The Molecules of Cells

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1 Chapter 3 The Molecules of Cells Chapter Objectives Opening Essay Explain why lactose intolerance is considered normal in adult humans. Explain why lactose tolerance might have evolved in people of European descent. Introduction To Organic Compounds 3.1 Explain why carbon is unparalleled in its ability to form large, diverse molecules. 3.1 Define organic compounds, hydrocarbons, a carbon skeleton, and an isomer. 3.2 Describe the properties of and distinguish between the six chemical groups important in the chemistry of life. 3.3 List the four main classes of macromolecules, explain the relationship between monomers and polymers, and compare the processes of dehydration synthesis and hydrolysis. Carbohydrates Describe the structures, functions, properties, and types of carbohydrate molecules common in the human diet. Lipids Describe the structures, functions, properties, and types of lipid molecules Describe the health risks associated with the use of anabolic steroids. Proteins Describe the structures, functions, properties, and types of proteins Describe the major achievements of Linus Pauling. Nucleic Acids 3.16 Compare the structures and functions of DNA and RNA Describe the adaptive advantage of lactose tolerance in people of East African decent. Key Terms alpha helix amine amino acid amino group anabolic steroid carbohydrate carbon skeleton carbonyl group carboxyl group carboxylic acid cellulose chitin cholesterol dehydration reaction denaturation deoxyribonucleic acid (DNA) disaccharide double helix enzyme fat functional group gene glycogen hydrocarbon hydrolysis hydrophilic 13

2 14 Instructor s Guide to Text and Media hydrophobic hydroxyl group isomers lipid macromolecule methyl group monomer monosaccharide nucleic acid nucleotide organic compound peptide bond phosphate group phospholipid pleated sheet polymer polypeptide polysaccharide primary structure protein quaternary structure ribonucleic acid (RNA) saturated secondary structure starch steroid tertiary structure unsaturated Word Roots de- without or remove; hydro- water (dehydration reaction: a chemical process in which two molecules become covalently bonded to each other with the removal of a water molecule) di- two; -sacchar sugar (disaccharide: a sugar molecule consisting of two monosaccharides linked by a dehydration reaction) carb- coal (carboxyl group: a functional group in an organic molecule, consisting of an oxygen atom double-bonded to a carbon atom that is also bonded to a hydroxyl group) glyco- sweet (glycogen: an extensively branched polysaccharide of many glucose monomers that serves as an energy-storage molecule in animal liver and muscle cells) helic- a spiral (alpha helix: spiral shape created by the coiling of polypeptides in a protein s secondary structure); double helix: the form of native DNA, composed of two adjacent polynucleotide strands wound into a spiral shape) hydro- water (hydrocarbon: a chemical compound composed only of the elements carbon and hydrogen) -lyse break (hydrolysis: a chemical process in which polymers are broken down by the chemical addition of water molecules to the bonds linking their monomers); -philos loving (hydrophilic: water-loving : refers to polar, or charged, molecules [or parts of molecules] that are soluble in water.) -phobos fearing (hydrophobic: water-fearing : refers to nonpolar molecules [or parts of molecules] that do not dissolve in water) iso- equal (isomer: one of several organic compounds with the same molecular formula but different structures and, therefore, different properties) macro- large (macromolecule: a giant molecule in a living organism formed by the joining of smaller molecules) mono- single (monosaccharide: simplest type of sugar; meros- = part (monomer: a chemical subunit that serves as a building block of a polymer) poly- many (polymer: a large molecule consisting of many monomers covalently joined together in a chain; polysaccharide: many monosaccharides joined together) quatr- four (quaternary structure: the fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits) terti- three (tertiary structure: the third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain)

3 Chapter 3 The Molecules of Cells 15 Student Media Introduction to Organic Compounds Activity: Diversity of Carbon-Based Molecules (3.1) Activity: Functional Groups (3.2) Activity: Making and Breaking Polymers (3.3) Carbohydrates Activity: Models of Glucose (3.4) Activity: Carbohydrates (3.7) You Decide: Low-Fat or Low-Carb Diets Which is Healthier? (3.6) Lipids Activity: Lipids (3.9) Proteins MP3 Tutor: Protein Structure and Function (3.13) Activity: Protein Functions (3.11) Activity: Protein Structure (3.14) BLAST Animation: Alpha Helix (3.14) BLAST Animation: Protein Primary Structure (3.14) BLAST Animation: Protein Secondary Structure (3.14) BLAST Animation: Protein Tertiary and Quaternary Structure (3.14) Nucleic Acids MP3 Tutor: DNA Structure (3.16) Activity: Nucleic Acid Structure (3.16) Process of Science: Connection: What Factors Determine the Effectiveness of Drugs? (3.16) Chapter Guide to Teaching Resources Introduction to Organic Compounds ( ) 1. General biology students might not have previously taken a chemistry course. The concept of molecular building blocks that cannot be seen can be abstract and difficult to comprehend for such students. Concrete examples from our diets and good images will increase comprehension. ( ) 2. Students might need to be reminded about the levels of biological organization. The relationship between atoms, monomers, and polymers can be confusing as each is discussed. Consider noting these relationships somewhere in the classroom (such as on the board) where students can quickly glance for reassurance. (3.1)

