McGraw-Hill Ryerson High School Biology PDF

 U N I T 1 Metabolic Processes Unit Like large emeralds encrusted with gold, thousands Preview of chrysalides (cocoons) hang from milkweed plants in southern Ontario. Wi...

 U N I T 1 Metabolic Processes Unit Like large emeralds encrusted with gold, thousands Preview of chrysalides (cocoons) hang from milkweed plants in southern Ontario. Within each of these In this Unit, you will discover chrysalides, a monarch butterfly caterpillar will undergo a metamorphosis to become an adult what molecules are butterfly. This process requires much energy to fuel necessary for metabolic the tremendous changes that occur in a caterpillar’s functions in cells, physical appearance and abilities. which major reactions All organisms require energy to survive. Cells occur in cells, in a eukaryotic organism contain organelles, such as how thermodynamic the mitochondria shown below, that transform the principles maintain energy in food into energy that can be used for metabolic function, various cellular processes. Without mitochondria, which processes are organisms such as the monarch caterpillar would involved in cellular not be able to perform the metabolic processes they respiration and need for metamorphosis. Metabolic processes involve photosynthesis, and all the chemical reactions that take place in cells, how knowledge of as well as the chemical reactions that need energy metabolic processes can to transport molecules and build the cellular contribute to technological structures necessary for all life processes. development. In this unit, you will learn about the chemical reactions that form molecules and see how the laws Unit of thermodynamics govern all reactions between Contents molecules. You will discover how special proteins are essential to metabolic processes in the cell. Chapter 1 You will explore the series of metabolic reactions The Chemistry that take place in cells and learn how energy is of Life.......... 4 transformed and used in these reactions. Finally, Chapter 2 you will explore how the study of cell biology Enzymes and relates to your life and lifestyle. Energy.......... 34 Chapter 3 How do organisms obtain the energy they need for life processes? Cellular Energy.... 62 Unit Investigation..... 98 UNIT INVESTIGATION Look ahead to pages 98–99. You can start planning your investigation well in advance by organizing what you will need. As you work through the unit, watch for ideas and materials that will help you prepare your experimental design. 2 3  C H A P T E R 1 The Chemistry of Life Reflecting Questions How are bonds formed between atoms? What is ATP, and what Within each living cell, chemical In this chapter, you will explore reactions within the cell reactions take place millions of times the basis for biochemical processes. govern its formation? every second. These reactions involve Although biologists are not usually What reactions build and the transport of material, the removal concerned with individual atoms, break down molecules? of wastes, and the formation of they must know how atoms combine Why are large molecules structures, such as the molecule of to form the molecules that animals essential for life? protein shown in the image on the and plant cells need to perform daily facing page. How do these reactions body functions such as growth, proceed and where are they carried maintenance, and repair. Metabolic out? Questions such as these processes involve the interactions have been at the centre of many of electrons and the formation or investigations into metabolic processes breaking of bonds between atoms to in unicellular and multicellular produce or break down molecules. organisms. Knowing how metabolic Understanding the chemistry of reactions take place and understanding metabolism is key to understanding the intricacies of the key steps its many reactions and the products in those reactions have helped of those reactions. researchers further their knowledge of metabolic processes. How do biologists use their knowledge of molecules and In the field of human biology, for chemical reactions in order to example, radiologists have been using understand metabolic processes? radioactive isotopes since the 1930s to treat and diagnose disease. The electron micrograph on the right shows healthy human thyroid tissue. Radioactive iodine is used as a marker to locate thyroid tissue that may be cancerous. Iodine can only be utilized in thyroid tissue. If the machine tracing the radioactive iodine shows that some of it remains in the patient’s body, doctors and technicians know that cancerous tissue remains to be removed. How are substances, like iodine, that are part of the non-living world related to substances that are part of the living world? What chemical processes are involved and what molecules play key roles in these processes? 4 Chapter Contents 1.1 Atoms and Bonding 6 MiniLab: Investigation 1-B: Finding the Reviewing Macromolecules 20 Products of Hydrolysis 24 MiniLab: Using Chemicals Safely 8 1.3 Making and Breaking Thinking Lab: Macromolecules 21 Polypeptides and Polarity 28 1.2 Biological Macromolecules and Their Subunits 14 Investigation 1-A: Acids, Bases, and Cellular pH 22 5  1.1 Atoms and Bonding E X P E C TAT I O N S Explain the term electronegativity. Express the relationship between electronegativity, bonding, and the polarity of molecules. L iving things are unique among all forms of matter. Atoms and Elements Unlike non-living things, all living things — from As you have learned in previous studies, all matter single-celled organisms such as the Euglena in is formed of atoms. The atom is the smallest unit Figure 1.1 to multicelled organisms such as whales of matter involved in chemical reactions. Although and redwood trees — interact with and manipulate tiny, atoms are complex structures, composed of matter and energy. For example, all cells take in even smaller subatomic particles. Most students essential substances such as oxygen, water, and of chemistry still study the model of the atom that nutrients from their external environment. Inside Danish physicist Niels Bohr presented in the early cells, these substances undergo chemical reactions twentieth century (see Figure 1.2). In this model, of several types. These reactions may be used to an atom consists of a small, dense core called a break down substances, synthesize