BCM301

Chapter 1:Bioenergetics

By: Zatilfarihiah Rasdi

Biochemistry II

By the end of the lecture, students By the end of the lecture, students should be able to know/define/state:should be able to know/define/state:

The first and second law of thermodynamicsThe first and second law of thermodynamics The enthalpy, entropy and free energyThe enthalpy, entropy and free energy Exothermic, endothermic, exergonic and endergonic Exothermic, endothermic, exergonic and endergonic

reactionsreactions Coupled reactionsCoupled reactions

Do revise this topic and refer to Do revise this topic and refer to textbook of biochemistry!!!textbook of biochemistry!!!

A Review: Thermodynamic A Review: Thermodynamic PrinciplesPrinciples

Living things require a continuous throughput of Living things require a continuous throughput of energy. eg. Photosynthesis process – plants convert energy. eg. Photosynthesis process – plants convert radiant energy from the Sun, the primary energy radiant energy from the Sun, the primary energy source for life on Earth, to the chemical energy of source for life on Earth, to the chemical energy of carbohydrates and other organic substances.carbohydrates and other organic substances.

The plants/ animals that eat them, then metabolize The plants/ animals that eat them, then metabolize these substances to power such functions as the these substances to power such functions as the synthesis of biomolecules, the maintenance of synthesis of biomolecules, the maintenance of concentration gradients and the movement of concentration gradients and the movement of muscles.muscles.

These processes transform the energy to heat, which is These processes transform the energy to heat, which is dissipated to the environment and must be devoted to the dissipated to the environment and must be devoted to the acquisition and utilization of energy.acquisition and utilization of energy.

Thermodynamics (Greek: Thermodynamics (Greek: thermetherme, heat + , heat + dynamicsdynamics, , power) is a description of the relationships among the power) is a description of the relationships among the various forms of energy and how energy affects matter various forms of energy and how energy affects matter on the macroscopic as opposed to the molecular level.on the macroscopic as opposed to the molecular level.

With a knowledge of thermodynamics we can determine With a knowledge of thermodynamics we can determine whether a physical process is possible. Thermodynamics whether a physical process is possible. Thermodynamics is essential for: is essential for: understanding why macromolecules fold to their native understanding why macromolecules fold to their native

conformationsconformations how metabolic pathways are designed, why molecules cross how metabolic pathways are designed, why molecules cross

biological membranesbiological membranes how muscles generate mechanical forcehow muscles generate mechanical force

1. First Law of Thermodynamics: 1. First Law of Thermodynamics: Energy Is ConservedEnergy Is Conserved

A A systemsystem is defined as that part of the universe that is of is defined as that part of the universe that is of interest, such as reaction vessel or an organism; the rest interest, such as reaction vessel or an organism; the rest of the universe is known as the of the universe is known as the surroundingssurroundings..

A system is said to be open, closed or isolated according A system is said to be open, closed or isolated according to whether or not it can exchange matter and energy to whether or not it can exchange matter and energy with its surroundings, only energy.with its surroundings, only energy.

Living organisms, which take up nutrients, release waste Living organisms, which take up nutrients, release waste products and generate work and heat (products and generate work and heat (openopen system). system).

If an organism were sealed inside an uninsulated box, it If an organism were sealed inside an uninsulated box, it would, together with the box, constitute a would, together with the box, constitute a closedclosed system.system.

If the box perfectly insulated, the system would be If the box perfectly insulated, the system would be isolatedisolated..

A.A. EnergyEnergy The 1The 1stst law of thermodynamics is a mathematical law of thermodynamics is a mathematical

statement of the law of conservation of energy. statement of the law of conservation of energy. Energy can be neither created or destroyedEnergy can be neither created or destroyed..

∆ ∆ U = UU = Ufinalfinal – U – Uinitialinitial = = qq – – ww

here here UU is energy, is energy, qq represents the heat absorbed by represents the heat absorbed by the system from surroundings and the system from surroundings and ww is the work done is the work done by the system on the surroundings.by the system on the surroundings.

Processes in which a negative Processes in which a negative qq, are known as , are known as exothermic processesexothermic processes (Greek: (Greek: exoexo, out of); those in , out of); those in which the system gains heat (positive which the system gains heat (positive qq) are known as ) are known as endothermic processesendothermic processes (Greek: (Greek: endonendon, within)., within).

