physical energetics

8/10/2019 Physical Energetics

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Chapter 8:

An Introduction

to Metabolism


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Important Point:


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Metab

olism(Overvie

w) Metabolism = Catabolism + Anabolism

Catabolic reactions are energy yielding

They are involved in the breakdown of

more-complex molecules into simpler

ones

Anabolic reactions are energy requiring

They are involved in the building up of

simpler molecules into more-complex

ones We can consider these bioenergetics in

terms of the physical laws of

thermodynamics


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1st& 2ndLaws of Thermodynamics

Energy can betransferred or

transformed but neither

created nor destroyed.p. 143, Campbell & Reece (2005)

Every energy transfer ortransformation increases the

disorder (entropy) of the

universe. p. 143, Campbell & Reece (2005)

Note especially the waste heat


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O

rganisms

areEnergyTrans

ducers

Organisms take in energy & transduce it to new

forms (1st law)

As energy transducers, organisms are less than

100% efficient (2nd law)

Organisms employ this energy to:

Grow

Protect Themselves Repair Themselves

Compete with other Organisms

Make new Organisms (I.e., babies)

In the process, organisms generate wastechemicals & heat

Organisms create local regions of order at the

expense of the total energy found in the

Universe!!! We are Energy Parasites!


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Wate

rFallAnalo

gy

Get it?


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awsof

Therm

odyna

mics

First Law of Thermodynamics:

Energy can be neither created nor destroyed

Therefore, energy generated in any system isenergy that has been transformed from one state

to another (e.g., chemically stored energy

transformed to heat)

Second Law of Thermodynamics:

Efficiencies of energy transformation never equal

100%

Therefore, all processes loseenergy, typically as

heat, and are not reversible unless the system isopen & the lost energy is resupplied from the

environment

Conversion to heat is the ultimate fate of

chemical energy


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ovemen

tsTowa

rdEquilibrium DownhillIncrease

stability

Greater

entropy

G < 0


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Entropy!
http://www.slvhs.slv.k12.ca.us/~pboomer/physicslectures/menu.html


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Free Energy & SpontaneityWhat is the name

of this molecule?


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Movement Toward Equilibrium

Potential

energy

Work

Spontaneous

Equilibrium

Forward

reaction


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Movement Toward Equilibrium

Viable organisms exist in a

chemical disequilibrium that

is maintained via the

harnessing of energy

obtained from theorganisms environment

(e.g., you eat to live)


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WaterfallA

nalog

y

Potential Energy

Kinetic Energy

Waste Heat

(once reaches

Bottom)

Stayring of a turbine

generator, Priest Rapids

Dam, 1958

Gravity (center Earth)
http://ccrh.org/comm/moses/phoarch.htmlhttp://ccrh.org/comm/moses/phoarch.htmlhttp://ccrh.org/comm/moses/phoarch.htmlhttp://ccrh.org/comm/moses/phoarch.htmlhttp://ccrh.org/comm/moses/phoarch.htmlhttp://members.aol.com/frank0509/bikepage/bike2.htmhttp://ski-zermatt.com/mattnet/pics/batch/3/photo8.htm


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oveme

ntTowa

rdEquilibrium

Potential

energy

Work

SpontaneousFood

Forward

reaction

Waste

heat


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Movement Toward Equilibrium in Steps

Note that Spontaneity is nota measure of speed of a

process, only its direction


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Exergonic Reactions

Energy

released

Food

Movement toward

equilibrium


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Exergonic Reaction (Spontaneous)DecreaseinGibbs free energy (-G)Increasein stabilitySpontaneous (gives off net energy upon going forward)Downhill (toward center of gravity well, e.g., of Earth)Movement towardsequilibriumCoupled to ATPproduction(ADP phosphorylation)

Catabolism

Endergonic Rxn (Non-Spontaneous)IncreaseinGibbs free energy (+G)

Decreasein stabilityNot Spontaneous (requires net input of energy to go forward)Uphill (away from center of gravity well, e.g., of Earth)Movement away fromequilibriumCoupled to ATP utilization(ATP dephosphorylation)

Anabolism


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CouplingR

eactions

Exergonic

reactions can

supply energyfor endergonic

reactions

Minus the

cut for the

2ndlaw


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nergyC

oupling

inMetabolism

Catabolic

reaction

Anabolic

reaction

Catabolic reactions provide the energy that

drives anabolic reactions forward


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Adenosine Triphosphate (ATP)

Call this A


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Energy Coupling via ATP


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Hydrolysis of ATP

Movement

toward

equilibrium


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Cou

pledR

eactions


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Howtha

treaction

reallyworks
http://fig.cox.miami.edu/~cmallery/150/metab/metabolism.htm


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Vario

usPiTransfers


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Summary of Metabolic Coupling

Endergonic

reaction

Exergonic

reaction

Exergonic

reaction

Endergonic

reaction

Get it? Exergonic processes drive Endergonic processes


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oveme

ntTowa

rdEquilibrium Food Endergonic

Exergonic


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Couplingthe

Biosphere

Anabolic

process

Catabolic

process

Chemically

stored energy


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Enzyme Catalyzed Reaction

Question: Isthis reaction

endergonic or

is it exergonic?

