2 The Nature of Matter fe depends on chemistry. When you eat food or inhale loxygen, your body uses these materials in chemical reactions that keep you alive. Just as buildings are made from bricks, stecl, glass, and wood, living things are made from chemical compounds. If the first task of an architect is to under- stand building materials, then the first job of a biologist is to understand the chemistry of life. Atoms ‘The study of chemistry begins with the basic unit of maiter, the atom, The Greek word atomos, which means “unable to be ent,” was first used to refer to matter by the Greek philosopher ‘Democritus nearly 2500 years ago, Democritus asked a simple question: If you take an object like a stick of chalk and break it, in half, are both halves still chalk? The answer, of course, is yes. ‘But what happens if you go on? Suppose you break it in half again and again and again. Can you continue to divide without limit, or does there come a point at which you cannot divide the fragment of chalk without changing it into something else? Democritus thought that there had to be a limit. He called the smallest fragment the atom, a name scientists still uso today. Atoms are incredibly small. Placed side by side, 100 million atoms would make a row only about 1 centimeter long—about the width of your little finger! Despite its extremely amall size, an atom contains subatomic particles that are even smaller. Figure 2-1 shows the subatomic particles in a helium atom, ® The cubatomic particles that make up atoms are protons, neutrons, and electrons. Protons and neutrons have about the same mass. However, protons are positively charged particles (+) and neutrons carry no charge. Their name is a reminder that they are neutral particles. Strong forces bind protons and neutrons together to form the nucleus, which is at the center of the atom. The electron is a negatively charged particle (~) with 1/1840 the mass of a proton. Electrons are in constant motion in the space surrounding the nucleus. They are attracted to the positively charged nucleus but remain outside the nucleus because of the energy of their motion. Because atoms have equal numbers of electrons and protons, and because these subatomic particles have equal but opposite charges, atoms are neutral. D> Figure 2-1 G Helium atoms contain protons, neu- trons, and electrons. The positively charged protons and uncharged neutrons are bound together in the dense nucleus, ‘while the negatively charged electrons move in the space around the nucieus. Guide for Reading Tienoreemcmnerenianmorennemate B Key Concepts * What three subatomic parti cles make up atoms? + How are all of the isotopes of an element similar? + What are the two main types of chemical bonds? Vocabulary atom nucleus electron element isotope compound ionic bond ion covalent bond molecule van der Waals forces Reading Strategy: Using Prior Knowledge Before you read, write down what you already know about atoms, elements, and com- pounds. As you read, note the ‘main new concepts you learn, Helium Atomic number = 2 Mass number = 4| V Figure 2-2 Because they have the same number of electrons, these Isotopes of carbon have the same chemical properties. The difference among the isotopes is the number of neutrons in their nuclei. Elements and isotopes A chomical clement is a pure substance that consists entirely ‘of one type of atom. More than 100 elements are known, but only about two dozen are commonly found in living organisms. Blemonts are represented by a one- or two-letter symbol. ©, for example, stands for carbon, H for hydrogen, and Na for sodium. ‘The number of protons in an atom of an clement is the element's atomiie number. Carbon’s atomic number is 6, meaning that each atom of carbon has six protons and, consequently, six electrons. ‘See Appendix G, The Periodie Table, which hows the elements, isellopes Atoms of an clement can have different numbers of neutrons. For example, some atoms of carbon have six neutrons, some have seven, and a few have cight. Atoms of the same ele- ment that differ in the number of neutrons they contain are known as isotopes. The sum of the protons and neutrons in the puclous of an atom is called its mass number. Isotopes are identi- fied by their mass numbers, Figure 2-2 shows the subatomic composition of carbon-12, carban-13, and carbon-14 atoms. The weighted average of the masses of an element's isotopes is called its atomic mass. “Weighted” means that the abundance of each isotope in nature is considered when the average is calculated. €® Because they have the same number of electrons, all isotopes of an element have the same chemical properties. Radioactive lsotapes Some isotopes are radioactive, meaning that their nuclei are unstable and break down at a constant rate over time. The radiation these isotopes give off can be dangerous, but radioactive isotopes have a number of impor- tant scientific and practical uses. Geologists can determine the ages of rocks and fossils by analyzing the isotopes found in them. Radiation from certain isotopes can be used to treat cancer and to kill bacteria that cause {fod to spoil. Radioactive isotopes can also be used a3 labels or “tracers” to follow tho movements of substances within organisms.Forensic Scientist Job Description: work as a forensic scientist for local, state, or federal investigative agencies in order to conduct scientific forensic exarnina- tons in criminal investigations