Metabolism Overview

8/12/2019 Metabolism Overview

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Energy is not Cycled

CO2 GlucoseCO2

Fat, muscle, etc.

Anabolism

Energy (light) Energy (heat)

Energy (heat)

Catabolism


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Catabolism Drives Analobolism

Catabolism

Breakdown of nutrients (e.g.

glucose)

Releases energy for anabolic

reactions

Releases heat

Anabolism (Biosynthesis) Synthesis of macromolecules

Requires energy

Releases heat

Intermediary Metabolism

Metabolic pathways involving low

molecular weight (


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Catabolism Driving Anabolism


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Separation of Anabolic and MeabolicPathways

Cellular Compartmentalization

Fatty acid catabolismin mitochondria

Fatty acid synthesisin cytoplasm

Different concentrations of products, reactants and regulators

Unique Cofactors

NAD/NADH for catabolism

NADP/NADPH for anabolism

When it goes wrong .


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Classes of Biochemical Reaction

Oxidation-reduction

Lactate dehydrogenase

Cleavage of carbon bonds

Adol condensations (aldose)

Claison condensations (citrate synthase)

Decarboxylations (acetoacetate decarboxylase)

Internal rearrangements, isomerizations and eliminations

Phosphohexose Isomerase

Group transfers (eg acyl,glucosyl, phosphoryl)

Hexokinase

Free radical reactions

Ribonucleotide reductase


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Oxidation-Reduction

Dehydrogenases

Dehydrogenations - loss of 2 electrons & 2 hydride ions

Oxidases

Oxygen becomes bonded to carbon

Oxygenases

Oxidases that use molecular oxygen

Oxidation

Reduction


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Phosphate and PhosphateTransfer

Transient Intermediate

Nucleophilic Attack (Glucokinase)


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Consider a Typical Enzymatic Reaction

ABCD

The reaction is reversible

Forward and backward reactions occur at the same time

The rate of each reaction is dependent on the concentration

of reactants

As A and B are used up, the forward rate decreases, C and D

increase and the rate of the reverse reaction increases

At the steady state, the forward and backward reaction rates

are the same

For the forward reaction;A and B are substrates

C and D are products


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Consider a Typical Enzymatic Reaction

ABCD

ForwardRate

Proportional to [A][B] = k1[A][B]

ReverseRate

Proportional to [C][D] = k2[C][D]

At Equilibrium: forward rate = reverse rate

k1and k2

are

constants

k1 [C][D]

k2 [A][B]

=

k1[A][B] = k2[C][D]Kd [C][D]

[A][B]=


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Equilibrium Constant

For the reaction:

At equilibrium:

Where Keq = the equilibrium constant

[A] = the molar concentration of A etc.

----------------------------------------------------------------------

K'eq

pH 7 (10-7

M H+) 55.5 M H2O

ABCD

Keq

[C][D][A][B]


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Equilibrium Constant

All enzymatic

reactions are

reversible

ABCD

Keq [C][D][A][B]

Enzymatic Reactions are reversible

AorB ForwardCorD

AorB

CorDBackwards

}

}

At dynamicequilibrium


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Change in Gibbs Free Energy G

The free energy change drives a reaction

A negativeG drives the reaction forward(as written)

A positiveG drives the reaction backwards(as written)

The G depends on the concentrations of reactants andproducts, temperature and pressure

Standard G(G)

One molar reactants and products, 298 K (25 C), 1 atm

Standard Biological G(G)

As G+ pH 7 (10-7M H+), 55.5 M H2O, 1 mM Mg2+

The standard free energy change of a reaction cannot

used to reliably predict the net direction of a reaction in

vivo since the reactants and products are not at 1 M


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Enzymes Lower the Activation Energy

Enzymes work by lowering the activation energy

Therefore:

Enzymes increase the dynamics of a reaction

Enzymes may increase the net rate of product formation

Enzymes do not change the Keq


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Free Energy Change

G = free energy change

G = standard G

G' = biological standard G

1 M, 298 K, 1 atm

10-7

M H+, 55.5 M H2O

ABCD

1 mM Mg2+


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Relationship between G and Keq

For the reaction

From thermodynamic principles:

At equilibrium

Therefore:

R= the gas constantT= the temperature in Kelvin

GG0' RTln[C][D][A][B]

ABCD

G

o'

