Learning Objectives
By the end of this section, you will be able to:
- Define matter and elements
- Describe the interrelationship between protons, neutrons, and electrons
- Compare the ways in which electrons can be donated or shared between atoms
- Explain the ways in which naturally occurring elements combine to create molecules, cells, tissues, organ systems, and organisms
At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 92 occur naturally. The remaining elements are synthesized in laboratories and are unstable.
Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already “taken” by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols derive from their Latin names; for example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium.
The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). In the non-living world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole, as shown in [Figure 1]. For example, the atmosphere is rich in nitrogen and oxygen but contains little carbon and hydrogen, while the earth’s crust, although it contains oxygen and a small amount of hydrogen, has little nitrogen and carbon. In spite of their differences in abundance, all elements and the chemical reactions between them obey the same chemical and physical laws regardless of whether they are a part of the living or non-living world.
Approximate Percentage of Elements in Living Organisms (Humans) Compared to the Non-living World | |||
---|---|---|---|
Element | Life (Humans) | Atmosphere | Earth’s Crust |
Oxygen (O) | 65% | 21% | 46% |
Carbon (C) | 18% | trace | trace |
Hydrogen (H) | 10% | trace | 0.1% |
Nitrogen (N) | 3% | 78% | trace |
Elements and Compounds
All matter in the natural world is composed of one or more of the 92 fundamental substances called elements. An element is a pure substance that is distinguished from all other matter by the fact that it cannot be created or broken down by ordinary chemical means. While your body can assemble many of the chemical compounds needed for life from their constituent elements, it cannot make elements. They must come from the environment. A familiar example of an element that you must take in is calcium (Ca++). Calcium is essential to the human body; it is absorbed and used for a number of processes, including strengthening bones. When you consume dairy products your digestive system breaks down the food into components small enough to cross into the bloodstream. Among these is calcium, which, because it is an element, cannot be broken down further. The elemental calcium in cheese, therefore, is the same as the calcium that forms your bones. Some other elements you might be familiar with are oxygen, sodium, and iron. The elements in the human body are shown in Table 1, beginning with the most abundant: oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). Each element’s name can be replaced by a one- or two-letter symbol; you will become familiar with some of these during this course. All the elements in your body are derived from the foods you eat and the air you breathe.
Table 1. Elements of the Human Body. The main elements that compose the human body are shown from most abundant to least abundant. | |||
---|---|---|---|
Element | Symbol | Percentage in Body | At a Look |
Oxygen | O | 65.0 | |
Carbon | C | 18.5 | |
Hydrogen | H | 9.5 | |
Nitrogen | N | 3.2 | |
Calcium | Ca | 1.5 | |
Phosphorus | P | 1.0 | |
Potassium | K | 0.4 | |
Sulfur | S | 0.3 | |
Sodium | Na | 0.2 | |
Chlorine | Cl | 0.2 | |
Magnesium | Mg | 0.1 | |
Trace elements include boron (B), chromium (Cr), cobalt (Co), copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), silicon (Si), tin (Sn), vanadium (V), and zinc (Zn) | less than 1.0 |
In nature, elements rarely occur alone. Instead, they combine to form compounds. A compound is a substance composed of two or more elements joined by chemical bonds. For example, the compound glucose is an important body fuel. It is always composed of the same three elements: carbon, hydrogen, and oxygen. Moreover, the elements that make up any given compound always occur in the same relative amounts. In glucose, there are always six carbon and six oxygen units for every twelve hydrogen units. But what, exactly, are these “units” of elements?
The Structure of the Atom
To understand how elements come together, we must first discuss the smallest component or building block of an element, the atom. An atom is the smallest unit of matter that retains all of the chemical properties of an element. For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and containing small amounts of other elements known as impurities. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold.
An atom is composed of two regions: the nucleus, which is in the center of the atom and contains protons and neutrons, and the outermost region of the atom which holds its electrons in orbit around the nucleus, as illustrated in [Figure 1]. Atoms contain protons, electrons, and neutrons, among other subatomic particles. The only exception is hydrogen (H), which is made of one proton and one electron with no neutrons.
Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams. Scientists arbitrarily define this amount of mass as one atomic mass unit (amu) or one Dalton, as shown in [Figure 2]. Although similar in mass, protons and neutrons differ in their electric charge. A proton is positively charged whereas a neutron is uncharged. Therefore, the number of neutrons in an atom contributes significantly to its mass, but not to its charge. Electrons are much smaller in mass than protons, weighing only 9.11 × 10-28 grams, or about 1/1800 of an atomic mass unit. Hence, they do not contribute much to an element’s overall atomic mass. Therefore, when considering atomic mass, it is customary to ignore the mass of any electrons and calculate the atom’s mass based on the number of protons and neutrons alone. Although not significant contributors to mass, electrons do contribute greatly to the atom’s charge, as each electron has a negative charge equal to the positive charge of a proton. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge.
Accounting for the sizes of protons, neutrons, and electrons, most of the volume of an atom—greater than 99 percent—is, in fact, empty space. With all this empty space, one might ask why so-called solid objects do not just pass through one another. The reason they do not is that the electrons that surround all atoms are negatively charged and negative charges repel each other.
Protons, Neutrons, and Electrons | |||
---|---|---|---|
Charge | Mass (amu) | Location | |
Proton | +1 | 1 | nucleus |
Neutron | 0 | 1 | nucleus |
Electron | –1 | 0 | orbitals |
Atomic Number and Mass Number
An atom of carbon is unique to carbon, but a proton of carbon is not. One proton is the same as another, whether it is found in an atom of carbon, sodium (Na), or iron (Fe). The same is true for neutrons and electrons. So, what gives an element its distinctive properties—what makes carbon so different from sodium or iron? The answer is the unique quantity of protons each contains. Carbon by definition is an element whose atoms contain six protons. No other element has exactly six protons in its atoms. Moreover, all atoms of carbon, whether found in your liver or in a lump of coal, contain six protons. Thus, the atomic number, which is the number of protons in the nucleus of the atom, identifies the element. Because an atom usually has the same number of electrons as protons, the atomic number identifies the usual number of electrons as well.
In their most common form, many elements also contain the same number of neutrons as protons. The most common form of carbon, for example, has six neutrons as well as six protons, for a total of 12 subatomic particles in its nucleus. An element’s mass number is the sum of the number of protons and neutrons in its nucleus. So the most common form of carbon’s mass number is 12. (Electrons have so little mass that they do not appreciably contribute to the mass of an atom.) Carbon is a relatively light element. Uranium (U), in contrast, has a mass number of 238 and is referred to as a heavy metal. Its atomic number is 92 (it has 92 protons) but it contains 146 neutrons; it has the most mass of all the naturally occurring elements.
Periodic Table Of Elements
By the twentieth century, it became apparent that the periodic relationship involved atomic numbers rather than atomic masses. The modern statement of this relationship, the periodic law, is as follows: the properties of the elements are periodic functions of their atomic numbers. A modern periodic table arranges the elements in increasing order of their atomic numbers and groups atoms with similar properties in the same vertical column (Figure 2). Each box represents an element and contains its atomic number, symbol, average atomic mass, and (sometimes) name. The elements are arranged in seven horizontal rows, called periods or series, and 18 vertical columns, called groups. Groups are labeled at the top of each column. In the United States, the labels traditionally were numerals with capital letters. However, IUPAC recommends that the numbers 1 through 18 be used, and these labels are more common. For the table to fit on a single page, parts of two of the rows, a total of 14 columns, are usually written below the main body of the table.
Many elements differ dramatically in their chemical and physical properties, but some elements are similar in their behaviors. For example, many elements appear shiny, are malleable (able to be deformed without breaking) and ductile (can be drawn into wires), and conduct heat and electricity well. Other elements are not shiny, malleable, or ductile, and are poor conductors of heat and electricity. We can sort the elements into large classes with common properties: metals (elements that are shiny, malleable, good conductors of heat and electricity—shaded yellow); nonmetals (elements that appear dull, poor conductors of heat and electricity—shaded green); and metalloids (elements that conduct heat and electricity moderately well, and possess some properties of metals and some properties of nonmetals—shaded purple).
