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

Lecture 1- Metabolism: Basic Concepts and Design

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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?

Introduction

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

For mechanical work

For active transport of molecules and ions

For synthesis of biomolecules

Introduction

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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

Introduction

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Reduced molecules are energy-richOxidized molecules are energy-poor

Introduction

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

The ion gradient can be used for

Oxidative phosphorylation to make ATP

Active transport across membranes

Nerve transmission

Introduction

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Ion gradients:

Introductions

See Chapter 2.3.3

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Metabolism is composed of many coupled interconnecting reactions

Metabolism

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Metabolism

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

Anabolic pathwaysThose that require an input of energy

Metabolism

Fuels (carbohydrates, fats) CO2 H2O + useful energy+

Useful energy + small molecules complex molecules

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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 equilibrium constant 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.

Metabolism

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Thermodynamically unfavorable reactions can be driven by favorable reactions.

Free energy change for a reactions:

Thermodynamics

†

DG = DG0' + RT ln C[ ] D[ ]A[ ] B[ ]

Ê

Ë Á

ˆ

¯ ˜

†

A + B Æ C + D

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Coupling unfavorable reactions with favorable ones

Thermodyamics

†

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 is the universal currency of free energy

ATP

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Hydrolysis of ATP:

ATP

ATP + H2O

ATP + H2O AMP + PPi

ADP + Pi DGo' = -7.3 kcal mol -1

DGo' = -10.9 kcal mol -1

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ATP hydrolysis drives metabolism by shifting the equilibrium of coupled reactions

ATP Hydrolysis

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Problem:Under standard conditions, the free energy for the hydrolysis of L-glycerol phosphate 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.

ATP Hydrolysis

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.

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Phosphoryl transfer is a common means of energy coupling

Molecular motors

Muscle contraction

Ion pumps

ATP Hydrolysis

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Structural basis for high transfer potential

Compare:

Phosphoryl Transfer

Glycerol 3-phosphate + H2O Glycerol + Pi

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

DGo' = -2.2 kcal mol -1

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Phosphate ester vs Phosphate anhydride

Phosphoryl Transfer

CH2 O PO

OO

O PO

OO

PO

OO

XY

O PO

OO

Phosphate ester Phosphate anhydryde

CH2

CH

CH2

OH

OH

O PO

OO

Glycerol 3-phosphate

O PO

OO

PO

OO

PO

OO

Adenosine

Adenosine triphosphate (ATP

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Stabilization of orthophosphate

resonance stabilization

electrostatic repulsion

hydration

Phosphoryl Transfer

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Resonance stabilization

Stabilization of Orthophosphate

Orthophosphate

Pyrophosphate

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There are other molelcules with favorable phosphoryl transferase energies

Phosphoryl Transfer and Energy Transfer

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

Phosphoryl Transfer

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

Phosphoryl Transfer

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

Phosphoryl Transfer

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

Cellular Energy

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

Cellular Energy

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

Cellular Energy

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

Example from glycolysis:

C

CH

CH2

OH

O PO

OO

Glyceraldehyde 3-phosphate

OH C

CH

CH2

OH

O PO

OO

OO

+ NAD+ + HO P OO

OP OO

O

+ NADH + H+

1,3-Bisphosphoglycerate

Coupling oxidation to ATP synthesis

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In the next step ATP is harvested from the high energy phosphate intermediate.

Coupling oxidation to ATP synthesis

C

CH

CH2

OH

O PO

OO

OO P O

O

O

+

1,3-Bisphosphoglycerate

ADP

C

CH

CH2

OH

O PO

OO

OO H

+

3-Phosphoglycerate

ATP

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Ion gradients across membranes provide an important form of cellular energy

Ion Gradients

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Ion gradients across membranes can be used to synthesize ATP

Cellular Energy

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Extraction of energy from foodstuffs is carried out in stages:

Cellular Energy

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Activated carriers exemplify the modular design and economy of metabolism.

Key reactions are reiterated throughout metabolism.

Metabolic processes are regulated in three principle way.

Recurring Motifs in Metabolism

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ATP is an activated carrier of phosphate groups

Other examples include:

Activated carriers of electrons in oxidation reactions

Activated carriers of electrons in reductive biosynthesis

Activated carriers of two-carbon fragments

Activated Carriers

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NAD+

(Nicotinamide Adenine Dinucleotide)

Activated carriers of electrons in catabolism

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FAD(Flavin Adenine Dinucleotide)

Activated carriers of electrons in catabolism

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Reduction of isoalloxazine ring of FAD

Activated carriers of electrons in catabolism

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NADPH(Nicotinamide Adenine Dinucleotide)

Activated carriers of electrons in biosynthesis

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Coenzyme A is a carrier of Acyl groups

Activated carriers of acyl groups

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Other common activated carriers:

Activated Carriers

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There are six basic reactions in metabolism:

Key Reactions

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Metabolic motifs

Key Reactions

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Metabolic processes are regulated in different ways:

Enzyme levels (Genetic control)

Enzyme activity (Allosteric control)

Accessiblity of substrates to the enzyme (Competitive inhibition)

Metabolic Regulation

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Degradative and biosynthesis pathways are usually distinct

Compartmentalization

Allosteric control

Metabolic Regulation

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The energy charge

Metabolic Regulation

†

Energy Charge = ATP[ ] + 12 ADP[ ]

ATP[ ] + ADP[ ] + AMP[ ]