Education: a bachelor’s degree in science— biology, physics, chemistry, metallurgy; some states require several yeats of forensic labora- tory experience Skills; analytical, togical, computer iterate, detail oriented, able to take meticulous notes and to prepare evidence for presentation in ‘court as well as to testify as an expert witness ‘ Discovery Seaeat Vitow To find out Highlights: have the opportunity to use ‘more about forensic science, view | ogic and science to solve unique or unusual track 1 “History's Mystery: An ‘problems in criminal investigations and to work Introduction to Forensic Science" collaboratively with other scientists | on the BioDetectives DVD. Chemical Compounds SpE Jn nature, most clements are found combined with other ele- ake PSchol com ments in compounds. A chemical compound is 2 substance ‘Web Cade: chb-1021 formed by the chemical combination of two or more elements in definite proportions. Scientists chow the composition of eom- pounds by a kind of shorthand known as 2 chemical formula. Water, which contains two atoms of hydrogen for each atom of oxygen, has the chemical formula H,O. The formula for table salt, NaCl, indicates that the elements from which table salt, forms—sodium and chlorine—eombine in a 1 : 1 ratio, ‘The physical and chemical properties of a compound are usually very different from those of the elements from which it is formed. For example, hydrogen and oxygen, which are gases ‘at room temperature, can combine explosively and form liquid water. Sodium ie a silver-colored metal that is soft enoagh to cut with a knife. It reacts explosively with cold water. Chlorine is very reactive, too. It is a poisonous, greonish gas that was used to kill many soldiers in World War I. Sodium and chlorine combine to form sodium chloride (NaC), or table salt. Sodium chloride is a white solid that dissolves easily in water. As you ‘know, sodium chloride is not poisonous. In fact, it is essential for the survival of most living things. yf ieceoonits What information is contained in a chemical formula? |i i f A Figure 2-3 The chemical bond in which electrons are transferred from one atom to another Is called an ionic bond. ‘The compound sodium chioride forms when sodium loses its valence ‘electron to chlorine. Water Molecule A Figure 2-4 (The chemical bond in which electrons are shared between atoms |s called a covalent bond. in a water molecule, ‘each hydrogen atom shares two electrons with the oxygen atom. Chemical Bonds ‘The atoms in compounds are held together by chemical bonds. ‘Much of chemistry is devoted to understanding how and when chemical bonds form. Bond formation involves the electrons that surround each atomic nuclous, The electrons that are available to form bonds are called valence electrons. 33 The main types of chemical bonds are ionic bonds and covalent bonds. fomic Bomels An ionic bond is formed when ane or more electrons are transferred from one atom to another. Recall thai. atoms are electrically neutral becaase they have equal numbers of protons and electrons. An atom that loses electrons has a positive charge, An atom that gains electrons has a negative charge. These positively and negatively charged atoms are ‘known as ions. Figure 2-3 shows how ionic bonds form between sodium and chlorine in table salt. A sodium atom easily loses its one valence electron and becomes a sodium ion (Na*).A chlorine atom easily gains an electron and becomes a chloride ion (CI). In a salt cexystal, there are trillions of sodium and chloride ions. These ‘oppositely charged ions have a strong attraction. The attraction between oppositely charged ions is an ionic bond. Covalent Bends Sometimes clectrons are shared by atoms instead of heing transferred. What does it mean to “share” electrons? It means that the moving clectrons aetually travel in the orbitals of both atoms. A covalent bond forms when clec- trons are shared between atoms. When the atoms share two electrons, the bond is called a single covalent bond. Sometimes the atoms share four electrons and form a double bond. In a few cases, atoms ean share six cloctrons and forma triple bond. ‘The structure that results when atoms are joined together by covalent bonds is called a molecule. The molecule is the smallest unit of most compounds. The diagram of a water molecule in Figure 2-8 shows that each hydrogen atom forms a single covalent bond with the oxygen atom.‘Van der Waals Forces Because of their structures, atoms of different elements do not all have the same ability to attract electrons. Some atoms have a stronger attraction for electrons than do other atoms. Therefore, when the atoms in a covalont bond share electrons, the sharing isnot | y sigure 2-5 Ven der Waas forces help always equal, Even when the sharing is equal, the rapid geckos to grip smooth, vertical surfaces. smovement of electrons can ereate regions on a molecale that Applying Concepts Which product(s) have a tiny positive or negative charge. might be developed based on van der Waals ‘When molecules are close together, a slight attraction forces? Explain. can develop between the oppositely charged regions of nearby molecules. Chemists call such intermolecular forces of attraction van der Waals forces, after the scientist who discovered them. Although van der Waals forces are not as strong as ionie bonds or cavalent bonds, they can hold molecules together, especially when the molecules are large. People