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CHAPTER 2 THE CHEMISTRY OF BIOLOGY Chemistry is introduced in this chapter. Matter, atoms, elements, and molecules are defined. Chemical bonds are discussed in terms of their strength and formation, and the concept of polar versus nonpolar compounds is highlighted. Chemical reactions, such as oxidation-reduction and ionization, are examined in terms of their importance in cellular metabolism. The structures of proteins, fats, carbohydrates, and lipids are elucidated. Finally, the idea that the structure of macromolecules determines their properties is discussed.

Learning Objectives A student should learn the following concepts: 1. Materials that occupy space and have mass are called matter. 2. The organization of matter begins with the atom which is a combination of protons (positive charge), neutrons (no charge), and electrons (negative charge). 3. An element is made up of only one kind of atom. 4. The properties of each element results from the numbers of protons, neutrons, and electrons it contains. 5. The number of electrons in an element’s outermost orbital determines its chemical properties and reactivity. 6. Most elements exist as molecules or compounds, which consist of atoms joined by chemical bonds. 7. Chemical bonds result when two or more atoms share electrons (covalent bonds), donate electrons (ionic bonds), or accept electrons (ionic bonds) between their outer orbitals. 8. When electrons are not shared equally between atoms, an unequal distribution of charges will result, and the molecule/compound is called polar (having a positive pole and a negative pole). 9. When electrons are equally shared between atoms, an equal distribution of charges will result, and the molecule/compound is called nonpolar (electrically neutral). 10. Hydrogen bonding and Van der Waals forces are due to attractive forces between nearby molecules and atoms. 11. Cells derive their energy from chemical reactions, by moving electrons from molecule to molecule. 12. Substances entering a reaction are reactants, while substances left after a reaction is complete are called products. 13. Reactions can involve the synthesis of substances, the decomposition of substances, or the exchange of portions between substances. 14. Polar molecules that attract water to their surface are called hydrophilic, while nonpolar molecules that repel water are called hydrophobic. 15. In pure water H+ and OH- are produced in equal amounts. 16. In an acidic solution the H+ ions outnumber the OH- ions.

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17. In a basic solution the OH- ions outnumber the H+ ions. 18. Inorganic chemicals do not contain both carbon and hydrogen. 19. Organic chemicals contain both carbon and hydrogen. 20. Carbohydrates, lipids, proteins, and nucleic acids consist of monomers bound together in various lengths to form polymers. 21. Carbohydrates (made of monomers of monosaccharides) contain carbon, hydrogen, and oxygen. 22. Lipids contain long carbon-hydrogen chains that are nonpolar or hydrophobic. 23. Phospholipids are unique in that they contain a polar region and a nonpolar region. 24. The structure, behavior, and unique qualities of living things are a consequence of their proteins (made of monomers of amino acids joined by peptide bonds). 25. Proteins contain up to four levels of structure, and the structure of a protein is critical for its function. 26. Nucleic acids (DNA and RNA) consist of monomers of nucleotides. 27. DNA is the hereditary material in cells. 28. RNA is involved in protein synthesis.

Chapter Outline (also see Chapter Summary with Key Terms p. 53) 2.1

Atoms, Bonds, and Molecules: Fundamental Building Blocks  Introduction o Matter Is Made Up of Atoms o Atoms Consist of:  Protons  Neutrons  Electrons  Different Types of Atoms: Elements and Their Properties  The Major Elements of Life and Their Primary Characteristics o Atomic Number, Mass Number, Isotopes, and Atomic Mass or Weight o Electron Orbitals and Shells o A Note About Mass, Weight, and Related Terms  Bonds and Molecules o Molecules, Compounds, and Valence o Covalent Bonds: Molecules with Shared Electrons  A Note about Diatomic Elements  Polarity in Molecules  Polar  Nonpolar o Ionic Bonds: Electron Transfer among Atoms o Ionization: Formation of Charged Particles o Hydrogen Bonding o Electron Transfer and Oxidation-Reduction Reactions o Chemical Shorthand: Formulas, Models, and Equations

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  2.2

 Reactants  Products  Chemical Equation  Synthesis Reaction  Decomposition Reactions  Catalysts Solutions: Homogeneous Mixtures of Molecules o Solutes o Solvents o Concentration o Hydrophilic o Hydrophobic o Amphipathic o Molarity Acidity, Alkalinity, and the pH Scale o Acidic o Basic o pH Scale o Neutralization Reactions o Metabolism The Chemistry of Carbon and Organic Compounds o Inorganic Chemicals o Organic Chemicals Functional Groups of Organic Compounds

Macromolecules: Superstructures of Life  Biochemistry: The Compounds of Life o Macromolecules o Monomers o Polymers  Carbohydrates: Sugars and Polysaccharides o Introduction  Aldehydes  Ketones  Saccharide  Monosaccharide  Disaccharide  Polysaccharide o The Nature of Carbohydrate Bonds  Glycosidic Bonds  Dehydration Synthesis o The Functions of Carbohydrates in Cells  Cellulose  Agar

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 Chitin  Peptigolycan  Lipopolysaccharide  Glycocalyx  Starch  Glycogen Lipids: Fats, Phospholipids, and Waxes o Storage Lipids  Triglycerides  Glycerol  Fatty Acids  Ester Bond o Membrane Lipids  Phospholipids o A Note about Membranes o Miscellaneous Lipids  Steroids  Cholesterol  Ergosterol  Prostaglandins Proteins: Shapers of Life o Proteins  Amino Acids  Peptide Bond  Peptide  Polypeptide o Protein Structure and Diversity  Primary Structure: Chain of Amino Acids  Secondary Structure: Alpha Helix or Beta-Pleated Sheet  Tertiary Structure: Bonds Between Functional Groups  Quaternary Structure: Two or More Polypeptides  Examples of Proteins:  Enzymes  Antibodies  Receptors The Nucleic Acids: A Cell Computer and Its Programs o Deoxyribonucleic Acid (DNA) o Ribonucleic Acid (RNA) o Nucleic Acids Are Made of Nucleotides, Which Contain:  A Nitrogen Base  A Pentose Sugar  A Phosphate The Double Helix of DNA o Making New DNA: Passing on the Genetic Message  Replication