others, and nucleus. It is composed of two kinds of subatomic repair defective structures. Chemical reactions also particles — the positively (+) charged protons and provide energy for these life-sustaining activities, the uncharged, or neutral, neutrons. Also in the as well as others such as reproduction. Unneeded Bohr model, negatively (−) charged electrons orbit (or harmful) products of the reactions are the nucleus in one or more energy levels, or shells. eliminated as wastes. Collectively, these processes — intake of substances, processing of substances, and = protons shells elimination of wastes — are called metabolic = neutrons nucleus processes, or metabolism. The substances involved = electrons in metabolism are molecules. The bonds that form between atoms define the structure and properties of these molecules. In this section, you will review Figure 1.2 Niels Bohr’s model of the neon atom several key ideas about atoms and bonding. An element is a substance that cannot be broken down into simpler substances by chemical means. Substances such as calcium, oxygen, potassium, iron, and carbon are all elements. A few elements, such as helium, occur as single atoms. Several elements, such as hydrogen, nitrogen, and oxygen, occur as molecules made up of two atoms. Such molecules are called diatomic. Other elements such as phosphorus and sulfur occur as molecules made up of more than two atoms. All atoms of an element have the same number of protons in their nuclei. This number, called the atomic number, is different for every element. The nuclei of carbon atoms, for example, each contain Figure 1.1 Euglena, a unicellular freshwater organism, six protons. Because the nuclei of most atoms also carries out the same metabolic processes that your cells do. contain neutrons, another important characteristic of an atom is its mass number. The mass number of an atom is the total number of protons and 6 MHR Unit 1 Metabolic Processes  neutron proton Carbon-14 Carbon-12 Carbon-13 6 protons 6 protons 6 protons 8 neutrons 6 neutrons 7 neutrons 6 electrons 6 electrons 6 electrons Figure 1.3 Carbon, one of the most important elements in of neutrons in the nucleus is 6, 7, or 8. In each isotope, living matter, has three naturally occurring isotopes. The 6 electrons exist outside the nucleus. nucleus of each isotope contains 6 protons, but the number neutrons in its nucleus. Atoms of the same element Table 1.1 shows the atomic masses of the that contain different numbers of neutrons are elements that are most abundant in living called isotopes of that element. Refer to Figure 1.3 organisms. Notice that, unlike atomic numbers and to see the numbers of protons, neutrons, and mass numbers, some atomic masses are not whole electrons in three isotopes of carbon. Their names numbers. This is the case because the atomic mass include the mass number of each isotope: of an element is the average mass of all the carbon-12, carbon-13, and carbon-14. naturally occurring isotopes of that element. Some isotopes are stable, whereas others are Chlorine, for example, naturally occurs as a unstable and break down (decay). The unstable mixture of two isotopes: chlorine-35 and chlorine- isotopes are known as radioactive isotopes. 37. There are three chlorine-35 atoms for every Carbon-12 and carbon-13 are both stable isotopes, chlorine-37 atom. Therefore, the average mass of whereas carbon-14 is unstable and decays. Many chlorine atoms is closer to 35 than to 37. The radioactive isotopes decay at known rates. The rate atomic mass of chlorine is, in fact, 35.5 u (atomic at which a radioactive isotope decays may be used mass units). Appendix 7 provides atomic masses scientifically. The decay of carbon-14 can be used for all the known elements. by archeologists, in a process called radiocarbon dating, to find the ages of some objects up to about Electron Energy 50 000 years old. Biologists usually study the groups of atoms that Table 1.1 make up molecules rather than atoms and The most abundant elements in living organisms subatomic particles themselves. All cells obtain the Atomic mass Abundance energy to function from chemical reactions that Element Symbol (u) (% by mass) involve molecules. The actions of electrons are key to this process. oxygen O 16.0 62.0 According to the Bohr model, electrons orbit the carbon C 12.0 20.0 nucleus of an atom within energy levels, or shells. hydrogen H 1.0 10.0 An electron in the first shell (nearest the nucleus) has the lowest amount of potential energy. Any nitrogen N 14.0 3.3 electrons in the remaining shells have more calcium Ca 40.1 2.5 potential energy. Each shell can hold a maximum number of electrons. The first shell, for example, phosphorus P 31.0 1.0 can hold a maximum of two electrons, while the sulfur S 32.1 0.25 second shell can hold a maximum of eight. Refer to potassium K 39.1 0.25 Figure 1.2, which shows that in a neon atom the first two shells are filled. In general, the maximum chlorine CI 35.5 0.2 number of electrons that a shell can hold is given sodium Na 23.0 0.1 by the formula 2n2 , where n is the number of the magnesium Mg 24.3 0.07 shell. For example, the third shell can hold a total of 2(3)2 = 18 electrons. iron Fe 55.9 0.01 Chapter 1 The Chemistry of Life MHR 7  The chemical properties of atoms rely mostly on Ionic and Covalent Bonds the number of electrons in the outermost, occupied Most atoms can form chemical bonds with other shell of an atom in its lowest energy state. This atoms. These bonds are the forces that hold the shell is known as the valence shell. The electrons atoms together in the form of compounds. For that occupy the valence shell of any atom are example, two chlorine atoms can combine called valence electrons. The elements in the (chemically react) to form a diatomic molecule of periodic table that are least reactive are the noble the element chlorine (Cl2). Atoms of sodium and gases, such as neon, found in group 18(8A) (see chlorine can combine to form the ionic compound Appendix 7). Atoms of the other elements in the sodium chloride (NaCl). periodic table are more reactive than the noble There are two general types of chemical bonds. gases. These elements can form chemical bonds One type involves the sharing of electrons between with each other. The MiniLab examines safety atoms, and is known as a covalent bond. The other issues involving the use of chemicals and how they type involves the transferring of one or more react with each other during chemical bonding. electrons from one atom to another, and is called an ionic bond. How are these bonds formed? MINI LAB Using Chemicals Safely Analyze Throughout this course, you will use solutions of chemicals 1. When you use these chemicals for a laboratory activity, such as hydrochloric acid and sodium hydroxide to help what personal safety supplies will you need? Explain you isolate, identify, or investigate the properties of various your choices. substances. Understanding how to use these chemicals 2. What concentration of substance are you likely to use properly, and what to do in case of an emergency, is vital to in your laboratory activities? ensure your safety as well as the safety of your classmates. 