who keep geckos as pets have already seen van der Waals forces in action. These remarkable little lizards can climb up vertical surfaces, even smooth glass walls, and then hang on by a single toe despite ‘the pull of gravity. How do they do it? No, they do not hhave some sort of glue on their fect and they don’t have suction cups. ‘A gecko foot like the one shown in Figure 2-5 is covered by as many os half a million tiny hairlike projections, Each projection is ftarther divided into hun- dreds of tiny, flat-surfaced fibers. This design allows the gecko’ foot to come in contact with an extremely large area “ of the wall at the molecular level. Van der Waals forces form between molecules on the surface of the gecko’s foot and molecules on the surface of the wall. The combined strength of all the van der Waals forces allows the gecko to balance ‘the pull of gravity. When the gecko needs to move its foot, it peels the foot off at an angle and reattaches it at another Jocation on the wall. ee2-2 Properties of Water i i : Guide for Reading fier soveral days in space, one of the first astronauts to we travel to the moon tooked back longingly at Earth and |B key Concepts marveled at its distant beauty. If there are other beings who i = Why are water melecules ‘have soen Harth, he said, they must surely call it “the blue j polar? planet." The astronaut was referring to the blue appearance of i + What are acidic solutions? the water in the oceans, which cover three fourths of Earth’s . ‘What are basic solutions? surface. Water is also the single most abundant compound in i ‘most living things. t ocabutery Water is one of the fow compounds that is a liquid at the adhesion temperatures found over much of Earth’s surface. Unlike most mixture substances, water expands as it freezes. Thus, ice is less dense t on than liquid water, which explains why ico floats on the surface of lakes and rivers. If the ice sank to the bottom, the situation would be disastrous for fish and plant life in regions with cold winters, to say nothing of the sport of ico skating! The Water Molecule Like all molecules, a water molecule (H,0) is neutral. The positive charges on its 10 protons balance out the negative ' ' i a f ‘and Plgure 2-9. As you read, ‘charges on its 10 electrons. However, there is more to the story. note how these two figures are celated. Polarity With 8 protons in its nucleus, an oxygen atom has a much stronger attraction for electrons than does the hydrogen atom with a single proton in its nucleus. Thus, at any moment, there is a greater probability of finding the shared electrons near the oxygen atom than near the hydrogen atom. Because the water molecule has a bent shape, as shown in Figure 2-6, tho oxygen atom is on one end of tho molecule and the hydrogen atoms are on the other. As a result, the oxygen end of the molecule has a \, slight negative change and the hydrogen end of | the molecule has a slight positive charge. Amelecule in whieh the charges are unevenly distributed is called a polar molecule boeanse the molecule is like a magnet with poles. DA water molecule is polar because there is an uneven distribution of electrons between the oxygen and hydrogen stoms. The negative pole is near the axygen stom and the positive pole is between, the hydrogen atoms. i 4 4 Figure 2-6 The unequal sharing of electrons causes the water molecuie to be polar. ‘The hydrogen end of the molecule i slightly positive, and the oxygen end is sightly negative.negative charges, polar molecules such as water can attract ‘each other, as shown in Figure 2-7. The charges on a polar molecule are written in parentheses, (-) or (+), to show that they ]rreoon tone are weaker than the charges on ions euch as Na* and CI.'The attraction between the hydrogen atom on one water molecule ©) @& and the oxygen atom on another water molecule is an example ¢ of a hydrogen bond. Hydrogen bonds are not as strong as cova- @ 4 lent ar ionic bonds, but water's ability to form multiple hydrogen S bonds is responsible for many of its special properties. @ GS Hydrogen Bomds Because of their partial positive and eP a Asingle water molecule may be involved in as many as four hydrogen bonds at the same time. 'The ability of water to form multiple hydrogen bonds is responsible for many of water's properties. Cohesion is an attraction between molecules of the ‘same substance. Because of hydrogen bonding, water is & Figure 2-7 The illustration extremely cohesive. Water's cohesion causes molecules on the ue surface of water to be drawn inward, which is why drops of inptmaa Cone nyo water form beads on a smooth surface. Cohesion also explains wwoter molecules attracted to ane why some insesta and spiders can wall on a pond’s surface, as another? shown in Figure 2-8, Adhesion is an attraction between molecules of different substances. Have you over been told to read the volume in a graduated cylinder at eye level? The surface of the water in the graduated cylinder dips slightly in the center because the adhesion between water molecules and glass molecules is stronger than the cohesion betweon water molecules. Adhesion between water and glass also causes water to rise in a narrow ‘tube against the force of gravity. This effect is called capillary Visit: youu So inks: action. Capillary action is one of the forces that draw water out ‘meee eae of the roots of a plant and up into its stems and leaves. Cohesion : holds the column