The elements can also be classified into the main-group elements (or representative elements) in the columns labeled 1, 2, and 13–18; the transition metals in the columns labeled 3–12; and inner transition metals in the two rows at the bottom of the table (the top-row elements are called lanthanides and the bottom-row elements are actinides; Figure 3). The elements can be subdivided further by more specific properties, such as the composition of the compounds they form. For example, the elements in group 1 (the first column) form compounds that consist of one atom of the element and one atom of hydrogen. These elements (except hydrogen) are known as alkali metals, and they all have similar chemical properties. The elements in group 2 (the second column) form compounds consisting of one atom of the element and two atoms of hydrogen: These are called alkaline earth metals, with similar properties among members of that group. Other groups with specific names are the pnictogens (group 15), chalcogens (group 16), halogens (group 17), and the noble gases (group 18, also known as inert gases). The groups can also be referred to by the first element of the group: For example, the chalcogens can be called the oxygen group or oxygen family. Hydrogen is a unique, nonmetallic element with properties similar to both group 1A and group 7A elements. For that reason, hydrogen may be shown at the top of both groups, or by itself.
In studying the periodic table, you might have noticed something about the atomic masses of some of the elements. Element 43 (technetium), element 61 (promethium), and most of the elements with atomic number 84 (polonium) and higher have their atomic mass given in square brackets. This is done for elements that consist entirely of unstable, radioactive isotopes (you will learn more about radioactivity in the nuclear chemistry chapter). An average atomic weight cannot be determined for these elements because their radioisotopes may vary significantly in relative abundance, depending on the source, or may not even exist in nature. The number in square brackets is the atomic mass number (and approximate atomic mass) of the most stable isotope of that element.
Isotopes
Although each element has a unique number of protons, it can exist as different isotopes. An isotope is one of the different forms of an element, distinguished from one another by different numbers of neutrons. The standard isotope of carbon is 12C, commonly called carbon twelve. 12C has six protons and six neutrons, for a mass number of twelve. All of the isotopes of carbon have the same number of protons; therefore, 13C has seven neutrons, and 14C has eight neutrons. The different isotopes of an element can also be indicated with the mass number hyphenated (for example, C-12 instead of 12C). Hydrogen has three common isotopes, shown in Figure 3.
An isotope that contains more than the usual number of neutrons is referred to as a heavy isotope. An example is 14C. Heavy isotopes tend to be unstable, and unstable isotopes are radioactive. A radioactive isotope is an isotope whose nucleus readily decays, giving off subatomic particles and electromagnetic energy. Different radioactive isotopes (also called radioisotopes) differ in their half-life, the time it takes for half of any size sample of an isotope to decay. For example, the half-life of tritium—a radioisotope of hydrogen—is about 12 years, indicating it takes 12 years for half of the tritium nuclei in a sample to decay. Excessive exposure to radioactive isotopes can damage human cells and even cause cancer and birth defects, but when exposure is controlled, some radioactive isotopes can be useful in medicine. For more information, see the Career Connections.
Career Connection: Interventional Radiologist
The controlled use of radioisotopes has advanced medical diagnosis and treatment of disease. Interventional radiologists are physicians who treat disease by using minimally invasive techniques involving radiation. Many conditions that could once only be treated with a lengthy and traumatic operation can now be treated non-surgically, reducing the cost, pain, length of hospital stay, and recovery time for patients. For example, in the past, the only options for a patient with one or more tumors in the liver were surgery and chemotherapy (the administration of drugs to treat cancer). Some liver tumors, however, are difficult to access surgically, and others could require the surgeon to remove too much of the liver. Moreover, chemotherapy is highly toxic to the liver, and certain tumors do not respond well to it anyway. In some such cases, an interventional radiologist can treat the tumors by disrupting their blood supply, which they need if they are to continue to grow. In this procedure, called radioembolization, the radiologist accesses the liver with a fine needle, threaded through one of the patient’s blood vessels. The radiologist then inserts tiny radioactive “seeds” into the blood vessels that supply the tumors. In the days and weeks following the procedure, the radiation emitted from the seeds destroys the vessels and directly kills the tumor cells in the vicinity of the treatment.