3. (a) Substance A is a clear, colourless liquid. How could Obtain a copy of an MSDS (Materials Data Safety Sheet) for you safely determine the identity of this liquid and/or the following: its components? hydrochloric acid sodium hydroxide (b) Substance B is a blue liquid. How could you safely Benedict’s solution Biuret solution determine the identity of this liquid and/or its (reagent) components? Lugol’s solution silver nitrate 4. Write a short scenario that involves a materials spill for Copy the chart below into your notebook, and use the dilute hydrochloric acid. Explain how to respond safely MSDS information to complete it. to the spill. Hydrolochloric acid Sodium hydroxide Benedict’s solution Biuret’s solution Lugol’s solution Silver nitrate Physical/Chemical Properties Appearance? Odour? Solubility in Water? Toxicity? Health Hazard Data List three health hazards. Safety Identify three safety precautions related to the health hazards listed above. Spill Procedure? Neutralizing Agent? 8 MHR Unit 1 Metabolic Processes Ionic Bonding one electron in outermost 8 electrons in outermost occupied shell occupied shell + 11p electron 11p 11 protons (+) = one 12n given up 12n 10 electrons (−) + charge sodium atom (Na) sodium ion (Na+) A When a sodium atom gives up an electron, it becomes a positive ion. 7 electrons in outermost 8 electrons in outermost occupied shell occupied shell – 17p electron 17p 18n 18n 17 protons (+) = one accepted 18 electrons (−) − charge chlorine atom (Cl) chloride ion (Cl−) B When a chlorine atom gains an electron, it becomes a negative ion. + – 11p 17p 11p 17p 12n + 18n 12n 18n Na Cl NaCl sodium chloride C When sodium reacts with chlorine, sodium chloride (NaCl) is formed. D In a sodium chloride crystal, ionic bonds between Na+ and CI− create Na+ a three-dimensional lattice. Each CI− sodium ion is surrounded by six chloride ions, and each chloride ion is surrounded by six sodium ions. 1 mm arrangement of sodium and chloride ions in one salt crystals salt crystal Figure 1.4 Reaction between sodium and chlorine to form ionic sodium chloride Chapter 1 The Chemistry of Life MHR 9  Any atom has the same number of electrons and chloride ion, with 17 protons and 18 electrons. protons. Therefore, the atom has no charge and is This number of electrons is arranged in the same said to be neutral. However, if an atom loses or way as the 18 electrons in an argon (Ar) atom. gains electrons, that atom becomes an ion. If an Because the sodium ion is positively charged and atom loses electrons, the ion formed has more the chloride ion is negatively charged, they attract protons than electrons and therefore has a positive each other to form an ionic bond. charge. A positively charged ion is called a cation. The tendency of chlorine to gain electrons is In contrast, if an atom gains one or more electrons characteristic of atoms with a few electrons less the ion formed has a negative charge. A negatively than a noble gas atom. For example, atoms of charged ion is called an anion. When sodium (Na) fluorine and oxygen also tend to gain electrons and chlorine (Cl) atoms react, they form an ionic when they form ionic bonds. One way to understand bond, as shown in Figure 1.4. The sodium atom which elements form ionic bonds when they react gives up its only valence electron and becomes a is to use the principle of electronegativity. sodium ion, with 11 protons and 10 electrons. This Electronegativity is a measure of the relative number of electrons is arranged in the same way abilities of bonding atoms to attract electrons. The that the 10 electrons are arranged in the neon atom. Pauling scale is the most commonly used measure The chlorine atom gains an electron and becomes a of electronegativities of atoms. Fluorine, the most Covalent Bonding 17p 18n + 17p 18n 17p 18n 17p 18n Cl Cl Cl Cl chlorine chlorine chlorine gas (CI2 ) 8p 8n + 8p 8n 8p 8n 8p 8n O O O O oxygen oxygen oxygen gas (O2 ) 1p 1p 8p 8n + 8p 8n 1p 1p O H oxygen 2H O H hydrogen water (H 2 O) Figure 1.5 In a covalent bond, electrons are shared between atoms. 10 MHR Unit 1 Metabolic Processes electronegative element, is found near the top Electron-Dot right corner of the periodic table and has an formula Structural formula Molecular formula electronegativity value of 4.0. Both cesium and francium, the least electronegative elements, are O C O O C O CO2 found near the bottom left corner of the periodic carbon dioxide carbon dioxide carbon dioxide table and each has an electronegativity value of 0.7. Elements that are most likely to form ionic bonds, H H such as sodium and chlorine, are far apart in the N H N H NH 3 periodic table and have a large difference in their H H electronegativity. ammonia ammonia ammonia Elements that are close together in the periodic table have a small difference in their electronegativity. If two of these elements react to H H form a compound, their similar abilities to attract H2O O H O H electrons results in the formation of a covalent bond, in which electrons are shared. In a covalent water water water bond, atoms share two valence electrons. An example of this is the covalent bonding of two Figure 1.6 In an electron-dot formula, only the electrons in chlorine atoms, as shown in Figure 1.5, top. Double the valence shell are shown. In a structural formula, each covalent bonds involve the sharing of two pairs line represents a pair of electrons shared by two atoms. A molecular formula shows only the number of each type of of shared valence electrons. The two oxygen atoms atom in a molecule. in