Chapter 1

Biochemistry: An Evolving Science

Concepts from Chemistry Explain the Properties of Biological Molecules
I. The double helix can form from its component strands a. When two DNA strands with appropriate, complementary sequences are mixed, they spontaneously assemble to form a double helix.

II.

b. What forces cause the two strands of DNA to bind to each other? To analyze this binding reaction, we must consider several factors. Covalent and noncovalent bonds are important for the structure and stability of biological molecules. a. Properties of water i. Two properties of water are especially relevant: ii. Water is a polar molecule 1. The water molecule is bent, not linear, and so the distribution of charge is asymmetric. iii. Water is highly cohesive. 1. Water molecules interact strongly with one another through hydrogen bonds. b. Covalent bonds i. The strongest bonds are covalent bonds 1. Because covalent bonds are so strong, considerable energy must be expended to break them. ii. A covalent bond is formed by the sharing of a pair of electrons between adjacent atoms. iii. For some molecules, more than one pattern of covalent bonding can be written; this are called resonance structures. 1. A molecule that can be written as several resonance structures of approximately equal energies has greater stability than does a molecule without multiple resonance structures.

Chapter 1 c. Noncovalent bonds i. Noncovalent bonds are weaker than covalent bonds. ii. Four fundamental noncovalent bond types: 1. Electrostatic Interactions a. A charged group on one molecule can attract an oppositely charged group on another molecule. The energy of an electrostatic interaction is given by Coulombs law: E = energy q1 & q2 = charges on the two atoms r = distance between the two atoms D= dielectric constant which is measure of the polarity of a molecule. D increases as the polarity of the molecule increases. D is unitless. 1. As D increases, E decreases. v. k = proportionality constant b. By convention, an attractive interaction has a negative energy. c. Note how important the dielectric constant of the medium is. i. For example: water = 80 (polar) hexane = 2 (nonpolar) 2. Hydrogen Bonds a. Hydrogen bonds are responsible for specific base-pair formation in the DNA double helix. b. The hydrogen atom in a hydrogen bond is partially shared by two electronegative atoms such as nitrogen or oxygen. c. The hydrogen-bond donor is the group that includes both the atom to which the hydrogen atom is more tightly linked and the hydrogen atom itself, whereas the hydrogen-bond acceptor is the atom less tightly linked to the hydrogen atom. i. ii. iii. iv.

Chapter 1

d. Hydrogen bonds are much weaker than covalent bonds. 3. van der Waals Interactions a. The basis of a van der Waals interaction is that the distribution of electronic charge around an atom fluctuates with time. i. At any instant, the charge distribution is not perfectly symmetric. 4. The hydrophobic effect A final fundamental interaction called the hydrophobic effect is a manifestation of the properties of water. The aggregation of nonpolar groups in water leads to the release of water molecules, initially interacting with the nonpolar surface, into bulk water. The release of water molecules into solution makes the aggregation of nonpolar groups favorable.

The double helix is an expression of the rules of chemistry. First, each phosphate group in a DNA strand carries a negative charge. Thus, unfavorable electrostatic interactions take place when two strands of DNA come together. Second, as already noted, hydrogen bonds are important in determining the formation of specific base pairs in the double helix. Because the number of hydrogen bonds broken is the same as the number formed, these hydrogen bonds do not contribute substantially to driving the overall process of double-helix formation.

Chapter 1 However, they contribute greatly to the specificity of binding. Third, within a double helix, the base pairs are parallel and stacked nearly on top of one another. This separation distance corresponds nicely to the van der Waals contact distance. Fourth, the hydrophobic effect also contributes to the favorability of base stacking. More-complete base stacking moves the nonpolar surfaces of the bases out of water into contact with each other. The laws of thermodynamics govern the behavior of biochemical systems. A system refers to the matter within a defined region of space. The matter in the rest of the universe is called the surroundings. The First Law of Thermodynamics states that the total energy of a system and its surroundings is constant. the energy content of the universe is constant; energy can be neither created nor destroyed. Energy can take different forms, however. Heat is a manifestation of the kinetic energy associated with the random motion of molecules. Alternatively, energy can be present as potential energyenergy that will be released on the occurrence of some process. entropy, a measure of the degree of randomness or disorder in a system. The Second Law of Thermodynamics states that the total entropy of a system plus that of its surroundings always increases.