Lehninger Principles of BiochemistryFourth Edition

David L. Nelson and Michael M. Cox

Fourth Edition

Chapter 13:

Principles of Bioenergetics

Copyright © 2004 by W. H. Freeman & Company

Energy

• Metabolism�energy

• Energy to perform work– Organisms use chemical energy of fuels– Organisms use chemical energy of fuels

– Photosynthetic organisms use light energy

. . . in general, respiration is nothing but a slowcombustion of carbon and hydrogen, which isentirelysimilar to that which occurs in a lighted lampsimilar to that which occurs in a lighted lampor candle, and that, from this point of view,animals thatrespire are true combustible bodies that burnand consume themselves . . .

Then, he lost his head�

Thermodynamics and bioenergitics

• Thermo:heat

• Dynamic:motion

• Thermodynamic:motion of heat(energy)• Thermodynamic:motion of heat(energy)

• Bioenergetics � quantitative study of the energy transductions that occur in living cells

Laws of Thermodynamics

• 1. Thermodynamics:

• Energy not destroyed or created• Energy not destroyed or created

• 2. Thermodynamics:

• Entropy increases

∆G= ∆H-T ∆S

• Gibbs free energy:G– Amount of energy

• Capable of doing work during rxn• Capable of doing work during rxn– Constant temperature

– Constant pressure

– Endergonic rxn: ∆G is pozitive

– Exergonic rxn: ∆G is negative (spont.)

∆G= ∆H-T ∆S

• Enthalpy: H– Heat content of system

~Total energy stored in the system~Total energy stored in the system

– # and kinds of chemical bonds – reactant and product

– Exothermic rxn release heat so ∆H� (-)– Hr>Hp

– Endothermic rxn recieve heat so ∆H� (+)

∆G= ∆H-T ∆S

• Entropy: S• Quantitative expression for the randomness

or disorder in a system.or disorder in a system.– Complexity ↓: entropy ↑

∆G= ∆H-T ∆S

• Entropy: S• Quantitative expression for the randomness

or disorder in a system.or disorder in a system.– Complexity ↓: entropy ↑

• ∆G� the change in Gibbs free energy of thereacting system

• ∆H� the change in enthalpy of the system.

∆G= ∆H-T ∆S

• ∆H� the change in enthalpy of the system.

• T� the absolute temperature,

• ∆S� the change in entropy of the system.

• ∆G�negative when rxn ..spontanous

• Chemical reactions

• System � reactants and products present, the solvent, atmospere

• Universe=system + surroundings

type energy Matter

closed no No

open yes Yes

isolated yes noisolated yes no

Living systems�open

System ⇔ surrounding

Entropy compansated by solar energy

Cells – energy

• isothermal systems (constant temperature)

• no work from heat

• Heterotrophic cell energy from nutrients

• Phototrophic cell from the sun

• Both convert it to ATP

Standart free-energy change

• To Standardize free energy for reactions

• Products and reactants are 1 M for chemicals, and 1 atm for gaseschemicals, and 1 atm for gases

• SFE change =∆Go

• Driving force until – equilibrium

• But biochemical reactions

• H+: constant �assumed as pH 7

• Water: 55.5 M

• Mg++ :1 mM

• So in biochemistry

• ∆Go in biological systems:∆G’o

Standard transformed constands in bioch. rxn

• ∆Go in biological systems:∆G’o

∆G’o is constant

Energy of product<e of reactant

No energy consumed

Exponentional interaction

Energy of product>e of reactant

Example

This is for my mother.

Actual energy change

• Depends on[product] & [reactant]

• ∆G’o: constant

• Everything ..standard except present concentration

•

Mass-action ratio, Q

Standard Free-Energy Additive• A ⇔C; ∆G’o

• A⇔B; ∆G’o

• B ⇔C; ∆G’o

• ∆G’o = ∆G’o + ∆G’o

1

2

total

total 1 2

P+

ATP and Phosphoryl Group

ATP⇔ADP + PATP ⇔AMP+P+P

Released P�resonanceOther product�H+

ATP hydrolysis�favorableATP hydrolysis�favorableWhy ATP stable at pH 7?

high activation energy

∆G of ATP(actual)

• ∆Gp (∆G in intact cell) of ATP at different tissues �far from ∆G’o

, -30.5 kJ/mol– Between -50 to -65 kJ/mol.

Other Phosphorylated Compounds

• Phosphoenolpyruvate (PEP)

•

PEP to enol form of pyruvate�keto form by tautomerization

Other Phosphorylated Compounds

• From anhydride bond between carboxyl group and phosphoric acid.