of water together as it rises. foe Solutions and Suspensions Water is not always pure—it is often found as part of a mixture. A mixture is a material composed of two or more elements or compounds that are physically mixed together but not chemically combined. Salt and pepper stirred together constitute a mixture. So do sugar and sand. Earth’s atmosphere is a mixture of gases. ‘Living things are in part composed of mixtures involving water. ‘Two types of mixtures that can be made with water are solutions and suspensions. PON How are cohesion and adhesion similar? Different? D> Figure 2-8 Cohesion is responsible for enabling this tarantula to rest on the water's surface. The strong attraction between water molecules produces a force sometimes called “surface tension,” which can support very light objects, including this spider. Observing How does the torantula’s physical structure help it to stay afloat?D> Figure 2-9 When an ionic compound such as sodium chioride is placed in water, water ‘molecules surround and separate the positive and negative ions. Intemreting Graphics What happens to the sodiura ions and chloride ions in the solution? | | Materials pH paper, samples of | | food, paper towel, scalpel, dropper pipette Procedure (fj GS 1, Predicting Predict whether most foods are acidic or basic. 26 a if using a pH probe, EES see your teacher for | instructions. 3. Tear off a 2-inch piece of pH paper for each sample you will fest. Place these pieces on a | paper towel. | 4 Construct data table in which | you will record the name and | _ pH of each food sample. | 5. Use a scalpel to cut a piece off each solid. CAUTION: Be careful | not t0 cut yourself. Do not eat the | food. Touch the cut surface of | ‘each sample to a square of pH \ | paper. Use a dropper pipette to place a drop of any liquid sample on a square of pH paper. Record the pH of each sample in your data table, Analyze and Conclude 1, Analyzing Data Were most of the samples acidic or basic? 2 Evaluating Was your [pre n correct? i i | | | | | i | | ' | | | | i i i t Solutions Ifa crystal of table salt is placed in a glass of warm ‘water, sodium and chloride ions on the surface of the erystal are attracted to the polar water molecules. Ions break away from the crystal and are surrounded by water molecules, as illustrated in Figure 2-9. The ions gradually become dispersed in the water, forming a type of mixture called a solution. All the components of a solution are evenly distributed throughout the solution. In a saltwater solution, table salt is the solute—the substance that is dissolved. Water is the solvent—the eubstance in which the solute dissolves. Water's polarity gives it the ability to dissolve both ionie compounds and other polar molecules, such as sugar. Without exaggeration, water is the greatest solvent on Earth. Suspensions Some materials do not dissolve when placed in water but separate into pieces so small that they do not settle out. The movement of water molecules keeps the small particles suspended. Such mixtures of water and nandissolved material are known as suspensions. Some of the most important biologi- cal fluids are both solutions and suspensions. The blood that circulates through your body ia mostly water, which contains many dissolved compounds. However, blood also contains cells and other undissolved particles that remain in suspension as the blood moves through the body. Acids, Bases, and pH A water molecule can react to form ions. This reaction can be summarized by a chemical equation in which double arrows are used to show that the reaction can occur in either direction. mOsm Ht + Of wor = EN 5 Ile ‘How often does this happen? In pure water, shout 1 water molecule in 550 million reacts and forms ions. Because tho number of positive hydrogen ions produced is equal to the number of nogative hydroxide ions produced, wator is neutral.‘The pH scale Chomiste dovised 2 measurement eystem, called the pH seale to indicate the concentration of H* ions in solution. As Figure 2-10 shows, the pH scale ranges from 0 to 14. At @ pH of 7, the concentration of H” ions and OH ions is equal. Pure water has a pH of 7. Salutions with a pH below 7 are called acidic because they have more H* ions than OH” ions. The lower the pH, the greater the acidity. Solutions with a pH above 7 are called basie because they ‘have more OH™ ions than H” ions. The higher the pH, the more basic the solution, Each step on the pH seale repre- sents a factor of 10. For example, a liter of a solution with a pH of has 10 times as many H ions as a liter of a solution ‘with a pH of 5. Acials Where do all those extra H* ions in a Jow-pH solution come from? They come from acids. An acid is any compound that forms H* ions in solution. C3) Acidie solutions contain higher coneentrations of H ions than pure water and have pH values helow 7. Strong acids tend to have pH values that range fiom 1 to 3. The hydrochlorie acid produced by the stomach to help digest. food is a strong acid. Bases A base is a compound that produces hydroxide ions (OH ions) in solution. (2> Basie, or alicaline, soln- tions contain lower concentrations of H’ ions than pure water and have pH values above 7. Strong bases, such as lye, tend to have pH values ranging from 11 to 14. Buffers The pH of the fluids within most cells in the human ‘body must generally be kept between 6.5 and 7.5, If the pH is lower or higher, it will affect the chemical reactions that take place within the cells, Thus, controlling pH is important for maintaining homeostasis. One of the ways that the body controis pH is through dissolved compounds called buffers. Buffers are weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH. 4 3 = . i i i Increasingly Acidic A Figure 2-10 The cancen- ‘ration of H ions determines whether solutions are acidic or basic. The most acidic material on this pH scale is stomach acid. The most basic material on this scale is oven cleaner.