4 16 Instructor s Guide to Text and Media 1. One of the great advantages of carbon is its ability to form up to four bonds, permitting the assembly of diverse components and branching configurations. Challenge your students to find another element that might also permit this sort of adaptability. (Like carbon, silicon has four electrons in its outer shell.) (3.1) 2. Toothpicks and gumdrops (or any other pliable small candy) permit the quick construction of chemical models. Different candy colors can represent certain atoms. The model of the methane molecule in Figure 3.1 can thus easily be demonstrated (and consumed!) (3.1) 3. A drill with interchangeable drill bits is a nice analogy to carbon skeletons with different functional groups. The analogy relates the role of different functions to different structures. (3.2) 4. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Considering adding that as the train cars are joined, a puff of steam appears a the reference to water production and a dehydration reaction when linking molecular monomers. (3.3) Carbohydrates ( ) 1. The abstract nature of chemistry can be discouraging to many students. Consider starting out this section of lecture by examining the chemical groups on a food nutrition label. Candy bars with peanuts are particularly useful, as they contain significant amounts of all three sources of calories (carbohydrates, proteins, and lipids). (3.4) 2. Consider reinforcing the three main sources of calories with food items that clearly represent each group. Bring clear examples to class as visual references. For example, a can of Coke or a bag of sugar for carbohydrates, a tub of margarine for lipids, and some beef jerky for protein (although some fat and carbohydrates might also be included). ( ) 1. If your lectures will eventually include details of glycolysis and aerobic respiration, this is a good point to introduce the basic concepts of glucose as fuel. Just introducing this conceptual formula might help: eating glucose breathing in oxygen water usable energy (used to build ATP) heat exhaling CO 2. (3.4) 2. Learning the definitions of word roots is invaluable when learning science. Learning the meaning of the prefix word roots mono (one), di (two), and poly (many) helps to distinguish the structures of various carbohydrates. (3.5) 3. The widespread use of high-fructose corn syrup can be surprising to students. Consider asking each student to bring to class a product label that indicates the use of high-fructose corn syrup (HFCS) as an ingredient. (3.6) 4. Consider an assignment for students to access the Internet and find reliable sources that discuss high rates of sugar consumption in the modern diet. The key, of course, is in the quality of the resource. Consider limiting their search to established nonprofit organizations (American Cancer Society, American Heart Association, etc.) and peer-reviewed journals. (3.6) 5. A simple exercise demonstrates the enzymatic breakdown of starches into sugars. If students place an unsalted cracker in their mouths, holding it in their mouths

5 Chapter 3 The Molecules of Cells 17 Lipids ( ) while it mixes well with saliva, they might soon notice that a sweeter taste begins to emerge. The salivary enzyme amylase begins the digestion of starches into disaccharides, which may be degraded further by other enzymes. These disaccharides are the source of the sweet taste. (3.7) 6. The text notes that cellulose is the most abundant organic molecule on Earth. Ask your students why this is true. (3.7) 7. The cellophane wrap often used to package foods is a biodegradable material derived from cellulose. Consider challenging students to create a list of other cellulose-derived products (such as paper.) (3.7) 8. An adult human may store about a half kilogram of glycogen in the liver and muscles of the body, depending up recent dietary habits. A person who begins dieting might soon notice an immediate weight loss of 2 4 pounds (1 2 kilograms) over several days, reflecting reductions in stored glycogen, water, and intestinal contents (among other factors). (3.7) 1. Students may struggle with the concept that a pound of fat contains more than twice the calories of a pound of sugar. It might seem that a pound of food would potentially add on a pound of weight. Other students may have never understood the concept of calories in the diet, simply following general guidelines of avoiding fatty foods. Furthermore, fiber and water have no caloric value but add to the weight of food. Consider class discussions that explore student misconceptions about calories, body weight, and healthy diets. (3.8) 2. Students might struggle to extrapolate the properties of lipids to their roles in an organism. Ducks float because their feathers repel water instead of attracting it. Hair on our heads remains flexible because of oils produced in our scalp. Examples such as these help connect the abstract properties of lipids to concrete examples in our world. ( ) 1. The text in Module 3.8 notes the common observation that vinegar and oil do not mix in this type of salad dressing. A simple demonstration can help make this point. In front of the class, mix together colored water and a yellow oil (corn or canola oil work well). Shake up the mixture and then watch as the two separate. (You may have a mixture already made ahead of time that remains separated; however, the dye may bleed between the oil and the water.) Placing the mixture on an overhead projector or other well-illuminated imaging device makes for a dramatic display of hydrophobic activity! (3.8) 2. The text notes that a gram of fat stores more than twice the energy of a gram of polysaccharide, such as starch. You might elaborate with a simple calculation to demonstrate how a person s body weight would vary if the energy stored in body fat were stored in carbohydrates instead. If a 100-kg man carried 25% body fat, he would have 25 kg of fat in his body. Fat stores about 2.25 times more energy per gram than carbohydrate. What would be the weight of the man if he stored the energy in the fat in the form of carbohydrate? ( kg of carbohydrate 75kg kg, an increase of 31.25%) (3.8) 3. Margarine in stores commonly comes in liquid squeeze containers, in tubs, and in sticks. These forms reflect increasing amounts of hydrogenation, gradually increasing