The SI unit of energy, the The SI unit of energy, the joule (J),joule (J), is steadily is steadily replacing the replacing the calorie (cal)calorie (cal) in modern scientific usage. in modern scientific usage.

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Table 3-1Table 3-1 Thermodynamic Units and Thermodynamic Units and Constants.Constants.

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B. EnthalpyB. Enthalpy- any combination of only state functions must also be a state any combination of only state functions must also be a state

functionfunction. One such combination, known as enthalpy (Greek: to . One such combination, known as enthalpy (Greek: to warm in) is definedwarm in) is defined

H = U + PVH = U + PV

wherewhere V V is the volume andis the volume and P P is its pressureis its pressure.. is a particularly convenient quantity with which to describe is a particularly convenient quantity with which to describe

biological systems because biological systems because under constant pressure, a condition under constant pressure, a condition typical of most biochemical processes, the enthalpy change typical of most biochemical processes, the enthalpy change between the initial and final states of a process, ∆H, is the easily between the initial and final states of a process, ∆H, is the easily measured heat that it generates or absorbsmeasured heat that it generates or absorbs..

a. State functions are independent of the path a systems follow

• Experiments have invariably demonstrated that the energy of a system depends only on its current properties or state, not on how it reached that state.

In general, the change of enthalpy in any In general, the change of enthalpy in any hypothetical reaction pathway can be hypothetical reaction pathway can be determined from the enthalpy change in any determined from the enthalpy change in any other reaction pathway between the same other reaction pathway between the same reactants and products.reactants and products.

Spontaneous processes are characterized by the Spontaneous processes are characterized by the conversion of order ( in this case the coherent motion conversion of order ( in this case the coherent motion of the swimmer’s body) to chaos ( here the random of the swimmer’s body) to chaos ( here the random thermal motion of the water molecules)thermal motion of the water molecules)

The 2The 2ndnd law of thermodynamics expresses this law of thermodynamics expresses this phenomenon, provide the criterion for determining phenomenon, provide the criterion for determining whether a process is spontaneous.whether a process is spontaneous.

1. Second Law of 1. Second Law of Thermodynamics: Thermodynamics: The universe The universe tends toward maximum disordertends toward maximum disorder

A.A. Spontaneity and disorderSpontaneity and disorder The spontaneous processes occur in directions that increase the The spontaneous processes occur in directions that increase the

overall disorder of the universe that is, of the systems and its overall disorder of the universe that is, of the systems and its surroundings.surroundings.

Disorder, in this context, is defined as the number of equivalent Disorder, in this context, is defined as the number of equivalent ways, ways, WW, of arranging the components of the universe., of arranging the components of the universe.

((Note: Find the equation that involved with Note: Find the equation that involved with WW))

Figure 3-1Figure 3-1 Two bulbs of equal volumes connected Two bulbs of equal volumes connected by a stopcock.by a stopcock.

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B. EntropyB. Entropy In a chemical systems, In a chemical systems, WW, the number of equivalent ways of , the number of equivalent ways of

arranging a system in a particular state, is usually arranging a system in a particular state, is usually inconveniently immense.inconveniently immense.

In order to be able to deal with In order to be able to deal with WW more easily, we define, as more easily, we define, as Ludwig Boltzman in 1877, a quantity known as entropy Ludwig Boltzman in 1877, a quantity known as entropy (Greek: (Greek: enen, in + , in + tropetrope, turning):, turning):

S = kS = kBB lnln W W

that increases with W but in more manageable way. Here that increases with W but in more manageable way. Here kkBB is is

the Boltzman constant. Eg. For twin bulb system, the Boltzman constant. Eg. For twin bulb system, S = kS = kBBN N lnln 2, 2,

so the entropy of the system in its most probable state is so the entropy of the system in its most probable state is proportional to the number of gas molecules contains.proportional to the number of gas molecules contains.

Note: Entropy is a state function because it depends only on the Note: Entropy is a state function because it depends only on the parameters that describe a state.parameters that describe a state.

