Lecture 2. Foundations (cont'd.)
Thursday 17 January 2019
Genetic and evolutionary foundations. Molecular biology. DNA and replication. Life and thermodynamics. The geometric, electronic, and bulk properties of water relevant to biological systems.
Reading: Lehninger, 4th ed. (Lehninger); Ch. 1, pp. 29-40; Part I (intro), pp.45-46; Ch.2, pp.47-58.
Summary
Reading summary.
§1.4 Genetic foundations.
Genetic continuity is vested in single DNA molecules.
The structure of DNA allows its replication and repair with near-perfect fidelity.
The linear sequence of DNA encodes proteins with three-dimensional structures.
§1.5 Evolutionary foundations.
Changes in the hereditary instructions allow evolution.
Biomolecules first arose by chemical evolution.
RNA or related precursors may have been the first genes and catalysts.
Biological evolution began more than three and a half billion years ago.
The first cell probably used inorganic fuels.
Eukaryotic cells evolved from simpler precursors in several stages.
Molecular anatomy reveals evolutionary relationships.
Functional genomics shows the allocations of genes to specific cellular processes.
Genomic comparisons have increasing importance in human biology and medicine.
§2.1 Weak interactions in aqueous systems.
Hydrogen bonding gives water its unusual properties.
Water forms hydrogen bonds with polar solutes.
Water interacts electrostatically with charged solutes.
Entropy increases as crystalline substances dissolve.
Nonpolar gases are poorly soluble in water.
Nonpolar compounds force energetically unfavorable changes in the structure of water.
van der Waals interactions are weak interatomic attractions.
Weak interactions are crucial to macromolecular structure and function.
Solutes affect the colligative properties of aqueous solutions.
Worked examples 2-1 & 2-2: Osmotic strength of an organelle.
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Biological systems are subject to the same physicochemical laws that govern non-living systems. It is important therefore to understand explicitly how basic thermodynamic principles are applied in biochemistry and biology. Therefore we undertake a review of the thermodynamics appropriate for application to biological systems. For example, we can usually treat processes in living organisms and tissues as occurring at constant pressure and temperature, with little or no change in volume. Thermodynamic methods valid in general for such processes will be useful in this specific biological context. To illustrate, the free energy function is used to interpret both the formation of a DNA double helix from separate single strands and the hydrophobic effect. The physical and chemical properties of water are of great relevance to biochemistry. The hydrophobic effect, an especially important case, is a consequence of the properties of water and aqueous environments.
Properties of water
Since so many of the processes of living organisms occur in aqueous media, it is of fundamental importance to understand physicochemical properties of water. Given the complexity of the liquid state, especially that of water, accomplishing this is much more of a challenge than one might first imagine. Let us nonetheless at least consider some of the outstanding features of water, and try to get at what are the most relevant and important from a biochemical viewpoint. With water making up most of the weight of typical organisms, it is appropriate to think of water as the solvent of life, and we'll examine the properties of water as a solvent and the principles of aqueous solution chemistry.
One very notable feature of water is its great capacity and tendency to form hydrogen bonds with itself and solutes with hydrogen-bonding ("H-bonding") groups. This underlies water's great cohesiveness, manifest in some unusual properties such as high melting point, boiling point, and surface tension. Molecules with a number of functional groups capable of hydrogen bonding with water tend to be quite soluble in water. Since water is a polar molecule, it also interacts well with ions and polar molecules.
Water is unquestionably an excellent solvent for many polar and charged species, yet it is a rather poor solvent for nonpolar molecules. Amphipathic molecules such as detergents or phospholipids can form micelles or bilayer structures in which the nonpolar portions of the amphipathic molecules are are sequestered together, while the polar or charged portions are exposed to the aqueous surroundings.
What is the basis of the solvent properties of water? The interactions of water with ions, dipoles, and H-bond acceptors and donors are strong. The dipole of water interacts strongly with charges, and we should note here that the rather large dielectric constant of water weakens electrostatic forces between charged solute groups. Water molecules ought to be able to interact somewhat favorably with nonpolar species by van der Waals attractions.
If we are to understand water as a solvent, we will have to venture beyond "like dissolves like" with some more careful analysis. If we imagine a process in which initially separated water and solute mix, the thermodynamics are tricky because although water interacts so well with solutes, its interacts with quite well with itself, as may some solutes such as salts. Thus, for the case of an ionic solid that dissolves endothermically, ΔH of the process is not favorable, but ΔS of forming the more dispersed solution is positive (and thus favorable). For solutes with nonpolar character, on the other hand, the interactions between solute molecules in the undissolved initial state and between solute molecules and water molecules in the dissolved state are both considerably weaker. Yet it is still possible for the solute-solvent interactions to be a little better than the interactions in the separated materials. The enthalpy change (ΔH) of the process is then slightly negative; even so, the solubility may still be quite low, indicating that ΔG is positive. We would be led in this case to the counterintuitive conclusion that ΔS is negative. This large negative ΔS for the formation of aqueous solutions of nonpolar solutes is the basis of the what is usually called the hydrophobic effect.