Chapter 3 The Molecules of Cells.

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1 Chapter 3 The Molecules of Cells

2 INTRODUCTION TO ORGANIC COMPOUNDS
© 2012 Pearson Education, Inc. 2

3 3.1 Life’s molecular diversity is based on the properties of carbon
Diverse molecules found in cells are composed of carbon bonded to other carbons and atoms of other elements. Carbon-based molecules are called organic compounds. Student Misconceptions and Concerns 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. 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. Teaching Tips 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.) 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)! © 2012 Pearson Education, Inc. 3

4 3.1 Life’s molecular diversity is based on the properties of carbon
By sharing electrons, carbon can bond to four other atoms and branch in up to four directions. Methane (CH4) is one of the simplest organic compounds. Four covalent bonds link four hydrogen atoms to the carbon atom. Each of the four lines in the formula for methane represents a pair of shared electrons. Student Misconceptions and Concerns 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. 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. Teaching Tips 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.) 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)! © 2012 Pearson Education, Inc. 4

5 3.1 Life’s molecular diversity is based on the properties of carbon
Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons. Carbon, with attached hydrogens, can bond together in chains of various lengths. Student Misconceptions and Concerns 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. 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. Teaching Tips 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.) 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)! © 2012 Pearson Education, Inc. 5

6 Structural formula Ball-and-stick model Space-filling model
Figure 3.1A Structural formula Ball-and-stick model Space-filling model Figure 3.1A Three representations of methane (CH4) The four single bonds of carbon point to the corners of a tetrahedron. 6

7 Animation: Carbon Skeletons
3.1 Life’s molecular diversity is based on the properties of carbon A carbon skeleton is a chain of carbon atoms that can be branched or unbranched. Compounds with the same formula but different structural arrangements are call isomers. Student Misconceptions and Concerns 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. 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. Teaching Tips 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.) 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)! Animation: L-Dopa Animation: Carbon Skeletons Animation: Isomers © 2012 Pearson Education, Inc. 7

8 Length. Carbon skeletons vary in length.
Figure 3.1B Length. Carbon skeletons vary in length. Ethane Propane Branching. Skeletons may be unbranched or branched. Butane Isobutane Double bonds. Skeletons may have double bonds. Figure 3.1B Four ways that carbon skeletons can vary 1-Butene 2-Butene Rings. Skeletons may be arranged in rings. Cyclohexane Benzene 8

9 Length. Carbon skeletons vary in length.
Figure 3.1B_1 Length. Carbon skeletons vary in length. Ethane Propane Figure 3.1B_1 Four ways that carbon skeletons can vary (part 1) 9

10 Skeletons may be unbranched or branched.
Figure 3.1B_2 Branching. Skeletons may be unbranched or branched. Figure 3.1B_2 Four ways that carbon skeletons can vary (part 2) Butane Isobutane 10

11 Skeletons may have double bonds.
Figure 3.1B_3 Double bonds. Skeletons may have double bonds. 1-Butene 2-Butene Figure 3.1B_3 Four ways that carbon skeletons can vary (part 3) 11

12 Rings. Skeletons may be arranged in rings.
Figure 3.1B_4 Rings. Skeletons may be arranged in rings. Figure 3.1B_4 Four ways that carbon skeletons can vary (part 4) Cyclohexane Benzene 12

13 3.2 A few chemical groups are key to the functioning of biological molecules
An organic compound has unique properties that depend upon the size and shape of the molecule and groups of atoms (functional groups) attached to it. A functional group affects a biological molecule’s function in a characteristic way. Compounds containing functional groups are hydrophilic (water-loving). Student Misconceptions and Concerns 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. Teaching Tips 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. © 2012 Pearson Education, Inc. 13

14 3.2 A few chemical groups are key to the functioning of biological molecules
The functional groups are hydroxyl group—consists of a hydrogen bonded to an oxygen, carbonyl group—a carbon linked by a double bond to an oxygen atom, carboxyl group—consists of a carbon double-bonded to both an oxygen and a hydroxyl group, amino group—composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton, and phosphate group—consists of a phosphorus atom bonded to four oxygen atoms. Student Misconceptions and Concerns 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. Teaching Tips 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. © 2012 Pearson Education, Inc. 14

15 Table 3.2 Table 3.2 Important chemical groups of organic compounds 15

16 Table 3.2_1 Table 3.2_1 Important chemical groups of organic compounds (part 1) 16

17 Table 3.2_2 Table 3.2_2 Important chemical groups of organic compounds (part 2) 17

18 3.2 A few chemical groups are key to the functioning of biological molecules
An example of similar compounds that differ only in functional groups is sex hormones. Male and female sex hormones differ only in functional groups. The differences cause varied molecular actions. The result is distinguishable features of males and females. Student Misconceptions and Concerns 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. Teaching Tips 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. © 2012 Pearson Education, Inc. 18

