Unit two. The Living Cell


2. The Chemistry of Life




These trees have been seriously damaged by acid rain. The death of this forest must have seemed a calamity to the animals that lived there. A porcupine knows no chemistry, has no way to comprehend what has happened, or why. Later in this chapter, you will explore what causes acid rain and snow, and how the acid has killed forests like this one. A famous conservation saying is that “you cannot save what you don’t understand.” In order to understand acid rain, you must first come to understand some simpler things, the nuts and bolts that underlie what happens in nature. All living things—in fact, everything you can see in the picture above—are made of tiny particles called atoms, linked together in assemblies called molecules. This is where we will have to start, if we want to understand things like what happened to this forest. Then, with molecules under our belt, we will need to get more specific and consider the nature of rain. What are rain and snow made of? Water. We will need to take a very careful look at water. When we do, we will see that when some chemicals are added to water, a chemically active mixture called an acid results. Acid rain is water containing such chemicals. Understanding this gives us the mental tool we need to attack the problem of what happened to this forest and determine how to stop it. In just this way, chemistry underlies much of what you will learn in biology.


2.1. Atoms


Biology is the science of life, and all life, in fact even all nonlife, is made of substances.

Chemistry is the study of the properties of these substances. So, while it may seem tedious or unrelated to examine chemistry in a biology text, it is essential. Organisms are chemical machines (figure 2.1), and to understand them we must learn a little chemistry.




Figure 2.1. Replacing electrolytes.

During extreme exercise, athletes will often consume drinks that contain "electrolytes," chemicals such as calcium, potassium, and sodium that play an important role in muscle contraction. Electrolytes can also be depleted in other types of dehydration.


Any substance in the universe that has mass and occupies space is defined as matter. All matter is composed of extremely small particles called atoms. An atom is the smallest particle into which a substance can be divided and still retain its chemical properties.

Every atom has the same basic structure you see in figure 2.2. At the center of every atom is a small, very dense nucleus formed of two types of subatomic particles, protons (illustrated by purple balls) and neutrons (the pink balls). Whizzing around the core is an orbiting cloud of a third kind of subatomic particle, the electron (depicted by yellow balls on concentric rings). Neutrons have no electrical charge, whereas protons have a positive charge and electrons have a negative one. In each atom, there is an orbiting electron for every proton in the nucleus. The electron’s negative charge balances the proton’s positive charge. The atom is said to be electrically neutral.




Figure 2.2. Basic structure of atoms.

All atoms have a nucleus consisting of protons and neutrons, except hydrogen, the smallest atom, which has only one proton and no neutrons in its nucleus. Carbon, for example, has six protons and six neutrons in its nucleus. Electrons spin around the nucleus in orbitals a far distance away from the nucleus. The electrons determine how atoms react with each other.


An atom is typically described by the number of protons in its nucleus or by the overall mass of the atom. The terms mass and weight are often used interchangeably, but they have slightly different meanings. Mass refers to the amount of a substance, whereas weight refers to the force gravity exerts on a substance. Hence, an object has the same mass whether it is on the earth or the moon, but its weight will be greater on the earth, because the earth’s gravitational force is greater than the moon’s. For example, an astronaut weighing 180 pounds on earth will weigh about 30 pounds on the moon. He didn’t lose any significant mass during his flight to the moon, there is just less gravitational pull on his mass.

The number of protons in the nucleus of an atom is called the atomic number. For example, the atomic number of carbon is 6 because it has six protons. Atoms with the same atomic number (that is, the same number of protons) have the same chemical properties and are said to belong to the same element. Formally speaking, an element is any substance that cannot be broken down into any other substance by ordinary chemical means.

Neutrons are similar to protons in mass, and the number of protons and neutrons in the nucleus of an atom is called the mass number. A carbon atom that has six protons and six neutrons has a mass number of 12. An electron’s contribution to the overall mass of an atom is negligible. The atomic numbers and mass numbers of some of the most common elements on earth are shown in table 2.1.






