The Biological Classification and Physiological Foundation of Domain of Eukarya Homeostasis

The domain of Eukarya Homeostasis is a completely new biological formation evolved from the domain of Eukarya. The name comes from the characteristic that the cells have Absolute Energy in Homeostasis. The great difference between Eukarya Homeostasis and Eukarya is cellular energetic status. Due to the different energetic status, the different biochemical reactions and functions were happened. Simply speaking, the biochemical functions and reactions of Eukarya were expedited by Thermodynamics and Eukarya Homeostasis was activated by the Absolute Homeostasis Energy Source.

In 1989, Mr. Yuan Lin discovered the Energy in Absolute Homeostasis that is the universal of all entities, this energy cannot be generated or annihilated, nor can it be increased or decreased. It does not have any form, cannot be changed but permeates everything and every place. It acts as the energy to construct the most fundamental forms of evolution for all and everything, including time and space, the universe and its background. Unlike other kinds of forces or catalysts, it will not be consumed and altered in any change of events or reactions. It does not have unique specificity to catalyze specific reactions or induce specific conformations. The progressive process of constituent energy for all and every event can take place only with the participation of this energy. It broadly affects the physical and chemical variations and reactions. Therefore the variations in physics (ΔP), chemistry (ΔC), mole (ΔM), and energy (ΔE) have a common function () under the same condition.

It can be shown that:

and the equations are represented as:

Where HAES is the Absolute Homeostasis Energy Source, and ΔP : physics; ΔC: chemistry; ΔM : mole; ΔE: energy; : free energy; t: time; x: substances
This equation is called the “Absolute Homeostasis Energy Source”.

The organism’s system of the Eukarya Homeostasis is a free system, it is a new style of organism independent of all organisms of modern stage, including, open system; close system; and isolated system. The physiological foundation of Eukarya Homeostasis is somewhat different from modern organism, we cannot apply wide range of knowledge in modern biology indiscriminately to the organism of the Eukarya Homeostasis. Before given an in depth explanation of this subject, we will review the theories of Bioenergetics; Thermodynamics; and Genetics.

Bioenergetics is a deep comprehension of biochemistry, specially, it is the required basic knowledge to understanding the biological organism metabolism regulation. It is the basic problems of living cells transition and energy utilization in biochemistry. Because the biochemistry relates to the basic problems of living cells transition and energy utilization. Bioenergetics is completely established on the foundation of Thermodynamic. For this reason, we have to review all basic concepts of Thermodynamics before we comprehend Bioenergetics.

The Basic Concepts of Thermodynamics

1. General concept, characteristics and states of system

Thermodynamics commonly uses two terminologies, one is system and the other is surroundings. System is also named material system or system of objects. The definition of system in Thermodynamics is the general term of whole substances which involve in research. In other words, system is substance within the limited range. Some people refer system as one part of universe of human research. Surrounding is outside of the system, it is the general term of substances outside the system, the outside environment that is directly connection with system. Figure 20-1 represents their simple relation.

The system and surrounding can exchange energy under the constant temperature and pressure reaction. The energy exchange must follow the laws of thermodynamics. The total energy of universe is constant (system + surroundings are constant). When system proceeds with physical or chemical changes, the entropy of universe increases and the free energy of the system decrease. Following these changes there is a change in thermal energy. Whether the energy flow is from system to the environment, or from the environment to the system, must always follow the relation, .

Depending on the different relation between system and surrounding, there are three types of whole systems: When the system has material exchanges and energy transfer with the surrounding is called open system. When the system only has energy transfer and no material exchange with the surrounding is called close system. When the system has no material exchange and no energy transfer with the surrounding is called isolated system. All organisms belong to open system.

The characteristics of system include pressure, volume, temperature, constituent, specific heat, and surface tension etc. Thermodynamics is using these system characteristics to describe the condition the whole system is situated. When all characteristics of system are definite, the whole system will be settled. On the other hand, when one system statue is fixed, every kind of characteristics of this system will have constant value. The relationship between this characteristics and statues was named state function by thermodynamics. Infinitesimal changes of the statue of one system would make infinitesimal change of state function. It is worth of attention that the change in state function is related to the beginning and ending statues of the system and has no relationship to the processes of statue changes.