-3 Carbon Compounds Guide for Reading ee | Bkey Concepe © What are the functions of each ‘group of organic compounds? nucleotide ribonucleic acid (RNA) deoxyribonucleic acid (DNA) protein Reading Strategy: Stemimarizing As you read, find the key ideas. Write down a few key words from each main idea. Then, use the key words in your summary. Reread your summary, keeping only the mast important ideas. 'Y Figure 2-11 Carbon can form single, double, or triple bonds with ‘other carbon atoms. Each line between atoms in a molecular drawing represents one covalent bond. Observing How many covalent bonds are there between the corbon atorns in acetylene? H HOH HOCH A Methane Acetylene i x i f ‘ntil the early 1800s, many chemists thought that eom- pounds created by organisms—rganie compounds—were distinetly difforent from compounds in nonliving things. In 1828, a German chemist was able to synthesize the organic compound urea from a mineral ealled ammonium cyanate. Chemists soon. realized that the principles governing the chemistry of nonliving things could be applied to living things. Scientists still use the term organic chemistry, but now it describes something a little different. Today, organic chemistry is the study of all compounds that contain bonds between carbon atoms. The Chemistry of Carbon Is carbon so interesting that a whole branch of chemistry should be set aside just to study earbon compounds? It is indeed, for two reasons. First, carbon atoms have four valence electrons. Bach electron can join with an electron from another atom to form a strong covalent bond. Carbon can bond with many elements, including hydrogen, oxygen, phosphorus, sulfur, and nitrogen. In fact, living organisms are made up of molecules that eonsist of carbon and these other elements. ‘Even more important, a carbon atom can bond to other carbon atoms, which gives carbon the ability to form chains that are almost unlimited in length. These carbon-carbon honds can be single, double, or triple covalent bonds. Chains of eazbon atoms can even close upon themselves to form rings, as shown in Figure 2-11. Carbon has the ability to form millions of differ- ‘ont large and complex structures. No other element even comes close to matching carhon’s versatility. fa ge ee nce a a o=c—t=d i of Seu | # Butadiene BenzeneMacromolecules Many of the molecules in living cells are eo large that they are known as macromolecules, which moans “giant molecules.” ‘Macromolecules are made from thousands or even hundreds of thousands of smaller molecules. ‘Macromolecules are formed by a process known as polymer- ization (pah-lih-mur-ih-ZA¥-shun), in which large compounds are built by joining smaller ones together. The smaller units, or monomers, join together to form polymers. The monomers in a polymer may be identical, like the links on a metal watch band; or the monomers may be different, like the beads in a multicolored necklace. Figure 2-12 illustrates the formation of a polymer from more than one type of monomer. ‘It would be difficult to study the millions of organic com- pounds if they were not classified into groups. (Ss Four groups of organic compounds found in living things are carbohydrates, lipids, nucleic acids, and proteins. Some- times these organie compounds are referred to as biomolecules, As you read about these molecules, compare their structures A Figure 2-12 When small and functions. ‘molecules called monomers join together, they form polyrners, or large sft) What is polymerization? molecules, Using Analogtes How are monomers similar to links ina chain? Carbohydrates Carbohydrates are compounds made up of earbon, hydrogen, and oxygen atoms, usually in a ratio of 1 : 2: 1. G2 Living things use carbohydrates as their main source of energy. Plans and some animals also use carbohydrates for structural purposes. The breakdown of sugars, such as glucose, supplies iramediate energy for all cell activities. Living thinge store extra sugar as complex carbohydrates known as starches, As shown in Figure 2-13, the monomers in starch polymers are sugar molecules. Starch o H / Aron Px [SNCS igure 2-13. starches and sugars are aoe ‘examples of carbohydrates that are used by 7 living things as a source of energy. The chef 1 1 show heres drying pasta, ‘made princi. HOH pally of starch, Starches form when sugars join together ina long chain.