From Atoms To Molecules

Most biologists think of what goes on in cells in terms of the activity of genes, RNAs, proteins, and other molecules. To understand how these molecules behave, it is necessary to go to a deeper level and examine their structures. The task is like that of an engineer. Building a copy of a machine or repairing it requires having a list of its parts. Each component has to have the right shape and size so that it can be combined with other components. And just as a motor has large parts that are built of smaller parts, molecules have different levels of structure, all of which are important to their functions. Proteins will be used as an example in this section to illustrate these levels of organization. The structures of DNA and RNA molecules are different and are covered in the second chapter, but the general principles needed to explain their behavior are similar.

Biological molecules are made of atoms that form bonds with each other. This is not a chemistry book, but it will be helpful to understand a little bit about the process of binding. Atoms have a central nucleus made of protons and neutrons, which is orbited by electrons. Early models of the atom depicted this as a sort of miniature solar system, but that changed in the early 20th century with the arrival of a new kind of physics called "quantum mechanics." In the new model of the atom, electrons have "fuzzy" positions that are located somewhere in orbital paths around the atom called "shells." There are several of these zones at various distances from the nucleus.

Each shell can hold a limited number of electrons. The innermost shell can hold two electrons, and each of the next two can hold eight. But often the shells are not filled; they lack one or more electrons. Atoms are not stable until their shells are filled; if their shells are not full, they try to fill them by binding to other atoms and sharing their electrons.

The simplest atom is hydrogen. It only has one electron, so its outer shell—which could hold two—is lacking one. Hydrogen easily forms bonds with other atoms that lack an electron in their own outer shells. Helium has two electrons and does not need to combine with other atoms. This makes it like neon, argon, and several other "noble gases," all of which have complete outer shells and are "inert" because they do not readily participate in chemical or biological reactions. This is much different from the behavior of oxygen, for example. Oxygen has eight electrons, split up in two shells: two in the inner shell and six in the outer one. This means that it lacks two electrons (to get a full set of eight in the outer shell). It can easily fill those spots by linking up with two hydrogen atoms, creating the molecule H2O, or water.

Atoms that bind to each other by sharing electrons are linked in what is called a "covalent bond." Groups of atoms (molecules) can also link to each other by covalent bonds, but as a group grows larger, its overall shape plays an increasingly important role in what it can bind to. Atoms have to be brought close to each other to share electrons. Sometimes the bonds in a molecule make it inflexible, putting atoms that could bind to each other out of reach. The situation is a bit like trying to mount a metal bracket onto a wall with holes that have been predrilled. If the holes in the bracket do not line up with those in the wall, mounting it may be impossible.

The formation and breakup of chemical bonds is essential to every biological process and will be discussed throughout this book. There are other "noncovalent" ways for one atom to link to others, such as ionic bonds, which occur when one atom "steals" an electron from another, rather than sharing it, and van der Waals interactions ("nonchemical" forces between atoms and molecules). But in general, the structures of proteins, DNA, and RNA and the linkage of biological molecules are mainly due to covalent bonds. They often involve hydrogen atoms because of the high quantity of water in the body and the ease with which this element is integrated into molecules.

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