THE CHEMICAL LEVEL OF ORGANIZATION

Figure 2.1IntroductionChapter ObjectivesAfter studying this chapter, you will be able to:

The smallest, most fundamental material components of the human body are basic chemical elements. In fact, chemicals called nucleotide bases are the foundation of the genetic code with the instructions on how to build and maintain the human body from conception through old age. There are about three billion of these base pairs in human DNA.

Human chemistry includes organic molecules (carbon-based) and biochemicals (those produced by the body). Human chemistry also includes elements. In fact, life cannot exist without many of the elements that are part of the earth. All of the elements that contribute to chemical reactions, to the transformation of energy, and to electrical activity and muscle contraction—elements that include phosphorus, carbon, sodium, and calcium, to name a few—originated in stars.

These elements, in turn, can form both the inorganic and organic chemical compounds important to life, including, for example, water, glucose, and proteins. This chapter begins by examining elements and how the structures of atoms, the basic units of matter, determine the characteristics of elements by the number of protons, neutrons, and electrons in the atoms. The chapter then builds the framework of life from there.

2.1 | Elements and Atoms: The Building Blocks of MatterBy the end of this section, you will be able to:

The substance of the universe—from a grain of sand to a star—is called matter. Scientists define matter as anything that occupies space and has mass. An object’s mass and its weight are related concepts, but not quite the same. An object’s mass is the amount of matter contained in the object, and the object’s mass is the same whether that object is on Earth or in the zero-gravity environment of outer space. An object’s weight, on the other hand, is its mass as affected by the pull of gravity. Where gravity strongly pulls on an object’s mass its weight is greater than it is where gravity is less strong. An object of a certain mass weighs less on the moon, for example, than it does on Earth because the gravity of the moon is less than that of Earth. In other words, weight is variable, and is influenced by gravity. A piece of cheese that weighs a pound on Earth weighs only a few ounces on the moon.

Elements and CompoundsAll 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 (Figure 2.2 ), 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.

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?

Atoms and Subatomic ParticlesAn atom is the smallest quantity of an element that retains the unique properties of that element. In other words, an atom of hydrogen is a unit of hydrogen—the smallest amount of hydrogen that can exist. As you might guess, atoms are almost unfathomably small. The period at the end of this sentence is millions of atoms wide.

Atomic Structure and EnergyAtoms are made up of even smaller subatomic particles, three types of which are important: the proton, neutron, and electron. The number of positively-charged protons and non-charged (“neutral”) neutrons, gives mass to the atom, and the number of each in the nucleus of the atom determine the element. The number of negatively-charged electrons that “spin” around the nucleus at close to the speed of light equals the number of protons. An electron has about 1/2000th the mass of a proton or neutron.

(Figure 2.3 )shows two models that can help you imagine the structure of an atom—in this case, helium (He). In the planetary model, helium’s two electrons are shown circling the nucleus in a fixed orbit depicted as a ring. Although this model is helpful in visualizing atomic structure, in reality, electrons do not travel in fixed orbits, but whiz around the nucleus erratically in a so-called electron cloud.

An atom’s protons and electrons carry electrical charges. Protons, with their positive charge, are designated p+. Electrons, which have a negative charge, are designated e–. An atom’s neutrons have no charge: they are electrically neutral. Just as a magnet sticks to a steel refrigerator because their opposite charges attract, the positively charged protons attract the negatively charged electrons. This mutual attraction gives the atom some structural stability. The attraction by the positively charged nucleus helps keep electrons from straying far. The number of protons and electrons within a neutral atom are equal, thus, the atom’s overall charge is balanced.

Atomic Number and Mass NumberAn 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.

The periodic table of the elements, shown in (Figure 2.4 ), is a chart identifying the 92 elements found in nature, as well as several larger, unstable elements discovered experimentally. The elements are arranged in order of their atomic number, with hydrogen and helium at the top of the table, and the more massive elements below. The periodic table is a useful device because for each element, it identifies the chemical symbol, the atomic number, and the mass number, while organizing elements according to their propensity to react with other elements. The number of protons and electrons in an element are equal. The number of protons and neutrons may be equal for some elements, but are not equal for all.

Click and ExploreVisit this website (http://openstaxcollege.org/l/ptable) to view the periodic table. In the periodic table of the elements, elements in a single column have the same number of electrons that can participate in a chemical reaction. These electrons are known as “valence electrons.” For example, the elements in the first column all have a single valence electron, an electron that can be “donated” in a chemical reaction with another atom. What is the meaning of a mass number shown in parentheses?

IsotopesAlthough 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 2.5 ).

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.

Interventional RadiologistThe 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 2.6 ). PET can reveal some cancerous masses because cancer cells consume glucose at a high rate to fuel their rapid reproduction.

The Behavior of ElectronsIn the human body, atoms do not exist as independent entities. Rather, they are constantly reacting with other atoms to form and to break down more complex substances. To fully understand anatomy and physiology you must grasp how atoms participate in such reactions. The key is understanding the behavior of electrons.

Although electrons do not follow rigid orbits a set distance away from the atom’s nucleus, they do tend to stay within certain regions of space called electron shells. An electron shell is a layer of electrons that encircle the nucleus at a distinct energy level.