RTlnKeq'

G 0


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Law of Mass Action


G 0G0' RTln[C][D]

[A][B]

At equilibrium

ABCD

Remove some of the productsCandD

G is zero:

G becomes negative G 0G0' RTln[C][D]

[A][B]

Remove some of the substratesAandB

G becomes positive G 0G0' RTln[C][D]

[A][B]

A +B C +D

A +B C +D

Forwards

Backwards

Keq

[C][D]

[A][B]


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Gs are Additive

Glucose + Pi G-6-P + H20

ATP + H20 ADP + Pi

Since only starting and final states are considered:

Glucose + ATP G-6-P + ADP

+13.8 kJ/mol

G'

-30.5 kJ/mol

-16.7 kJ/mol

The hydrolysis of ATP is used to drive the reaction forward

Consider the reaction:

Energetically unfavorable reactions are coupled to favorable ones


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Keqs are Multiplicative

Glucose + Pi G-6-P + H20

ATP + H20 ADP + Pi

Since only starting and final states are considered:

Glucose + ATP G-6-P + ADP

3.9 x10-3M

Keq

2.0 x 105M

7.8 x 102M

The hydrolysis of ATP is used to drive the reaction forward


Energetically unfavorable reactions are coupled to favorable ones

Overall G = G1+ G2where G1= RTln Keq1

Overall G = RTln Keq1 + RTln Keq2 (adding logs = multiplication)


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Operational Gs

ATP + H20 ADP + Pi

G'

-30.5 kJ/mol


Observed versus biological standard Gs

Conditions vary, but in general the true G of ATP

hydrolysis in vivo is more negative than standard G

In human erythrocytes at 25 C

[ADP] = 0.25 x 10-3

[Pi] = 1.65 x 10-3

[ATP] = 2.25 x 10-3

Gp = G + RT ln [ADP][Pi]

[ATP]

Gp = -30.5 + 21 kJ/mol

G of ATP hydrolysis = 51.5 kJ/mol


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Metabolic Pathways & Law of Mass Action

Products are moved through pathways by:Increasing the level of substrate

Decreasing the level of product

Especially useful for energetically unfavorable

reactions

ABCD Keq [C][D][A][B]



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Relationship Between Keqand G

Keq G (kJ/mol)

0.001 17.1

0.01 11.4

0.1 5.7

1 0.0

10 -5.7

100 -11.41,000 -17.1

Why is G 0 when Keq

is 1?


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ATP

Adenosine

ATP

AMP

ADP

Phosphoester

bonds

Phosphoanhydride

bonds


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ATP Hydrolysis

Hydrolysis with relief of charge repulsion

Resonance stabilization Ionization


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ATP Forms a Complex With Mg2+


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ATP is a High-Energy Compound


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1,3-BPG Hydrolysis

H+

1,3-Bisphosphoglycerate4- + H2O

3-phosphoglycerate3- Pi2- + H+

G = -49.3 kJ/mol

ionization

Resonance Stabilization and Ionization


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TransphosphorylationsPhosphocreatine is an Energy Reservoir

ADP + phosphocreatine ATP + creatine G = -12.5 kJ/mol

2ADP ATP + AMP G = ~ 0

ATP + NDP ADP + NTP G = ~ 0

Creatine Kinase

Other Transphosphorylations

Adenylate Kinase

Nucleoside diphosphate Kinase


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Acetyl-CoA HydrolysisResonance Stabilization and Ionization


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Thioesters Versus Oxygen EstersNo Resonance Stabilization in Thioesters


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Comparison of Gs of Hydrolysis

Standard Free Energies of Hydrolysis

G kJ/mol(approx)

Phospoenolpyruvate - 62

1,3-bisphoshoglycerate to 3-BPG - 49

Phosphocreatine - 43ATP to ADP

ATP to AMP + PPi

ADP to AMP

PPi

AcetylCoA - 31

Hexose phosphates - 13 to - 21

AMP - 14

Gycerol-1-phosphate - 9.2

{~ - 31


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ATP Coupling is Multi-StepGlutamine Synthetase


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Na+K+ ATPaseATP Hydrolysis Powers the Pump


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ATPase Pumping MechanismPhosphorylation changes the conformation of the pump


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Palmitoyl-CoA SynthesisAMP is conjugated to palmitate


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RNA ElongationTwo High-Energy Bonds are Used


