Biomol1

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.

ระเบียบการแต่งกายของนิสิตจุฬาฯ ผู้แต่งกายผิดระเบียบ หักคะแนน & แจ้งฝ่ายกิจการนิสิต ห้ามเข้าปฏิบัติการ ห้ามเข้าสอบ

ติดต่อภาควิชาได้ที่ ชั้น 2 ตึกพรีคลินิก โทรฯ 02-218-8670-1

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. Thermodynamics The quantitative description of heat and energy changes and of chemical equilibria. Bioenergetics The quantitative study of the energy transductions that occur in living cells.

Thermodynamics The laws of thermodynamics deal with measurable quantities whose values are determined only by the state of the system. 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. System + Surroundings = Universe A biochemical cell is an open system because nutrients and waste can pass cell membrane.

The First Law of Thermodynamics Principle of the conservation of energy For any physical change or chemical change, the total amount of energy in universe remains constant. Energy may change form or it may be transported from one region to another but it cannot be created or destroyed. Cellular works Nutrients (complex molecules) sugars, proteins, fats

Mechanical works Chemical synthesis Osmotic gradients

Chemical transformation in cells

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 work and heat. Work: a transfer of energy that can cause motion against opposite force Heat: 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 Entropy All 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 temperature Disorder: degradation of macromolecules Dissipation of heat

C6H12O6 + 6O2 7 molecule

6CO2 + 6H2O 12 molecule Increase in entropy

Organism require energy for maintaining internal order. I Chemical components in living organisms are different from surroundings. II Cells try to maintain chemical components as a constant but not equilibrium between system and surroundings. III The constancy of concentration inside cells is the dynamic steady state (balance between synthesis and breakdown)

Dynamic steady state

Organism require energy for maintaining internal order. Heat

Nutrients

Free energy

Conserve internal order -biosynthesis -cell structure -steady-state dynamics

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).

∆G = ∆H − T∆S G; amount of energy capable of doing work under constant temperature and pressure. H; heat content of the reaction system, which is referred to a 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 system ΔG: total change in term of system alone

Standard transformed constants Standard conditions

∆G0, ∆H0, ∆S0

Temperature = 298 K (25 C) Concentration of reactants = 1 M Pressure = 1 atm or 101.3 kilopascals Physical constants used in thermodynamics

∆G and the Equilibrium Constant aA + bB

cC + dD

[C ]c [ D]d K eq = [ A]a [ B]b

The energy that drives system to equilibrium state equals to ΔG.

∆G = ∆G 0 + RT ln K eq The ∆G of a chemical reaction can be expressed mathematically as equilibrium constant (Keq). At equilibrium ∆G = 0

∴ ∆G 0 = − RT ln K eq

∆G and the Equilibrium Constant

aA + bB

cC + dD

[C ]c [ D]d K eq = [ A]a [ B]b

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 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

− ∆G − 3.40 ×103 ln K eq = = RT 8.31× ( 273 + 25)

Summing Changes in Gibbs energy

Glucose + Pi ATP + H2O Glucose + ATP

A

B

∆G01

B

C

∆G02

A

C

∆G01 + ∆G02

Glucose 6-P + H2O ADP + Pi Glucose 6-P + ADP

∆G01 = 13.8 kJ/mol ∆G02 = -30.5 kJ/mol ∆G01 + ∆G02 = -16.7 kJ/mol

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 ∆G is 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 ATP I Energy currency in cell metabolism II Donation the energy for edogernic processes, macromolecule synthesis or mechanical work in cells and organisms.

Free energy for driving endergonic processes The hydrolytic cleavage of the phosphoric acid anhydride bonds provides large negative ∆G0 = -30.5 kJ/mol

ATP hydrolysis provides large negative ΔG.

I Electrostatic repulsion II Releasing of more stabilizing compound as a resonance hybrid III Increasing of entropy by increasing in degree of solvation

Other negative free energy phosphorylated compounds These compounds produce the product more stable relative to reactant after being hydrolyzed (always in tautomerized or resonance form).

Other negative free energy phosphorylated compounds

Other negative free energy phosphorylated compounds

-Thioester; a usaul oxygen atom is replaced with a sulfur atom. -Acetyl-CoA is one of thioesters important in metabolism.

