AGM101 - Metabolism - Energetics

Metabolism - Energetics

Energetics in microbial metabolism

[Note: Energetics (also called energy economics) is the study of energy under transformation. Energetics is a very broad discipline, encompassing for example thermodynamics, chemistry, biological energetics, biochemistry and ecological energetics].

Regardless of how a microorganism makes a living—whether by chemoorganotrophy, chemolithotrophy, or phototrophy, it must be able to conserve some of the energy released in its energy-yielding reactions. Here we discuss the principles of energy conservation, using some simple laws of chemistry and physics to guide our understanding. We then consider enzymes, the cell’s catalysts.

Energy is the ability to do work. In microbiology, energy is measured in kilojoules (kJ), a unit of heat energy. All chemical reactions in a cell are accompanied by changes in energy, energy either being required for or released during the reaction. One k calorie is the energy required to raise 1°C of 1 kg of water. 1 calorie = 4.184 Joules. Chemical energy referred as the energy released during oxidation of organic or inorganic compounds.

First Law of Thermodynamics: Energy can neither be created nor be destroyed in the universe: So, the living things should collect the energy from existing sources and convert them to a suitable form for the biological process. Plants grab the energy from light and convert them to high energy chemical compounds. Similarly, animals can derive their energy by oxidizing the chemicals. Microorganisms especially the bacteria have both the ways (from chemicals and sun light).

Second law of Thermodynamics: In all the reactions, some of the energy involved loses its ability to do work: We can refer this energy lose as “disorder”. Generally living systems are “ordered”, but universe always prefers disordered. The living systems are always against the disorder and the living systems have constant battle against disorder and when they lose the battle, they die. The quantity of energy which is unable to do work in a reaction is referred as entropy. The energy released from a reaction, that is available to do some useful work is referred as free energy [indicated as ΔG (Δ “change in”, G “free-energy)].

Hence, total energy = free energy (ΔG) + entropy

The change in free energy during a reaction is expressed as ∆G^0` (Delta G 0 and prime refers free energy at standard conditions; pH 7.5; Temp 25°C at 1 atmospheric pressure.

A reaction may release or require free energy. If a reaction needs energy, it is referred as endergonic reaction and if a reaction releases energy, it is referred as exergonic reaction.

A + B → C + D + energy [exergonic reaction]

A + B + energy → C + D [endergonic reaction]

ΔG of some compounds are H₂0 = -237.2; CO₂ = -396.4; H₂= 0; O₂ = 0; N₂O = +104.2; Glucose = -917.3 Negative ΔG is good and available to do work in the cell.

How to calculate ∆G^0`

For a reaction, A + B → C + D, calculate the net free energy of A+B (Reactants) and net free energy of C+D (Product) and measure the ∆G^0` as “product minus reactant”. If ∆G^0`is negative, it is exergonic, can conserve or release energy for ATP production. If, ∆G^0` is positive, it is endergonic which requires energy.

Activation energy

Consider the formation of water from gaseous oxygen (O2) and hydrogen (H2). The energetics of this reaction are quite favorable:

H2 + ½O2 → H2O, ∆G0` -2237 kJ

However, if we were to mix O2 and H2 together in a sealed bottle and leave it for years, no measurable amount of water would form. This is because the bonding of oxygen and hydrogen atoms to form water requires that their chemical bonds first be broken. The breaking of these bonds requires some energy, and this energy is called activation energy. Activation energy is the energy required to bring all molecules in a chemical reaction into the reactive state.

The concept of activation energy leads us to consider catalysis and enzymes. A catalyst is a substance that lowers the activation energy of a reaction, thereby increasing the reaction rate. Most cellular reactions do not proceed at useful rates without catalysis. Biological catalysts are called enzymes. Enzymes are proteins (or in a few cases, RNAs) that are highly specific for the reactions they catalyze. That is, each enzyme catalyzes only a single type of chemical reaction, or in the case of some enzymes, a single class of closely related reactions. This specificity is a function of the precise three-dimensional structure of the enzyme molecule.

Oxidation and Reduction

The energy released in oxidation–reduction (redox) reactions is conserved in cells by the simultaneous synthesis of energy rich compounds, such as ATP. We will consider oxidation–reduction reactions and the major electron carriers present in the cell. An oxidation is the removal of an electron or electrons from a substance, and a reduction is the addition of an electron or electrons to a substance. Oxidations and reductions are common in cellular biochemistry and can involve just electrons or an electron plus a proton (a hydrogen atom; H).

