Biochemistry/Thermodynamics

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Why Do Substances React?
Chemical (and thus, biochemical) reactions only occur to a significant extent if they are energetically favorable. If the products are more stable than the reactants, then in general the reaction will, over time, tend to go forward. Ashes are more stable than wood, so once the energy of activation is supplied (e.g., by a match), the wood will burn. There are plenty of exceptions to the rule, of course, but as a rule of thumb it's pretty safe to say that if the products of a reaction represent a more stable state, then that reaction will go in the forward direction.

There are two factors that determine whether or not reactions changing reactants into products are considered to be favorable: these two factors are simply called enthalpy and entropy.

Enthalpy
Simply put, enthalpy is the heat content of a substance (H). Most people have an intuitive understanding of what heat is... we learn as children not to touch the burners on the stove when they are glowing orange. Enthalpy is not the same as that kind of heat. Enthalpy is the sum of all the internal energy of a substance's matter plus its pressure times its volume. Enthalpy is therefore defined by the following equation:


 * $$H = U + PV \,$$

where (all units given in SI)
 * H is the enthalpy
 * U is the internal energy, (joules)
 * P is the pressure of the system, (Pascals)
 * and V is the volume, (cubic meters)

If the enthalpy of the reactants while being converted to products ends up decreasing (&Delta;H < 0), that means that the products have less enthalpy than the reactants and energy is released to the environment. This reaction type is termed exothermic. In the course of most biochemical processes there is little change in pressure or volume, so the change in enthalpy accompanying a reaction generally reflects the change in the internal energy of the system. Thus, exothermic reactions in biochemistry are processes in which the products are lower in energy than the starting materials.

As an example, consider the reaction of glucose with oxygen to give carbon dioxide and water. Strong bonds form in the products, reducing the internal energy of the system relative to the reactants. This is a highly exothermic reaction, releasing 2805 kJ of energy per mole of glucose that burns (&Delta;H = -2805 kJ/mol). That energy is given off as heat.

Entropy
Entropy (symbol S) is the measure of randomness in something. It represents the most likely of statistical possibilities of a system, so the concept has extremely broad applications. In chemistry of all types, entropy is generally considered important in determining whether or not a reaction goes forward based on the principle that a less-ordered system is more statistically probable than a more-ordered system.

What does that mean, really? Well, if the volcano Mt. Vesuvius erupted next to a Roman-Empire era Mediterranean city, would the volcano be more likely to destroy the city, or build a couple of skyscrapers there? It's pretty obvious what would happen (or, rather, what did happen) because it makes sense to us that natural occurrences favor randomness (destruction) over order (construction, or in this case, skyscrapers). Entropy is just a mathematical way of expressing these essential differences.

When it comes to chemistry, there are three major concepts based on the concept of entropy:
 * 1) Intramolecular states (Degrees of freedom)
 * 2) * The more degrees of freedom (how much the molecules can move in space) a molecule has, the greater the degree of randomness, and thus, the greater the entropy.
 * 3) * There are three ways molecules can move in space, and each has a name: rotation = movement around an axis, vibration = intramolecular movement of two bonded atoms in relation to each other, and translation = a molecule moving from place to place.
 * 4) Intermolecular structures
 * 5) * When molecules can interact with each other by forming non-covalent bonds a structure is often created.
 * 6) * This tends to reduce randomness (and thus entropy) since any such association between molecules stabilizes the motion of both and decreases the possibilities for a random distribution.
 * 7) Number of possibilities
 * 8) * The more molecules present, the more ways of distributing the molecules in space - which because of statistical probabilities means more potential for randomness.
 * 9) * Also, if there is more space available to distribute the molecules within, the randomness increases for precisely the same reason
 * 10) * solid matter (least entropy) << liquids << gases (most entropy)

Changes in entropy are denoted as &Delta;S. For the reasons stated above (in the volcano situation), the increase of entropy (&Delta;S > 0) is considered to be favorable as far as the Universe in general is concerned. A decrease in entropy is generally not considered favorable unless an energetic component in the reaction system can make up for the decrease in entropy (see free energy below).

Gibbs Free Energy
Changes of both enthalpy (&Delta;H) and entropy (&Delta;S) combined decide how favorable a reaction is. For instance, burning a piece of wood releases energy (exothermic, favorable) and results in a substance with less structure (CO2 and H2O gas, both of which are less 'ordered' than solid wood). Thus, one could predict that once a piece of wood was set on fire, it would continue to burn until it was gone. The fact that it does so is ascribed to the change in its Gibbs Free Energy.

The overall favorability of a reaction was first described by the prominent chemist Josiah Willard Gibbs, who defined the free energy of a reaction as
 * &Delta;G = &Delta;H - T &Delta;S

where T is the temperature on the Kelvin temperature scale. The formula above assumes that pressure and temperature are constant during the reaction, which is almost always the case for biochemical reactions, and so this book makes the same assumption throughout.

The unit of &Delta;G (for Gibbs) is the "joule" in SI systems, but the unit of "calorie" is also often used because of its convenient relation to the properties of water. This book will use both terms as convenient, but the preference should really be for the SI notation.

What Does &Delta;G Really Mean?
If &Delta;G < 0 then the reactants should convert into products (signifying a forward reaction)... eventually. (Gibbs free energy says nothing about a reaction's rate, only its probability.) Likewise, for a given reaction if &Delta;G > 0 then it is known that the reverse reaction is favored to take place. A state where &Delta;G = 0 is called equilibrium, and this is the state where the reaction in both the forward and reverse directions take place at the same rate, thus not changing the net effect on the system.