Radioisotopes emit subatomic particles that can be detected and tracked by imaging technologies. One of the most advanced uses of radioisotopes in medicine is the positron emission tomography (PET) scanner, which detects the activity in the body of a very small injection of radioactive glucose, the simple sugar that cells use for energy. The PET camera reveals to the medical team which of the patient’s tissues are taking up the most glucose. Thus, the most metabolically active tissues show up as bright “hot spots” on the images (Figure 4). PET can reveal some cancerous masses because cancer cells consume glucose at a high rate to fuel their rapid reproduction.
Carbon Dating
Carbon is normally present in the atmosphere in the form of gaseous compounds like carbon dioxide and methane. Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere from atmospheric 14N (nitrogen) by the addition of a neutron and the loss of a proton because of cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism incorporates 14C initially as carbon dioxide fixed in the process of photosynthesis, the relative amount of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio between 14C and 12C will decline as 14C decays gradually to 14N by a process called beta decay—the emission of electrons or positrons. This decay gives off energy in a slow process.
After approximately 5,730 years, half of the starting concentration of 14C will have been converted back to 14N. The time it takes for half of the original concentration of an isotope to decay back to its more stable form is called its half-life. Because the half-life of 14C is long, it is used to date formerly living objects such as old bones or wood. Comparing the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. On the basis of this amount, the age of the material, such as the pygmy mammoth shown in [Figure 3], can be calculated with accuracy if it is not much older than about 50,000 years. Other elements have isotopes with different half lives. For example, 40K (potassium-40) has a half-life of 1.25 billion years, and 235U (Uranium 235) has a half-life of about 700 million years. Through the use of radiometric dating, scientists can study the age of fossils or other remains of extinct organisms to understand how organisms have evolved from earlier species.
It should be stressed that there is a connection between the number of protons in an element, the atomic number that distinguishes one element from another, and the number of electrons it has. In all electrically neutral atoms, the number of electrons is the same as the number of protons. Thus, each element, at least when electrically neutral, has a characteristic number of electrons equal to its atomic number.
Electrons fill orbitals in a consistent order: they first fill the orbitals closest to the nucleus, then they continue to fill orbitals of increasing energy further from the nucleus. If there are multiple orbitals of equal energy, they will be filled with one electron in each energy level before a second electron is added. The electrons of the outermost energy level determine the energetic stability of the atom and its tendency to form chemical bonds with other atoms to form molecules.
Under standard conditions, atoms fill the inner shells first, often resulting in a variable number of electrons in the outermost shell. The innermost shell has a maximum of two electrons but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule, which states, with the exception of the innermost shell, that atoms are more stable energetically when they have eight electrons in their valence shell, the outermost electron shell. Examples of some neutral atoms and their electron configurations are shown in [Figure 6]. Notice that in this [Figure 6], helium has a complete outer electron shell, with two electrons filling its first and only shell. Similarly, neon has a complete outer 2n shell containing eight electrons. In contrast, chlorine and sodium have seven and one in their outer shells, respectively, but theoretically they would be more energetically stable if they followed the octet rule and had eight.
Art Connection
An atom may give, take, or share electrons with another atom to achieve a full valence shell, the most stable electron configuration. Looking at this figure, how many electrons do elements in group 1 need to lose in order to achieve a stable electron configuration? How many electrons do elements in groups 14 and 17 need to gain to achieve a stable configuration?