6 18 Instructor s Guide to Text and Media Proteins ( ) the stiffness from a liquid, to a firmer spread, to a firm stick of margarine. As noted in the text, recent studies have suggested that unsaturated oils become increasingly unhealthy as they are hydrogenated. Public attention to hydrogenation and the health risks of the resulting trans fats are causing changes in the use of products containing trans fats. (3.8) 4. Before explaining the properties of a polar molecule such as a phospholipid, have students predict the consequences of adding phospholipids to water. See if the class can generate the two most common configurations: (1) a lipid bilayer encircling water (water surrounding the bilayer and contained internally) and (2) a micelle (polar heads in contact with water and hydrophobic tails clustered centrally). (3.9) 5. The consequences of steroid abuse will likely be of great interest to your students. However, the reasons for the damaging consequences might not be immediately clear. As time permits, consider noting the diverse homeostatic mechanisms that normally regulate the traits affected by steroid abuse. (3.9) 1. The functional significance of protein shape is an abstract molecular example of form and function relationships, which might be new to some students. The binding of an enzyme to its substrate is a type of molecular handshake, which permits specific interactions. To help students think about form and function relationships, share some concrete analogies in their lives perhaps flathead and Phillips screwdrivers that match the proper type of screws or the fit of a hand into a glove. (3.13) 1. Many analogies help students appreciate the diversity of proteins that can be made from just 20 amino acids. The authors note that our language uses combinations of 26 letters to form words. Proteins are much longer words, creating even more diversity. Another analogy is to trains. This builds upon the earlier analogy when polymers were introduced. Imagine making different trains about 100 cars long, using any combination of 20 types of railroad cars. Mathematically, the number of possible trains is ,a number beyond imagination. ( ) 2. The authors note that the difference between a polypeptide and a protein is analogous to the relationship between a long strand of yarn and a sweater knitted from yarn. Proteins are clearly more complex! (3.12) 3. Most cooking results in changes in the texture and color of food. The brown color of a cooked steak is the product of the denaturation of proteins. Fixatives such as formalin also denature proteins and cause color changes. Students who have dissected vertebrates will realize that the brown color of the muscles makes it look as if the animal has been cooked. (3.13) 4. Consider this assignment to review the organic molecules in our diets. Have students, working individually or in small groups, analyze a food label listing the components of a McDonalds Big Mac or other fast-food sandwich. Note the most abundant organic molecule class (perhaps by weight) found in each component. (3.14) 5. An examination of the fabrics and weave of a sweater might help students understand the levels of protein structure. Although not a perfect analogy, levels of organization can be better appreciated. Teasing apart a single thread reveals a simpler organization of smaller fibers woven together. In turn, threads are interlaced into a connected fabric, which may be further twisted and organized into a pattern or structural component of a

7 Chapter 3 The Molecules of Cells 19 sleeve. Challenge students to identify the limits of this analogy and identify aspects of protein structure not included (such as the primary structure of a protein, its sequence of amino acids). (3.15) 6. Additional details of Linus Pauling s career can be found on the website of the Linus Pauling Institute at Oregon State University, (3.15) Nucleic Acids ( ) 1. Module 3.16 is the first time the authors present the concept of transcription and translation, discussed extensively in later chapters. The basic conceptual flow of information from DNA to RNA to proteins is essential to these later discussions. (3.16) 2. The evolution of lactose tolerance within human groups in East Africa does not represent a deliberate decision, yet this evolutionary change appears logical. Many students perceive adaptations as deliberate events with purpose. As students develop a better understanding of the mechanisms of evolution, it will be important to point out that mutations arise by chance, with the culling hand of natural selection favoring traits that convey advantage. Organisms cannot plan evolutionary change. (3.17) 1. The NA in the acronyms DNA and RNA stands for nucleic acid. Students often do not make this association without assistance. (3.16) 2. When discussing the sequence of nucleotides in DNA and RNA, consider challenging your students with the following questions based upon prior analogies. If the 20 possible amino acids in a polypeptide represent words in a long polypeptide sentence, how many possible words are in the language of a DNA molecule? (Four nucleotides, GCAT, are possible). Are these the same words used in RNA? (Answer: No. Uracil substitutes for thymine.) (3.17)

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