Biochemistry aims to explain biological form and function in chemical terms. One of the most fruitful approaches to understanding biological phenomena has been to purify an individual chemical component, such as a protein, from a living organism and to characterize its chemical structure or catalytic activity. As we begin the study of biomolecules and their interactions, some basic questions deserve attention. What chemical elements are found in cells? What kinds of molecules are present in living matter? In what proportions do they occur? How did they come to be there? In what ways are the kinds of molecules found in living cells especially suited to their roles?
We review here some of the chemical principles that govern the properties of biological molecules: the covalent bonding of carbon with itself and with other elements, the functional groups that occur in common biological molecules, the three-dimensional structure and stereochemistry of carbon compounds, and the common classes of chemical reactions that occur in living organisms. Next, we discuss the monomeric units and the contribution of entropy to the free-energy changes of reactions in which these units are polymerized to form macromolecules. Finally, we consider the origin of the monomeric units from simple compounds in the earth's atmosphere during prebiological timesthat is, chemical evolution.
By the beginning of the nineteenth century, it had become clear to chemists that the composition of living matter is strikingly different from that of the inanimate world. Antoine Lavoisier (1743-1794) noted the relative chemical simplicity of the "mineral world," and contrasted it with the complexity of the "plant and animal worlds"; the latter, he knew, were composed of compounds rich in the elements carbon, oxygen, nitrogen, and phosphorus. The development of organic chemistry preceded, and provided invaluable insights for, the development of biochemistry.
We will briefly review some fundamental concepts of organic chemistry: the nature of bonding between atoms of carbon and of hydrogen, oxygen, and nitrogen; the functional groups that result from these combinations; and the diversity of organic compounds that are derived from these elements
Only about 30 of the more than 90 naturally occurring chemical elements are essential to living organisms. Most of the elements in living matter have relatively low atomic numbers; only five have atomic numbers above that of selenium, 34 (Fig. 3-1). The four most abundant elements in living organisms, in terms of the percentage of the total number of atoms, are hydrogen, oxygen, nitrogen, and carbon, which together make up over 99% of the mass of most cells. They are the lightest elements capable of forming one, two, three, and four bonds, respectively (Fig. 3-2). In general, the lightest elements form the strongest bonds. Six of the eight most abundant elements in the human body are also among the nine most abundant elements in seawater (Table 3-1), and several of the elements abundant in humans are components of the atmosphere and were probably present in the atmosphere before the appearance of life on earth. Primitive seawater was most likely the liquid medium in which living organisms first arose, and the primitive atmosphere was probably a source of methane, ammonia, water, and hydrogen, the starting materials for the evolution of life. The trace elements (Fig. 3-1) represent a miniscule fraction of the weight of the human body, but all are absolutely essential to life, usually because they are essential to the function of specific enzymes (Table 3-2).
The chemistry of living organisms is organized around the element carbon, which accounts for more than one-half the dry weight of cells. In methane (CH4), a carbon atom shares four electron pairs with four hydrogen atoms; each of the shared electron pairs forms a single bond. Carbon can also form single and double bonds to oxygen and nitrogen atoms (Fig. 3-3). Of greatest signiiicance in biology is the ability of carbon atoms to share electron pairs with each other to form very stable carbon-carbon single bonds. Each carbon atom can form single bonds with one, two, three, or four other carbon atoms. Two carbon atoms also can share two (or three) electron pairs, thus forming carbon-carbon double (or triple) bonds (Fig. 3-3). Covalently linked carbon atoms can form linear chains, branched chains, and cyclic and cagelike structures. To these carbon skeletons are added groups of other atoms, called functional groups, which confer specific chemical properties on the molecule. Molecules containing covalently bonded carbon backbones are called organic compounds; they occur in an almost limitless variety. Most biomolecules are organic compounds; we can therefore infer that the bonding versatility of carbon was a major factor in the selection of carbon compounds for the molecular machinery of cells during the origin and evolution of living organisms.
The four covalent single bonds that can be formed by a carbon atom are arranged tetrahedrally, with an angle of about 109.5°between any two bonds (Fig. 3-4) and an average length of 0.154 nm. There is free rotation around each carbon-carbon single bond unless very large or highly charged groups are attached to both carbon atoms, in which case rotation may be restricted. A carbon-carbon double bond is shorter (about 0.134 nm long) and rigid and allows little rotation about its axis. (Fig. 3-4). No other chemical element can form molecules of such widely different sizes and shapes or with such a variety of functional groups.
Functional Groups Determine Chemical Properties
Most biomolecules can be regarded as derivatives of hydrocarbons, compounds with a covalently linked carbon backbone to which only hydrogen atoms are bonded. The backbones of hydrocarbons are very stable. The hydrogen atoms may be replaced by a variety of functional groups to yield different families of organic compounds. Typical families of organic compounds are the alcohols, which have one or more hydroxyl groups; amines, which have amino groups; aldehydes and ketones, which have carbonyl groups; and carboxylic acids, which have carboxyl groups (Fig. 3-5).
Many biomolecules are poiyfunctional, containing two or more different kinds of functional groups (Fig. 3-6), each with its own chemical characteristics and reactions. Amino acids, an important family of molecules that serve primarily as monomeric subunits of proteins, contain at least two different kinds of functional groups: an amino group and a carboxyl group, as shown for histidine in Figure 3-6. The ability of an amino acid to condense (see Fig. 3-14e) with other amino acids to form proteins is dependent on the chemical properties of these two functional groups.
Three-Dimensional Structure
Although the covalent bonds and functional groups of biomolecules are central to their function, they do not tell the whole story. The arrangement in three-dimensional space of the atoms of a biomolecule is also crucially important. Compounds of carbon can often exist in two or more chemically indistinguishable three-dimensional forms, only one of which is biologically active. This specificity for one particular molecular configuration is a universal feature of biological interactions. All biochemistry is three-dimensional.
Each Cellular Component Has a Characteristic Three-Dimensional Structnre
Biomolecules have characteristic sizes and three-dimensional structures, which derive from their backbone structures and their substituent functional groups. Figure 3-7 shows three ways to illustrate the three-dimensional structures of molecules. The perspective diagram specifies unambiguously the three-dimensional structure (stereochemistry) of a compound. Bond angles and center-to-center bond lengths are best represented with ball-and-stick models, whereas the outer contours of molecules are better represented by space-filling models. In space-filling models, the radius of each atom is proportional to its van der Waals radius (Table 3-3),and the contours of the molecule represent the outer limits of the region from which atoms of other molecules are excluded.
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