<!–<para> Elements in group 1 need to lose one electron to achieve a stable electron configuration. Elements in groups 14 and 17 need to gain four and one electrons, respectively, to achieve a stable configuration.–>
Understanding that the organization of the periodic table is based on the total number of protons (and electrons) helps us know how electrons are distributed among the outer shell. The periodic table is arranged in columns and rows based on the number of electrons and where these electrons are located. Take a closer look at the some of the elements in the table’s far right column in [Figure 4]. The group 18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells, making it unnecessary for them to share electrons with other atoms to attain stability; they are highly stable as single atoms. Their non-reactivity has resulted in their being named the inert gases (or noble gases). Compare this to the group 1 elements in the left-hand column. These elements, including hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means that they can achieve a stable configuration and a filled outer shell by donating or sharing one electron with another atom or a molecule such as water. Hydrogen will donate or share its electron to achieve this configuration, while lithium and sodium will donate their electron to become stable. As a result of losing a negatively charged electron, they become positively charged ions. Group 17 elements, including fluorine and chlorine, have seven electrons in their outmost shells, so they tend to fill this shell with an electron from other atoms or molecules, making them negatively charged ions. Group 14 elements, of which carbon is the most important to living systems, have four electrons in their outer shell allowing them to make several covalent bonds (discussed below) with other atoms. Thus, the columns of the periodic table represent the potential shared state of these elements’ outer electron shells that is responsible for their similar chemical characteristics.
Chemical Reactions and Molecules
All elements are most stable when their outermost shell is filled with electrons according to the octet rule. This is because it is energetically favorable for atoms to be in that configuration and it makes them stable. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom; these bond together to form water, as illustrated in [Figure 8]. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.
Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in the beginning of a chemical reaction are called the reactants (usually found on the left side of a chemical equation), and the substances found at the end of the reaction are known as the products (usually found on the right side of a chemical equation). An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction; this direction is not always a “one-way street.” For the creation of the water molecule shown above, the chemical equation would be:
An example of a simple chemical reaction is the breaking down of hydrogen peroxide molecules, each of which consists of two hydrogen atoms bonded to two oxygen atoms (H2O2). The reactant hydrogen peroxide is broken down into water, containing one oxygen atom bound to two hydrogen atoms (H2O), and oxygen, which consists of two bonded oxygen atoms (O2). In the equation below, the reaction includes two hydrogen peroxide molecules and two water molecules. This is an example of a balanced chemical equation, wherein the number of atoms of each element is the same on each side of the equation. According to the law of conservation of matter, the number of atoms before and after a chemical reaction should be equal, such that no atoms are, under normal circumstances, created or destroyed.
Even though all of the reactants and products of this reaction are molecules (each atom remains bonded to at least one other atom), in this reaction only hydrogen peroxide and water are representatives of compounds: they contain atoms of more than one type of element. Molecular oxygen, on the other hand, as shown in [Figure 9],consists of two doubly bonded oxygen atoms and is not classified as a compound but as a mononuclear molecule.
Some chemical reactions, such as the one shown above, can proceed in one direction until the reactants are all used up. The equations that describe these reactions contain a unidirectional arrow and are irreversible. Reversible reactions are those that can go in either direction. In reversible reactions, reactants are turned into products, but when the concentration of product goes beyond a certain threshold (characteristic of the particular reaction), some of these products will be converted back into reactants; at this point, the designations of products and reactants are reversed. This back and forth continues until a certain relative balance between reactants and products occurs—a state called equilibrium. These situations of reversible reactions are often denoted by a chemical equation with a double headed arrow pointing towards both the reactants and products.
For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3–) forming an equilibrium state with carbonic acid (H2CO3). If carbonic acid were added to this system, some of it would be converted to bicarbonate and hydrogen ions.
In biological reactions, however, equilibrium is rarely obtained because the concentrations of the reactants or products or both are constantly changing, often with a product of one reaction being a reactant for another. To return to the example of excess hydrogen ions in the blood, the formation of carbonic acid will be the major direction of the reaction. However, the carbonic acid can also leave the body as carbon dioxide gas (via exhalation) instead of being converted back to bicarbonate ion, thus driving the reaction to the right by the chemical law known as law of mass action. These reactions are important for maintaining the homeostasis of our blood.
Ions and Ionic Bonds
Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that are formed by losing electrons. Negative ions are formed by gaining electrons and are called anions. Anions are designated by their elemental name being altered to end in “-ide”: the anion of chlorine is called chloride, and the anion of sulfur is called sulfide, for example.