19 Testosterone Estradiol Figure 3.2_1
Figure 3.2_1 Differences in the chemical groups of sex hormones (part 1) 19

20 Figure 3.2_2 Figure 3.2_2 Differences in the chemical groups of sex hormones (part 2) 20

21 Figure 3.2_3 Figure 3.2_3 Differences in the chemical groups of sex hormones (part 3) 21

22 3.3 Cells make a huge number of large molecules from a limited set of small molecules
There are four classes of molecules important to organisms: carbohydrates, proteins, lipids, and nucleic acids. Student Misconceptions and Concerns 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. Teaching Tips 1. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Consider adding that as the train cars are joined, a puff of steam appears—a reference to water production and a dehydration reaction when linking molecular monomers. 2. The authors note that the great diversity of polymers mainly results from the arrangement of polymers, the different sequences made possible by combinations or permutations of the same monomers. Consider illustrating this by simply asking students how many different ways can we arrange the letters A, B, and C, using each letter, and only once, to form 3-lettered words. The answer is 6 permutations: ABC, ACB, BAC, BCA, CBA, CAB (the factorial of 3). And if letters can be repeated, the answer is 27 (= 33): AAA, BBB, CCC, ABB, ACC, etc. © 2012 Pearson Education, Inc. 22

23 3.3 Cells make a huge number of large molecules from a limited set of small molecules
The four classes of biological molecules contain very large molecules. They are often called macromolecules because of their large size. They are also called polymers because they are made from identical building blocks strung together. The building blocks of polymers are called monomers. Student Misconceptions and Concerns 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. Teaching Tips 1. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Consider adding that as the train cars are joined, a puff of steam appears—a reference to water production and a dehydration reaction when linking molecular monomers. 2. The authors note that the great diversity of polymers mainly results from the arrangement of polymers, the different sequences made possible by combinations or permutations of the same monomers. Consider illustrating this by simply asking students how many different ways can we arrange the letters A, B, and C, using each letter, and only once, to form 3-lettered words. The answer is 6 permutations: ABC, ACB, BAC, BCA, CBA, CAB (the factorial of 3). And if letters can be repeated, the answer is 27 (= 33): AAA, BBB, CCC, ABB, ACC, etc. © 2012 Pearson Education, Inc. 23

24 3.3 Cells make a huge number of large molecules from a limited set of small molecules
Monomers are linked together to form polymers through dehydration reactions, which remove water. Polymers are broken apart by hydrolysis, the addition of water. All biological reactions of this sort are mediated by enzymes, which speed up chemical reactions in cells. Student Misconceptions and Concerns 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. Teaching Tips 1. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Consider adding that as the train cars are joined, a puff of steam appears—a reference to water production and a dehydration reaction when linking molecular monomers. 2. The authors note that the great diversity of polymers mainly results from the arrangement of polymers, the different sequences made possible by combinations or permutations of the same monomers. Consider illustrating this by simply asking students how many different ways can we arrange the letters A, B, and C, using each letter, and only once, to form 3-lettered words. The answer is 6 permutations: ABC, ACB, BAC, BCA, CBA, CAB (the factorial of 3). And if letters can be repeated, the answer is 27 (= 33): AAA, BBB, CCC, ABB, ACC, etc. Animation: Polymers © 2012 Pearson Education, Inc. 24

25 3.3 Cells make a huge number of large molecules from a limited set of small molecules
A cell makes a large number of polymers from a small group of monomers. For example, proteins are made from only 20 different amino acids and DNA is built from just four kinds of nucleotides. The monomers used to make polymers are universal. Student Misconceptions and Concerns 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. Teaching Tips 1. Train cars linking together to form a train is a nice analogy to linking monomers to form polymers. Consider adding that as the train cars are joined, a puff of steam appears—a reference to water production and a dehydration reaction when linking molecular monomers. 2. The authors note that the great diversity of polymers mainly results from the arrangement of polymers, the different sequences made possible by combinations or permutations of the same monomers. Consider illustrating this by simply asking students how many different ways can we arrange the letters A, B, and C, using each letter, and only once, to form 3-lettered words. The answer is 6 permutations: ABC, ACB, BAC, BCA, CBA, CAB (the factorial of 3). And if letters can be repeated, the answer is 27 (= 33): AAA, BBB, CCC, ABB, ACC, etc. © 2012 Pearson Education, Inc. 25