an oxygen molecule are joined by a double covalent bond, as shown in Figure 1.5, middle. The shared electrons in covalent bonds belong ELECTRONIC LEARNING PARTNER exclusively to neither one nor the other atom. However, by sharing these valence electrons, both To learn more about ionic and covalent bonding, go to your atoms appear to have the same number of valence Electronic Learning Partner now. electrons as a noble gas atom. In a covalent bond formed by two atoms of the same element, the electronegativity difference is zero. Therefore, the electrons in the bond are shared equally between Hydrogen Bonds and the the two atoms. This type of bond is described as Properties of Water non-polar covalent. Examples of non-polar Some molecules with polar covalent bonds are covalent bonds are found in chlorine and carbon known as polar molecules. A polar molecule has dioxide molecules. an unequal distribution of charge as a result of its A covalent bond is said to be polar covalent when polar bonds and its shape. More information about the electronegativity difference between the atoms polar molecules is provided in Appendix 6. Water is not zero and the electrons are therefore shared is a common example of a polar molecule. In a unequally. In a water molecule (see Figure 1.5, water molecule, as shown in Figure 1.7, the bottom), oxygen is more electronegative than is slightly negative end of each bond can be labelled hydrogen. The shared electrons spend more of δ − and the slightly positive end can be labelled δ +. their time near the oxygen nucleus than near the These two ends, with slightly different charges, are hydrogen nucleus. As a result, the oxygen atom sometimes referred to as “poles.” Because a water gains a slight negative charge and the hydrogen molecule is polar, it can attract other water atoms become slightly positively charged. molecules, due to the attraction between negative Chemists represent molecules formed through poles and positive poles (see Figure 1.7). The covalent bonds with various formulas, such as attractions between water molecules are called those in Figure 1.6. Electron-dot and structural hydrogen bonds. Hydrogen bonds can also be formulas are simplified ways of showing what found between other molecules that contain electrons are being shared. hydrogen atoms bonded covalently to atoms of a much more electronegative element. Examples include ammonia (NH3 ) and hydrogen fluoride (HF) in their liquid states. Chapter 1 The Chemistry of Life MHR 11  A hydrogen bond is a force between molecules, δ− not a chemical bond within a molecule. Hydrogen O δ+ H H δ+ δ+ H H δ+ bonds are usually weaker than chemical bonds. For O δ− instance, a hydrogen bond may be only five percent CI − Na + the strength of a covalent bond, but it is sufficient to hold one water molecule to another in liquid water or ice. Under normal conditions, water Figure 1.8 The salt NaCl dissolves in water because molecules are attracted to each other in such a way chloride ions and sodium ions attract water molecules. that they are neither attracted too strongly (to form a solid) nor too weakly (allowing water to become a Compounds that interact with water — for vapour). For this reason, under normal conditions example, by dissolving in it — are called on Earth, water exists as a liquid. hydrophilic. In contrast, compounds that do not interact with water are called hydrophobic. Non- polar compounds are hydrophobic. They cannot form hydrogen bonds with water in the same way that ionic or polar compounds can. Therefore, hydrophobic molecules are insoluble in water. For δ+ example, when you place a drop of oil (a non-polar δ– compound of carbon and hydrogen) into water, the oil does not mix with the water — they δ+ remain separate. In this section, you have learned that the type of chemical bond that joins individual atoms together hydrogen determines whether the resulting compound is bond ionic or covalent. Covalent molecules may be polar Figure 1.7 Hydrogen bonding (shown via dotted lines) or non-polar, depending on the electronegativities between water molecules of the bonded atoms and shape of the molecule. You have learned that hydrogen bonds form Solubility of Substances in Water between molecules in water, which interacts very differently with hydrophobic and hydrophilic All cells depend on liquid water. In fact, living compounds. Hydrophobic interactions especially organisms contain more molecules of water than have a great effect on many biological molecules. any other substance; water comprises as much as For instance, many protein molecules have 90 percent of a typical cell. Water is a perfect fluid hydrophobic regions in portions of their structure. environment through which other molecules can Interactions of these regions with water cause move and interact. the molecules to adopt specific shapes. You will Sodium chloride (table salt), and many other see examples of this in the next section, which ionic compounds or salts, dissolve readily in water. reviews the four main kinds of molecules that This occurs because the positively charged poles of make up all cells. the water molecule are attracted to the anions (chloride ions) in the salt. The negatively charged pole of the water molecule is similarly attracted to COURSE CHALLENGE the cations (sodium ions) in the salt as shown in What you have learned about molecules and polarity may Figure 1.8. These two attractions pull the sodium be useful in preparing your Biology Course Challenge. How ions and chloride ions away from each other. The could you use this knowledge to help you prepare for your salt is now dissociated, which means that the science symposium? sodium ions and chloride ions have separated and have dissolved in the water. 12 MHR Unit 1 Metabolic Processes  SECTION REVIEW 1. K/U Is this atom chemically unreactive or chemically 6. I If you pour a few drops of oil into water, you reactive? Explain your answer in terms of valence will notice that the oil forms a thin layer at the surface electrons. of the water almost immediately. Based on your knowledge of hydrophobic and hydrophilic compounds and bonding, form a hypothesis as to why oil and water interact in this way. How would you test your hypothesis? 