This movement of electrons from one element to another is referred to as electron transfer. As [Figure 10] illustrates, sodium (Na) only has one electron in its outer electron shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. It is now referred to as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, giving it a net negative (–1) charge. It is now referred to as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium cation) or –1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.
Ionic bonds are formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.
Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.
Covalent Bonds and Other Bonds and Interactions
Another way the octet rule can be satisfied is by the sharing of electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. Covalent bonds are commonly found in carbon-based organic molecules, such as our DNA and proteins. Covalent bonds are also found in inorganic molecules like H2O, CO2, and O2. One, two, or three pairs of electrons may be shared, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.
The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, the sharing of these three pairs of electrons between the two nitrogen atoms allows for the filling of their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA.
The formation of water molecules provides an example of covalent bonding. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds, as shown in [Figure 8]. The electron from the hydrogen splits its time between the incomplete outer shell of the hydrogen atoms and the incomplete outer shell of the oxygen atoms. To completely fill the outer shell of oxygen, which has six electrons in its outer shell but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence the well-known formula H2O. The electrons are shared between the two elements to fill the outer shell of each, making both elements more stable.
Polar Covalent Bonds
There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, shown in [Figure 11], the electrons are unequally shared by the atoms and are attracted more to one nucleus than the other. Because of the unequal distribution of electrons between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ–) charge develops. This partial charge is an important property of water and accounts for many of its characteristics.
Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge. This occurs because the nucleus of the oxygen atom is more attractive to the electrons of the hydrogen atoms than the hydrogen nucleus is to the oxygen’s electrons. Thus oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time in the vicinity of the oxygen nucleus than they do near the nucleus of the hydrogen atoms, giving the atoms of oxygen and hydrogen slightly negative and positive charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is more likely than finding it near a hydrogen nucleus. Either way, the atom’s relative electronegativity contributes to the development of partial charges whenever one element is significantly more electronegative than the other, and the charges generated by these polar bonds may then be used for the formation of hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which are discussed in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar bonds are often present in organic molecules.
Nonpolar Covalent Bonds
Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons will be equally distributed between the two oxygen atoms.
Another example of a nonpolar covalent bond is methane (CH4), also shown in [Figure 11]. Carbon has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule.
Hydrogen Bonds and Van Der Waals Interactions
Ionic and covalent bonds between elements require energy to break. Ionic bonds are not as strong as covalent, which determines their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between molecules. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells.
When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly positive charge because hydrogen’s electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the δ+of the hydrogen from one molecule and the δ– charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule. This interaction is called a hydrogen bond. This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix.
Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one another. These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the three-dimensional structure of the proteins in our cells that is necessary for their proper function.
Pharmaceutical Chemist
Pharmaceutical chemists are responsible for the development of new drugs and trying to determine the mode of action of both old and new drugs. They are involved in every step of the drug development process. Drugs can be found in the natural environment or can be synthesized in the laboratory. In many cases, potential drugs found in nature are changed chemically in the laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version found in nature.
After the initial discovery or synthesis of a drug, the chemist then develops the drug, perhaps chemically altering it, testing it to see if the drug is toxic, and then designing methods for efficient large-scale production. Then, the process of getting the drug approved for human use begins. In the United States, drug approval is handled by the Food and Drug Administration (FDA) and involves a series of large-scale experiments using human subjects to make sure the drug is not harmful and effectively treats the condition it aims to treat. This process often takes several years and requires the participation of physicians and scientists, in addition to chemists, to complete testing and gain approval.
An example of a drug that was originally discovered in a living organism is Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer. This drug was discovered in the bark of the pacific yew tree. Another example is aspirin, originally isolated from willow tree bark. Finding drugs often means testing hundreds of samples of plants, fungi, and other forms of life to see if any biologically active compounds are found within them. Sometimes, traditional medicine can give modern medicine clues to where an active compound can be found. For example, the use of willow bark to make medicine has been known for thousands of years, dating back to ancient Egypt. It was not until the late 1800s, however, that the aspirin molecule, known as acetylsalicylic acid, was purified and marketed for human use.