2. Two Forms of Energy- Heat and Work

There are many kinds of appearance of energy, heat and work are the two major forms among them. Heat and work are the two forms of exchangeable energy between the surroundings and the system statue when changes occur. Heat is an energy transmission way due to the temperature differential. Heat transmission always accompanies the random exercise of particles. Work is another energy exchange way between system and surroundings. For example: volume changes in resist to outside pressure; surface area changes in resist to surface tension; electric work and mechanical work in resist of outside electric field, etc. are all works. Work is accompaniment to the fix direction movement of particles of system, it is an order movement.

3. General Concept of Internal Energy and Enthalpy:

The internal energy is the total energy contained by particle energy inside the system. Generally use the symbol is U or E to represent. The energy of every particle inside the system is associated with the characteristics, structure, movement state, and exchange function of system. Therefore, internal energy is the function of system state. The nature of internal energy is due to the molecular motion of horizontal kinetic energy, rotational energy, vibrating energy, electronic energy, electron and nucleus steady static mass energy, and potential energy of interaction of molecules. It shows that the absolute value of internal energy is beyond measurement. But, when the state of the system happens to change, the amount of change of the internal energy is measurable. That is to say, when the system state is definite, the internal energy will be constant value. The experiment proved that internal energy is related to the definite statue, and has no relationship with the pathway of how to reach the condition.

Enthalpy is represented by the symbol H. It is state function of system; it is a measure of the total energy of the system including the internal energy and the amount of energy to change pressure and volume of total molecules. Due to each particle in system collides, it makes interaction between particles. Enthalpy is related to the interaction of particles inside system and energy of particle itself. The change in enthalpy is represented by symbol . The formula shows the relationship between Enthalpy and internal energy change:

Based on the above basic concept, it is not difficult to comprehend the two laws of thermodynamics.

4. First Law of Thermodynamics:

First law of thermodynamics is an expression of the principle of conservation of energy. This law points out that the total energy of system and surrounding is constant. Even though the form of energy can convert, but it will not disappear.

System and surroundings are the two functional parts in internal energy of universe. The internal energy of universe is never change, no matter what the energy flowing direction between system and surroundings. Any special system has two ways to get energy from surroundings or to give energy to the surroundings; one is to get heat from the surroundings or to give heat to the surroundings, the other is to work on the surroundings or the surroundings work on the system. If the system state is changed, the internal energy of the system also changes. The change of internal energy of the system is equal to the heat absorption by the system subtract the work done by the system.

Mathematical formula of the first law of thermodynamics is represented as:

　　If the internal energy is an infinitesimal change, one writes:

Under constant pressure process, it is only volume work by system, no work on surroundings, therefore dW = PdV, equation (3) can be rewrite as:

One writes when enthalpy is infinitesimal change:

Substitute equation (4) into equation (5)

Since dU = dQ – PdV, For the system only has volume work, the enthalpy is represented as:

In equations (4) and (7), dQ, P, V, dP, dV are measurable values, therefore, we can calculate dU and dH value. If volume is unchanged, dV = 0, then

If pressure is unchanged, dP = 0, then

From the above derivations, they expressed that absorption heat of system is equal to internal energy change under volume unchanged condition. The absorption heat of system is equal to enthalpy change under pressure unchanged condition.

Organisms are open system. The special characteristics of system are not only mass exchange but also energy transmission between system and surroundings. Most of biochemical processes of organisms are happened under pressure unchanged condition; the absorptive or emitting energy is enthalpy change in system. Most of biochemical procedures processed under liquid or solid condition, so their change in volume is very small. Therefore, all biochemical procedures in organisms processed under almost constant pressure and volume, then dP = 0, dV = 0, so ΔH is almost equal to ΔU, that is (ΔH ≈ΔU). They neglected the difference between ΔH and ΔU in biochemistry, it is called energy change of accompaniment reaction.