26 Unlinked monomer Short polymer Figure 3.3A_s1
Figure 3.3A_s1 Dehydration reaction building a polymer chain (step 1) 26

27 Dehydration reaction forms a new bond
Figure 3.3A_s2 Unlinked monomer Short polymer Dehydration reaction forms a new bond Figure 3.3A_s2 Dehydration reaction building a polymer chain (step 2) Longer polymer 27

28 Figure 3.3B_s1 Figure 3.3B_s1 Hydrolysis breaking down a polymer (step 1) 28

29 Hydrolysis breaks a bond
Figure 3.3B_s2 Hydrolysis breaks a bond Figure 3.3B_s2 Hydrolysis breaking down a polymer (step 2) 29

30 CARBOHYDRATES Carbohydrates range from small sugar molecules (monomers) to large polysaccharides. Glucose (an aldose) Fructose (a ketose) © 2012 Pearson Education, Inc. 30

31 Abbreviated structure
Figure 3.4C 6 5 4 1 3 2 Figure 3.4C Three representations of the ring form of glucose Structural formula Abbreviated structure Simplified structure 31

32 Examples of Carbohydrates
Monosaccharides: Glucose, fructose, galactose Range from 3 to 7 Carbons in length Disaccharides: Maltose = Glucose---Glucose Lactose = Glucose---Galactose Sucrose = Glucose---Fructose Polysaccharides: Long chains of monosaccharides Glycogen, starch, cellulose are all long glucose chains Student Misconceptions and Concerns 1. 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). 2. 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). Teaching Tips 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 and breathing oxygen produces water and usable energy (used to build ATP) plus heat and carbon dioxide exhaled in our breath. © 2012 Pearson Education, Inc. 32

33 Function of Carbohydrates
Carbohydrates are used as: the main fuels for cellular work (immediate energy) used as raw materials to manufacture other organic molecules. Student Misconceptions and Concerns 1. 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). 2. 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). Teaching Tips 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 and breathing oxygen produces water and usable energy (used to build ATP) plus heat and carbon dioxide exhaled in our breath. © 2012 Pearson Education, Inc. 33

34 Monosaccharides can be linked together by a dehydration reaction
Figure 3.5_s1 Glucose Glucose Monosaccharides can be linked together by a dehydration reaction Figure 3.5_s1 Disaccharide formation by a dehydration reaction (step 1) 34

35 Monosaccharides can be linked together by a dehydration reaction
Figure 3.5_s2 Glucose Glucose Monosaccharides can be linked together by a dehydration reaction Figure 3.5_s2 Disaccharide formation by a dehydration reaction (step 2) Maltose 35

36 Polysaccharides are long chains of sugar units
Polysaccharides may function as storage molecules or structural compounds. Starch is used by plants for energy storage. Glycogen is used by animals for energy storage Cellulose forms plant cell walls. Student Misconceptions and Concerns 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). Teaching Tips 1. 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 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. 2. The text notes that cellulose is the most abundant organic molecule on Earth. Ask your students why this is true. 3. 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.) 4. An adult human may store about a half of a 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). © 2012 Pearson Education, Inc. 36

37 Starch granules in potato tuber cells Starch
Figure 3.7 Starch granules in potato tuber cells Starch Glucose monomer Glycogen granules in muscle tissue Glycogen Cellulose microfibrils in a plant cell wall Cellulose Figure 3.7 Polysaccharides Hydrogen bonds Cellulose molecules 37

38 LIPIDS © 2012 Pearson Education, Inc. 38

39 3.8 Fats are lipids that are mostly energy-storage molecules
are water insoluble (hydrophobic, or water-fearing) compounds, are important in long-term energy storage, contain twice as much energy as a polysaccharide, and consist mainly of carbon and hydrogen atoms linked by nonpolar covalent bonds. Student Misconceptions and Concerns 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. 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. Teaching Tips 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! 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? (2.25 x 25 = kg of carbohydrate + 75kg (nonfat body weight) = kg, an increase of 31.25%) 3. Margarine in stores commonly comes in liquid squeeze containers, in tubs, and in sticks. 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 in the text, recent studies have suggested that unsaturated oils become increasingly unhealthy as they are hydrogenated. Students might therefore remember that as margarine products increase in stiffness, they generally become less healthy. Public attention to hydrogenation and the health risks of the resulting trans fats are causing changes in the use of products containing trans fats. © 2012 Pearson Education, Inc. 39

