The Molecules of Cells - Honors Biology · PDF file03.09.2011 · Chapter 3 The Molecules of Cells Chapter Objectives Opening Essay Explain why lactose intolerance is considered normal

C h a p t e r 3

The Molecules of Cells

Chapter Objectives

Opening EssayExplain why lactose intolerance is considered normal in adult humans. Explain why lactosetolerance might have evolved in people of European descent.

Introduction To Organic Compounds3.1 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.

Carbohydrates3.4–3.7 Describe the structures, functions, properties, and types of carbohydrate molecules

common in the human diet.

Lipids3.8–3.10 Describe the structures, functions, properties, and types of lipid molecules.

3.10 Describe the health risks associated with the use of anabolic steroids.

Proteins3.11–3.14 Describe the structures, functions, properties, and types of proteins.

3.15 Describe the major achievements of Linus Pauling.

Nucleic Acids3.16 Compare the structures and functions of DNA and RNA.3.17 Describe the adaptive advantage of lactose tolerance in people of East African decent.

13

alpha helixamineamino acidamino groupanabolic steroidcarbohydratecarbon skeletoncarbonyl groupcarboxyl group

carboxylic acidcellulosechitincholesteroldehydration reactiondenaturationdeoxyribonucleic acid

(DNA)disaccharide

double helixenzymefatfunctional groupgeneglycogenhydrocarbonhydrolysishydrophilic

Key Terms

M03_CAMB3215_06_SE_C03.QXD 4/2/08 2:11 PM Page 13

Word Rootsde- � without or remove; hydro- � water (dehydration reaction: a chemical process in which two mole-cules 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 linkedby a dehydration reaction)

carb- � coal (carboxyl group: a functional group in an organic molecule, consisting of an oxygen atomdouble-bonded to a carbon atom that is also bonded to a hydroxyl group)

glyco- � sweet (glycogen: an extensively branched polysaccharide of many glucose monomers thatserves 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 secondarystructure); double helix: the form of native DNA, composed of two adjacent polynucleotide strandswound 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 chemicaladdition 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 differentstructures and, therefore, different properties)

macro- � large (macromolecule: a giant molecule in a living organism formed by the joining of smallermolecules)

mono- � single (monosaccharide: simplest type of sugar; meros- = part (monomer: a chemical subunitthat serves as a building block of a polymer)

poly- � many (polymer: a large molecule consisting of many monomers covalently joined together in achain; polysaccharide: many monosaccharides joined together)

quatr- � four (quaternary structure: the fourth level of protein structure; the shape resulting from theassociation of two or more polypeptide subunits)

terti- � three (tertiary structure: the third level of protein structure; the overall, three-dimensional shapeof a polypeptide due to interactions of the R groups of the amino acids making up the chain)

14 Instructor’s Guide to Text and Media

hydrophobichydroxyl groupisomerslipidmacromoleculemethyl groupmonomermonosaccharidenucleic acidnucleotide

organic compoundpeptide bondphosphate groupphospholipidpleated sheetpolymerpolypeptidepolysaccharideprimary structureprotein

quaternary structureribonucleic acid

(RNA)saturatedsecondary structurestarchsteroidtertiary structureunsaturated


Student MediaIntroduction 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 (3.1–3.3)Student Misconceptions and Concerns

1. General biology students might not have previously taken a chemistry course. Theconcept of molecular building blocks that cannot be seen can be abstract and diffi-cult to comprehend for such students. Concrete examples from our diets and goodimages will increase comprehension. (3.1–3.3)

2. Students might need to be reminded about the levels of biological organization. Therelationship between atoms, monomers, and polymers can be confusing as each isdiscussed. Consider noting these relationships somewhere in the classroom (such ason the board) where students can quickly glance for reassurance. (3.1)

Chapter 3 The Molecules of Cells 15


Teaching Tips1. 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 thissort 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 quickconstruction 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 withdifferent functional groups. The analogy relates the role of different functions todifferent structures. (3.2)

4. Train cars linking together to form a train is a nice analogy to linking monomers toform polymers. Considering adding that as the train cars are joined, a puff of steamappears—a the reference to water production and a dehydration reaction whenlinking molecular monomers. (3.3)

Carbohydrates (3.4–3.7)

Student Misconceptions and Concerns1. 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 foodnutrition label. Candy bars with peanuts are particularly useful, as they containsignificant amounts of all three sources of calories (carbohydrates, proteins, andlipids). (3.4)

2. Consider reinforcing the three main sources of calories with food items that clearlyrepresent each group. Bring clear examples to class as visual references. Forexample, a can of Coke or a bag of sugar for carbohydrates, a tub of margarine forlipids, and some beef jerky for protein (although some fat and carbohydrates mightalso be included). (3.4–3.7)

Teaching Tips1. 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 intro-ducing this conceptual formula might help: eating glucose � breathing in oxygen → water � usable energy (used to build ATP) � heat � exhaling CO2. (3.4)

2. Learning the definitions of word roots is invaluable when learning science. Learningthe 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. Con-sider asking each student to bring to class a product label that indicates the use ofhigh-fructose corn syrup (HFCS) as an ingredient. (3.6)

4. Consider an assignment for students to access the Internet and find reliable sourcesthat 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 non-profit 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



while it mixes well with saliva, they might soon notice that a sweeter taste beginsto emerge. The salivary enzyme amylase begins the digestion of starches intodisaccharides, which may be degraded further by other enzymes. These disaccha-rides 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 materialderived from cellulose. Consider challenging students to create a list of othercellulose-derived products (such as paper.) (3.7)