5. Chemical Energy Transformation:

Different chemical materials store different chemical energy which can convert to other forms of energy in reactions. For example: light energy converts to chemical energy in photosynthesis. This chemical energy is stored in form of chemical substances. Heterotroph can utilize the release energy in chemical substances through metabolism to convert to mechanical work or supply biological synthesis.

During the metabolism process, organic chemical substances convert to low energy new chemical substances step by step and release free energy and heat in organisms.

When chemical substances are completely oxidized, the large amount chemical energy convert to fire energy (thermal energy). It is the oxidized heat; its definition is the large amount energy to be released when one mole organic compound is completely oxidized. Fire is very drastic oxidization form. Under slow oxidation, the released energy from chemical substance is equal to the difference between the chemical bond energy of substance subtracting the chemical bond energy of products. The total released energy from oxidation has no relationship with the oxidation pathway of substance. If the products are same then the total released energy must be equal.

Biological oxidation is chemical substances to be oxidized in organism. The end of products are the same as burning, they are CO2 and H2O. It is slow process of oxidization in organ body, it gradually releases heat and the greater portion of energy transforms to other special compounds.

For example: release energy from burning glucose is 2868.852kJ/mol (equal to 686Kcal/mol). At body temperature, glucose is oxidized to CO2 and H2O and releases the same amount of energy. There are many steps for oxidization processes of glucose in the body, the stored energy will gradually release and greater portion of energy is transformed to special stored compound ATP.

6. General Idea of Second Law of Thermodynamics:

Second law of thermodynamics is an expression that heat flows from regions of higher temperature to lower temperature regions. It is impossible to have spontaneous and reversible reactions. The second law describes that system motion in thermodynamics has a constant direction of progress; it flows from high temperature to low temperature.

Living experiences tell us, many procedures can process spontaneous reactions under special condition. For example: heat can conduct from high temperature substances to low temperature environment; diamond and oxygen (gas) produce CO2, it is possible spontaneous reaction. If all reactions that are reverse to above reaction, it will be non spontaneous reaction.

When heat flows from the high temperature object to low temperature environment, it is to spread the concentrated energy of high temperature object to all particles of the connected environment. This demonstrates the increase degree of separation energy. The reversed procedure is not spontaneous process. CO2 produced from diamond is also the procedure of spread out from a concentrated energy. The common characteristics of spontaneous processes are that energy flows to the direction of increase degree of separation. The degree of separation of energy in system is the collected macro characteristics of total appearance from large amount of micro particles doing exercise in system; this characteristics changes following the status of the system, it is the statue function to system. The statue function of degree of separation energy in system is generally expressed as Entropy, the symbol is S, it is a measure of randomness associate with particles in the system. When the particles are more random, the entropy value increases, the change in entropy is represented as ΔS, it is a positive value.

The second law of thermodynamics describes that a progress can be spontaneous process when the sum of total entropy value of system and surroundings increases in an isolated system, one writes:

ΔS = Qr/T or dS = dQr/T 　　　（10）

Entropy change in isolated system equals to the sum of entropy change from system and surroundings. One writes:

ΔS =ΔSsys. + ΔSsur. ≧ 0　　　（11）

the “=” in equation represents reversible process. The entropy will be zero, and the system will be in equilibrium state. The “＞“ represents irreversible reaction, Entropy will increase in system. In fact, all spontaneous processes are irreversible. Entropy always increases, until reaches the maximum value, and then the process will be stopped.

Something worthy of attention is that when the spontaneous procedure is proceeding, the entropy of the system may decrease but the entropy of surroundings will increase, their total entropy must be positive value. Besides, on the stand point of Thermodynamics, a possible spontaneous process is not really to indicate that the process is progressing. Whether the process is moving forward, depends on the existence of suitable condition. For non organism, we can change pressure, temperature, and raise the concentration of reactants to induce the process. For organism, all reactions must restrict under constant temperature and pressure to process. The concentration of reactants has to be within limited range in the body. How to follow the law of thermodynamic to activate chemical reactions and release energy to support life activity? It is the question to be revealed in biochemistry.