The atoms of the elements found in the human body have from one to five electron shells, and all electron shells hold eight electrons except the first shell, which can only hold two. This configuration of electron shells is the same for all atoms. The precise number of shells depends on the number of electrons in the atom. Hydrogen and helium have just one and two electrons, respectively. If you take a look at the periodic table of the elements, you will notice that hydrogen and helium are placed alone on either sides of the top row; they are the only elements that have just one electron shell (Figure 2.7 ). A second shell is necessary to hold the electrons in all elements larger than hydrogen and helium.

Lithium (Li), whose atomic number is 3, has three electrons. Two of these fill the first electron shell, and the third spills over into a second shell. The second electron shell can accommodate as many as eight electrons. Carbon, with its six electrons, entirely fills its first shell, and half-fills its second. With ten electrons, neon (Ne) entirely fills its two electron shells. Again, a look at the periodic table reveals that all of the elements in the second row, from lithium to neon, have just two electron shells. Atoms with more than ten electrons require more than two shells. These elements occupy the third and subsequent rows of the periodic table.

The factor that most strongly governs the tendency of an atom to participate in chemical reactions is the number of electrons in its valence shell. A valence shell is an atom’s outermost electron shell. If the valence shell is full, the atom is stable; meaning its electrons are unlikely to be pulled away from the nucleus by the electrical charge of other atoms. If the valence shell is not full, the atom is reactive; meaning it will tend to react with other atoms in ways that make the valence shell full.

Consider hydrogen, with its one electron only half-filling its valence shell. This single electron is likely to be drawn into relationships with the atoms of other elements, so that hydrogen’s single valence shell can be stabilized.

All atoms (except hydrogen and helium with their single electron shells) are most stable when there are exactly eight electrons in their valence shell. This principle is referred to as the octet rule, and it states that an atom will give up, gain, or share electrons with another atom so that it ends up with eight electrons in its own valence shell. For example, oxygen, with six electrons in its valence shell, is likely to react with other atoms in a way that results in the addition of two electrons to oxygen’s valence shell, bringing the number to eight. When two hydrogen atoms each share their single electron with oxygen, covalent bonds are formed, resulting in a molecule of water, H2O.

In nature, atoms of one element tend to join with atoms of other elements in characteristic ways. For example, carbon commonly fills its valence shell by linking up with four atoms of hydrogen. In so doing, the two elements form the simplest of organic molecules, methane, which also is one of the most abundant and stable carbon-containing compounds on Earth. As stated above, another example is water; oxygen needs two electrons to fill its valence shell. It commonly interacts with two atoms of hydrogen, forming H2O. Incidentally, the name “hydrogen” reflects its contribution to water (hydro- = “water”; -gen = “maker”). Thus, hydrogen is the “water maker.”

2.2 | Chemical BondsBy the end of this section, you will be able to:

Atoms separated by a great distance cannot link; rather, they must come close enough for the electrons in their valence shells to interact. But do atoms ever actually touch one another? Most physicists would say no, because the negatively charged electrons in their valence shells repel one another. No force within the human body—or anywhere in the natural world—is strong enough to overcome this electrical repulsion. So when you read about atoms linking together or colliding, bear in mind that the atoms are not merging in a physical sense.

Instead, atoms link by forming a chemical bond. A bond is a weak or strong electrical attraction that holds atoms in the same vicinity. The new grouping is typically more stable—less likely to react again—than its component atoms were when they were separate. A more or less stable grouping of two or more atoms held together by chemical bonds is called a molecule. The bonded atoms may be of the same element, as in the case of H2, which is called molecular hydrogen or hydrogen gas. When a molecule is made up of two or more atoms of different elements, it is called a chemical compound. Thus, a unit of water, or H2O, is a compound, as is a single molecule of the gas methane, or CH4.

Three types of chemical bonds are important in human physiology, because they hold together substances that are used by the body for critical aspects of homeostasis, signaling, and energy production, to name just a few important processes. These are ionic bonds, covalent bonds, and hydrogen bonds.

Ions and Ionic BondsRecall that an atom typically has the same number of positively charged protons and negatively charged electrons. As long as this situation remains, the atom is electrically neutral. But when an atom participates in a chemical reaction that results in the donation or acceptance of one or more electrons, the atom will then become positively or negatively charged. This happens frequently for most atoms in order to have a full valence shell, as described previously. This can happen either by gaining electrons to fill a shell that is more than half-full, or by giving away electrons to empty a shell than is less than half-full, thereby leaving the next smaller electron shell as the new, full, valence shell. An atom that has an electrical charge—whether positive or negative—is an ion.

Click and ExploreVisit this website (http://openstaxcollege.org/l/electenergy) to learn about electrical energy and the attraction/ repulsion of charges. What happens to the charged electroscope when a conductor is moved between its plastic sheets, and why?

Potassium (K), for instance, is an important element in all body cells. Its atomic number is 19. It has just one electron in its valence shell. This characteristic makes potassium highly likely to participate in chemical reactions in which it donates one electron. (It is easier for potassium to donate one electron than to gain seven electrons.) The loss will cause the positive charge of potassium’s protons to be more influential than the negative charge of potassium’s electrons. In other words, the resulting potassium ion will be slightly positive. A potassium ion is written K+, indicating that it has lost a single electron. A positively charged ion is known as a cation.

Now consider fluorine (F), a component of bones and teeth. Its atomic number is nine, and it has seven electrons in its valence shell. Thus, it is highly likely to bond with other atoms in such a way that fluorine accepts one electron (it is easier for fluorine to gain one electron than to donate seven electrons). When it does, its electrons will outnumber its protons by one, and it will have an overall negative charge. The ionized form of fluorine is called fluoride, and is written as F–. A negatively charged ion is known as an anion.