8. An adult human may store about a half kilogram of glycogen in the liver and mus-cles of the body, depending up recent dietary habits. A person who begins dietingmight soon notice an immediate weight loss of 2–4 pounds (1–2 kilograms) overseveral days, reflecting reductions in stored glycogen, water, and intestinal contents(among other factors). (3.7)

Lipids (3.8–3.10)Student Misconceptions and Concerns

1. Students may struggle with the concept that a pound of fat contains more than twicethe calories of a pound of sugar. It might seem that a pound of food would potentiallyadd on a pound of weight. Other students may have never understood the concept ofcalories 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, bodyweight, and healthy diets. (3.8)

2. Students might struggle to extrapolate the properties of lipids to their roles in anorganism. Ducks float because their feathers repel water instead of attracting it. Hair onour heads remains flexible because of oils produced in our scalp. Examples such asthese help connect the abstract properties of lipids to concrete examples in our world.(3.8–3.10)

Teaching Tips1. 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 frontof 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 mixturealready made ahead of time that remains separated; however, the dye may bleedbetween the oil and the water.) Placing the mixture on an overhead projector or other well-illuminated imaging device makes for a dramatic display of hydrophobicactivity! (3.8)

2. The text notes that a gram of fat stores more than twice the energy of a gram of poly-saccharide, such as starch. You might elaborate with a simple calculation to demonstratehow a person’s body weight would vary if the energy stored in body fat were stored incarbohydrates instead. If a 100-kg man carried 25% body fat, he would have 25 kg offat 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 ofcarbohydrate? (2.25 � 25 � 56.25 kg of carbohydrate �75kg � 131.25 kg, an increaseof 31.25%) (3.8)

3. Margarine in stores commonly comes in liquid squeeze containers, in tubs, and insticks. These forms reflect increasing amounts of hydrogenation, gradually increasing



the stiffness from a liquid, to a firmer spread, to a firm stick of margarine. As noted inthe text, recent studies have suggested that unsaturated oils become increasinglyunhealthy as they are hydrogenated. Public attention to hydrogenation and the healthrisks of the resulting trans fats are causing changes in the use of products containingtrans 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 cangenerate the two most common configurations: (1) a lipid bilayer encircling water(water surrounding the bilayer and contained internally) and (2) a micelle (polar headsin 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 normallyregulate the traits affected by steroid abuse. (3.9)

Proteins (3.11–3.15)Student Misconceptions and Concerns

1. The functional significance of protein shape is an abstract molecular example of formand function relationships, which might be new to some students. The binding of anenzyme to its substrate is a type of molecular handshake, which permits specificinteractions. To help students think about form and function relationships, share someconcrete analogies in their lives—perhaps flathead and Phillips screwdrivers that matchthe proper type of screws or the fit of a hand into a glove. (3.13)

Teaching Tips1. 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 lettersto form words. Proteins are much longer “words,” creating even more diversity. Anotheranalogy is to trains. This builds upon the earlier analogy when polymers were intro-duced. Imagine making different trains about 100 cars long, using any combination of20 types of railroad cars. Mathematically, the number of possible trains is 20100, anumber beyond imagination. (3.11–3.12)

2. The authors note that the difference between a polypeptide and a protein is analogousto 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 acooked steak is the product of the denaturation of proteins. Fixatives such as formalinalso denature proteins and cause color changes. Students who have dissected vertebrateswill realize that the brown color of the muscles makes it look as if the animal has beencooked. (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 ofa McDonalds’ Big Mac or other fast-food sandwich. Note the most abundant organicmolecule class (perhaps by weight) found in each component. (3.14)

5. An examination of the fabrics and weave of a sweater might help students understandthe levels of protein structure. Although not a perfect analogy, levels of organization canbe better appreciated. Teasing apart a single thread reveals a simpler organization ofsmaller 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



sleeve. Challenge students to identify the limits of this analogy and identify aspects ofprotein structure not included (such as the primary structure of a protein, its sequenceof amino acids). (3.15)

6. Additional details of Linus Pauling’s career can be found on the website of the LinusPauling Institute at Oregon State University, http://lpi.oregonstate.edu/lpbio/lpbio2.html.(3.15)

Nucleic Acids (3.16 –3.17)Student Misconceptions and Concerns

1. Module 3.16 is the first time the authors present the concept of transcription and trans-lation, discussed extensively in later chapters. The basic conceptual flow of informationfrom 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 repre-sent a deliberate decision, yet this evolutionary change appears logical. Many studentsperceive adaptations as deliberate events with purpose. As students develop a betterunderstanding of the mechanisms of evolution, it will be important to point out thatmutations arise by chance, with the culling hand of natural selection favoring traits thatconvey advantage. Organisms cannot plan evolutionary change. (3.17)

Teaching Tips1. 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 challengingyour students with the following questions based upon prior analogies. If the 20 possibleamino acids in a polypeptide represent “words” in a long polypeptide sentence, howmany 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 substitutesfor thymine.) (3.17)




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The Molecules of Cells - Honors Biology · PDF file03.09.2011 · Chapter 3 The Molecules of Cells Chapter Objectives Opening Essay Explain why lactose intolerance is considered normal