According to second law of thermodynamics, we will understand what procedures can happen in organism and predict what factor is limiting in the procedures. For example: It is possible to form high degree of order organism structure because the decrease in entropy of high degree of order organism structure formation is offset by the increase of entropy of surroundings and it still retains some of entropy. For example: the irreversible process in organism continuously produced positive entropy, it would bring danger to organisms themselves due to greater entropy. The maximum of entropy will implies the stop of the life, organism will die too. When organism can ingenuously and continuously absorb negative entropy from surroundings then organisms can maintain life. The processes of metabolism let the organisms successfully release to the surroundings, the whole positive entropy had to produce while conducting life activity.Because of this, any kind of organisms eventually cannot escape death.

It is very difficult to use entropy to judge the biochemical procedures whether it is spontaneous process or not. From equation (11), it is necessary to know entropy change in system and entropy change in surroundings. Because it is difficult to measure of entropy from chemical reactions, we can use free energy as the standard of measure and also can get rid of difficult problem. Free energy is the status function; it is another base judgment of nature procedure and spontaneous motion derived from the second law of thermodynamics.

7. General idea of Free Energy:

The general idea of free energy has a special important meaning for studying biochemical procedures in energy mechanics. The organisms use the free energy releasing from chemical reactions inside the body to work. The energy released from biological oxidation is exactly the free energy utilized by the organism. It is not only can be used to judge whether the process is spontaneous or not, but also can utilize free energy function to calculate other reference numbers.

In 1878, Josiah Willard Gibbs described this general idea of free energy. In order to understand the general idea of free energy, a simple example is due: put a gas containing thermal energy Q in a frictionless thermal mechanism, the temperature of gas is T1, assume the temperature of gas goes down to absolute zero after gas does work in thermal mechanism. Due to frictionless, all heat energy Q converts to work. All the energy which can do the work, Gibbs named it as free energy. So Q is free energy. In fact, the temperature of gas was much higher than absolute zero after work. Assume temperature decreased to T2, only part of total energy can do the work, and presented as free energy. The frictionless thermal mechanism having energy Q does the work between temperature T1 and T2, then the work can be represented by the equation:

Rewrite equation (12) to:

If T2 is absolute zero, that is T2 = 0, then W = Q
If T2≠0, then portion of energy cannot do work.
Where (Q/ T1) T2 is the energy cannot do work, and Q/ T1 is entropy of system, represented by (S).
The free energy can do work, is represented by the symbol (G). Earlier literatures use the symbol (F).
There are two kinds of energy, one is thermal energy, that does work and induces temperature or pressure change, the other is free energy that does work under constant temperature and pressure.
Gibbs defined free energy as:

From Gibbs free energy formula, free energy is enthalpy and entropy combined function. We can find the combined relationship between the first law and second law.

Gibbs found that at constant temperature and reversible process, the following relation exists:

Or
Substitute equation (15) into (14) to obtain
ΔG = 0, that is the free energy is zero in the reversible processes.

Following discussion should help to further comprehend the definition of free energy.
When a system involves in work, there are two kinds of work. One is due to change in volume to do work and it is named volume work, the other is to do work toward outside system and it is named useful work. The infinitesimal process of work (total work), includes volume work (PdV) and useful work (dW’). The relationship of them is shown following:

According to the first law of thermodynamics:

Substitute equation (3) into equation (16) to obtain

If it is reversible reaction in system, then dQ = TdS (equation 10). Where dW is the maximum work, also it is the total work of reversible process. dW represents the useful work, but not the total work. dQ represents the absorption of heat energy in an infinitesimal reversible process of system.

Substitute dQ = TdS into equation (17)
　　
According to definition of free energy:

Differentiation of the above equation to obtain dG:

　　Due to , substitutes dH into equation (19)

Substitute dU in equation (18) into equation (20) to obtain

If temperature unchanged, SdT =0, equation (21) becomes

Integration of equation (22) to obtain the following

If temperature unchanged and no work, W’ = 0

If temperature and pressure unchanged

It is concluded that decrease in free energy (ΔG is negative value), it is the maximum amount of usable work under constant temperature and pressure in reversible processes. If in the process, there is only volume work in system but is not useful work, then W’ = 0, equation (25) is simplified to

It is reversible processes.