| Word Origins Re Monomer comes from the Greek || words monos, meaning “single,” © and meres, meaning “part.” || Monomer means “single part.” The || prefix poly- comes from the Greek | word polus, meaning “many,” so polymer means “many parts.” The word saccharide comes from the Latin word saccharum, meaning “sugar.” What do you think the terms monosaccharide and polysaccharide mean? V Figure 2-14 Lipids are used to store energy. Lipid molecules are made up of fatty acids and glycerol. Liquid lipids, such as olive of, contain mainly unsaturated fatty acids, Single sugar molecules are also called monosaccharides (mahn-oh-SAK-uh-rydz). Besides glucose, monosaccharides include galactose, which is a component of milk, and fructose, which is found in many fruits. ‘The large macromolecules formed from monosaccharides are known as polysaccharides. Many animals store excess sugar in a polysaccharide called glycogen, or animal starch. When the Ievel of glucose in your blood runs low, glycogen is released from your liver. The glyeogen stored in your muscles supplies the energy for muscle contraction and, thus, for movement. Plants use a lightly different polysaccharide, called plant starch, to store excoss sugar. Plants also make another impor- tant polysaccharide called cellulase, Tough, flexible cellulose fibers give plants much of their strength and rigidity. Cellulose is tho major component of both wood and paper, so you are actually looking at eellulose as you read these words! Lipids Lipids are a large and varied group of biological molecules that are generally not soluble in water. Lipids are made mostly from carbon and hydrogen atoms. The common categories of lipids are fats, oils, and waxes. (> Lipids can be used to store energy. Some lipids are important parts of biological membranes and waterproof coverings. Steroids are lipids as well. Many steraids serve as chemical mossengers. Many lipids are formed when a glycerol molecule combines with compounds ealled fatty acids, as shown in Figure 2-14, If each carbon atom in a lipid’s fatty acid chains is joined to another carbon atom by a single bond, the lipid is said to be saturated. The term saturated is used because the fatty acids contain the maximum possible number of hydrogen atoms. igs me aeIf there is at least one carbon-carbon double bond in a fatty acid, the fatty acid is said to be unsaturated. Lipids whose fatty acids contain more than one donble bond are said to be polyun- saturated, If the terms saturated and polyunsaturated seem familiar, you have probably soon them on food package labels. Lipids such as olive oil, which contains unsaturated fatty acids, tend to be liquid at room temperature. Cooking ofis, such a3 corn «il, sesame oil, canola oil, and peanut oil, contain polyunsatu- rated lipids. Nucleic Acids Nucleic acids are macromolecules containing hydrogen, oxygen, nitrogen, carbon, and phosphorus. Nucleic acids are polymers assembled from individual monomers known as nucleotides. Nucleotides consist of three parts: a 5-carbon sugax; a phosphate group, and a nitrogenous base, as shown in Figure 2-15. Individual nucleotides can be joined by covalent bonds to form a polynucleotide, or nucleic acid. €@ Nucleic acids store and transmit hereditary, or genetic, information. There are two kinds of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). As their names indicate, RNA contains the sugar ribose and DNA contains the sugar deoxyribose. av Proteins Proteins are macromolecules that contain nitrogen as well as carbon, hydrogen, and oxygen. Proteins are polymers of molecules called amino acids. Amino acids are compounds with an asaino group (-NH;) on one end and a carboxyl group (~COOH) on the other end. Figure 2-16 shows one reason why proteins are among the most diverse macromolecules. More than 20 different amino acids are found in nature, All amine acids are identical in the regions where they may be joined together by covalent bonds. ‘This uniformity allows any amino acid to be joined to any other amino acid—by bonding an amino group to a carboxyl group. What are the three parts of a nucleotide? D> Figure 2-46 Amino acids are the monomers of proteins. All aH 29 ‘amino acids have an amino group NL oe at one end and a carboxyl group at_ «NG Secret wnccmngaee Cf ‘one amino acid from another is the R-group section af the molecule. Amina Cartoxyl Comparing and Contrasting eee How are proteins and carbohydrates. General structure shits? How are they different? A Figure 2-15 store and transmi mation. The mon nitrogenous base. Amino Acids, S-earbon sugar Nudelc acids it genetic infor- jomers that make ‘up anucleic acid are nucleotides. Each nucleotide has a S-carbon sugar, a phosphate group, and aA Figure 2-17 C2 Proteins help ‘to carry out chemical reactions, transport small molecules in and out Of cells, and fight diseases. Proteins ‘are made up of chains of amino acids {folded into complex structures. ‘The portion of each amino acid that is different is a side chain called an B-group. Some R-groups are acidie and some are basic. Some are polar and some are nonpolar: Some eontain carbon rings, The instructions for arranging amino acids into many different, proteins are stored in DNA. Each protein has a specific role. C23 Seme proteins control the rate of reac- tions and regulate cell processes. Some are used to form bones and muscles. Others transport substances into or out of cells or help to fight disease. Proteins can have up to four levels of organization. The first evel is the sequenee of amino acids in a protein chain. Sceond, ‘the amino acids within 2 chain can be twisted or folded. Third, the chain itself is folded. If 2 protein has more than one chain, each chain has a specific arrangement in space as shown by the red and blue structures in Figure 2-17. Van der Waals forces and hydrogen bonds help maintain a protein’s shape. In the next seetion, you will learn why a protein’s shape is so important.2-4 Chemical Reactions and Enzymes iving things, as you have seen, are made up of