40 3 Categories of Lipids We will consider three types of lipids:
Triglycerides (fats), phospholipids, and steroids. A triglyceride is a large lipid made from two kinds of smaller molecules, glycerol and 3 fatty acids. Student Misconceptions and Concerns 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. 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. Teaching Tips 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! 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? (2.25 x 25 = kg of carbohydrate + 75kg (nonfat body weight) = kg, an increase of 31.25%) 3. Margarine in stores commonly comes in liquid squeeze containers, in tubs, and in sticks. 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 in the text, recent studies have suggested that unsaturated oils become increasingly unhealthy as they are hydrogenated. Students might therefore remember that as margarine products increase in stiffness, they generally become less healthy. Public attention to hydrogenation and the health risks of the resulting trans fats are causing changes in the use of products containing trans fats. © 2012 Pearson Education, Inc. 40

41 Triglyceride = 1 glycerol covalently attached to 3 fatty acids
Figure 3.8B Glycerol Triglyceride = 1 glycerol covalently attached to 3 fatty acids Fatty acid Figure 3.8B A dehydration reaction linking a fatty acid molecule to a glycerol molecule 41

42 1 glycerol covalently attached to 3 fatty acids
Figure 3.8C Triglyceride = 1 glycerol covalently attached to 3 fatty acids Glycerol Fatty acids can be: Saturated Unsaturated Fatty acids Figure 3.8C A fat molecule (triglyceride) consisting of three fatty acids linked to glycerol 42

43 Phospholipids Phospholipids contain two fatty acids attached to glycerol. A phosphate functional group replaces the other fatty acid Used to build cell membranes Student Misconceptions and Concerns 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. Teaching Tips 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 water contained internally) and (2) a micelle (polar heads in contact with water and hydrophobic tails clustered centrally). © 2012 Pearson Education, Inc. 43

44 Phospholipids Phosphate group Glycerol Water Hydrophilic heads
Figure 3.9A-B Phospholipids Phosphate group Glycerol Water Hydrophilic heads Hydrophobic tails Symbol for phospholipid Water Figure 3.9A-B Detail of a phospholipid membrane 44

45 Steroids and Cholesterol
Steroids are lipids in which the carbon skeleton contains four fused rings. Cholesterol is a common component in animal cell membranes and starting material for making steroids, including sex hormones. Student Misconceptions and Concerns 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. Teaching Tips 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 water contained internally) and (2) a micelle (polar heads in contact with water and hydrophobic tails clustered centrally). © 2012 Pearson Education, Inc. 45

46 Testosterone Estradiol Figure 3.2
Figure 3.2 Differences in the chemical groups of sex hormones 46

47 PROTEINS © 2012 Pearson Education, Inc. 47

48 Proteins are made from amino acids
involved in nearly every function in your body and very diverse, 50, ,000 proteins, each with a specific structure and function, in the human body. Proteins are composed of differing arrangements of a common set of just 20 amino acids. Amino group Carboxyl group Teaching Tips 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 20100, 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! © 2012 Pearson Education, Inc. 48

49 Proteins are made from amino acids
Amino acids are classified as either hydrophobic or hydrophilic. Hydrophobic Hydrophilic Teaching Tips 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 20100, 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! Leucine (Leu) Serine (Ser) Aspartic acid (Asp) © 2012 Pearson Education, Inc. 49

50 Amino acids are joined together by a dehydration reaction
Figure 3.11C_s1 Amino acids are joined together by a dehydration reaction Carboxyl group Amino group Amino acid Amino acid Figure 3.11C_s1 Peptide bond formation (step 1) 50

51 Amino acids are joined together by a dehydration reaction
Figure 3.11C_s2 Amino acids are joined together by a dehydration reaction Peptide bond Carboxyl group Amino group Dehydration reaction Amino acid Amino acid Dipeptide Figure 3.11C_s2 Peptide bond formation (step 2) 51

52 A protein’s specific shape determines its function
Proteins are distinguished by: The combination of sequence of amino acids The linear sequence of amino acids in a protein is called the PRIMARY STRUCTURE of the protein 3D structure The amino acid sequence causes the protein to assume a particular shape. The shape of a protein determines its specific function. Student Misconceptions and Concerns 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. Teaching Tips 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. © 2012 Pearson Education, Inc. 52

53 Primary structure Amino acid Figure 3.13A
Figure 3.13A Primary Structure: linear sequence of amino acids 53

54 Beta pleated sheet Alpha helix
Figure 3.13A-D_s4 Four Levels of Protein Structure Primary structure Amino acids Amino acids Secondary structure Hydrogen bond Beta pleated sheet Alpha helix Tertiary structure Transthyretin polypeptide Figure 3.13A-D_s4 Four Levels of Protein Structure (step 4) Quaternary structure Transthyretin, with four identical polypeptides 54