7. MC A graduated cylinder with 10 mL of dilute sodium hydroxide solution is accidentally spilled onto your work surface. List the steps you will follow in 2. K/U Use examples of ionic, covalent, and polar response to this spill. covalent bonds to help explain how they are different. 8. MC If the spill in question 7 came in contact with 3. K/U Describe a polar covalent bond using the term human skin, how would your list of steps change? “electronegativity.” 4. K/U How is a hydrogen bond different from other UNIT INVESTIGATION PREP bonds described in this chapter? The reactivity of atoms is a concept central to metabolic 5. C Explain why hydrophobic and hydrophilic processes. How might this knowledge help you plan an compounds behave differently in water. experiment to study a metabolic process? Chapter 1 The Chemistry of Life MHR 13  1.2 Biological Macromolecules and Their Subunits E X P E C TAT I O N S Identify functional groups and explain their effect on the properties of molecules. Review the types of macromolecules. Explain the meaning of the term isomer, with examples. The atoms of four elements make up roughly The Central Atom: Carbon 99 percent of the mass of most cells: hydrogen, The diversity of life relies greatly upon the nitrogen, carbon, and oxygen. With only a few versatility of carbon. Recall that a carbon atom in exceptions, molecules that contain carbon atoms its most stable state has two occupied energy levels, are called organic compounds. There are millions the second of which contains four valence electrons. of different organic compounds. Nearly all organic This means that, in covalent molecules, a carbon compounds contain hydrogen as well as carbon, atom can form bonds with as many as four other and most of these also include oxygen. Pure carbon atoms. In biological systems, these atoms are mainly and carbon compounds that lack hydrogen — such hydrogen, oxygen, nitrogen, phosphorus, sulfur, as carbon dioxide and calcium carbonate — are and — importantly — carbon itself. Carbon’s ability considered inorganic. Inorganic compounds are, to bond covalently with other carbon atoms enables nevertheless, integral components of living systems. carbon to form a variety of geometrical structures, See Figure 1.9. For example, water — an inorganic including straight chains, branched chains, and compound — provides a medium in which various rings. Figure 1.10 shows the shapes of several substances may be dissolved and transported simple organic molecules that contain only carbon within and between cells. and hydrogen atoms. These molecules, called hydrocarbons, comprise the fossil fuels that serve as the main fuel source for much of the world’s industrial activities. Hydrocarbons are themselves not components of living systems. However, Name Molecular formula Structural formula H methane CH4 H C H H H H ethane C2 H6 H C C H H H H H C H benzene C6 H6 C C C C H C H H Figure 1.10 Carbon atoms can bond in several ways — from the simple tetrahedral structure of methane, to the short chain of carbon atoms in ethane, to the ring of carbon Figure 1.9 In what ways do living and non-living systems, atoms in benzene. and organic and inorganic compounds interact? 14 MHR Unit 1 Metabolic Processes substantial portions of many biological molecules usually have similar chemical and physical consist of bonded chains of carbon and hydrogen. properties, but enzymes or proteins on the cell membrane can distinguish between them. Usually, Molecular Isomers one optical isomer is biologically active and the other biologically inactive. In some cases however, Because carbon can form so many compounds with this is not always true. For example, sometimes so many elements, it is common to encounter one optical isomer of a drug is not as effective as several organic compounds with the same the other or can even cause complications. In the molecular formula but different structures. Such early 1960s, many pregnant women were prescribed compounds are known as isomers. For example, a drug called thalidomide for morning sickness. two isomers of glucose, a six-carbon sugar, are Thalidomide is a mixture of two optical isomers; one fructose and galactose. Glucose, fructose, and produced the desired effect, but the other caused galactose all have the same molecular formula major birth defects. As the thalidomide example (C6H12O6 ). However, they differ in their molecular demonstrates, organisms can be very sensitive to structures, as shown in Figure 1.11. minute variations in molecular geometry. H2 COH C O O H H H2 COH H2 COH H C C C C OH H H OH HO OH H2 COH H OH C C C C C O H OH OH H OH H H glucose C C fructose OH H H OH C C H OH galactose Figure 1.11 The different ways in which the same atoms are arranged in glucose, galactose, and fructose make them isomers. There are two main types of isomers. Structural isomers are two or more compounds with the same Figure 1.12 Optical isomers, such as these molecules of the amino acid, alanine, are identical in their structures atoms bonded differently. Glucose and fructose, for except that they are non-superimposable mirror images example, are structural isomers. Notice that a of each other. Your left and right hands are also glucose molecule contains a ring of five carbon non-superimposable images of each other. atoms and an oxygen atom, whereas a fructose molecule contains a ring of four carbon atoms and The Functional Groups an oxygen atom. Because their structures are different, glucose and fructose have different Chemical reactions involve breaking or forming properties, and cells metabolize them differently. chemical bonds. These processes can transform Stereoisomers are two or more compounds with simple molecules such as glucose into complex their atoms bonded in the same way, but with molecules such as starch or cellulose. Many of atoms arranged differently in space. Stereoisomers these complex molecules contain groups of atoms may be geometrical or optical. Geometrical isomers with characteristic chemical properties. These can have very different physical properties (such groups of atoms, known as functional groups, as different melting points), but they tend to have include hydroxyl, carbonyl, carboxyl, amino, the same chemical properties. Glucose and sulfhydryl, and phosphate groups, as shown in galactose are examples of geometrical isomers. Figure 1.13 on page 16. Many compounds have Optical isomers, shown in Figure 1.12, are non- more than one functional group in their structure. superimposable mirror