Atoms that have more than one electron to donate or accept will end up with stronger positive or negative charges. A cation that has donated two electrons has a net charge of +2. Using magnesium (Mg) as an example, this can be written Mg++ or Mg2+. An anion that has accepted two electrons has a net charge of –2. The ionic form of selenium (Se), for example, is typically written Se2–.

The opposite charges of cations and anions exert a moderately strong mutual attraction that keeps the atoms in close proximity forming an ionic bond. An ionic bond is an ongoing, close association between ions of opposite charge. The table salt you sprinkle on your food owes its existence to ionic bonding. As shown in (Figure 2.8 ), sodium commonly donates an electron to chlorine, becoming the cation Na+. When chlorine accepts the electron, it becomes the chloride anion, Cl–. With their opposing charges, these two ions strongly attract each other.

Water is an essential component of life because it is able to break the ionic bonds in salts to free the ions. In fact, in biological fluids, most individual atoms exist as ions. These dissolved ions produce electrical charges within the body. The behavior of these ions produces the tracings of heart and brain function observed as waves on an electrocardiogram (EKG or ECG) or an electroencephalogram (EEG). The electrical activity that derives from the interactions of the charged ions is why they are also called electrolytes.

Covalent BondsUnlike ionic bonds formed by the attraction between a cation’s positive charge and an anion’s negative charge, molecules formed by a covalent bond share electrons in a mutually stabilizing relationship. Like next-door neighbors whose kids hang out first at one home and then at the other, the atoms do not lose or gain electrons permanently. Instead, the electrons move

back and forth between the elements. Because of the close sharing of pairs of electrons (one electron from each of two atoms), covalent bonds are stronger than ionic bonds.

Nonpolar Covalent Bonds Figure 2.9 shows several common types of covalent bonds. Notice that the two covalently bonded atoms typically share just one or two electron pairs, though larger sharings are possible. The important concept to take from this is that in covalent bonds, electrons in the outermost valence shell are shared to fill the valence shells of both atoms, ultimately stabilizing both of the atoms involved. In a single covalent bond, a single electron is shared between two atoms, while in a double covalent bond, two pairs of electrons are shared between two atoms. There even are triple covalent bonds, where three atoms are shared.

You can see that the covalent bonds shown in (Figure 2.9 )are balanced. The sharing of the negative electrons is relatively equal, as is the electrical pull of the positive protons in the nucleus of the atoms involved. This is why covalently bonded molecules that are electrically balanced in this way are described as nonpolar; that is, no region of the molecule is either more positive or more negative than any other.

Polar Covalent BondsGroups of legislators with completely opposite views on a particular issue are often described as “polarized” by news writers. In chemistry, a polar molecule is a molecule that contains regions that have opposite electrical charges. Polar molecules occur when atoms share electrons unequally, in polar covalent bonds.

The most familiar example of a polar molecule is water (Figure 2.10 ). The molecule has three parts: one atom of oxygen, the nucleus of which contains eight protons, and two hydrogen atoms, whose nuclei each contain only one proton. Because every proton exerts an identical positive charge, a nucleus that contains eight protons exerts a charge eight times greater than a nucleus that contains one proton. This means that the negatively charged electrons present in the water molecule are more strongly attracted to the oxygen nucleus than to the hydrogen nuclei. Each hydrogen atom’s single negative electron therefore migrates toward the oxygen atom, making the oxygen end of their bond slightly more negative than the hydrogen end of their bond.

What is true for the bonds is true for the water molecule as a whole; that is, the oxygen region has a slightly negative charge and the regions of the hydrogen atoms have a slightly positive charge. These charges are often referred to as “partial charges” because the strength of the charge is less than one full electron, as would occur in an ionic bond. As shown in (Figure 2.10 ), regions of weak polarity are indicated with the Greek letter delta (∂) and a plus (+) or minus (–) sign.

Even though a single water molecule is unimaginably tiny, it has mass, and the opposing electrical charges on the molecule pull that mass in such a way that it creates a shape somewhat like a triangular tent (see (Figure 2.10b ). This dipole, with the positive charges at one end formed by the hydrogen atoms at the “bottom” of the tent and the negative charge at the opposite end (the oxygen atom at the “top” of the tent) makes the charged regions highly likely to interact with charged regions of other polar molecules. For human physiology, the resulting bond is one of the most important formed by water—the hydrogen bond.

Hydrogen BondsA hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another molecule. In other words, hydrogen bonds always include hydrogen that is already part of a polar molecule.

The most common example of hydrogen bonding in the natural world occurs between molecules of water. It happens before your eyes whenever two raindrops merge into a larger bead, or a creek spills into a river. Hydrogen bonding occurs because the weakly negative oxygen atom in one water molecule is attracted to the weakly positive hydrogen atoms of two other water molecules (Figure 2.11 ).

Water molecules also strongly attract other types of charged molecules as well as ions. This explains why “table salt,” for example, actually is a molecule called a “salt” in chemistry, which consists of equal numbers of positively-charged sodium (Na+) and negatively-charged chloride (Cl–), dissolves so readily in water, in this case forming dipole-ion bonds between the water and the electrically-charged ions (electrolytes). Water molecules also repel molecules with nonpolar covalent bonds, like fats, lipids, and oils. You can demonstrate this with a simple kitchen experiment: pour a teaspoon of vegetable oil, a compound formed by nonpolar covalent bonds, into a glass of water. Instead of instantly dissolving in the water, the oil forms a distinct bead because the polar water molecules repel the nonpolar oil.