H2 + ½O2 → H2O, In this reaction, the redox reactions occur in pairs. For example, hydrogen gas (H2) can release electrons and protons and become oxidized. However, electrons cannot exist alone in solution; they must be part of atoms or molecules. Thus, the reaction is only a half reaction, which needs for a second half reaction. This is because for any substance to be oxidized, another substance must be reduced. The oxidation of H2 can be coupled to the reduction of many different substances, including oxygen (O2), in a second half reaction. This reduction half reaction, when coupled to the oxidation of H2, yields the overall balanced reaction. In reactions of this type, we refer to the substance oxidized (in this case, H2) as the electron donor, and the substance reduced (in this case, O2) as the electron acceptor. The concept of electron donors and electron acceptors is very important in microbiology and underlies virtually all aspects of energy metabolism.

Electron carriers

Substrates or compounds vary their ability to donate or accept the electrons (in other words, to become oxidized or reduced). The tendency of a substrate to donate or accept the electron is referred as oxidation – reduction Potential or redox potential. The redox potential of each substance was calculated by means of electrical volt with reference substance as H2. The redox potential is –ve means, the substance is rich of electrons, (means reduced form) and +ve means it already lost the electrons (means oxidized form). The reduced forms can give or donate electrons and oxidized form can accept the electrons. If series of oxidation – reduction reactions occur, the electrons from one reaction can be carried out to another by means of electron carriers. They can accept the electrons from a reaction and can donate the same in some other reaction. They are called as electron carriers. Very common carrier is the coenzyme nicotinamide adenine dinucleotide (NAD+) NAD+ is an electron plus proton carrier, transporting 2 e- and 2 H+ at the same time. The reduction potential of the NAD+/NADH couple is -0.32 V, which places it fairly high on the electron tower; that is, NADH is a good electron donor.

Please see the above reaction. When substrate X gets oxidized, the electron released can be taken up by NAD+ (oxidized form) and reduced to NADH. The NADH (reduced form) then moves to some other reaction and can donate the electron to substrate A which may give the products A and B. This is how the electron carriers functioned in oxidation-reduction reactions or in metabolic path ways.

Phosphorylation (ATP synthesis)

Addition of phosphorus is referred as phosphorylation. The energy released during oxidation reaction is stored in the form of high energy phosphate bonds in ATP. When energy is released, the ADP and Pi reacted and form ATP. This process of addition of Pi to from ATP is referred as phosphorylation.

(Note: The high energy phosphate bonds are differing from normal phosphate bonds and the energy released from ATP is higher than glucose phosphates).

Phosphate can be bonded to organic compounds by either ester or anhydride bonds. However, not all phosphate bonds are energy-rich. ∆G0` of hydrolysis of the phosphate ester bond in glucose 6-phosphate is only -13.8 kJ/mol. By contrast, the ∆G0` of hydrolysis of the phosphate anhydride bond in phosphoenolpyruvate is -51.6 kJ/mol, almost four times that of glucose 6-phosphate. ATP to ADP gives -31.8 8 kJ/mol.

ATP

The most important energy-rich phosphate compound in cells is adenosine triphosphate (ATP). ATP consists of the ribonucleoside adenosine to which three phosphate molecules are bonded in series. ATP is the prime energy currency in all cells, being generated during exergonic reactions and consumed in endergonic reactions. From the structure of ATP, it can be seen that two of the phosphate bonds are phosphoanhydrides that have free energies of hydrolysis greater than 30 kJ. Thus, the reactions ATP → ADP + Pi and ADP → AMP + Pi each release roughly 32 kJ/mol of energy. By contrast, AMP is not energy-rich because its free energy of hydrolysis is only about half that of ADP or ATP.

The phosphorylation or ATP formation occurs in three different ways in bacteria.

Substrate level phosphorylation: Energy released during oxidation of one organic molecule to another will be used for ATP production. There won’t be any external electron acceptor and the organic substrate itself acts as electron acceptor. This kind of phosphorylation is referred as substrate level phosphorylation.
Oxidative or Electron transport phosphorylation: ATP formation during electron transport chain by proton motive force is referred as oxidative phosphorylation. The electrons were carried by several electron carriers and finally the terminal electron acceptor (like O2) will accept the electron and form H20. The proton motive force of ATPase used for ATP synthesis.
Photophosphorylation: The ATP formation using light energy is referred as photophosphorylation. The proton motive force during photosynthesis is used for ATP synthesis.

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