images of each other. They Chapter 1 The Chemistry of Life MHR 15  These functional groups are hydrophilic. Except Each functional group has a specific role in for the phosphate group, they are polar and so cell metabolism. Phosphates are essential to the they increase the solubility in water of the organic metabolic processes of photosynthesis and cellular molecules to which they are attached. Each respiration. For example, the transfer of a phosphate functional group also has capabilities to change group from ATP (adenosine triphosphate) begins the chemical properties of the organic molecules to the very important process of glycolysis — the first which it bonds. For example, if a hydrogen atom in step in cellular respiration. You will discover more ethane is replaced by a sulfhydryl group, the result about this process in Chapter 3. is ethanethiol, also known as ethyl mercaptan. While amino and phosphate groups contribute to While ethanethiol in small amounts stabilizes energy transactions in the cell, the sulfhydryl (–SH) protein structures, it is also a dangerous neurotoxin group is essential to protein stabilization. Amino and respiratory toxin. acids with –SH groups form bonds called disulfide bridges (S–S bonds) that help protein molecules to take on and maintain a specific shape. Functional group Formula Name of compound Structural example H H hydroxyl OH alcohols H C C OH H H ethanol H O O carbonyl C aldehydes H C C H H H acetaldehyde (ethanal) H O H O H C C C H ketones C H H acetone H O O O carboxyl C C carboxylic acids H C C OH O− OH H (non-ionized) (ionized) acetic acid H H H H + amino N N H amines H C N H H H H (non-ionized) (ionized) methylamine H H H H sulfhydryl SH thiols H C C C C SH H H H H butanethiol HO O C O H C OH O phosphate O P O− organic phosphates H C O P O− O− H O− Figure 1.13 Functional groups of 3-phosphoglyceric acid organic compounds 16 MHR Unit 1 Metabolic Processes Monomers and Macromolecules Table 1.2 Macromolecules and their subunits and functions As you know, atoms can join together — bond — to form small compounds called molecules. Similarly, Macromolecule Sub-unit Function molecules can join together to form large structures Carbohydrates called macromolecules. The small, molecular glucose – energy storage subunits that make up macromolecules are called (monosaccharide) monomers. The macromolecules themselves are starch, glycogen glucose energy storage built up of long chains of monomers. These chains (polysaccharides) cellulose glucose component of plant cell are called polymers. (polysaccharide) walls Table 1.2 lists the main types of macromolecules chitin modified glucose cell walls of fungi; outer and their monomer subunits. Figure 1.14 depicts (polysaccharide) skeleton of insects and the subunits that comprise carbohydrates, selected related groups lipids, proteins, and nucleic acids. Chemical Proteins reactions in cells synthesize macromolecules from globular amino acids catalysis these subunits, and break the molecules apart to structural amino acids support and structure release their subunits. Refer to Figure 1.14 often as Lipids you examine these chemical reactions in the final fats glycerol + three fatty energy storage section of this chapter. acids phospholipids glycerol + two fatty component of cell acids + phosphate membranes WEB LINK steroids four carbon rings message transmission www.mcgrawhill.ca/links/biology12 (hormones) To learn how researchers use molecular models to help them terpenes long carbon chains pigments in photosynthesis investigate the structure of complex molecules, go to the web Nucleic acids site above, and click on Web Links. Identify a scientific DNA nucleotides encoding of heredity discovery in which molecular modelling played a significant information role. What techniques or technologies were used in the RNA nucleotides blueprint of heredity construction of the model? Present your findings in a class information workshop on methods of molecular modelling. CH2OH A glucose molecule, the phosphate subunit for carbohydrates group C O H H O nitrogen base H C C O P O− OH H HO OH O C C H H H H H H H OH O CH2 O O glucose H C OH C C C C C C H C HO H H H H H H C C A nucleotide H H H H H H O molecule, the H C OH + OH H C C C C C C C H subunit for sugar nucleic acids HO (deoxyribose) H H H H H H H H H H H C OH O C C C C C H H HO glycerol H H H H Glycerol and three fatty acid molecules, 3 fatty acids the subunits for fats (triglycerides) Figure 1.14A Notice the prevalence of carbon, hydrogen, and oxygen atoms in the monomers that comprise the macromolecules of life. Chapter 1 The Chemistry of Life MHR 17  H H H H H O O O O O H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C O− O− O− O− O− H CH3 CH CH2 H 3C CH glycine alanine CH3 CH3 CH CH2 valine CH3 CH3 CH3 leucine isoleucine non-polar H H H H O O O O + + + + H3N C C H3N C C H3N C C H3N C C O− O− O− O− CH2 CH2 CH2 H2C CH2 CH2 CH2 proline S NH CH3 methionine phenylalanine tryptophan H H H H H O O O O O H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C O− O− O− O− O− CH2 CH2 CH2 CH2 CH2 C CH2 polar OH H SH O serine cysteine NH2 O H3N+ C C C O − asparagine NH2 O CH glutamine OH CH3 OH threonine tyrosine H H H H H O O O O O + + + + + H3N C C H3N C C H3N C C H3N C C H3N C C O− O− O− O− O− electrically charged CH2 CH2 CH2 CH2 CH2 NH C CH2 CH2 CH2 O− O C CH2 CH2 aspartic acid − O O NH+ CH2 NH glutamic acid histidine NH3+ C NH2+ lysine NH2 arginine acidic basic The 20 major amino acids, the subunits for proteins. Notice is highlighted in colour. Biologists refer to this group as a that each amino acid has one carbon that is bonded to side-chain or an R-group. The R-group is different for each both an amino group and a carboxyl group. Notice also that amino acid, and is responsible for its chemical properties. bonded to this same carbon atom is a molecular group that Figure 1.14B Notice that each amino acid has an amine at one end and a carboxyl group at the other. 