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Bioenergetics and Principles of Thermodynamic in Life Science
Department of Biochemistry
Jeerus Sucharitakul
Biomolecules
Fundamental Biochemistry Lab
Molecular Biology
Cell Biology
Professionalism I, II, III
Bioethics
Human Body I, II
Human Body Lab II
Development and Basic Human Tissue
Craniofacial complex
Dental Cariology I
Bio Dent Science I etc.
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Bioenergetics and thermodynamics
Living cells and organism-perform work to stay alive (growth and reproduction)-carry out a variety of energy transduction, conversion of one form energy to another.
ThermodynamicsThe quantitative description of heat and energy changes and of chemical equilibria.
BioenergeticsThe quantitative study of the energy transductions that occur in living cells.
Thermodynamics
Systems and surroundings
An open system; exchange of both energy and matter.A closed system; exchange of only energy.An isolated system; no exchange of both energy and matter.
A biochemical cell is an open system because nutrients and waste can pass cell membrane.
The laws of thermodynamics deal with measurable quantities whose values are determined only by the state of the system.
System + Surroundings = Universe
The First Law of Thermodynamics
Principle of the conservation of energy
For any physical change or chemical change, the total amountof energy in universe remains constant.
Energy may change form or it may be transported from oneregion to another but it cannot be created or destroyed.
Nutrients (complex molecules)sugars, proteins, fats
Mechanical worksChemical synthesisOsmotic gradients
Chemical transformation in cells
Cellular works
The First Law of Thermodynamics
Energy exchanges
Energy can be exchanged between system and surroundings.Two of the most common types of energy exchanges are workand heat.
Work: a transfer of energy that can cause motion against opposite forceHeat: a transfer of energy as a result of a temperature difference between system and its surroundings.
System that allows heat transfer: diathermic, exothermic (releasing of heat) and endothermic system (absorbing of heat)
System that does not allow heat transfer: adiabatic
The Second Law of Thermodynamics
EntropyAll natural processes, the entropy of the universe increases.The tendency in nature is toward disorder in the universe.
Entropy: quantitatively meaning randomness and disorder
Randomness: heat transfer from system to surroundings without changes of temperatureDisorder: degradation of macromolecules
C6H12O6 + 6O2 6CO2 + 6H2O
Dissipation of heat
7 molecule 12 moleculeIncrease in entropy
Organism require energy for maintaining internal order.
I Chemical components in living organisms are different fromsurroundings.II Cells try to maintain chemical components as a constant butnot equilibrium between system and surroundings.III The constancy of concentration inside cells is the dynamicsteady state (balance between synthesis and breakdown)
Dynamic steady state
Organism require energy for maintaining internal order.
Free energy
Conserve internal order-biosynthesis-cell structure-steady-state dynamics
Nutrients Heat
The Gibbs Energy Changes
Energy changes that cell can harvest to do any work during chemical reactions are called free energy or Gibbs free energy (G).
STHG
G; amount of energy capable of doing work under constanttemperature and pressure.H; heat content of the reaction system, which is referred toa number of bond formation and bond breaking.S; an expression for randomness or disorder of the system.
Properties of the Gibbs Free Energy
Spontaneous process: ΔStotal > 0, ΔG < 0
Non-spontaneous process: ΔStotal 0, ΔG > 0
ΔS: total change in term of surroundings and systemΔG: total change in term of system alone
Standard transformed constants
Standard conditions
Temperature = 298 K (25 C)Concentration of reactants = 1 MPressure = 1 atm or 101.3 kilopascals
Physical constants used in thermodynamics
G0, H0, S0
aA + bB cC + dD
G and the Equilibrium Constant
ba
dc
eq BA
DCK
][][
][][
The energy that drives system to equilibrium state equals to ΔG.
The G of a chemical reaction can be expressed mathematically as equilibrium constant (Keq).
At equilibrium 0G
eqKRTG ln0
eqKRTGG ln0
aA + bB cC + dD ba
dc
eq BA
DCK
][][
][][
ΔG >0: Reaction prefers to proceed reverse (endogernic reaction)
ΔG =0: Reaction is at equilibrium.