Occasionally, drugs developed for one use are found to have unforeseen effects that allow these drugs to be used in other, unrelated ways. For example, the drug minoxidil (Rogaine) was originally developed to treat high blood pressure. When tested on humans, it was noticed that individuals taking the drug would grow new hair. Eventually the drug was marketed to men and women with baldness to restore lost hair.
The career of the pharmaceutical chemist may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier.
Section Summary
Matter is anything that occupies space and has mass. It is made up of elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create molecules, which in turn combine to form cells, tissues, organ systems, and organisms. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
Glossary
- anion
- negative ion that is formed by an atom gaining one or more electrons
- atom
- the smallest unit of matter that retains all of the chemical properties of an element
- atomic mass
- calculated mean of the mass number for an element’s isotopes
- atomic number
- total number of protons in an atom
- balanced chemical equation
- statement of a chemical reaction with the number of each type of atom equalized for both the products and reactants
- cation
- positive ion that is formed by an atom losing one or more electrons
- chemical bond
- interaction between two or more of the same or different atoms that results in the formation of molecules
- chemical reaction
- process leading to the rearrangement of atoms in molecules
- chemical reactivity
- the ability to combine and to chemically bond with each other
- compound
- substance composed of molecules consisting of atoms of at least two different elements
- covalent bond
- type of strong bond formed between two of the same or different elements; forms when electrons are shared between atoms
- electrolyte
- ion necessary for nerve impulse conduction, muscle contractions and water balance
- electron
- negatively charged subatomic particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a negative charge of –1 unit
- electron configuration
- arrangement of electrons in an atom’s electron shell (for example, 1s22s22p6)
- electron orbital
- how electrons are spatially distributed surrounding the nucleus; the area where an electron is most likely to be found
- electron transfer
- movement of electrons from one element to another; important in creation of ionic bonds
- electronegativity
- ability of some elements to attract electrons (often of hydrogen atoms), acquiring partial negative charges in molecules and creating partial positive charges on the hydrogen atoms
- element
- one of 118 unique substances that cannot be broken down into smaller substances; each element has unique properties and a specified number of protons
- equilibrium
- steady state of relative reactant and product concentration in reversible chemical reactions in a closed system
- hydrogen bond
- weak bond between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules
- inert gas
- (also, noble gas) element with filled outer electron shell that is unreactive with other atoms
- ion
- atom or chemical group that does not contain equal numbers of protons and electrons
- ionic bond
- chemical bond that forms between ions with opposite charges (cations and anions)
- irreversible chemical reaction
- chemical reaction where reactants proceed uni-directionally to form products
- isotope
- one or more forms of an element that have different numbers of neutrons
- law of mass action
- chemical law stating that the rate of a reaction is proportional to the concentration of the reacting substances
- mass number
- total number of protons and neutrons in an atom
- matter
- anything that has mass and occupies space
- molecule
- two or more atoms chemically bonded together
- neutron
- uncharged particle that resides in the nucleus of an atom; has a mass of one amu
- noble gas
- see inert gas
- nonpolar covalent bond
- type of covalent bond that forms between atoms when electrons are shared equally between them
- nucleus
- core of an atom; contains protons and neutrons
- octet rule
- rule that atoms are most stable when they hold eight electrons in their outermost shells
- orbital
- region surrounding the nucleus; contains electrons
- periodic table
- organizational chart of elements indicating the atomic number and atomic mass of each element; provides key information about the properties of the elements
- polar covalent bond
- type of covalent bond that forms as a result of unequal sharing of electrons, resulting in the creation of slightly positive and slightly negative charged regions of the molecule
- product
- molecule found on the right side of a chemical equation
- proton
- positively charged particle that resides in the nucleus of an atom; has a mass of one amu and a charge of +1
- radioisotope
- isotope that emits radiation composed of subatomic particles to form more stable elements
- reactant
- molecule found on the left side of a chemical equation
- reversible chemical reaction
- chemical reaction that functions bi-directionally, where products may turn into reactants if their concentration is great enough
- valence shell
- outermost shell of an atom
- van der Waals interaction
- very weak interaction between molecules due to temporary charges attracting atoms that are very close together