18 MHR Unit 1 Metabolic Processes Biology Magazine TECHNOLOGY SOCIETY ENVIRONMENT The Thalidomide Dilemma chemical is made by blood cells as part of the body’s immune response. However, large quantities of TNF In the late 1950s, a new drug called thalidomide was result in harmful inflammation — a common symptom widely sold as a sleeping pill and cure for morning of autoimmune disorders such as rheumatoid arthritis, sickness during pregnancy. Research had shown that AIDS, and lupus. Thalidomide is the most effective drug thalidomide is remarkably non-toxic, even in very high known to relieve this symptom. doses. Tragically, tests did not show that the drug affects the normal development and growth of a fetus. As a result, thousands of women who had taken thalidomide when pregnant gave birth to babies with missing or malformed limbs, facial deformities, and defective internal organs. The drug was banned for general use in 1964. In the years since the catastrophe caused by thalidomide, researchers have discovered more effects that the drug has on the body. Not only does thalidomide induce sleep and reduce nausea, but also it is a powerful anti- inflammatory agent. It can also moderate extreme and damaging reactions of the immune system. These effects make it a valuable tool for treating leprosy, rheumatoid arthritis, lupus, certain conditions associated with AIDS, and other diseases. The dilemma is how to control and market the use of a drug that can cause great damage, Thalidomide can be used to prevent the growth of yet has great benefits as well. cancerous tumours. One Drug, Many Effects The Bottom Line It is quite common to find that pharmaceuticals developed for one purpose have other applications. For example, With little or no toxicity and a wide range of applications, Aspirin™ was originally prescribed as a painkiller, but thalidomide is a valuable drug for medical use. However, much later was found to help prevent the formation of the drug’s effect on babies born a generation ago still blood clots. Prozac™ was marketed as an appetite makes its use controversial. The Thalidomide Victims suppressant before it was recognized as an effective Association of Canada is a group of individuals born with antidepressant. Minoxidil™, used to control hypertension, physical defects caused by this drug. They lobby drug is now used to treat baldness. The interactions between companies and governments to help ensure that another a particular drug and the body’s cells and organ systems generation does not experience the same effects as are often complex and poorly understood, even after a they did. drug has been in use for many years. Follow-up Thalidomide and Disease 1. Debate in class the arguments for and against How does thalidomide produce its effects? Since the prescribing a therapeutic drug that has been proven mid-1990s, scientists have learned that: to pose serious health risks. Who should decide on its use? What might be the view of a person who has Thalidomide inhibits the movement of cells needed to physical disabilities that were caused by thalidomide? form new blood vessels. This is the property of the What might be the view of a person who suffers from drug that affects fetal development and results in life-threatening symptoms of a disease (such as malformed limbs and organs. However, inhibition of AIDS) that thalidomide can relieve? blood vessel growth also has important clinical value. For example, cancerous tumours can only grow by 2. Thalidomide is dangerous to fetal development for developing new blood supplies to provide them with only a very short time in early pregnancy, three to oxygen and nutrients and to carry away wastes. By five weeks after conception. Other approved drugs preventing the growth of new blood vessels, on the market, including an acne drug, also have side thalidomide starves tumours and stunts their growth. effects that include producing fetal malformations. Thalidomide suppresses the production of a chemical What other examples can you think of where lack messenger called tumour necrosis factor, or TNF. This of complete information might distort the evaluation of a drug? Chapter 1 The Chemistry of Life MHR 19  MINI LAB Reviewing Macromolecules principal functions of these polymers in living systems You have studied carbohydrates, lipids, proteins, and sources in nature from which cells and other living nucleic acids in previous science courses. Use the systems may obtain these essential compounds molecules shown in Figure 1.14 as a starting point for Analyze designing a reference resource on the structure and 1. Cells metabolize macromolecules in a fluid environment. function of these four main types of macromolecules. Your Why is water necessary for metabolic processes? reference resource can incorporate one or several media, Would these processes be possible in a non-fluid and should include the following information, as well as any environment? Defend your answer. additional details you deem appropriate: types of polymers formed from the monomer subunits shown in Figure 1.14 SECTION REVIEW 1. C Biologists usually consider inorganic compounds 5. K/U What is a functional group? State two as part of the non-living world and organic characteristics of a functional group that make compounds as part of the living world. it important to biological systems. (a) What property of water makes it an inorganic 6. C Name three macromolecules and sketch the compound? monomer subunit for each. (b) Why is water, nevertheless, an essential 7. MC Like carbon, atoms of the element silicon component of all living systems? can form bonds with as many as four other atoms. 2. C In this section you read, “The diversity of life relies Ammonia is a more polar substance than water. In greatly upon the versatility of carbon.” Explain your your opinion, why is life on Earth based on carbon understanding of the significance of this statement. chains in water, instead of silicon chains in ammonia? Use examples to support and enhance your 8. I Examine the carbon “skeletons” shown below. explanation. How many additional atoms can bond with the 3. K/U Explain why glucose, fructose, and galactose highlighted carbon atom in each case? are isomers. C 4. K/U Describe the differences between a C C C C C C C C C C stereoisomer and a structural isomer. Give an example of each. C A B C D 20 MHR Unit 1 Metabolic Processes  1.3 Making and Breaking Macromolecules E X P E C TAT I O N S Identify and describe the four main kinds of biochemical reactions. Use molecular models to infer the polarity of molecules. Investigate the structures and properties of macromolecules and functional groups using models. Large molecules can be broken down to release the concentration of these ions is low. In pure water