ΔG <0: Reaction proceeds forward. (exogernic reaction)
G and the Equilibrium Constant
G and the Equilibrium Constant
H2 + I2 2HI
Suppose It has been known that G0 = 3.4 kJ/mol for this reaction at 25 C; then to calculate the equilibrium constant
)25273(31.8
1040.3ln
3
RT
GKeq
Summing Changes in Gibbs energy
A B
B C
G01
G02
A C G01 + G0
2
G01 + G0
2 = -16.7 kJ/mol
Glucose + Pi Glucose 6-P + H2O
ATP + H2O ADP + Pi
G01 = 13.8 kJ/mol
G02 = -30.5 kJ/mol
Glucose + ATP Glucose 6-P + ADP
Coupled reactions
I A reaction that is not spontaneous may be driven forward by a reaction that is spontaneous.II The overall reaction is spontaneous because the sum of Gis negative.III ATP is employed to drive the endogernic reaction(G >0) in cell such as synthesis of macromolecules, membrane transport and motion of muscle cell.
Exergonic reaction Endogernic reaction
Phosphoryl group transfers and ATP
Roles of ATPI Energy currency in cell metabolismII Donation the energy for edogernic processes, macromoleculesynthesis or mechanical work in cells and organisms.
Free energy for driving endergonic processesThe hydrolytic cleavage of the phosphoric acid anhydride bonds provides large negative G0 = -30.5 kJ/mol
ATP hydrolysis provides large negative ΔG.
I Electrostatic repulsionII Releasing of more stabilizing compound as a resonance hybridIII Increasing of entropy by increasingin degree of solvation
Other negative free energy phosphorylated compounds
These compounds produce the product more stable relativeto reactant after being hydrolyzed (always in tautomerized or resonance form).
Other negative free energy phosphorylated compounds
-Thioester; a usaul oxygen atom is replaced with a sulfur atom.-Acetyl-CoA is one of thioesters importantin metabolism.
Other negative free energy phosphorylated compounds
Biological Oxidation-Reduction Reaction
The flow of electron can do biological work.
Low electron affinity compound
Electron motive force (emf)
High electron affinity compound
Electron transfer in biological oxidation-reduction reactions are exergonic process for driving endogernic reactions.
Fe2+ + Cu2+ Fe3+ + Cu+
Two Half-reactions in oxidoreduction
Fe2+ Fe3++ e
Oxidative half-reaction
Reducing agent
Cu2++ e Cu+
Reductive half-reaction
Oxidizing agent
Oxidation reaction Reduction reaction
Oxidation state of carbon atom
A change in oxidation number of carbon atom can be usedfor indicating a reducing or oxidizing agent. Revise !
C HH
H
H
H3C CH3
H2C CH2
HC CH
H3CH2C OH
H3CC OH
O
C OO
Nernst Equation
About century ago, Walther Hermann Nernst derived an equation that relates standard reduction potential (E0) at any oxidized and reduced species.
][
][ln0
acceptorelectron
donorelectron
nF
RTEE
Fe2+ Fe3++ e
][
][ln
3
20
Fe
Fe
nF
RTEE
n; number of electron transfer per moleculeF; Faraday constant = 9.648x104 J/V.mol
Walter Hermann Nernst(1864-1941)
Redox potential is used as parameters for capability to accept electron
Sign convention of redox potential values
A + e B E = -200 mV
A + e E = 200 mVB
Standard reduction potentials can be used to calculate the redox potential under non-standard state.
][
][ln0
acceptorelectron
donorelectron
nF
RTEE
EnFG 00 EnFG
Relation between redoxpotential and free energy change
Standard reduction potentials can be used to calculate the free-Energy change.
H3C CH
O
Acetaldehyde
+ NADH H3C CH2OH + NAD
Ethanol
Acetaldehyde + 2H+ +2e Ethanol
NAD+ + 2H+ +2e NADH+H+
E0 = -197 mV
E0 = -320 mV
The overall net reduction potential of reaction E0 = 123 mV[-197-(-320) mV]
00 EnFG
G0 = -2 x 96.5 kJ/V/mol x 0.123 V
Standard reduction potentials can be used to calculate the free-energy change.