2.3 | Chemical ReactionsBy the end of this section, you will be able to:

Characteristics of Chemical ReactionsAll chemical reactions begin with a reactant, the general term for the one or more substances that enter into the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. The one or more substances produced by a chemical reaction are called the product.

In chemical reactions, the components of the reactants—the elements involved and the number of atoms of each—are all present in the product(s). Similarly, there is nothing present in the products that are not present in the reactants. This is because chemical reactions are governed by the law of conservation of mass, which states that matter cannot be created or destroyed in a chemical reaction.

Just as you can express mathematical calculations in equations such as 2 + 7 = 9, you can use chemical equations to show how reactants become products. As in math, chemical equations proceed from left to right, but instead of an equal sign, they employ an arrow or arrows indicating the direction in which the chemical reaction proceeds. For example, the chemical reaction in which one atom of nitrogen and three atoms of hydrogen produce ammonia would be written as N + 3H → NH3 . Correspondingly, the breakdown of ammonia into its components would be written as NH3 → N + 3H.

Notice that, in the first example, a nitrogen (N) atom and three hydrogen (H) atoms bond to form a compound. This anabolic reaction requires energy, which is then stored within the compound’s bonds. Such reactions are referred to as synthesis reactions. A synthesis reaction is a chemical reaction that results in the synthesis (joining) of components that were formerly separate (Figure 2.12a ). Again, nitrogen and hydrogen are reactants in a synthesis reaction that yields ammonia as the product. The general equation for a synthesis reaction is A + B → AB.

In the second example, ammonia is catabolized into its smaller components, and the potential energy that had been stored in its bonds is released. Such reactions are referred to as decomposition reactions. A decomposition reaction is a chemical reaction that breaks down or “de-composes” something larger into its constituent parts (see (Figure 2.12b ). The general equation for a decomposition reaction is: AB → A + B .

An exchange reaction is a chemical reaction in which both synthesis and decomposition occur, chemical bonds are both formed and broken, and chemical energy is absorbed, stored, and released (see (Figure 2.12c ). The simplest form of an exchange reaction might be: A + BC → AB + C . Notice that, to produce these products, B and C had to break apart in a decomposition reaction, whereas A and B had to bond in a synthesis reaction. A more complex exchange reaction might be: AB + CD → AC + BD . Another example might be: AB + CD → AD + BC .

In theory, any chemical reaction can proceed in either direction under the right conditions. Reactants may synthesize into a product that is later decomposed. Reversibility is also a quality of exchange reactions. For instance, A + BC → AB + C could then reverse to AB + C → A + BC . This reversibility of a chemical reaction is indicated with a double arrow: A + BC ⇄ AB + C . Still, in the human body, many chemical reactions do proceed in a predictable direction, either one way or the other. You can think of this more predictable path as the path of least resistance because, typically, the alternate direction requires more energy.

Factors Influencing the Rate of Chemical ReactionsIf you pour vinegar into baking soda, the reaction is instantaneous; the concoction will bubble and fizz. But many chemical reactions take time. A variety of factors influence the rate of chemical reactions. This section, however, will consider only the most important in human functioning.

Properties of the ReactantsIf chemical reactions are to occur quickly, the atoms in the reactants have to have easy access to one another. Thus, the greater the surface area of the reactants, the more readily they will interact. When you pop a cube of cheese into your mouth, you chew it before you swallow it. Among other things, chewing increases the surface area of the food so that digestive chemicals can more easily get at it. As a general rule, gases tend to react faster than liquids or solids, again because it takes energy to separate particles of a substance, and gases by definition already have space between their particles. Similarly, the larger the molecule, the greater the number of total bonds, so reactions involving smaller molecules, with fewer total bonds, would be expected to proceed faster.

In addition, recall that some elements are more reactive than others. Reactions that involve highly reactive elements like hydrogen proceed more quickly than reactions that involve less reactive elements. Reactions involving stable elements like helium are not likely to happen at all.

TemperatureNearly all chemical reactions occur at a faster rate at higher temperatures. Recall that kinetic energy is the energy of matter in motion. The kinetic energy of subatomic particles increases in response to increases in thermal energy. The higher the temperature, the faster the particles move, and the more likely they are to come in contact and react.

Concentration and PressureIf just a few people are dancing at a club, they are unlikely to step on each other’s toes. But as more and more people get up to dance—especially if the music is fast—collisions are likely to occur. It is the same with chemical reactions: the more particles present within a given space, the more likely those particles are to bump into one another. This means that chemists can speed up chemical reactions not only by increasing the concentration of particles—the number of particles in the space—but also by decreasing the volume of the space, which would correspondingly increase the pressure. If there were 100 dancers in that club, and the manager abruptly moved the party to a room half the size, the concentration of the dancers would double in the new space, and the likelihood of collisions would increase accordingly.

Enzymes and Other CatalystsFor two chemicals in nature to react with each other they first have to come into contact, and this occurs through random collisions. Because heat helps increase the kinetic energy of atoms, ions, and molecules, it promotes their collision. But in the body, extremely high heat—such as a very high fever—can damage body cells and be life-threatening. On the other hand, normal body temperature is not high enough to promote the chemical reactions that sustain life. That is where catalysts come in.