Biological Oxidation-Reduction Reaction

The flow of electron can do biological work. Low electron affinity compound

High electron affinity compound

Electron motive force (emf) Electron transfer in biological oxidation-reduction reactions are exergonic process for driving endogernic reactions.

Two Half-reactions in oxidoreduction

Fe2+ + Cu2+ Oxidative half-reaction Fe2+

Fe3++ e

Reducing agent

Oxidation reaction

Fe3+ + Cu+ Reductive half-reaction Cu2++ e

Cu+

Oxidizing agent

Reduction reaction

Oxidation state of carbon atom A change in oxidation number of carbon atom can be used for indicating a reducing or oxidizing agent. Revise ! H H C H

H3CH2C

OH

H O H3C

CH3

H3CC

OH

H2C

CH2

O C

O

HC

CH

Nernst Equation About century ago, Walther Hermann Nernst derived an equation that relates standard reduction potential (E0) at any oxidized and reduced species.

RT [electron donor ] E=E − ln nF [electron acceptor ] 0

Fe2+ Walter Hermann Nernst (1864-1941)

Fe3++ e

2+ RT [ Fe ] 0 E=E − ln nF [ Fe 3+ ]

n; number of electron transfer per molecule F; Faraday constant = 9.648x104 J/V.mol

Redox potential is used as parameters for capability to accept electron

Sign convention of redox potential values B

A+e

A+e

B

∆E = -200 mV ∆E = 200 mV

Standard reduction potentials can be used to calculate the redox potential under non-standard state.

RT [electron donor ] E=E − ln nF [electron acceptor ] 0

Relation between redoxpotential and free energy change

∆G 0 = −nF∆E 0

∆G = −nF∆E

Standard reduction potentials can be used to calculate the free-Energy change. O H3C CH2OH + NAD

H3C CH + NADH

Ethanol

Acetaldehyde Acetaldehyde + 2H+ +2e NAD+ + 2H+ +2e

Ethanol NADH+H+

E0 = -197 mV E0 = -320 mV

The overall net reduction potential of reaction ∆E0 = 123 mV [-197-(-320) mV]

∆G 0 = − nF∆E 0 ∆G0 = -2 x 96.5 kJ/V/mol x 0.123 V

Standard reduction potentials can be used to calculate the free-energy change. O H3C CH + NADH

Acetaldehyde

H3C CH2OH + NAD

Ethanol

At equilibrium, [NADH] and [Acetaldehyde] = 1 M [Ethanol] and [NAD+] = 0.1 M

RT [eth] Eacet = E − ln nF [acet ] RT [ NADH ] 0 E NADH = E NADH − ln nF [ NAD + ] 0 acet

Coenzymes that serve as electron carriers Some enzymes require additional component for activity, and these component are called cofactor.

Cofactor Coenzymes

In organic ions Fe2+, Mg2+, Mn2+ or Zn2+

NAD+, NADP+, FMN, FAD, metalloorganic molecules such as heme or chlorophyll

Non covalently linked to enzyme

covalently linked to enzyme; prosthetic group

Coenzymes serve as universal electron carriers. Degradation of nutrients in cells results in the conservation of 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 form NAD(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 either one-electron or two-electron process.

NADH and NADPH involve in catalysis of redox reaction. Alcohol dehydrogenase H3C CH2 OH + NAD+

Ethanol

O H3C CH + NADH + H+

Acetaldehyde

The general name for enzyme this type is oxidoreductase, and also commonly called dehydrogenase.

NAD(P) and NAD(P)H Total concentration of [NAD+ + NADH] in most tissue is around 10 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 utilize free 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 energy Anabolism; or biosynthesis of complexe biomolecules from simpler 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. The irreversible step (large negative free energy) commits the intermediates the it produces to continue down path way. B1

P1

A

B

Product accumulation sometimes can inhibit catalytic activity of the first enzyme, called feed back inhibition.

B2

P2

Principal characteristics of metabolic pathways. 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. 3) Metabolic pathways in eukaryotic cells occur in specific cellular locations. The compartmentation of the eukaryotic cell allows different metabolic pathway