Atomic Number

Mass Number














































Electrons Determine What Atoms Are Like

Electrons have very little mass (only about 1/1,840 the mass of a proton). Of all the mass contributing to your weight, the portion that is contributed by electrons is less than the mass of your eyelashes. And yet electrons determine the chemical behavior of atoms because they are the parts of atoms that come close enough to each other in nature to interact. Almost all the volume of an atom is empty space. Protons and neutrons lie at the core of this space, whereas orbiting electrons are very far from the nucleus. If the nucleus of an atom were the size of an apple, the orbit of the nearest electron would be more than a mile out!


Electrons Carry Energy

Because electrons are negatively charged, they are attracted to the positively charged nucleus, but they also repel the negative charges of each other. It takes work to keep them in orbit, just as it takes work to hold an apple in your hand when gravity is pulling the apple down toward the ground. The apple in your hand is said to possess energy, the ability to do work, because of its position—if you were to release it, the apple would fall. Similarly, electrons have energy of position, called potential energy. It takes work to oppose the attraction of the nucleus, so moving the electron farther out from the nucleus, as shown by the set of arrows on the right side of figure 2.3, requires an input of energy and results in an electron with greater potential energy. Moving an electron in toward the nucleus has the opposite effect (the set of arrows on the left side); energy is released, and the electron has less potential energy. Consider again an apple held in your hand. If you carry the apple up to a second-story window, it has a greater potential energy when you drop it, compared to when it is dropped at ground level. Similarly, if you lower the apple until it is 6 inches from the ground, it has less potential energy. Cells use the potential energy of atoms to drive chemical reactions, as we will discuss in chapter 5.




Figure 2.3. The electrons of atoms possess potential energy.

Electrons that circulate rapidly around the nucleus contain energy, and depending on their distance from the nucleus, they may contain more or less energy. Energy level 1 is the lowest potential energy level because it is closest to the nucleus. When an electron absorbs energy, it moves from level 1 to the next higher energy level (level 2). When an electron loses energy, it falls to a lower energy level closer to the nucleus.


While the energy levels of an atom are often visualized as well-defined circular orbits around a central nucleus as was shown in figure 2.2, such a simple picture is not accurate. These energy levels, called electron shells, often consist of complex three-dimensional shapes, and the exact location of an individual electron at any given time is impossible to specify. However, some locations are more probable than others, and it is often possible to say where an electron is most likely to be located. The volume of space around a nucleus where an electron is most likely to be found is called the orbital of that electron.

Each electron shell has a specific number of orbitals, and each orbital can hold up to two electrons. The first shell in any atom contains one orbital. Helium, shown in figure 2.4a, has one electron shell with one orbital that corresponds to the lowest energy level. The orbital contains two electrons, shown above and below the nucleus. In atoms with more than one electron shell, the second shell contains four orbitals and holds up to eight electrons. Nitrogen, shown in figure 2.4b, has two electron shells; the first one is completely filled with two electrons, but three of the four orbitals in the second electron shell are not filled because nitrogen’s second shell contains only five electrons (openings in orbitals are indicated with dotted circles). In atoms with more than two electron shells, subsequent shells also contain up to four orbitals and a maximum of eight electrons. Atoms with unfilled electron orbitals tend to be more reactive because they lose, gain, or share electrons in order to fill their outermost electron shell. Losing, gaining, or sharing electrons is the basis for chemical reactions in which chemical bonds form between atoms. Chemical bonds will be discussed later in this chapter.




Figure 2.4. Electrons in electron shells.

(a) An atom of helium has two protons, two neutrons, and two electrons. The electrons fill the one orbital in its one electron shell, the lowest energy level. (b) An atom of nitrogen has seven protons, seven neutrons, and seven electrons. Two electrons fill the orbital in the innermost electron shell, and five electrons occupy orbitals in the second electron shell (the second energy level). The orbitals in the second electron shell can hold up to eight electrons; therefore there are three vacancies in the outer electron shell of a nitrogen atom.


Key Learning Outcome 2.1. Atoms, the smallest particles into which a substance can be divided, are composed of electrons orbiting a nucleus that contains protons and neutrons. Electrons determine the chemical behavior of atoms.