In chemistry, a catalyst is a substance that increases the rate of a chemical reaction without itself undergoing any change. You can think of a catalyst as a chemical change agent. They help increase the rate and force at which atoms, ions, and molecules collide, thereby increasing the probability that their valence shell electrons will interact.

The most important catalysts in the human body are enzymes. An enzyme is a catalyst composed of protein or ribonucleic acid (RNA), both of which will be discussed later in this chapter. Like all catalysts, enzymes work by lowering the level of energy that needs to be invested in a chemical reaction. A chemical reaction’s activation energy is the “threshold” level of energy needed to break the bonds in the reactants. Once those bonds are broken, new arrangements can form. Without an enzyme to act as a catalyst, a much larger investment of energy is needed to ignite a chemical reaction (Figure 2.13 ).

Enzymes are critical to the body’s healthy functioning. They assist, for example, with the breakdown of food and its conversion to energy. In fact, most of the chemical reactions in the body are facilitated by enzymes.

2.4 | Inorganic Compounds Essential to Human FunctioningBy the end of this section, you will be able to:

These reactions are reversible, and play an important role in the chemistry of organic compounds (which will be discussed shortly).

SaltsRecall that salts are formed when ions form ionic bonds. In these reactions, one atom gives up one or more electrons, and thus becomes positively charged, whereas the other accepts one or more electrons and becomes negatively charged. You can now define a salt as a substance that, when dissolved in water, dissociates into ions other than H+ or OH–. This fact is important in distinguishing salts from acids and bases, discussed next.

A typical salt, NaCl, dissociates completely in water (Figure 2.15 ). The positive and negative regions on the water molecule (the hydrogen and oxygen ends respectively) attract the negative chloride and positive sodium ions, pulling them away from each other. Again, whereas nonpolar and polar covalently bonded compounds break apart into molecules in solution, salts dissociate into ions. These ions are electrolytes; they are capable of conducting an electrical current in solution. This property is critical to the function of ions in transmitting nerve impulses and prompting muscle contraction.

Many other salts are important in the body. For example, bile salts produced by the liver help break apart dietary fats, and calcium phosphate salts form the mineral portion of teeth and bones.

Acids and BasesAcids and bases, like salts, dissociate in water into electrolytes. Acids and bases can very much change the properties of the solutions in which they are dissolved.

Acids

An acid is a substance that releases hydrogen ions (H+) in solution (Figure 2.16a ). Because an atom of hydrogen has just one proton and one electron, a positively charged hydrogen ion is simply a proton. This solitary proton is highly likely to participate in chemical reactions. Strong acids are compounds that release all of their H+ in solution; that is, they ionize completely. Hydrochloric acid (HCl), which is released from cells in the lining of the stomach, is a strong acid because it releases all of its H+ in the stomach’s watery environment. This strong acid aids in digestion and kills ingested microbes. Weak acids do not ionize completely; that is, some of their hydrogen ions remain bonded within a compound in solution. An example of a weak acid is vinegar, or acetic acid; it is called acetate after it gives up a proton.

Bases

A base is a substance that releases hydroxyl ions (OH–) in solution, or one that accepts H+ already present in solution (see (Figure 2.16b ). The hydroxyl ions (also known as hydroxide ions) or other basic substances combine with H+ present to form a water molecule, thereby removing H+ and reducing the solution’s acidity. Strong bases release most or all of their hydroxyl ions; weak bases release only some hydroxyl ions or absorb only a few H+. Food mixed with hydrochloric acid from the stomach would burn the small intestine, the next portion of the digestive tract after the stomach, if it were not for the release of bicarbonate (HCO3–), a weak base that attracts H+. Bicarbonate accepts some of the H+ protons, thereby reducing the acidity of the solution.

The Concept of pHThe relative acidity or alkalinity of a solution can be indicated by its pH. A solution’s pH is the negative, base-10 logarithm of the hydrogen ion (H+) concentration of the solution. As an example, a pH 4 solution has an H+ concentration that is ten times greater than that of a pH 5 solution. That is, a solution with a pH of 4 is ten times more acidic than a solution with a pH of 5. The concept of pH will begin to make more sense when you study the pH scale, like that shown in (Figure 2.17 ). The scale consists of a series of increments ranging from 0 to 14. A solution with a pH of 7 is considered neutral—neither acidic nor basic. Pure water has a pH of 7. The lower the number below 7, the more acidic the solution, or the greater the concentration of H+. The concentration of hydrogen ions at each pH value is 10 times different than the next pH. For instance, a pH value of 4 corresponds to a proton concentration of 10–4 M, or 0.0001M, while a pH value of 5 corresponds to a proton concentration of 10–5 M, or 0.00001M. The higher the number above 7, the more basic (alkaline) the solution, or the lower the concentration of H+. Human urine, for example, is ten times more acidic than pure water, and HCl is 10,000,000 times more acidic than water.

BuffersThe pH of human blood normally ranges from 7.35 to 7.45, although it is typically identified as pH 7.4. At this slightly basic pH, blood can reduce the acidity resulting from the carbon dioxide (CO2) constantly being released into the bloodstream by the trillions of cells in the body. Homeostatic mechanisms (along with exhaling CO2 while breathing) normally keep the pH of blood within this narrow range. This is critical, because fluctuations—either too acidic or too alkaline—can lead to life-threatening disorders.