55 A protein’s specific shape determines its function
Functions of proteins: Enzymes catalyze chemical reactions. Structural proteins provide associations between body parts. Contractile proteins are found within muscle. Defensive proteins include antibodies of the immune system. Signal proteins are best exemplified by hormones and other chemical messengers. Receptor proteins transmit signals into cells. Transport proteins carry oxygen. Storage proteins serve as a source of amino acids for developing embryos. Student Misconceptions and Concerns 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. Teaching Tips 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. © 2012 Pearson Education, Inc. 55

56 NUCLEIC ACIDS © 2012 Pearson Education, Inc. 56

57 3.14 DNA and RNA are the two types of nucleic acids
DNA(deoxyribonucleic acid) DNA is provides genetic information DNA is inherited from an organism’s parents. DNA provides instructions for production of proteins in a cell. DNA works through an intermediary, ribonucleic acid (RNA). DNA is transcribed into RNA. RNA is translated into proteins. Student Misconceptions and Concerns Module 3.14 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. Teaching Tips The “NA” in the acronyms DNA and RNA stands for “Nucleic acid.” Students often do not make this association without assistance. © 2012 Pearson Education, Inc. 57

58 Figure 3.14_s1 Gene DNA Figure 3.14_s1 The flow of genetic information in the building of a protein (step 1) 58

59 Gene DNA Transcription Nucleic acids RNA Figure 3.14_s2
Figure 3.14_s2 The flow of genetic information in the building of a protein (step 2) 59

60 Gene DNA Transcription Nucleic acids RNA Translation Protein
Figure 3.14_s3 Gene DNA Transcription Nucleic acids RNA Figure 3.14_s3 The flow of genetic information in the building of a protein (step 3) Translation Protein Amino acid 60

61 Nucleic acids are built from nucleotides
Nucleotides have three parts: a five-carbon sugar called ribose in RNA and deoxyribose in DNA, a phosphate group, and a nitrogenous base. Nitrogenous base (adenine) Teaching Tips 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? (Answer: Four nucleotides, GCAT, are possible). Are these the same “words” used in RNA? (Answer: No. Uracil substitutes for thymine.) Phosphate group Sugar 61

62 DNA vs. RNA DNA nitrogenous bases are DNA sugar = deoxyribose RNA
adenine (A), thymine (T), cytosine (C), and guanine (G). DNA sugar = deoxyribose RNA also has A, C, and G, but instead of T, it has uracil (U). RNA sugar = ribose Teaching Tips 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? (Answer: Four nucleotides, GCAT, are possible). Are these the same “words” used in RNA? (Answer: No. Uracil substitutes for thymine.) © 2012 Pearson Education, Inc. 62

63 Sugar-phosphate backbone
Figure 3.15B A Nucleotide T C G Figure 3.15B Part of a polynucleotide T Sugar-phosphate backbone 63

64 DNA vs. RNA DNA = 2 strands of nucleotides that form a double helix.
The two strands pair thru contacts with nucleotide bases A pairs with T C pairs with G RNA is usually a single polynucleotide strand. Teaching Tips 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? (Answer: Four nucleotides, GCAT, are possible). Are these the same “words” used in RNA? (Answer: No. Uracil substitutes for thymine.) © 2012 Pearson Education, Inc. 64

65 Base pair C A T C G C G T A C G A T A T G C A T A T T A Figure 3.15C
Figure 3.15C DNA double helix G C A T A T T A 65

66 Short polymer Monomer Longer polymer Dehydration Hydrolysis
Figure 3.UN01 Dehydration Hydrolysis Short polymer Monomer Longer polymer Figure 3.UN01 Reviewing the Concepts, 3.3 66

67 Classes of Molecules and Their Components Functions Examples
Figure 3.UN03_1 Classes of Molecules and Their Components Functions Examples Carbohydrates Energy for cell, raw material a. b. Starch, glycogen Plant cell support c. Monosaccharides Lipids (don’t form polymers) Energy storage d. Figure 3.UN03_1 Connecting the Concepts, question 2 (part 1) e. Phospholipids Glycerol Fatty acid Hormones f. Components of a fat molecule 67

68 Classes of Molecules and Their Components Functions Examples
Figure 3.UN03_2 Classes of Molecules and Their Components Functions Examples j. Lactase Proteins k. Hair, tendons g. h. l. Muscles Transport m. Communication Signal proteins n. Antibodies Storage Egg albumin i. Receive signals Receptor protein Amino acid Nucleic Acids Heredity r. Figure 3.UN03_2 Connecting the Concepts, question 2 (part 2) p. o. s. DNA and RNA Nucleotide q. 68