chemical Guide for Reading compounds—some simple and some complex. But chemistry _STenininesonemecnecatontnt isn't just what life is made of&~chemistry is also what life does. Everything that happons in an organism—its growth, its intor- Ss etopeero chemical action with the environment, its reproduction, and even its bonds during chemical movement—is based on chemical reactions. reactions? + How do energy changes affect heer a chemical reaction \ s occur Chemical Reactions = Why are enzymes important to A chemical reaction is a process that changes, or transforms, tiving things? one set of chemicals into another. An important scientific princi- Vocabulary ple is that mass and onorgy are conserved during chemical chemical reaction transformations, This is also true for chemical reactions that reactant occur in living organiams, Some chemical reactions occur slowly, product such as the combination of iron and oxygen to form an iron activation eneray oxide called rust, shown in Figure 2-18. Other reactions occur — ‘quickly. The elements or compounds that enter into a chemical ba reaction are known as reactants. The elements or compounds produced by a chemical reaction are known as products. Reading Strategy: Chemical reactions always invalve changes in the Suliding Vocabulary chemical bonds that join atoms in compounds. eerie ‘One example of an important chemical reaetion that occurs Santa coment in your body involves carbon dioxide. Your cells constantly highlighted, boldface term. produce carbon dioxide as a normal part of their activity. This ‘carbon dioxide is carried to your lungs through the bloodstream, and then is eliminated as you exhale, However, carbon dioxide is not very soluble in water. The bloodstream could not possibly dissolve enough carbon dioxide to carry it away from your tissues were it not for a chemical reaction. As it enters the Blood, carbon dioxide reacts with water to produce a highly soluble compound ealled earbonie acid, H,COs. 60 +H,0 —> 1,60, The reaction shown above enables the bloodstream to carry carbon dioxide to the lungs, In the lungs, the reaction is reversed. H,COs—» CO» + HO ‘This reverse reaction produces carbon dioxide gas, which is released as you exhale. D> Figure 2-18 <> Chemical reactions always involve changes in ‘chemical bonds. The iron in these chin finks gradually combined with ‘oxygen to produce a compound known as rust.po, (Go Wnline | active art, | For: Erayme dtion acy Vist: PHSchoot.com ‘Web Caste: cbp-1024 J oo eee Y Figure 2-19 Chemical reactions that release energy often ‘occur spontaneously. Chemical reactions that absorb energy will occur only with a source of energy. “The peak of each graph represents the ‘energy needed for the reaction to go forward, The difference between this required energy and the energy of the reactants is the activation energy. Course of Reaction Energy in Reactions Energy is released or absorbed whenever chemical bonds form or are broken. Because chemical reactions involve breaking and forming bonds, they involve changes in energy. Energy Changes Some chemical rosctions relesse energy, and other reactions absorb energy. Energy changes are one of the most important factors in determining whether a chemical reaction will occur. (3 Chemical reactions that release energy often occur spontaneously. Chemical reactions that absorb energy will not occur without a source of energy. An example of an onergy-releasing reaction is hydrogen gas burning, or reacting, with oxygen to produce water vapor. 28a + Oy—> 2H,0 ‘The energy is released in the form ofheat, and sometimes— when hydrogen gas explodes—light and sound. ‘The reverse reaction, in which water is changed into hydro- gen and oxygen gas, absorbs so much energy that it generally doesn’t occur by itself. In fact, the only practical way to reverse the reaction is to pass an clectrical curront through water to decompose water into hydrogen gas and oxygen gas. Thus, in one direction the reaction produces energy, and in the other direction the reaction requires energy. In order to stay alive, organisms need to carry out reactions that require energy. Because matter and energy are conserved in chemical reaetions, every organism must have 2 source of energy to carry out chemical reactions. Plants get that energy by trap- ping and storing the energy from sunlight in energy- rich compounds, Animals get their energy when they consume plants or other animals, Humans release the energy needed to grow tall, to breathe, to think, and even to dream through the chemical reactions that occur when humans metabolize, or break dows, digested food. Activation Energy Even chemical reactions that release energy do not always occur spontaneously. ‘That's a good thing becauso if they did, the pages of this book might burst into flames. The cellulose in paper burns in the presence of oxygen and releases heat and light. However, the cellulose will bum only if you light it with a match, which supplies enough ‘energy to get the reaction started. Chemists eall the energy that is needed to get a reaction started the activation energy. As Figure 2-19 shows, activa- tion energy is a factor in whether the overall chemi- cal reaction releases energy or absorbs energy. & -eQhit What is activation energy?33 How Does pH Affect an Enzyme? || Catalase is an enzyme that helps decompose the toxic |_ hydrogen peroxide that is produced during normal cell activities. The products