Enzyme


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Activa

tionEnergy(EA

)Anything that

doesnt require

an input ofenergy to get

started has

already

happened!


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ow-(i.e.

,body-)Temp.S

tability

Why don't energy-rich molecules, e.g., glucose,

spontaneously degrade into CO2and Water?

To be unstable, something must have thepotential to change into something else,

typically something that possesses less free

energy (e.g., rocks)

To be unstable, releasing somethings ability tochange into something else must also be

relatively easy (i.e., little input energy)

Therefore, stability = already low free energy

Alternatively, stability = high activation energy

Things, therefore, can be high in free energy

but still quite stable, e.g., glucose


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Catalysis

Lowering of

activation

energy


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Catalysis

At a given

temperature,

catalyzed reactionscan run faster

because less energy

is required to achieve

the transition state

This is instead of

adding heat; heat is

an inefficient means

of speeding up

reactions since it

simply is a means of

increasing the

random jostlings of

molecules


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nzyme

-mediatedCatalysis

= Subtle

application

of energy


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echanismsofCata

lysis Active sites can hold two or more

substrates in proper orientations so that

new bonds between substrates can form

Active sites can stress the substrate into

the transition state

Active sites can maintain conducive

physical environments (e.g., pH)

Active sites can participate directly in the

reaction (e.g., forming transient covalent

bonds with substrates) Active sites can carry out a sequence of

manipulations in a defined temporal order

(e.g., step Astep Bstep C)


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Catalysis as Viewed in 3D

Active site is

site of

catalysis

The rest of an

enzyme is involvedin supporting active

site, controlling

reaction rates,

attaching to other

things, etc.


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Induce

dFit(ActiveSite)

Induced fit not only allows the enzyme to bindthe substrate(s), but also provides a subtle

application of energy (e.g., bending chemical

bonds) that causes the substrate(s) to

destabilize into the transition state
http://www.blc.arizona.edu/marty/181/181Lectures/SO2Lecture4.html


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EnzymeSaturation

Enzyme Activity at Saturation is a

Function of EnzymeTurnover Rate
http://www.stark.kent.edu/~cearley/PChem/protein/protein.htmhttp://cwx.prenhall.com/bookbind/pubbooks/mcmurrygob/medialib/media_portfolio/19.html


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EnzymeSaturation

Turnover rate
http://cwx.prenhall.com/bookbind/pubbooks/mcmurrygob/medialib/media_portfolio/19.htmlhttp://cwx.prenhall.com/bookbind/pubbooks/mcmurrygob/medialib/media_portfolio/19.html


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Non-Specific Inhibition of Enzyme Activity

Instability

& shape

change

(too fluid)

Reduced rate of

chemical

reaction

Reduced

enzyme fluidity

Change in

R groupionization

Change in

R group

ionization

Denatured?

Turnover

rate

Even at saturation, rates

of enzymatic reactions

can be modified


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Activators of Catalysis

Metal Ion or =Organic Molecule

= OrganicCofactor

Polypeptide

Dont worry about

apoenzyme and

holoenzyme


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SpecificInhibitio

nCompetitive

inhibitors can

be competedoff by

supplying

sufficient

substrate

densities

Non-competitive

inhibitors cannotbe competed off

by substrate


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AllostericInteractions

Reversible

interactions,

sometimes

on,sometimes

off, dependent

on binding

constant anddensity of

effector

C ti it


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Cooperativity

Cooperativity

is when theactivity of

other

subunits are

increased by

substrate

binding to

one subunits

active site


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FeedbackInhibition

E M t b li R l ti


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Energy-Metabolism Regulation
http://cwx.prenhall.com/bookbind/pubbooks/mcmurrygob/medialib/media_portfolio/21.html


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EnzymeLo

calization

Organization of

Electron

Transport

Chain of

CellularRespiration:

Substrate

Enzyme

Product

Enzyme chainsare co-localized

Enzymes in single pathway

may be co-localized so that

the product of one enzyme

increases the local

concentration of the substrate

for another
http://ntri.tamuk.edu/cell/mitochondrion.htmlhttp://cwx.prenhall.com/bookbind/pubbooks/mcmurrygob/medialib/media_portfolio/21.html


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physical energetics

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