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Oxidation


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Food for WorkComparison to an electrical motor

BatteryElectric

MotorWORK

e.g. movement

Food Mitochondria WORKe.g. muscle use

Electrons

Physical

Coupling

Electrons ATP

Electromotif Force (emf)

Proton Motive Force


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Redox Pair

Fe 2+ Cu2+ Fe3+ Cu++ +

Fe2+

Cu2+Fe

3+

Cu+++

e-e

-

Reducing agent(reductant,

Oxidizing agent(oxidant, electron

acceptor)electron donor)

Ferrous FerricCupric Cuprous

Oxidation

loss of electrons

Reduction

gain of electrons

T f f El t i O i C d


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Transfer of Electrons in Organic CompoundsOxidation of a reducing sugar by cupric ions

CR

O

H

+ 4OH - + 2Cu2+ Cu2O+ 2H 2OCR

O

OH

+

CR

O

H

+ 2OH - + H2OCR

O

OH

+

2OH - + 2Cu2+ Cu2O H2O++2e -

2e -

Oxidation - loss of electrons

Reduction - gain of electrons

cupric ion

T f f El t i O i C d


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Transfer of Electrons in Organic CompoundsOxidation of a reducing sugar by cupric ions

CR

O

H

+ 2OH - + H2OCR

O

OH

+

2OH - + 2Cu2+ Cu2O H2O++2e -

2e -

2OH-give H2O plus O2-

2Cu2++ 2e-give 2Cu+

2Cu

+

+ O

2-

give Cu2O

OH replaces H yields 1e-

H combines with OH-

to give H2O plus 1e-


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Oxidation States of CarbonOwnership of Electrons H< C < S < N < O

Electronsbelongingto

carbon


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Methods of Electron Flow

Fe 2+ + Cu 2+ Fe 3+ + Cu+

Direct Electron Transfer

Use of Hydride Ions

Use of Hydrogen Atoms

Direct Oxidation by Oxygen to Give

a Covalently Bound Oxygen

AH 2 + B A + BH 2

AH 2 A + 2H + 2e -

NAD + + H - + H + e - NADH + H+

NAD + + AH 2 NADH + H +

R-CH 3 +1 /2O2 R-CH 2 -OH

Electron acceptor

Electron acceptor

Electron acceptor


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Nernst Equation

E = E0+RT

nFln

[electron acceptor]

[electron donor]

__ _______________

E = E0+n

ln[electron acceptor]

[electron donor]_______________0.026 V

n =no. of electrons/moleculeF = Faraday Const.

T= temp (K)

R = gas constant

Relates Standard Reduction Potential to True Reduction Potential

E is the biological reduction

potential (pH 7)

f G


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Relationship of G to E

G = -n F E

or

G 0' = -n F E0'

F = Faraday Const.

Th H d Q i h E


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The Hardest Question on the Exam

G = -n F E

or

G 0' = -n F E0'F = Faraday Const.

Given E for two reactions, predict thefavorable direction the reaction; what

becomes oxidized and what reduced

Preparation

Work through the example in Lehninger pages 510/1

NAD A t 2 El t


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NAD+ Accepts 2 ElectronsTransferred as a Hydride Ion (H-)

E l f NAD ifi it


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Examples of NAD specificity

NADH Ab b t 340


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NADH Absorbs at 340 nmCan be used to measure concentration

Pellagra


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PellagraDermatitis, diarrhea, dementia, death

Maize is deficient in tryptophan and niacin

Alcoholics have reduced absorption of niacin

QuickTime and a

TIFF (Uncompressed) decompressorare needed to see this picture.

P ll hi t


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Pellagra, a history

Once common in the Southern

US, pellagra was thought to becontagious

1914 - Dr Joseph Goldberg wentto the S. to find a cure

Came to believe it was related to

nutrition

Controlled trials in orphanagesand a convict camp (inducedpellagra using a restricted diet)

In 1937 vitamin B3 was identified

Native Americans did not sufferfrom pellagra because they treatedcorn with lime which made niacinavailable

QuickTime and a

TIFF (Uncompressed) decompressorare neede d to see this picture.

Fl i d i di l tid (FAD)


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Flavin adenine dinucleotide (FAD)Accepts One or Two Electrons

Fl t i


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Flavoproteins

Metabolism Overview

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