Other Phosphorylated Compounds

• Hydrolysis of phosphocreatine: Breakage of the P-N bond in phosphocreatine produces creatine, which is stabilized by formation of a resonance hybrid. The other product,Pi, is also resonance stabilized.product,Pi, is also resonance stabilized.

Others: Thioesters

• Ester with a S instead of O

• Acetyl-CoA has a key role in the • Acetyl-CoA has a key role in the metabolism.

• Standar free energy change is high

Energy from ATP by P transfer

Energy transfered by group transfer.But, in some processes ATP directly hydrolyzed and released energy used for motion. Ex: muscles, G-prot.

Classification of compound with P

• Two– High-energy compounds

• <-25 kJ/mol (standard free energy change)• <-25 kJ/mol (standard free energy change)

– Low energy compounds• >-25 kJ/mol (standard free energy change)

any phosphorylated compound �synthesized by coupling the synthesis

to the breakdown of another phosphoryl-ated compound with a more

negative free energy of hydrolysis. Example: PEP�ATP

Energy transfer• Much of catabolism �toward the synthesis of high-

energy phosphate compounds• The transfer of a phosphoryl group to a compound

effectively puts free energy into that compound, – it has more free energy

• ATP�universal Why:• ATP�universal Why:• thermodynamically unstable

– A good phosphoryl group donor

• Kinetically stable– Not spontenously donate because of huge activation

energy (200-400 kJ/mol)» Specific enzymes

Phosphoryl,Pyrophosphoryl, and Adenylyl Groups from ATP

• ATP reactions�generally SN2 nculeophilic displacement– the oxygen of an alcohol or carboxylate,

– a nitrogen of creatine or of the side chain of arginine or histidine

A question: Which

Example:

Phosphoryl to glucose5-phosphoribosyl-1-pyrophosphate5-phosphoribosyl-1-pyrophosphate

A question: Which oxygen is the bridge?

Solution: radioactive O

Realities: gammaO from alcoholPhosphoryl n not phosphate

Realities: betaTransfer a pyrophosphoryl Not pyrophosphate

Realities: alfaTransfer an adenylyladenylylation

30.532.8

45.6

19.2

ATP�ADP + P+

↓AMP

+P

63.3ATP�AMP + PP

↓P+P

63.3

65.8

19.2

inorganic pyrophosphotase

65.8

65.8>63.3

•Polymerization:•Proteins and nucleic acids

•Energy required•Procursor: nucleoside triphosphates

WHERE ATP USED

WHERE ATP USED

ATP for Active Transport

• To transport ions from [low] to [high]• Transportation � Major ATP consumption

– Brain-kidney�2/3 ATP consumed for Na+ and K+

•Na-dependent phosphorylation of the NaK ATPase forces a change in the protein’s conformation•K-dependent dephosphorylation favors return to the original conformation. •Each cycle in the transport process results in the conversion of ATPto ADP and Pi, (free-energy change)�the electrogenic pumping of Na and K. – Brain-kidney�2/3 ATP consumed for Naand K

WHERE ATP USED

ATP for muscle contraction

• Reading assignment �page 186

Transphosphorylation btwn nucleotides

• All dNTPs�energetically equal to ATP

• ATP is the primary high-energy phosphate compoundproduced by catabolism, in the processes of glycolysis,oxidative phosphorylation, and, in photosyntheticcells, oxidative phosphorylation, and, in photosyntheticcells, photophosphorylation.

• Several enzymes then carry phosphoryl groups from ATP to the other nucleotides.

Right (ATP/ADP�high)

Ping-Pong mechanism of nucleoside diphosphate kinase.

• High ADP�problem– in muscles

• ATP↓ � muscle constraction ↓• Cell lowers [ADP] and acquires ATP

similar enzyme, guanylate kinase, converts GMP to GDP at the expense of ATP.

Phosphocreatine (PCr)�ATP

• ATP production from PCr

[Pcrmuscle]=30mM -- [ATP m]=~3mM[Pcr

brain,kidney,smooth_muscle]=5-10mM

PCr�energy reservoir; extra ATP demant�PCr for ATP (not catabolism)////demant slower�extra ATP to PCr to full reservoir

Inorganic polyphosphate

polyP accumulate in cells (vacuols in yeast)polyP accumulate in cells (vacuols in yeast)Role:

a phophogen, a P reserviorPP�energy source for active transport of H+ in plantsPP�phosphoryl donor in microbes and animals

Simplify Biochemical reactions

3. Oxidation-Reduction Reactions

• Energy transfer– Phosphoryl group transfer

– Electron transfer (oxidation-reduction) • Nonphotosynthetic organisms:• Nonphotosynthetic organisms:

– reduced compounds����source

• Photosynthetic organisms:– Excited ones by light����source

– How flow of electron����complex– A����B���� …. D���� specialized electron carriers����

acceptor with higher electron affinity

Flow electron & Biowork• Electricity: a flow of electrons from

battery�flow through wires�motor =work �electromotive force (emf)

• Electron flow in cell

ExergonicEmf�Biological workProton increase �protone-motive force �ATP synthases � ATPe.coli�emf�proton motive force�flagglar motion

Question

“JUMBING TO THE MOON” is more possible

– HOW MANY ENZYMES TAKE A ROLE IN ENERGY METABOLIM

– WHAT are THEIR RATE ENHANCEMENT VALUEs

– WHAT IS THE OVERALL RATE

Think!