energy. Alternatively, they can be formed to build at 25°C, the concentration of each of these ions is cellular structures or store information. In the same: 1 × 10−7 mol/L. Because hydrogen and biological systems there are four major types of hydroxide ions are very reactive, changes in their chemical reactions involved in breaking apart and concentrations can drastically affect cells and the building molecules: macromolecules within them. Acids and bases, and acid-base or neutralization reactions, which more specifically the concentrations of hydrogen transfer hydrogen ions between molecules, and hydroxide ions within cells, determine how effectively cellular processes are carried out. redox, or oxidation-reduction reactions, which transfer electrons between molecules, pH hydrolysis reactions, in which molecules react 14 1 mol/L NaOH (14.0) with H2O to form other molecules, and condensation reactions, in which molecules react 13 lye (sodium hydroxide) to form H2O and other molecules. (13.0) These types of chemical reactions are described 12 below. household ammonia (11.9) MORE BASIC 11 Acids, Bases, and milk of magnesia (antacid) (10.5) Neutralization Reactions 10 detergent solution Acids and bases are compounds that may be (approximately 10) inorganic or organic. Hydrochloric acid, found in 9 the mammalian stomach, is an inorganic acid. Acetic acid and amino acids are examples of 8 ocean water (7.0–8.3) organic acids. Sodium hydroxide, a key component blood (7.4) of oven cleaners, is an inorganic base. Purines and 7 NEUTRAL pyrimidines, the molecules that form part of the milk (6.4) subunits of nucleic acids, are examples of organic 6 urine (4.8–7.5) bases; they are often referred to as nitrogenous rain water (5.6) bases, because they include the nitrogen-containing MORE ACIDIC 5 amine group. What is it, however, that makes one substance an tomatoes (4.2) 4 acid and another a base? In biology, acids and bases are understood in relation to their behaviour in vinegar (2.4–3.4) 3 water. Under normal conditions, pure water exists lemon juice (2.2–2.4) Figure 1.15 in the form of H2O molecules. A small number of 2 Substances that these molecules dissociate, which means that they are acidic have a break up into ions. When a water molecule stomach acid pH less than 7, 1 (mainly HCl) (1.0–3.0) dissociates, it forms a positively charged hydrogen while substances ion, H+ , and a negatively charged hydroxide ion, that are basic 1 mol/L HCl (0.0) have a pH OH−. Since very few water molecules dissociate, 0 greater than 7. Chapter 1 The Chemistry of Life MHR 21  An acid is any substance that donates H+ ions according to the relative concentrations of their when it dissolves or dissociates in water. Therefore, hydrogen and hydroxide ions. Water, with equal acids increase the concentration of H+ ions in water concentrations of these ions, is considered neutral solutions. Bases, on the other hand, decrease the and has a pH of 7. Substances with a pH that is concentration of H+ ions in solution. Usually this lower than 7 have higher concentrations of H+ ions occurs because bases attract H+ ions, thus reducing (and lower concentrations of OH− ions), so they are their concentration. As a result, the concentration acids. Substances with a pH that is higher than 7 of OH− ions increases when bases dissolve or have lower concentrations of H+ ions (and higher dissociate in water. The pH scale, shown in concentrations of OH− ions), so they are bases. Figure 1.15, is a means for ranking substances When acids and bases react, they produce two products: water and a salt (an ionic compound). This Investigation 1 A SKILL FOCUS Predicting Acids, Bases, and Cellular pH Performing and recording The pH value indicates whether a substance is acidic or basic. Acids have a pH Analyzing and interpreting value less than 7 and bases have a pH value greater than 7. Most cells function at around pH 7, which is considered to be a neutral environment. To maintain Communicating results this neutral environment, cells must control, or buffer, the pH level so it does not become too acidic or too basic. In this investigation you will determine the effects of adding an acid and a base to several solutions. You will use a commercially prepared buffer solution and a solution made from living cells. Pre-lab Questions 0.1 mol/L HCl 0.1 mol/L NaOH What factors might influence the pH of cells? commercial buffer solution, pH 7 Why might cells need to maintain a constant pH 10% homogenized potato solution environment? 50 mL beaker distilled water in squirt bottle How do cells regulate pH? medicine dropper tap water Problem graphing paper How do acids and bases affect living cells? Procedure Prediction 1. Work in a small group. Read steps 2 to 7, then Make a prediction about how cells maintain a design a data table to record your results. constant pH. 2. Add 20 mL of tap water to a clean beaker, and CAUTION: Acids and bases are corrosive and measure the pH of the water. If you are using universal indicator paper, use only a small piece. caustic substances. Avoid any contact with skin, Immerse the paper into the water using the forceps. eyes, or clothes. If contact does occur, rinse Compare the colour of the paper against the pH thoroughly with water and inform your teacher. chart and determine the pH. Clean up any spill immediately. Dispose of any materials as instructed by your teacher. Wash 3. To the 20 mL of tap water, add one drop of the your hands before leaving the laboratory. HCl solution. Gently swirl the contents, and then measure the pH. Continue adding drops of the HCl solution to the beaker, recording the pH after each drop, until a total of five drops has been added. Materials Gently swirl the contents of the beaker after each drop is added. universal indicator paper or pH meter forceps pH scale 22 MHR Unit 1 Metabolic Processes chemical process in which acids and bases react to proteins require a certain pH in order to take on product a salt and water is called a neutralization their characteristic shapes. Therefore, it is important reaction. In such a reaction, the acid no longer acts for pH in organisms to be maintained at specific as an acid and the base no longer acts as a base; levels. Certain chemicals or combinations of their properties have been neutralized. chemicals known as buffers minimize changes in pH. Buffers maintain pH levels by