of this reaction are water ‘and oxygen gas. The pressure of the oxygen gas in 2 closed container increases as oxygen is produced. Any increase in the rate of the reaction will cause an increase in the pressure of the oxygen. ‘The purple fine on the graph represents the normal ‘ate of the reaction in a water solution of hydrogen peroxide and catalase. The red! line represents the rate ‘of reaction when an acid is added to the solution. The | biue line represents the rate of reaction when a base is 4. Drawing Conclustons What effect do acids and | PE Prossure of Oxygen (KPa) ze 2% a3 20 4d 69 80 100 120 140 160 ‘Time (secontis) added to the solution. bbases have on the enzyme catalase? } 1. Applying Concepts What variable is plotted on _5, Drawing Conelustons Would tt be valid to Wi | the x-axis? What variable is plotted on the y-axis? conclude that i base were added, the rate ofthe | | 2. mnterpreting Graphles How did the rate of ‘reaction would slow down? Explain. I reaction change over time in the control reaction? Going Further Predict what wouldhappen it. | | 3. linferrimg Suggest an explanation for the change vinegar were added to a water salution of hydrogen | | in the contrat reaction at about 40 seconds. peroxide and catalase. Enzymes Some chemical reactions that-malke life possible Y figure 2-20 Coen sae are hoo slow or have activation energies that are reachons that take place In ete, Note ow the too high to make them practical for living tissue. | _Sauston nan entre Toners te avvation energy in ‘These chemical reactions are made possible by a tisresebn. Th elon spends up the reaction process that would make any chemist proud— . cells make catalysts. A catalyst is a substance that speeds up the rate of a chemical reaction. Gatalyats work by lowering a reaction’s activa- Reaction pathway tion energy. without enzyme Enzymes aro proteins that act as biological catalysts. (S> Enzymes speed up chemical reactions that take place in cells. Like other catalysts, enzymes act by lowering the activation ‘energios, as illustrated by the graph in Figure 2-20, Lowering the activation onergy has a dramatic offeet on how quickly the reaction is completed. How big an effect does it have? Consider the reaction in which carbon dioxide combines with water to produce carbonic acid. CO, + H,0—> HCO,V Figure 2-21 The enzyme hexokinase converts the substrates glucose and ATP into glucose-6- phosphate and ADP. Predicting What happens to the hexokinase after ‘the products ore released? Left to itself, this reaction is ¢o slow that carbon dioxide smight build up in the body faster than the bloodstream could ‘remove it. Your bloodstream contains an enzyme called carbonic anhydrase that epoods up the reaction by a factor of 10 million. ‘With carbonic anhydrase on the job, the reaction takes place immediately and carbon dioxide is removed from the blood quickly. ‘Enzymes are very specific, generally catalyzing only one chemical reaction. For this reason, part of an enzyme’s name is asually derived from the reaction it catalyzes, Carbonic anhy- drase gets its name because it catalyzes the reaction that removes water from carbonic acid. Enzyme Action ‘How do enzymes do their jobs? For a chemical reaction to take place, the reactants must collide with enough energy so that existing bonds will be broken and new bonds will be formed. If the reactants do not have enough energy, they will be un- changed after the collision. The Enzyme-Substrate Complex Enzymes provide a site where reactants can be brought together to react, Such a site reduces the energy needed for reaction. The reactants of ‘enzyme-catalyzed reactions are known as substrates.Figure 2-21 provides an example of an enzyme- catalyzed reaction. The enzyme is hexokinase. The substrates are ghneose and ATP. During the reaction, a phosphate group is transferred from ATP to the glucose molecule. Recall that each protein has a specific, complex shape. The substrates bind to a site on the enzyme called the active site. The active site and the substrates have complementary shapes. The {fit is so precise that the active site and substrates are often compared to a lock and key. Figure 2-22 shows a substrate fitting into an active site on an enzyme. The enzyme and substrate are bound together by intermolecular forces and form an enzyme-substrate complex. They remain bound together until the reaction is done. Once the reaction is over, the products of the reaction are released and the enzyme is fro to start the process again, Regulation of Enzyme Activity Because they are catalysts for reactions, enzymes can be affected by any variable that influences a chemical reaction. Enzymes, including those that help digest food, work best at certain pH values. Many enzymes are affected by changes in temperature. Not surprisingly, those enzymes produced by human cells generally work best at temperatures close to 37°C, the normal tem- perature of the human body. Celis can regulate the activities of enzymes ina variety of ways. Most cells contain proteins that holp to turn key enzymes “on” or “of” at critical stages in the A Figure 2-22 This space-filling model shows life of the cell. Enzymes play essential roles in regulating _how a substrate binds to an active site on an chemical pathways, making materials that cells need, enzyme. interpreting Graphics What happens releasing energy, and transferring information, Raincadeenieheodhetecledlasere nial