How is equilibrium best explained? Alright, as an example set yourself on the living room carpet with your most gullible younger relative (a little nephew, niece or cousin will work fine). Take out a set of Monopoly, take one ten dollar bill for yourself and give your little relative the rest. Now both of you give the other 5% of all that you have. Do this again, and again, and again-again-again until eventually... you both have the same amount of money. This is precisely what the equilibrium of a reaction means, though equilibrium only very rarely results in an even, 50-50% split of products and reactants.

&Delta;G naturally varies with the concentration of reactants and products. When &Delta;G reaches 0, the reaction rate in the forward direction and the reaction rate in the reverse direction are the same, and the concentration of reactants and products no longer appears to change; this state is called the point of chemical equilibrium. You and your gullible little relative have stopped gaining and losing Monopoly money, respectively; you both keep exchanging the same amount each turn. Note again that equilibrium is dynamic. Chemical reaction does not cease at equilibrium, but products are converted to reactants and reactants are converted to products at exactly the same rate.

A small &Delta;G (that is, a value of &Delta;G close to 0) indicates that a reaction is somewhat reversible; the reaction can actually run backwards, converting products back to reactants. A very large &Delta;G (that is, &Delta;G >> 0 or &Delta;G << 0) is precisely the opposite, because it indicates that a given reaction is irreversible, i.e., once the reactants become products there are very few molecules that go back to reactants.

Metabolic pathways
The food we consume is processed to become a part of our cells; DNA, proteins, etc. If the biochemical reactions involved in this process were reversible, we would convert our own DNA back to food molecules if we stop eating even for a short period of time. To prevent this from happening, our metabolism is organized in metabolic pathways. These pathways are a series of biochemical reactions which are, as a whole, irreversible. The reactions of a pathway occur in a row, with the products of the first reaction being the reactants of the second, and so on:
 * A &#8652; B &#8652; C &#8652; D &#8652; E

At least one of these reactions has to be irreversible, e.g.:
 * A &#8640; B &#8652; C &#8652; D &#8640; E

The control of the irreversible steps (e.g., A &rarr; B) enables the cell to control the whole pathway and, thus, the amount of reactants used, as well as the amount of products generated.

Some metabolic pathways do have a "way back", but it is not the same pathway backwards. Instead, while using the reversible steps of the existing pathway, at least one of the irreversible reactions is bypassed by another (irreversible) one on the way back from E to A:
 * E &#8640; X &#8652; C &#8652; B &#8640; A

This reaction is itself controlled, letting the cell choose the direction in which the pathway is running.

Free energy and equilibrium
For &Delta;G, the free energy of a reaction, standard conditions were defined: Under these standard conditions, &Delta;G0' is defined as the standard free energy change.
 * concentration of reactants and products at 1Mol/dm³
 * temperature at 25&deg;C
 * acidity at pH 7.0

For a reaction
 * A + B &#8652; C + D

the ratio of products to reactants is given by keq' (=keq at pH 7.0):
 * $$k_{eq}^\prime = {\text{products} \over \text{reactants}} = {[C][D] \over [A][B]}$$

The relationship of &Delta;G0' and keq' is
 * &Delta;G0' = - R T ln keq' = - R T 2.30 log10 keq'

with
 * R = 8.315 [J mol-1 K-1] (molar gas constant)
 * T = temperature [K]
 * In = loge ("e" equals to 2.71828...)

In theory, we can now decide if a reaction is favorable (&Delta;G0' < 0). However, the reaction might need a catalyst to occur within a reasonable amount of time. In biochemistry, such a catalyst is called an enzyme.

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The purpose of DNA melting or DNA denaturation is emphasizing and demonstrating the life cycles of all organisms and the origin of replication. The origin of replication specific structure varies from species to species. Furthermore, the particular sequence of the origin of replication is in a genome which is the human genes. Nevertheless, DNA replication is also part of origin of replication which examen in the living organism such as prokaryotes and eukaryotes.

Thermodynamically, there are two important contributions on the DNA denaturation. One of them is the breaking all of the hydrogen bonds between the bases in the double helix; the other one is to overcome the stacking stability/energy of bases on top of each other. There are several methods to denature DNA; heat is known as the most common one use in laboratory. We just have to heat the sample to reach above its melting point, the unstack ability of DNA can be then monitored. Melting point and denaturation of DNA depend on several factors: the length of DNA, base-composition of DNA, the condition of the DNA and also the composition of buffer. For instance, the longer DNA will contain more H-bonds and more intermolecular forces compared to the shorter one; therefore, denaturations of longer DNA requires more time and more heat. Base-composition of DNA can also play as a key factor because A:T requires two hydrogen bonds and G:C interaction requires three hydrogen bonds. The region of DNA which contains more A:T will melt/denature more rapidly compared to G:C. We can also see how the condition of DNA is important because condition of DNA is related to whether the DNA is relax, supercoiled, linear or heavily nicked. It is important because it allow us to examine how much intermolecular forces existing in the double helix. Finally, condition of buffer is also playing an essential role to study DNA denaturation because it allow us to control the amount of ions present in the solution during the entire process.

Biologically, DNA denaturation can happen inside the cell during DNA replication or translation. In both cases, DNA denaturation is an essential step and a beginning to start each of the process. Most of the time, denaturation happened because of binding of protein or enzymes to a specific region of DNA, the binding will likely lead to open or denature of the helix. However, the actual meaning of the DNA melting is the denaturation of DNA which changes the structure of DNA from double stranded into single stranded. The processes of DNA denaturation is unwinding the double stranded deoxyribonucleic acid and breaks it into two single stranded by breaking the hydrogen bonding between the bases. DNA denaturation is also known of DNA annealing because it is reservable. The main steps DNA annealing are double helical will go through the denaturation to become partially denatured DNA then it will separated the strands into two single strand of DNA in random coils.