Chemical Foundations

Polysaccharide chains on the surface of cellulose visualized by atomic force microscopy. [Courtesy of M. Miles from A. A. Baker et al., 2000, Biophys J. 79:1139-1145.]

The life of a cell depends on thousands of chemical interactions and reactions exquisitely coordinated with one another in time and space and under the influence of the cell's genetic instructions and its environment. How does a cell extract critical nutrients and information from its environment? How does a cell convert the energy stored in nutrients into work (movement, synthesis of critical components)? How does a cell transform nutrients into the fundamental structures required for its survival (cell wall, nucleus, nucleic acids, proteins, cytoskeleton)? How does a cell link itself to other cells to form a tissue? How do cells communicate with one another so that the organism as a whole can function? One of the goals of molecular cell biology is to answer such questions about the structure and function of cells and organisms in terms of the properties of individual molecules and ions.

Life first arose in a watery environment, and the properties of this ubiquitous substance have a profound influence on the chemistry of life. Constituting 70-80 percent by weight of most cells, water is the most abundant molecule in biological systems. About 7 percent of the weight of living matter is composed of inorganic ions and small molecules such as amino acids (the building blocks of proteins), nucleotides (the building blocks of DNA and RNA), lipids (the building blocks of biomembranes), and sugars (the building blocks of starches and cellulose), the remainder being the macromolecules and macromolecular aggregates composed of these building blocks.

Many biomolecules (e.g., sugars) readily dissolve in water; these water-liking molecules are described as hy-drophilic. Other biomolecules (e.g., fats like triacylglycerols)

shun water; these are said to be hydrophobic (water-fearing). Still other biomolecules (e.g., phospholipids), referred to as amphipathic, are a bit schizophrenic, containing both hy-drophilic and hydrophobic regions. These are used to build the membranes that surround cells and their internal organelles (Chapter 5). The smooth functioning of cells, tissues, and organisms depends on all these molecules, from the smallest to the largest. Indeed, the chemistry of the simple proton (H+) with a mass of 1 dalton (Da) can be as important to the survival of a human cell as that of each gigantic DNA molecule with a mass as large as 8.6 X 1010 Da (single strand of DNA from human chromosome 1).

A relatively small number of principles and facts of chemistry are essential for understanding cellular processes at the molecular level (Figure 2-1). In this chapter we review some of these key principles and facts, beginning with the cova-lent bonds that connect atoms into a molecule and the non-covalent forces that stabilize groups of atoms within and between molecules. We then consider the key properties of the basic building blocks of cellular structures. After reviewing those aspects of chemical equilibrium that are most relevant to biological systems, we end the chapter with basic

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