>> Key Terms (indicated in blue within the text below):

adenine amino acid chiral center cytosine DNA (deoxyribonucleic acid) enantiomer endothermic enthalpy (H) enthalpy of hydration (Hhydration) entropy (S) equilibrium ester

esterification fat fatty acid free energy (G) guanine heat of solution hydration ion–dipole lipid messenger RNA (mRNA) nucleotide

peptide bond protein ribosome second law of thermodynamics spontaneously stereoisomer third law of thermodynamics thymine transcription transfer RNA (tRNA) translation

Chapter 13 extends the discussion of energy in Chapter 11 from enthalpy to entropy and free energy. It also extends the discussion of organic compounds in Chapter 12 to fats, proteins and DNA. The two ideas are connected by the use of fats, proteins and carbohydrates as biological sources of energy.

Enthalpy (H) is the measure of the internal energy of a system, studied in Chapter 11.

                              >> Explore: Enthalpy Tutorial

That chapter discussed the heat of fusion (melting or freezing), heat of vaporization (boiling or condensing), and heat of reaction. This chapter adds heat of solution (H_soln). Heat of solution is the energy involved in creating a solution from solute and solvent. It may be either endothermic (+H) or exothermic (–H). The heat of solution for ionic compounds may be understood by considering the dilution process. First, the ions of the compound must be separated, and the lattice energy (H_ionic or U) must be overcome. This process requires energy (is endothermic). In addition, the solvent–solvent attraction must be overcome, so that the ions can mix by getting between the solvent molecules. Since the most common solvent, especially for ionic compounds, is water, the intermolecular force of hydrogen bonding must be overcome (H_H-bond).This is another endothermic process. However, the mixing of the ions with the water will create ion–dipole forces of attraction and release energy (H_ion-dipole). The breaking of hydrogen bonds of the water and creation of ion–dipole forces together is called hydration. The enthalpy of hydration (H_hydration) is the sum of H_H-bond and H_ion–dipole.The heat of solution is the enthalpy of hydration minus the lattice energy. (Lattice energy refers to the creation of the salt. Since dissolution separates the ions of the salt, the sign of H is opposite, thus the "minus.")

                              >> Explore: Dissolution of Ammonium Nitrate Tutorial

Many dissolutions happen spontaneously; that is, without outside intervention. Since systems spontaneously move toward lower internal energies, exothermic reactions should be spontaneous and endothermic reactions should be nonspontaneous. However, experimental evidence shows that neither is always true. Therefore some other type of energy must be involved in chemical reactions. This other type of energy is called entropy (S) and it is a measure of the randomness of a system. The second law of thermodynamics states that in spontaneous reaction, the entropy of the universe (which includes both the system and the surroundings) increases. Therefore the entropy of either the system or the surroundings must increase, not necessarily both.

                              >> Explore: Entropy Tutorial

The entropy of a substance is linked to temperature. At higher temperatures, kinetic energy and randomness increase. As temperature decreases, so does entropy. This leads to the third law of thermodynamics, which states that a perfect crystal at 0 K (temperature where there is no movement) has an entropy of zero. Crystals (ordered solids studied in Chapter 10) have the least entropy of all the physical states. Liquids have higher values of entropy, and gases have values that are higher yet. Mixtures have higher entropy than pure substances. Thus any substance has its own intrinsic value of entropy.

                              >> Explore: Molecular Motion Tutorial

The third law of thermodynamics allows the entropy of a variety of substances to be determined. Some of these are listed in the appendix. The entropy change of substances in a chemical reaction can be calculated from Equation 13.5.

S° = nS°_products – mS°_reactants         (Equation 13.5)

Since higher values of S indicate a more random system, positive values of S show an increase in randomness, whereas negative values show a decrease.

Spontaneous reactions depend on two forces, enthalpy (H) and entropy (S). If both of these forces decrease the energy of the system (–H and +S), the reaction will be spontaneous. If both of these forces increase the energy of the system (+H and –S), the reaction will be nonspontaneous. If one force increases the energy of the system and the other decreases it, spontaneity will be determined by the larger force. Since entropy is linked to temperature, higher temperatures increase the effect of entropy.

J. Willard Gibbs used the ideas of enthalpy, entropy, and spontaneity in a concept called free energy
(G). Free energy refers to the maximum amount of energy free to do useful work. It is related to enthalpy (H), temperature (T), and entropy (S) by Equation 13.12.