It is spontaneous processes.

The Free Energy Change and Meanings in Chemical Reactions

For explanation of free energy in chemical reactions, especially for the function and meaning of biochemical reactions, we have to analyze free energy change in chemical reactions. The basic general idea of free energy was described in first section; the free energy change in chemical reactions must gain the same free energy formula.

1. Change in Free Energy Formula in Chemical reaction:

Consider the chemical reaction:

If total energy of A + B are larger than that of C + D, then release energy is ΔH.

Written the C + D energetic state after the reaction:

Under constant temperature, the change in free energy is obtained by (30) – (29)

Equation (31) can be rewritten to

Equation (32) is same as equation (14), it is the free energy formula.

2. The Relationship between Standard Free Energy Change and Chemical Equilibrium:

Reactants and products have specific free energy in chemical reactions. The difference between total of free energy of reactants and products is free energy change in reaction. For convenience in calculation, we set up some conditions as standard condition and all free energy change in chemical reaction under those conditions is named standard free energy change. The standard condition refers to the temperature at 25oC (298K), atmosphere pressure of 101,325pa (1 atm), the concentration of reactants (A, B) and products (C, D) is 1 mol/L. The symbol of standard free energy change is ΔGo. With respect to biochemical reactions, the standard condition requires the reactions proceeds under the environment of pH =7, the standard free energy change at these conditions is represented as ΔGo’.

We must pay attention to the difference between ΔG and ΔGo. ΔGo is a constant in chemical reactions, it is under specific condition and the number is decided by reaction substances themselves, every chemical reaction has the specific free energy change. ΔG is free energy which is changed by concentration of reaction substances, pH in reaction and temperature change in chemical reactions. From the concentration of reactants and products to calculate ΔG, then we can judge the direction of procedures which follow the chemical reactions or not. When ΔG is negative value, the reaction can process. Because negative value means during the reaction happens, there will be a release of energy. If ΔGo is positive value and the calculated value of ΔG is negative; the procedure still will follow the direction to process. To all chemical equilibriums reactions, the ΔG is negative value. Moreover this absolute value will gradually reduce until it reaches zero, it is the equilibrium point of reaction.

Below we discuss the relationship between free energy change of chemical reaction and equilibrium
constant.

Consider the following chemical reaction:

a,b,c,d represents molecule numbers for A, B, C, D reacting materials.
Under constant temperature and pressure, free energy change in this reaction is:

ΔGo: free energy change, when reactants and products stay standard condition, it is standard free energy change
R: gas constant
T: absolute temperature

[A], [B], [C], [D] represents the mole concentration of reactants and products. Strictly speaking, they are activity.

The free energy change (ΔG) in chemical reactions depended on one part of unchanged factors, the nature of reactants; other part of change factors, the concentration of reactants and products, chemical equivalent and temperature in reactions.

According to the requirement, we can calculate the free energy change in reactions if we know the free energy change of reactants and products and concentration.

When formula (33) stayed at equilibrium point, no reaction was happened again, then free energy change was zero (ΔG=0). This reaction system could not do any works.

Rewrite equation (35) into the following :

The equilibrium constant of biochemistry is represented as the follows:

Note: K’eq  represents the measured equilibrium constant under a definite condition, which is slightly different with the real equilibrium constant defined in Thermodynamics.
Substitute equation (37) into equation (36) to obtain (38) where ΔG0 is ΔG0'

Rewrite equation (38) in logarithm form to obtain

Equation (39) can also write in the following form:

R is gas constant, R=1.98x10-3 Kcal/mol K (K is absolute temperature, equal to 298 K; it is 25oC), the unit of ΔGo is Kcal/mol or KJ/mol. R= 8.31x10-3 KJ/mol K.

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