

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Key Reactions Metabolic motifs

44 44 Metabolic Regulation Metabolic processes are regulated in different ways:

Enzyme levels (Genetic control)

Enzyme activity (Allosteric control)

Accessiblity of substrates to the enzyme (Competitive inhibition)

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Metabolic Regulation Degradative and biosynthesis pathways are usually distinct

Compartmentalization

Allosteric control

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Metabolic Regulation

The energy charge

ATP + 1 ADP Energy Charge = [ ] 2 [ ] [ATP] + [ADP] + [AMP]

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