G = H – T S         (Equation 13.12)

                              >> Explore: Gibbs Free Energy Tutorial

Free energy is also a measure of spontaneity. Negative values of G indicate a spontaneous or forward (reactants make products) reaction. Positive values of G indicate a nonspontaneous or reverse (products make reactants)system. If G = 0, the system is in equilibrium, where there is no forward or reverse reaction. At equilibrium, the composition of the system (amount of products and reactants) is constant.

Like enthalpy (H) and entropy (S), free energy (G) is a state function. Therefore the free energy of a sum of a series of equations is the sum of the free energies of those equations. One form of this is Equation 13.14.

G°_rxn = n G°_f,product – m G°_f,reactant         (Equation 13.14)

where G°_f refers to the free energy of the formation reaction.

Fuel for biological reactions comes from food. Food can be divided into three categories: carbohydrates, proteins and fats. The fuel value of carbohydrates and proteins is about the same (averaging 17 kJ/g) and is higher for fats (averaging38 kJ/g).

Carbohydrates were discussed in Chapter 12. In that chapter it was noted that only certain arrangements of atoms, isomers, can be used by the body. Isomers with different bonding patterns are called structural isomers. Isomers that differ in the orientation of atoms bonded to the same atom (different orientation)are called stereoisomers. Chapter 12 discussed one type of stereoisomer,the arrangement of atoms around a double bond (cis and trans).Another type of stereoisomer is two molecules arranged as nonsuperimposable mirror images, called enantiomers. The atom location where the mirror image is formed is called the chiral center. Four different groups that are bonded to an sp³ carbon form a chiral center that can be arranged as enantiomers. Enantiomers can be labeled either R or S, depending on the orientation of groups around a chiral carbon.

                              >> Explore: Chiral Centers Tutorial

                              >> Explore: Chirality Tutorial

Proteins are long chains of amino acids. An amino acid has a carbon with a primary amine, carboxylic acid, hydrogen, and one other group. The amine group on one amino acid reacts with the hydroxyl of carboxylic acid group of another amino acid in a condensation reaction that links the two amino acids together. The two amino acids are linked through the nitrogen as a secondary amine. The link, consisting of a carbonyl and the secondary amine, is called a peptide bond.

                              >> Explore: Condensation of Biological Polymers Tutorial

Fats or lipids are formed from the esterification reaction of a fatty acid with glycerol. A fatty acid is a long carbon chain with a carboxylic acid group at the end. If the carbon chain consists only of single bonds between carbons or between carbons and hydrogens, the fatty acid is called saturated (has the maximum number of hydrogens). If there is one carbon–carbon double bond, the fatty acid is monounsaturated. If there is more than one carbon–carbon double bond, the fatty acid is polyunsaturated. Because saturated fatty acids pack better, and therefore have stronger dispersion forces, they are more likely to be solids. Unsaturated fatty acids are less organized and therefore are more likely to be liquids. Unsaturated fatty acids are also more reactive, particularly at the site of the double bonds.

Glycerol is a three-carbon chain with an alcohol group on each carbon. When the carboxylic acid of the fatty acid reacts in a condensation reaction with the alcohol of the glycerol, a lipid is formed. The link between the fatty acid and alcohol is called an ester. Thus the reaction is also called esterification. An ester is a functional group that consists of a carbon with a carbonyl group and an ether link to another carbon.

Another biological compound is deoxyribonucleic acid (DNA). This compound is not used for fuel, but as a way of transmitting genetic information needed to synthesize proteins. DNA is made of repeating units called nucleotides. Each nucleotide is made of a phosphate (PO₄^3–) and a nitrogen base bonded to a deoxyribose (five-carbon cyclic sugar). The nucleotide is characterized by the nitrogen base. There are four of these bases in DNA: thymine, cytosine, adenine, and guanine. There are two chains of nucleotides in DNA in the form of a double helix held together by the hydrogen bonds between the nitrogen bases. Thus a thymine is always paired with an adenine in the opposite chain, and a cytosine is always paired with a guanine.

Proteins are synthesized at sites in the nuclei of cells called ribosomes. The information from the DNA is transferred to messenger RNA (mRNA) in a process called transcription. The nucleotides of RNA are slightly different. The sugar is ribose rather than deoxyribose, and uracil replaces thymine as one of the nitrogen bases. mRNA pairs with DNA in the same way the complimentary strand of DNA does (except that uracil replaces thymine). The mRNA carries the genetic information to the site of protein synthesis. The mRNA binds to transfer RNA (tRNA) with hydrogen bonding of the nitrogen bases in the same way as the double helix of DNA and the creation of RNA. The tRNA binds to only one type of amino acid and is used in the actual synthesis of proteins. The conversion of the genetic code into an amino acid sequence of a protein is called translation.