The conclusions based on the twin-bulb apparatus The conclusions based on the twin-bulb apparatus may be applied to explain, why blood transports may be applied to explain, why blood transports between the lungs and the tissues. Solutes in between the lungs and the tissues. Solutes in solution behave analogously to gases in that they solution behave analogously to gases in that they intend to maintain a uniform concentration intend to maintain a uniform concentration throughout their occupied volume – this is their throughout their occupied volume – this is their most probable arrangement.most probable arrangement.

In the lungs-concentration of OIn the lungs-concentration of O22 is higher than in is higher than in

venous blood passing through them, more Ovenous blood passing through them, more O22 enters enters

the blood than leaves it. On the other hand, in the the blood than leaves it. On the other hand, in the tissues- where the Otissues- where the O22 concentration is lower than in concentration is lower than in

arterial blood, there is net diffusion of Oarterial blood, there is net diffusion of O22 from from

blood to the tissues.blood to the tissues.

Figure 3-3Figure 3-3 Relationship of entropy and temperature.Relationship of entropy and temperature.The structure of water or any other substance becomes The structure of water or any other substance becomes

increasingly disordered, that is, its entropy increases, as its increasingly disordered, that is, its entropy increases, as its temperature rises.temperature rises.

3. Free energy change, ∆G – indicator of spontaneity• Thermodynamic view: metabolism is an energy

transforming process whereby catabolism provides energy for anabolism.

• What is energy?- “the capacity to cause or undergo change”

• Cell and organisms are able to harness forms of energy and convert them to other suitable forms to support movement, active transport and biosynthesis.

The most important medium of energy exchange The most important medium of energy exchange is ATP – “universal carrier of biological energy”is ATP – “universal carrier of biological energy”

Fundamental concept of metabolism:Fundamental concept of metabolism:

i. exergonic – i. exergonic – the overall process of catabolism the overall process of catabolism releases energy (spontaneous)releases energy (spontaneous)

ii. endergonic – ii. endergonic – the overall process of anabolism the overall process of anabolism requires nergy input (nonspontaneous)requires nergy input (nonspontaneous)

Goal of thermodynamic: to predict the spontaneity Goal of thermodynamic: to predict the spontaneity of a process or reaction. The most useful of a process or reaction. The most useful thermodynamic terms is free energy, thermodynamic terms is free energy, GG or known or known as Gibbs free energy.as Gibbs free energy.

GG is an indicator of the energy available from the is an indicator of the energy available from the reaction to do work;composed of two components, reaction to do work;composed of two components, enthalpyenthalpy ( (HH) and ) and entropyentropy ( (SS).).

G = H – TS…………………………….(1)

where T = temperature in Kelvin (K)units for G = joules/mol or kJ/mol

∆G = ∆H –T ∆S……………………....(2)

whether a reaction is spontaneous may be predicted from the following values of ∆G:

If ∆G < 0 energy is released;reaction is spontaneous and exergonic∆G = 0 reaction is at equilibrium∆G > 0 energy is required;reaction is nonspontaneous and

endergonic

Note: it is very difficult to measure ∆G for a biochemical reaction because the cellular concentrations of the reactants are very small and hard to determine experimentally. In order to calculate the energy associated with biochemical reactions, we must resort to the measurement under a set of standard.

Standard Free Energy Change,Standard Free Energy Change, ∆G°’ ∆G°’ This section focus on the most important energy This section focus on the most important energy

molecule, ATP.molecule, ATP. The breakdown of ATP must be exergonic reaction, but The breakdown of ATP must be exergonic reaction, but

what is the what is the quantitative amount quantitative amount of energy released under of energy released under std. conditions?std. conditions?

ATP ADP + PATP ADP + Pii + energy + energy

In your introductory chemistry courses, std. conditions for solute In your introductory chemistry courses, std. conditions for solute reactions were defined as:reactions were defined as:

1 atm of pressure, 25°C and initial and products concentration of 1 1 atm of pressure, 25°C and initial and products concentration of 1 MM. (but in biochemical process) + condition of a pH of 7 the . (but in biochemical process) + condition of a pH of 7 the modified modified ∆G°’.∆G°’.

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Table 3-2Table 3-2 Variation of Reaction Spontaneity Variation of Reaction Spontaneity (Sign of (Sign of GG) with the signs of ) with the signs of HH and and SS..