All cells of the body depend on homeostatic regulation of acid–base balance at a pH of approximately 7.4. The body therefore has several mechanisms for this regulation, involving breathing, the excretion of chemicals in urine, and the internal release of chemicals collectively called buffers into body fluids. A buffer is a solution of a weak acid and its conjugate base. A buffer can neutralize small amounts of acids or bases in body fluids. For example, if there is even a slight

decrease below 7.35 in the pH of a bodily fluid, the buffer in the fluid—in this case, acting as a weak base—will bind the excess hydrogen ions. In contrast, if pH rises above 7.45, the buffer will act as a weak acid and contribute hydrogen ions.

Acids and BasesExcessive acidity of the blood and other body fluids is known as acidosis. Common causes of acidosis are situations and disorders that reduce the effectiveness of breathing, especially the person’s ability to exhale fully, which causes a buildup of CO2 (and H+) in the bloodstream. Acidosis can also be caused by metabolic problems that reduce the level or function of buffers that act as bases, or that promote the production of acids. For instance, with severe diarrhea, too much bicarbonate can be lost from the body, allowing acids to build up in body fluids. In people with poorly managed diabetes (ineffective regulation of blood sugar), acids called ketones are produced as a form of body fuel. These can build up in the blood, causing a serious condition called diabetic ketoacidosis. Kidney failure, liver failure, heart failure, cancer, and other disorders also can prompt metabolic acidosis.

In contrast, alkalosis is a condition in which the blood and other body fluids are too alkaline (basic). As with acidosis, respiratory disorders are a major cause; however, in respiratory alkalosis, carbon dioxide levels fall too low. Lung disease, aspirin overdose, shock, and ordinary anxiety can cause respiratory alkalosis, which reduces the normal concentration of H+.

Metabolic alkalosis often results from prolonged, severe vomiting, which causes a loss of hydrogen and chloride ions (as components of HCl). Medications also can prompt alkalosis. These include diuretics that cause the body to lose potassium ions, as well as antacids when taken in excessive amounts, for instance by someone with persistent heartburn or an ulcer.

2.5 | Organic Compounds Essential to Human FunctioningBy the end of this section, you will be able to:

Nucleotides can be assembled into nucleic acids (DNA or RNA) or the energy compound adenosine triphosphate.

Nucleic AcidsThe nucleic acids differ in their type of pentose sugar. Deoxyribonucleic acid (DNA) is nucleotide that stores genetic information. DNA contains deoxyribose (so-called because it has one less atom of oxygen than ribose) plus one phosphate group and one nitrogen-containing base. The “choices” of base for DNA are adenine, cytosine, guanine, and thymine. Ribonucleic acid (RNA) is a ribose-containing nucleotide that helps manifest the genetic code as protein. RNA contains ribose, one phosphate group, and one nitrogen-containing base, but the “choices” of base for RNA are adenine, cytosine, guanine, and uracil.

The nitrogen-containing bases adenine and guanine are classified as purines. A purine is a nitrogen-containing molecule with a double ring structure, which accommodates several nitrogen atoms. The bases cytosine, thymine (found in DNA only) and uracil (found in RNA only) are pyramidines. A pyramidine is a nitrogen-containing base with a single ring structure

Bonds formed by dehydration synthesis between the pentose sugar of one nucleic acid monomer and the phosphate group of another form a “backbone,” from which the components’ nitrogen-containing bases protrude. In DNA, two such backbones attach at their protruding bases via hydrogen bonds. These twist to form a shape known as a double helix (Figure 2.29 ). The sequence of nitrogen-containing bases within a strand of DNA form the genes that act as a molecular code instructing cells in the assembly of amino acids into proteins. Humans have almost 22,000 genes in their DNA, locked up in the 46 chromosomes inside the nucleus of each cell (except red blood cells which lose their nuclei during development). These genes carry the genetic code to build one’s body, and are unique for each individual except identical twins.

In contrast, RNA consists of a single strand of sugar-phosphate backbone studded with bases. Messenger RNA (mRNA) is created during protein synthesis to carry the genetic instructions from the DNA to the cell’s protein manufacturing plants in the cytoplasm, the ribosomes.

Adenosine TriphosphateThe nucleotide adenosine triphosphate (ATP), is composed of a ribose sugar, an adenine base, and three phosphate groups (Figure 2.30 ). ATP is classified as a high energy compound because the two covalent bonds linking its three phosphates store a significant amount of potential energy. In the body, the energy released from these high energy bonds helps fuel the body’s activities, from muscle contraction to the transport of substances in and out of cells to anabolic chemical reactions.

When a phosphate group is cleaved from ATP, the products are adenosine diphosphate (ADP) and inorganic phosphate (Pi). This hydrolysis reaction can be written:

ATP + H2 O →

ADP + Pi

+ energy

Removal of a second phosphate leaves adenosine monophosphate (AMP) and two phosphate groups. Again, these reactions also liberate the energy that had been stored in the phosphate-phosphate bonds. They are reversible, too, as when ADP undergoes phosphorylation. Phosphorylation is the addition of a phosphate group to an organic compound, in this case, resulting in ATP. In such cases, the same level of energy that had been released during hydrolysis must be reinvested to power dehydration synthesis.

Cells can also transfer a phosphate group from ATP to another organic compound. For example, when glucose first enters a cell, a phosphate group is transferred from ATP, forming glucose phosphate (C6H12O6—P) and ADP. Once glucose is phosphorylated in this way, it can be stored as glycogen or metabolized for immediate energy.

