BCM301

Chapter 1:Bioenergetics

By: Zatilfarihiah Rasdi

Biochemistry II

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

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

reactions Coupled reactions

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

A Review: Thermodynamic Principles

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

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

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

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

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

conformations how metabolic pathways are designed, why molecules cross

biological membranes how muscles generate mechanical force

1. First Law of Thermodynamics:Energy Is Conserved

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

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

1. Open system: Living organisms, which take up nutrients, release waste products and generate work and heat.

2. Closed system: If an organism were sealed inside an uninsulated box.

3. Isolated system: If the box perfectly insulated.

A. Energy The 1st law of thermodynamics is a mathematical

statement of the law of conservation of energy. Energy can be neither created nor destroyed.

∆ U = Ufinal – Uinitial = q – where U is energy, q represents the heat absorbed by the system from surroundings and w is the work done by the system on the surroundings.

Processes in which a negative q, are known as exothermic processes (Greek: exo, out of); those in which the system gains heat (positive q) are known as endothermic processes (Greek: endon, within).

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

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Table 3-1 Thermodynamic Units and Constants.P

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

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

H = U + PV

where V is the volume and P is its pressure. is a particularly convenient quantity with which to describe biological

systems because under constant pressure, a condition typical of most biochemical processes, the enthalpy change between the initial and final states of a process, ∆H, is the easily measured 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 hypothetical reaction pathway can be determined from the enthalpy change in any other reaction pathway between the same reactants and products.

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

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

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

disorder

A. Spontaneity and disorder The spontaneous processes occur in directions

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

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

(Note: Find the equation that involved with W)

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

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

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

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

S = kB ln W

that increases with W but in more manageable way. Here kB is the Boltzman constant. Eg. For twin bulb system, S = kBN ln 2, so the entropy of the system in its most probable state is proportional to the number of gas molecules contains.

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

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

In the lungs-concentration of O2 is higher than in venous blood passing through them, more O2 enters the blood than leaves it. On the other hand, in the tissues- where the O2 concentration is lower than in arterial blood, there is net diffusion of O2 from blood to the tissues.

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

increasingly disordered, that is, its entropy increases, as its 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 is ATP – “universal carrier of biological energy”

Fundamental concept of metabolism:

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

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

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

G is an indicator of the energy available from the reaction to do work;composed of two components, enthalpy (H) and entropy (S).

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, ∆G°’ This section focus on the most important energy

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

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

ATP ADP + Pi + energy

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

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

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Table 3-2 Variation of Reaction Spontaneity (Sign of DG) with the signs of DH and DS.

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

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

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

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

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

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Table 3-3 Variation of Keq with DG° at 25°C.P

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

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

Biochemical Interest.

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

Biochemical Interest.

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

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

(1) A + B C + D ∆G1

(2) D + E F + G ∆G2

If ∆G1 ≥ 0, reaction (1) will not occur spontaneously. However, if ∆G2 is sufficiently exergonic so that ∆G1 + ∆G2 < 0, then

although the equilibrium concentration of D in reaction (1) 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 the forward direction to replenish the equilibrium concentration of D.

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

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

(3) A + B + E C + F + G ∆G3

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