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o RNA: Organizers of Protein Synthesis  Messenger RNA  Transfer RNA  Ribosomal RNA o ATP: The Energy Molecule of Cells

Student Activities 1. After covering the section on Protein Structure and Diversity (p. 48), and discussing the primary, secondary, tertiary, and quaternary structures of proteins, have students research diseases which have been attributed to improperly folded proteins. The list will vary but should include Alzheimer’s disease, cystic fibrosis, cancer, Creutzfeldt-Jakob disease (CJD), and diabetes. 2. Visualizing molecules, compounds, and macromolecules is often difficult for students, particularly when they always see the structures on a flat sheet of paper. Use molecular model kits (most likely available in your chemistry department) to build methane, a polysaccharide, and lipids. These kits can also be used to demonstrate the formation of covalent bonds. To do this, first construct two separate monosaccharides (monomers), then remove an OH group from one monomer and an H group from the other monomer, join them together—thus performing dehydration synthesis (see pp. 42-43). 3. Bring two see-through bottles with lids, water, salt, and cooking oil to class. Fill both the bottles ¾ full with water, then add some oil to one bottle and some salt to the other. Have students shake the bottles, then discuss the concept of hydrophilic versus hydrophobic as the salt dissolves in the water and the oil coalesces into droplets. 4. Bring some pH paper, small paper cups, and ammonia (any household cleaner with a basic pH will work) to class. As students enter the classroom have them pour small amounts of their beverages (cola, flavored water, coffee) into the cups. Determine the pH of the beverages and ammonia using the pH paper. Then place their beverages and the cleaner onto the pH scale in Figure 2.13. Have them determine the concentration of hydrogen ions in the beverages and the concentration of hydrogen ions in the cleaner. 5. After discussing Figure 2.26 on DNA replication, have students visit the site and click on the link “DNA workshop activity.” After selecting replication, students will be led through the steps in DNA replication (unzipping and matching the base pairs).

Classroom Discussion 1. Ask students the following question: changing the number of which subatomic particle (proton, neutron, or electron) changes the element? Through answering this question students will define isotopes and ions.

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2. Students may have a pre-formed opinion of the definition of organic. Spend time discussing the definition of organic as it relates to chemistry as opposed to the definition of organic in terms of agriculture. 3. As you cover the periodic table (Figure 2.2), explain that the table is arranged vertically according to the number of electrons present in the outer shell (except for helium). With this knowledge it is easy for students to determine the reactivity of the different atoms (without having to draw out all the shells). Also, it is a good way for students to check their models to make sure they have the proper number of electrons present in the outer shell. 4. When lecturing on the various types of chemical bonds, have students discuss which bonds they think would be the strongest. List the order of strength of the bonds (covalent, ionic, hydrogen, and Van der Waals) and discuss how the strength of the bond correlates with the structure of the bond. This discussion will allow you to focus on the difference between sharing electrons and donating or accepting electrons as opposed to electrostatic forces. 5. Show Figure 2.15 and discuss the fact that glucose, fructose, and galactose all have the same chemical formula (C6H12O6). Then look at the structures of maltose, sucrose, and lactose that also have the same chemical formulas, but have different structures. The difference in their structures becomes readily apparent in lactose intolerant individuals, who can digest sucrose but not lactose. This discussion can also highlight the specificity of enzymes and proteins, and how the structure of compounds influences their function.

Applicable Online Quizzes Chapter 2 Multiple Choice Quiz Protein Denaturation Quiz

Key Terms and Phrases matter atom protons neutrons electrons nucleus elements atomic number (AN) mass number (MN) isotopes atomic mass/weight

orbitals molecule compounds formula mass molecular weight chemical bonds valence covalent bonds polar nonpolar ionic bonds

ionization ions cations anions electrolytes hydrogen bond Van der Waals forces oxidation reaction reduction reaction redox reaction reducing agent

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oxidizing agent products reactants synthesis reaction catalyst solution solute solvent hydrated hydrophilic hydrophobic amphipathic concentration hydrogen ion hydroxide ion acidic basic pH neutralization metabolism inorganic chemicals organic chemicals functional groups biochemistry macromolecules monomers polymers carbohydrate

aldehydes ketones monosaccharide disaccharide polysaccharide hexose pentose fructose lactose maltose sucrose glycosidic bonds dehydration synthesis cellulose agar chitin peptidoglycan lipopolysaccharide glycocalyx starch glycogen hydrolysis lipid triglycerides fatty acids glycerol ester bond membrane lipids

phospholipids cholesterol proteins amino acids peptide bond peptide polypeptide primary structure secondary structure tertiary structure cysteine quaternary structure enzymes antibodies deoxyribonucleic acid (DNA) ribonucleic acid (RNA) nucleotides nitrogen base adenine (A) guanine (G) thymine (T) cytosine (C) uracil (U) replication adenine triphosphate (ATP) electronegativity

Instructors are encouraged to visit the Foundations in Microbiology ARIS (Assessment, Review, Instruction System) site at for animations of key processes, online quizzing, case presentations, and more.

Solution manual foundations in microbiology 7th edition talaro