KEY TERMSKEYTERMacidcompound that releases hydrogen ions (H+) in solutionactivation energyamount of energy greater than the energy contained in the reactants, which must be overcome for a reaction to proceedadenosine triphosphate (ATP)nucleotide containing ribose and an adenine base that is essential in energy transferamino acidbuilding block of proteins; characterized by an amino and carboxyl functional groups and a variable side- chainanionatom with a negative chargeatomsmallest unit of an element that retains the unique properties of that elementatomic numbernumber of protons in the nucleus of an atombasecompound that accepts hydrogen ions (H+) in solutionbondelectrical force linking atomsbuffersolution containing a weak acid or a weak base that opposes wide fluctuations in the pH of body fluidscarbohydrateclass of organic compounds built from sugars, molecules containing carbon, hydrogen, and oxygen in a 1-2-1 ratiocatalystsubstance that increases the rate of a chemical reaction without itself being changed in the processcationatom with a positive chargechemical energyform of energy that is absorbed as chemical bonds form, stored as they are maintained, and released as they are brokencolloidliquid mixture in which the solute particles consist of clumps of molecules large enough to scatter lightcompoundsubstance composed of two or more different elements joined by chemical bondsconcentrationnumber of particles within a given spacecovalent bondchemical bond in which two atoms share electrons, thereby completing their valence shellsdecomposition reactiontype of catabolic reaction in which one or more bonds within a larger molecule are broken, resulting in the release of smaller molecules or atomsdenaturationchange in the structure of a molecule through physical or chemical meansdeoxyribonucleic acid (DNA)deoxyribose-containing nucleotide that stores genetic informationdisaccharidepair of carbohydrate monomers bonded by dehydration synthesis via a glycosidic bonddisulfide bondcovalent bond formed within a polypeptide between sulfide groups of sulfur-containing amino acids, for example, cysteineelectronsubatomic particle having a negative charge and nearly no mass; found orbiting the atom’s nucleuselectron shellarea of space a given distance from an atom’s nucleus in which electrons are groupedelementsubstance that cannot be created or broken down by ordinary chemical meansenzymeprotein or RNA that catalyzes chemical reactionsexchange reactiontype of chemical reaction in which bonds are both formed and broken, resulting in the transfer of componentsfunctional groupgroup of atoms linked by strong covalent bonds that tends to behave as a distinct unit in chemical reactions with other atomshydrogen bonddipole-dipole bond in which a hydrogen atom covalently bonded to an electronegative atom is weakly attracted to a second electronegative atominorganic compoundsubstance that does not contain both carbon and hydrogenionatom with an overall positive or negative chargeionic bondattraction between an anion and a cationisotopeone of the variations of an element in which the number of neutrons differ from each otherkinetic energyenergy that matter possesses because of its motionlipidclass of nonpolar organic compounds built from hydrocarbons and distinguished by the fact that they are not soluble in watermacromoleculelarge molecule formed by covalent bondingmass numbersum of the number of protons and neutrons in the nucleus of an atommatterphysical substance; that which occupies space and has massmoleculetwo or more atoms covalently bonded togethermonosaccharidemonomer of carbohydrate; also known as a simple sugarneutronheavy subatomic particle having no electrical charge and found in the atom’s nucleusnucleotideclass of organic compounds composed of one or more phosphate groups, a pentose sugar, and a baseorganic compoundsubstance that contains both carbon and hydrogenpeptide bondcovalent bond formed by dehydration synthesis between two amino acidsperiodic table of the elementsarrangement of the elements in a table according to their atomic number; elements having similar properties because of their electron arrangements compose columns in the table, while elements having the same number of valence shells compose rows in the tablepHnegative logarithm of the hydrogen ion (H+) concentration of a solutionphospholipida lipid compound in which a phosphate group is combined with a diglyceridephosphorylationaddition of one or more phosphate groups to an organic compoundpolar moleculemolecule with regions that have opposite charges resulting from uneven numbers of electrons in the nuclei of the atoms participating in the covalent bondpolysaccharidecompound consisting of more than two carbohydrate monomers bonded by dehydration synthesis via glycosidic bondspotential energystored energy matter possesses because of the positioning or structure of its componentsproductone or more substances produced by a chemical reactionprostaglandinlipid compound derived from fatty acid chains and important in regulating several body processesproteinclass of organic compounds that are composed of many amino acids linked together by peptide bondsprotonheavy subatomic particle having a positive charge and found in the atom’s nucleuspurinenitrogen-containing base with a double ring structure; adenine and guaninepyrimidinenitrogen-containing base with a single ring structure; cytosine, thiamine, and uracilradioactive isotopeunstable, heavy isotope that gives off subatomic particles, or electromagnetic energy, as it decays; also called radioisotopesreactantone or more substances that enter into the reactionribonucleic acid (RNA)ribose-containing nucleotide that helps manifest the genetic code as proteinsolutionhomogeneous liquid mixture in which a solute is dissolved into molecules within a solventsteroid(also, sterol) lipid compound composed of four hydrocarbon rings bonded to a variety of other atoms and moleculessubstratereactant in an enzymatic reactionsuspensionliquid mixture in which particles distributed in the liquid settle out over timesynthesis reactiontype of anabolic reaction in which two or more atoms or molecules bond, resulting in the formation of a larger moleculetriglyceridelipid compound composed of a glycerol molecule bonded with three fatty acid chainsvalence shelloutermost electron shell of an atomCHAPTER REVIEW

INTERACTIVE LINK QUESTIONSClick and Explore1.Visit this website (http://openstaxcollege.org/l/ptable)to view the periodic table. In the periodic table of the

elements, elements in a single column have the same number of electrons that can participate in a chemical

reaction. These electrons are known as “valence electrons.” For example, the elements in the first column all have a single valence electron—an electron that can be “donated” in a chemical reaction with another atom. What is the meaning of a mass number shown in parentheses?

