U N I T 1 Metabolic Processes Unit L ike 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 chrysalides, a monarch butterfly caterpillar will discover 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 How do organisms obtain the energy they Chapter 3 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? W What is ATP, and what ithin 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: Polypeptides and Polarity 28 Macromolecules 21 1.2 Biological Macromolecules and Their Subunits 14 Investigation 1-A: Acids, Bases, and Cellular pH 22 5 Atoms and Bonding 1.1 EXPECTATIONS Explain the term electronegativity. Express the relationship between electronegativity, bonding, and the polarity of molecules. Living 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 energy to function from chemical reactions that Atomic mass Abundance 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. An electron in the first shell (nearest the nucleus) hydrogen H 1.0 10.0 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 shell. For example, the third shell can hold a total magnesium Mg 24.3 0.07 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 (Cl ). Atoms of sodium and 2 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 1.When you use these chemicals for a laboratory activity, Throughout this course, you will use solutions of chemicals what personal safety supplies will you need? Explain such as hydrochloric acid and sodium hydroxide to help your choices. you isolate, identify, or investigate the properties of various 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 – 1178pn electron 1178pn 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 + 17p 17p 17p 18n 18n 18n 18n Cl Cl Cl Cl chlorine chlorine chlorine gas (C I ) 2 8p + 8p 8p 8p 8n 8n 8n 8n O O O O oxygen oxygen oxygen gas (O ) 2 1p 1p + 8p 8p 8n 8n 1p 1p O H oxygen 2H O H hydrogen water ( H O ) 2 Figure 1.5 In a covalent bond, electrons are shared between atoms. 10 MHR • Unit 1 Metabolic Processes