H3C CH
O
Acetaldehyde
+ NADH H3C CH2OH + NAD
Ethanol
At equilibrium, [NADH] and [Acetaldehyde] = 1 M
[Ethanol] and [NAD+] = 0.1 M
][
][ln
][
][ln
0
0
NAD
NADH
nF
RTEE
acet
eth
nF
RTEE
NADHNADH
acetacet
Coenzymes that serve as electron carriers
Some enzymes require additional component for activity, and these component are called cofactor.
Cofactor
In organic ionsFe2+, Mg2+, Mn2+ or Zn2+
CoenzymesNAD+, NADP+, FMN, FAD, metalloorganic molecules such as heme or chlorophyll
covalently linked to enzyme; prosthetic group
Non covalently linked to enzyme
Coenzymes serve as universal electron carriers.
Degradation of nutrients in cells results in the conservationof free energy from those processes in compounds of
- NAD or NADPH (nicotinamide adenine dinucleotide or Nicotinamide adenine dinucleotide phosphate)
- Flavin-derivative compounds riboflavin FAD (flavin adenine dinucleotide) FMN (flavin mono nucleotide)
NADH and NADPH
NAD(P)/NAD(P)+ ; oxidized formNAD(P)H/NAD(P)H+H+; reduced form
NAD(P)++ 2e + 2H+ NAD(P)H + H+
The NAD reactions occur via two-electron reduction or oxidation.
NAD is derived from vitamin niacin.
-Human can synthesize niacin but not sufficient.-Essential dietary-Function as a coenzyme-Nicotinic deficiency: pellagra
Pellagra
•black tongue•dermatitis•diarrhea•dementia•alcoholism
Flavin-derivative compounds
Flavin can donate or accept eitherone-electron or two-electron process.
NADH and NADPH involve in catalysis of redox reaction.
The general name for enzyme this type is oxidoreductase,and also commonly called dehydrogenase.
H3C CH2 OH + NAD+ H3C CH
O
+ NADH + H+
Alcohol dehydrogenase
Ethanol Acetaldehyde
NAD(P) and NAD(P)H
Total concentration of [NAD+ + NADH] in most tissue is around10 μM whereas [NADP+ + NADPH] is around 1 μM.
The ratio of [NAD+]/NADH is high, favoring hydride transfer from a substrate to NAD+ but the ratio of [NADP+]/[NADPH] is low, favoring hydride transfer from NADPH to substrate.
The difference of concentration ratio between NAD and NADP in cell reflect the specialized metabolic role of two coenzymes.
Metabolism
The process through which living organism acquire and utilizefree energy they need to carry out various functions.
This process is always rendered by coupling the exogernic reaction (G< 0) of nutrient oxidation to endogernic process
(G> 0) required to maintain living state.
The reaction pathways in metabolism can be categorized into
Catabolism; or degradation of nutrient to break down exergonically to salvage their component/or to release free energyAnabolism; or biosynthesis of complexe biomolecules fromsimpler molecules
Energy relationships between catabolism and anabolism
Energy relationships between catabolism and anabolism
Principal characteristics of metabolic pathways
1) The first step in multi-step metabolic pathways is a committed step but not true in all cases.
A
B
B1 B2
The irreversible step (large negative free energy) commits the intermediates the it produces to continue down path way.
P1 P2
Product accumulation sometimes can inhibit catalytic activity of the first enzyme, called feed back inhibition.
2) All metabolic pathways are regulated.
- The first committed step is always a regulation step, and also acts as rate-limiting step.
- It is controlled by regulating the enzyme that catalyzes its first committed step.
- The reason is a prevention of unnecessary synthesis of metabolites.
Principal characteristics of metabolic pathways.
Principal characteristics of metabolic pathways.
3) Metabolic pathways in eukaryotic cells occur in specificcellular locations.The compartmentation of the eukaryotic cell allows different metabolic pathway