Click and Explore2.Visit this website (http://openstaxcollege.org/l/ electenergy)to learn about electrical energy and the

attraction/repulsion of charges. What happens to the charged electroscope when a conductor is moved between its plastic sheets, and why?

Click and Explore3.Watch this video (http://openstaxcollege.org/l/ disaccharide)to observe the formation of a disaccharide. What happens when water encounters a glycosidic bond?

Review QuestionsQuestion 2.4

Together, just four elements make up more than 95 percent of the body’s mass. These include ________.calcium, magnesium, iron, and carbon oxygen, calcium, iron, and nitrogen sodium, chlorine, carbon, and hydrogen oxygen, carbon, hydrogen, and nitrogenQuestion 2.5

The smallest unit of an element that still retains the distinctive behavior of that element is an ________.electron atom elemental particle isotopeQuestion 2.6

The characteristic that gives an element its distinctive properties is its number of ________.protons neutrons electrons atomsQuestion 2.7

On the periodic table of the elements, mercury (Hg) has an atomic number of 80 and a mass number of 200.59. It has seven stable isotopes. The most abundant of these probably have ________.about 80 neutrons each fewer than 80 neutrons each more than 80 neutrons each more electrons than neutronsQuestion 2.8

Nitrogen has an atomic number of seven. How many electron shells does it likely have?one two three fourQuestion 2.9

Which of the following is a molecule, but not a compound?H2O 2H H2 H+Question 2.10

A molecule of ammonia contains one atom of nitrogen and three atoms of hydrogen. These are linked with ________.ionic bonds nonpolar covalent bonds

polar covalent bonds hydrogen bondsQuestion 2.11

When an atom donates an electron to another atom, it becomesan ion an anion nonpolar all of the aboveQuestion 2.12

A substance formed of crystals of equal numbers of cations and anions held together by ionic bonds is called a(n) ________.noble gas salt electrolyte dipoleQuestion 2.13

Which of the following statements about chemical bonds is true?Covalent bonds are stronger than ionic bonds. Hydrogen bonds occur between two atoms of

hydrogen. Bonding readily occurs between nonpolar and

polar molecules. A molecule of water is unlikely to bond with anQuestion 2.14

The energy stored in a foot of snow on a steep roof is ________.potential energy kinetic energy radiant energy activation energyQuestion 2.15

The bonding of calcium, phosphorus, and other elements produces mineral crystals that are found in bone. This is an example of a(n) ________ reaction.catabolic synthesis decomposition exchangeQuestion 2.16

AB → A + B is a general notation for a(n) ________ reaction.anabolic endergonic decomposition exchangeQuestion 2.17

________ reactions release energy. a. Catabolichydrogen and hydrogen hydrogen and helium helium and helium neon and heliumQuestion 2.19

Chewing a bite of bread mixes it with saliva and facilitates its chemical breakdown. This is most likely due to the fact that ________.the inside of the mouth maintains a very high temperature

chewing stores potential energy chewing facilitates synthesis reactions saliva contains enzymesQuestion 2.20

CH4 is methane. This compound is ________.inorganic organic reactive a crystalQuestion 2.21

Which of the following is most likely to be found evenly distributed in water in a homogeneous solution?sodium ions and chloride ions NaCl molecules salt crystals red blood cellsQuestion 2.22

Jenny mixes up a batch of pancake batter, then stirs in some chocolate chips. As she is waiting for the first few pancakes to cook, she notices the chocolate chips sinking to the bottom of the clear glass mixing bowl. The chocolate- chip batter is an example of a ________.solvent solute solution suspensionQuestion 2.23

A substance dissociates into K+ and Cl– in solution. The substance is a(n) ________.acid base salt bufferQuestion 2.24

Ty is three years old and as a result of a “stomach bug” has been vomiting for about 24 hours. His blood pH is 7.48. What does this mean?Ty’s blood is slightly acidic. Ty’s blood is slightly alkaline. Ty’s blood is highly acidic.

Ty’s blood is within the normal rangeQuestion 2.25

C6H12O6 is the chemical formula for a ________.polymer of carbohydrate pentose monosaccharide hexose monosaccharide all of the aboveQuestion 2.26

What organic compound do brain cells primarily rely on for fuel?glucose glycogen galactose glycerolQuestion 2.27

Which of the following is a functional group that is part of a building block of proteins?phosphate adenine amino riboseQuestion 2.28

A pentose sugar is a part of the monomer used to build which type of macromolecule?polysaccharides nucleic acids phosphorylated glucose glycogenQuestion 2.29

A phospholipid ________. a. has both polar and nonpolar regions b. is made up of a triglyceride bonded to abeta chain pleated sheet alpha helix double helixQuestion 2.31

Uracil ________. a. contains nitrogen b. is a pyrimidine c. is found in RNA d. all of the aboveselectivity specificity subjectivity specialtyCRITICAL THINKING QUESTIONS

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