– WHAT IS THE OVERALL RATE ENHANCEMENT OF ONLY ONE STEP rxn CASCADE?

– MORE THAN THE 1000000000000000000xWORLD AGE

Two half-reactions

oxidation of ferrous ion by cupric ion

reducing agent (reductant): Electron-donating molecule in

reductant oxidant

reducing agent (reductant): Electron-donating molecule in an oxidation-reduction reactionoxidizing agent (oxidant): the electron-accepting moleculeelectron donor ⇔ e + electron acceptor. � a conjugate reductant-oxidant pair (redox pair)

Dehydorgenation

• Carbon share electron with others unequally

• H<C <S < N < O

• More electronehative�”owns”�e• More electronehative�”owns”�e

• Alkane oxidezed to alkene (no Oxygen)

• Loss H

• Loss of H�loss of e

Dehydorgenation

• Loss of H�loss of e

• Dehydregnation � oxidation

• Dehydrogenases �enzyme– More reduced �more H but less O

– More oxidized �less H but more O

Ways of electron transfer

1. Directly as electron

2. As hydrogen atomsA reducing equivalent � a single electron equivalent participating in anoxidation-reduction reaction2. As hydrogen atoms

3. As a hydrogen ion (NADH, later)

4. Through direct combination with oxygen

E donorE acceptor

participating in anoxidation-reduction reactionOxygen� 2 RE

2. As Hydrogen atoms

• H atom=proton + a single eelectron

• Đf transfer H atoms, it means transfer of electron ( bases����receive only proton)

• H atom=proton + a single eelectron

• Đf transfer H atoms, it means transfer of electron ( bases����receive only proton)electron ( bases����receive only proton)electron ( bases����receive only proton)

3. Hydrogen ino (:H-)

• Like NAD-linked dehydrogenase (later)

4.Direct combination with oxygen4.Direct combination with oxygen

• Oxygen combines with an organic reductant

• Electron flow from less affinity to more

Electron flow

Counter ion flow

Nernst’s Equation

Why knowing E is improtant

• Đf we know E, we know the direction of electron flow

• Electron flow to more positive E cell• Electron flow to more positive E cell

• For example

A B

EA: 1EB:0,5

Electron flow from B to A

Strengt�on ∆E

ExampleExample

Acetaldehyde accepts 2 electron =>

n=2

But their actual concentration differentBut their actual concentration different

[acetaldehyde]=[NADH]=1.00M[ethanol]=[NAD]=0.1 M

[acetaldehyde]=[NADH]=1.00M[ethanol]=[NAD]=0.1 M

Electron carriers

• Many enzymes for electron flow use a few types of coenzymes: such as NAD, NADP, FAD, FMN, quinons etcFAD, FMN, quinons etc

• NAD, NADP, FAD, FMN, �water soluble

NADH and NADPH Act with Dehydrogenasesas Soluble Electron Carriers

Energy currencies

• Like many

• Reduced compounds�sallary

• Sallary�1000 $ (glucose)• Sallary�1000 $ (glucose)

• Nothing you can buy

• You should change your money.

Deficiency of Niacin�pellagra

• Pyridine ring of NAD & NADP niacin vitamine (B3) tryptophan

• We can’t synthesize B3 enough

• Low B3 in diet�affect NAD and NADP metabolism�pellegra disease

• 3 Ds: dermatitis, diarrhea, dementia

• 10000 died btwn 1912-16 in USA

• Niacin for treatment

• Pellegra still in alcholics (intestinal absorption)

In 1937 Frank Strong, D. Wayne Wolley, Conrad Elvehjem identified niacin as the curative agent for blacktongue

Flavin Nucleotides

• FADH2 and FMNH2�reduced�fully reduced

• Fully reduced one accept 2 electrons

B2

360 nm

Flavin nucleotide�prostetic group

• Cofactor�inorganic and coenzyme (organic)

• Prostetic group�covalently bonded one to • Prostetic group�covalently bonded one to enzyme

• FN binds covalently to some enzymes, succinate dehydrogenase (citric acid cycle)