lehninger principles of biochemistry, fourth edition.pdf
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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
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Energy
• Metabolism�energy
• Energy to perform work– Organisms use chemical energy of fuels– Organisms use chemical energy of fuels
– Photosynthetic organisms use light energy
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. . . 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�
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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
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Laws of Thermodynamics
• 1. Thermodynamics:
• Energy not destroyed or created• Energy not destroyed or created
• 2. Thermodynamics:
• Entropy increases
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∆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.)
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∆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� (+)
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∆G= ∆H-T ∆S
• Entropy: S• Quantitative expression for the randomness
or disorder in a system.or disorder in a system.– Complexity ↓: entropy ↑
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∆G= ∆H-T ∆S
• Entropy: S• Quantitative expression for the randomness
or disorder in a system.or disorder in a system.– Complexity ↓: entropy ↑
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• ∆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
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• 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
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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
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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
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• 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
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∆G’o is constant
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Energy of product<e of reactant
No energy consumed
Exponentional interaction
Energy of product>e of reactant
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Example
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This is for my mother.
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Actual energy change
• Depends on[product] & [reactant]
• ∆G’o: constant
• Everything ..standard except present concentration
•
Mass-action ratio, Q
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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
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P+
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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
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∆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.
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Other Phosphorylated Compounds
• Phosphoenolpyruvate (PEP)
•
PEP to enol form of pyruvate�keto form by tautomerization
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Other Phosphorylated Compounds
• From anhydride bond between carboxyl group and phosphoric acid.
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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.
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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
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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.
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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)
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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
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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
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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
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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
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•Polymerization:•Proteins and nucleic acids
•Energy required•Procursor: nucleoside triphosphates
WHERE ATP USED
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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
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WHERE ATP USED
ATP for muscle contraction
• Reading assignment �page 186
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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.
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• 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.
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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
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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
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Simplify Biochemical reactions
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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
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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
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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
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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)
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Dehydorgenation
• Carbon share electron with others unequally
• H<C <S < N < O
• More electronehative�”owns”�e• More electronehative�”owns”�e
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• 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
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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
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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)
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3. Hydrogen ino (:H-)
• Like NAD-linked dehydrogenase (later)
4.Direct combination with oxygen4.Direct combination with oxygen
• Oxygen combines with an organic reductant
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• Electron flow from less affinity to more
Electron flow
Counter ion flow
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Nernst’s Equation
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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
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ExampleExample
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Acetaldehyde accepts 2 electron =>
n=2
But their actual concentration differentBut their actual concentration different
[acetaldehyde]=[NADH]=1.00M[ethanol]=[NAD]=0.1 M
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[acetaldehyde]=[NADH]=1.00M[ethanol]=[NAD]=0.1 M
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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
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NADH and NADPH Act with Dehydrogenasesas Soluble Electron Carriers
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Energy currencies
• Like many
• Reduced compounds�sallary
• Sallary�1000 $ (glucose)• Sallary�1000 $ (glucose)
• Nothing you can buy
• You should change your money.
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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)
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In 1937 Frank Strong, D. Wayne Wolley, Conrad Elvehjem identified niacin as the curative agent for blacktongue
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Flavin Nucleotides
• FADH2 and FMNH2�reduced�fully reduced
• Fully reduced one accept 2 electrons
B2
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360 nm
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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)