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4. Chemical equilibria4. Chemical equilibria The entropy (disorder) of a substance increases with its volume. The entropy (disorder) of a substance increases with its volume.

eg. Twin-bulb apparatus – a collection of gas molecules occupied eg. Twin-bulb apparatus – a collection of gas molecules occupied all of the volume available to it, maximizes its entropy. Entropy is all of the volume available to it, maximizes its entropy. Entropy is a function of concentration.a function of concentration.

If entropy varies with concentration, so do free energy. The free If entropy varies with concentration, so do free energy. The free energy change of chemical reaction depends on the concentrations energy change of chemical reaction depends on the concentrations of both its reactants and products. eg enzymatic reactions which of both its reactants and products. eg enzymatic reactions which needs substrates (reactants) and on the metabolic demand for their needs substrates (reactants) and on the metabolic demand for their products.products.

The equilibrium constant of a reaction may therefore be The equilibrium constant of a reaction may therefore be calculated from standard free energy data and vice versa.calculated from standard free energy data and vice versa.

Note: For more information on equilibrium constants, students may Note: For more information on equilibrium constants, students may refer to textbook and reference book of Biochemistry.refer to textbook and reference book of Biochemistry.

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Table 3-3Table 3-3 Variation of Variation of KKeq eq with with G°G° at 25°C. at 25°C.P

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Table 3-4Table 3-4 ((toptop) Free Energies of Formation of ) Free Energies of Formation of Some Compounds of Biochemical Interest.Some Compounds of Biochemical Interest.

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Table 3-4Table 3-4 ((middlemiddle) Free Energies of ) Free Energies of Formation of Some Compounds of Formation of Some Compounds of

Biochemical Interest.Biochemical Interest.

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Table 3-4Table 3-4 ((bottombottom) Free Energies of ) Free Energies of Formation of Some Compounds of Formation of Some Compounds of

Biochemical Interest.Biochemical Interest.

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A.A. Coupled reactionsCoupled reactions The additivity of free energy changes allows an The additivity of free energy changes allows an

endergonic reaction to be driven by an exergonic endergonic reaction to be driven by an exergonic reaction under the proper conditions.reaction under the proper conditions. (thermodynamic basis for the operation of the (thermodynamic basis for the operation of the metabolic pathways since most of these reaction metabolic pathways since most of these reaction sequences comprise endergonic as well as sequences comprise endergonic as well as exergonic reactions.exergonic reactions.

(1)(1) A + B C + DA + B C + D ∆G∆G11

(2)(2) D + E F + GD + E F + G ∆G∆G22

If ∆GIf ∆G1 1 ≥ 0, reaction (1) will not occur spontaneously.≥ 0, reaction (1) will not occur spontaneously. However, if ∆GHowever, if ∆G22 is sufficiently exergonic so that ∆G is sufficiently exergonic so that ∆G1 1 + ∆G+ ∆G22 < 0, < 0,

then although the equilibrium concentration of D in reaction (1) then although the equilibrium concentration of D in reaction (1) will be relatively small, it will be larger than that in reaction (2). will be relatively small, it will be larger than that in reaction (2). As reaction (2) converts D to product, reaction (1) will operate in As reaction (2) converts D to product, reaction (1) will operate in the forward direction to replenish the equilibrium concentration of the forward direction to replenish the equilibrium concentration of D.D.

The highly exergonic reaction (2) therefore drives the endergonic The highly exergonic reaction (2) therefore drives the endergonic reaction (1), and the two reactions are said to be coupled through reaction (1), and the two reactions are said to be coupled through their common intermediate D.their common intermediate D.

These coupled reactions proceed spontaneously can also be seen These coupled reactions proceed spontaneously can also be seen by summing reactions (1) and (2) to yield overall reactionby summing reactions (1) and (2) to yield overall reaction

(3)(3) A + B + E C + F + GA + B + E C + F + G ∆G ∆G33

As long as the overall pathway (reaction sequence) is exergonic, it As long as the overall pathway (reaction sequence) is exergonic, it will operate in the forward directionwill operate in the forward direction. Thus, the free energy of ATP . Thus, the free energy of ATP hydrolysis, a highly exergonic process, is harnessed to drive many hydrolysis, a highly exergonic process, is harnessed to drive many otherwise endergonic biological processes to completion.otherwise endergonic biological processes to completion.