Life and Chemistry: Atoms and Small Molecules

Atoms: The Constituents of Matter

More than a trillion (1012) atoms could fit over the period at the end of this sentence. Each atom consists of a dense, positively charged nucleus, around which one or more negatively charged electrons move The nucleus contains one or more protons and may contain one or more neutrons. Atoms and their component particles have volume and mass, which are properties of all matter. Mass measures the quantity of matter present; the greater the mass, the greater the quantity of matter. The mass of a proton serves as a standard unit of measure: the atomic mass unit (amu) or dalton (named after the English chemist John Dalton). A single proton or neutron has a mass of about 1 dalton (Da). Because the mass of an electron is negligible compare to the mass of a proton or a neutron, the contribution of electrons to the mass of an atom can usually be ignored when measurements and calculations are made.

These are electrons, however, that determine how atoms will interact in chemical reactions and they will be discussed extensively later in this chapter. Each proton has a positive electric charge defined as +1 unit of charge. An electron has a negative charge equal and opposite to that of a proton; thus, the charge of an electron is –1 unit. The neutron, as its name suggests, is electrically neutral, so its charge is 0 unit. Unlike charges (+/–) attract each other; like charges (+/+ or –/–) repel each other. Atoms are electrically neutral: the number of protons in an atom equals the number of electrons.

An element is made up of only one kind of atom

An element is a pure substance that contains only one type of atom. The element hydrogen consists only of hydrogen atoms; the element iron consists only of iron atoms. The atoms of each element have certain characteristics or properties that distinguish them from the atoms of other elements. The more than 100 elements, found in the universe, are arranged in the periodic table. These elements are not found in equal amounts. Stars have abundant hydrogen and helium. The earth’s crust and those of the neighboring planets are almost half oxygen, 28 percent silicon, 8 percent aluminum, 2–5 percent each of sodium, magnesium, potassium, calcium and iron, and contain much smaller amounts of the other elements. About 98 percent of the mass of every living organism (bacterium, turnip or human) is composed of just six elements: carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur. The chemistry of these six elements will be the primary concern here but the others are not unimportant. Sodium and potassium, for example, are essential for nerves to function; calcium can act as a biological signal; iodine is a component of a vital hormone; and plants need magnesium as part of their green pigment (chlorophyll) and molybdenum in order to incorporate nitrogen into biologically useful substances.

The number of protons identifies the element

An element is distinguished from other elements by the number of protons in each of its atoms. This number which does not change, is called the atomic number. An atom of helium has 2 protons, and an atom of oxygen has 8 protons; the atomic numbers of these elements are thus 2 and 8, respectively. Along with a definitive number of protons, every element except hydrogen has one or more neutrons in its nucleus. The mass number of an atom is the total number of protons and neutrons in its nucleus. The nucleus of a helium atom contains 2 protons and 2 neutrons; oxygen has 8 protons and 8 neutrons. Therefore, helium has a mass number of 4 and oxygen a mass number of 16. The mass number may be thought of as the mass of the atom in daltons. Each element has its own one- or two-letter chemical symbol. For example, H stands for hydrogen, He for helium and O for oxygen. Some symbols come from other languages: Fe (from the Latin ferrum) stands for iron, Na (Latin natrium) for sodium and W (German Wolfram) for tungsten.

Electron behavior determines chemical bonding

When considering atoms, biologists are concerned primarily with electrons because the behavior of electrons explains how chemical changes occur in living cells. These changes, called chemical reactions or just reactions, are changes in the atomic composition of substances. The characteristic number of electrons in each atom of an element determines how its atoms will react with other atoms. All chemical reactions involve changes in the relationships of electrons with one another.

The location of a given electron in an atom at any given time is impossible to determine. We can only describe a volume of space within the atom where the electron is likely to be. The region of space where the electron is found at least 90 percent of the time is the electron’s orbital. In an atom, a given orbital can be occupied by at most two electrons. Thus, any atom larger than helium (atomic number 2) must have electrons in two or more orbitals. The different orbitals have characteristic forms and orientations in space. The orbitals, in turn, constitute a series of electron shells or energy levels, around the nucleus. The innermost electron shell consists of only one orbital called an s orbital. Hydrogen (1H) has one electron in its first shell; helium (2He) has two of them. All other elements have two first-shell electrons, as well as electrons in other shells. The second shell is made up of four orbitals (an s orbital and three p orbitals) and hence can hold up to eight electrons. The s orbitals fill with electrons first and their electrons have the lowest energy. Subsequent shells have different numbers of orbitals but the outermost shells usually hold only eight electrons. In any atom, the outermost electron shell determines how the atom combines with other atoms—that is, how the atom behaves chemically. When an outermost shell consisting of four orbitals contains eight electrons, there are no unpaired electrons. Such an atom is stable and will not react with other atoms. Examples of chemically stable elements are helium, neon and argon. Reactive atoms seek to attain the stable condition of having no unpaired electrons in their outermost shells. They attain this stability by sharing electrons with other atoms or by gaining or losing one or more electrons. In either case, the atoms are bonded together. Such bonds create stable associations of atoms called molecules.

A molecule is two or more atoms linked by chemical bonds. The tendency of atoms in stable molecules to have eight electrons in their outermost shells is known as the octet rule. Many atoms in biologically important molecules—for example, carbon (C) and nitrogen (N)—follow the octet rule. However, some biologically important atoms are exceptions to the rule. Hydrogen (H) is the most obvious exception attaining stability when only two electrons occupy its single shell.

Date: 2014-12-22; view: 1229