Pattern Matching Classifying Organic Molecules

Name AP Biology / Rodgers Date Per Pattern Matching: Classifying Organic Molecules Background: You have previously learned about the four classes of large biological molecules: lipids, nucleic acids, proteins, and carbohydrates. In this activity, you will work with a group to identify the major classes of organic molecules and distinguish the features of each class of molecules. There may be as many as 10,000 different kinds of molecules in a living thing. In this activity you will examine, distinguish the features of, and classify 45 different molecules. Which elements are present in each type of molecule? Start by filling in the table, writing “Always,” “Sometimes,” or “Never” in each box. Carbon Hydrogen Nitrogen Oxygen Phosphorus Sulfur Proteins Always Always Always Always Never Sometimes Carbohydrates Always Always Never Always Never Never Nucleic Acids Always Always Always Always Always Lipids Always Always Never Always Never Never Never With your chart complete, begin your work by removing your cards from the bag. Count them to ensure that you have all 45. You will notice that the cards are numbered; these are their identifiers: you will use them to answer the questions in this activity. You do not need to put them in number order. After you have ensured you have a complete set of cards, work together to put the cards into FIVE stacks: Proteins, Carbohydrates, Nucleic Acids, Lipids, and Unknown. Use the chart above to help you sort your molecules. Remember, work as a group does not mean “divide and conquer” where each student does a handful. Work as a group means you discuss the features of each card and determine together where it should belong. Once all the cards have been sorted, describe the patterns, shapes, and/or function groups you noticed that led you to sort the cards as you did. Things we noticed… Proteins Carbohydrates Nucleic Acids Lipids Look more closely at the stack of “Unknowns” – Can you group those into smaller groups? Do any have similar structures? Describe the features of the unknowns that seem to be patterns among two or more of the cards in your unknown. For example, “Card X and Y both have…” Check in with your teacher before you move on. PROTEINS Proteins are molecules that play many important roles in the body, including muscle structure, hormones, antibodies to neutralize pathogens, hemoglobin for carrying oxygen, transport proteins for moving molecules across cell membranes, chemical messengers in the nervous system, and many, many more. What is the monomer of a protein called? Amino Acid Figure 1 shows a “generic” amino acid, or one that doesn’t have a side chain, or “R group.” Two amino acids are joined by dehydration synthesis reactions to form a dipeptide; when three or more amino acids are joined they are referred to as a polypeptide. Once a polypeptide has folded into a functional conformation (shape) it is referred to as a protein. When amino acids are joined together, the “-N-C-C-“ in the center of the molecule is known as its backbone and is a defining feature of amino acids. A typical protein chain may contain 150 – 1000 or more amino acids. There are 20 common amino acids that are used to build protein molecules. Cells string amino acids together end-to-end as shown in Figure 2. Each amino acid has a different side group that is represented by “R” in Figures 1 and 2. Two amino acids with their particular side groups are shown in Figure 3. Focusing only on the cards you placed in “Proteins,” lay out all of the amino acids. How many did you originally identify? You should have 14. If you don’t have all 14 amino acids, sort through your other piles, beginning with “Unknown” until you find all 14 amino acids. List the cards numbers here of your amino acids: 2 6 9 13 15 16 18 20 21 24 25 26 27 28 We will now look more closely at these 14 amino acids. Bearing in mind that the properties of the Rgroup determine the behavior of the amino acid, separate the amino acids into two stacks: polar and non-polar. Hint: A highly electronegative atom on the end of an R-group will cause the amino acid to be polar and a series of hydrocarbons on the end of an R-group will cause the amino acid to be nonpolar. You should find 6 non-polar amino acids. List the cards here of the non-polar amino acids: 2 6 13 20 21 25 Are these amino acids more likely to be found on the interior or exterior of a globular protein that exists in the cytosol of a cell? Interior, away from the aqueous cytosol. You should find 8 polar amino acids. List the cards here of the polar amino acids: 9 15 16 18 24 26 27 28 Are these amino acids more likely to be found on the interior or exterior of a globular protein that exists in the cytosol of a cell? Exterior, in contact with the aqueous cytosol. Looking even more closely at the polar amino acids, you should find three that have a charged R-group. List the cards here of the charged amino acids: 15 16 18 Last, find the ONE amino acid that has a terminal (end) sulfur atom that could engage in a “di-sulfide bridge.” What’s its card number? Card 26 CARBOHYDRATES Carbohydrates are also versatile molecules that store energy and provide structure to organisms. You may have heard of simple carbohydrates, sugar, or complex carbohydrates, such a fiber. Sugars occur as ring structures. There are monosaccharides (single rings), disaccharides (double rings), and larger structures called polysaccharides. In solution, single rings can dynamically change from straight chains to rings and back to straight chains. A straight chain sugar is shown below. Notice that ever carbon has an oxygen atom attached to it. Sugars can be joined together in long chains to form macromolecules called starch, cellulose, and glycogen. A plant’s starch and an animal’s glycogen are easily broken down into sugars for energy. Cellulose, on the other hand, which is made primarily in plants, can be broken down only by a few organisms in the world – primarily the bacteria in the guts of termites. Yet all three types of macromolecules are made of long chains of monosaccharides, and cellulose differs only by a small change in the connecting bond between each pair of sugars. Pick up your pile of carbohydrate cards. You should have 11 of them. If you don’t, sort through your pile of unknowns to search for more. Remember, carbohydrates only contain carbon, oxygen, and hydrogen in a very specific 1 carbon:2 hydrogen:1 oxygen ratio. List the card numbers for the 11 carbohydrate molecules: 1 3 5 10 12 14 17 22 23 29 34 Further divide your set of 11 cards into monosaccharides, disaccharides, and polysaccharides. Which cards are straight chain monosaccharides? 1 5 12 14 17 22 Which cards are ring monosaccharides? 3 29 Which cards are disaccharides? 10 23 Which card is a polysaccharide? 34 Look again at your two disaccharides. One of them is common table sugar. Look up “sucrose” in your book or online. Which two monosaccharides combine to form sucrose? Draw them below. Which atoms are removed during the bonding of the two monosaccharides? Glucose and Fructose Lipids Lipids are a diverse group of molecules that share one important trait: they are hydrophobic. Lipids are most easily recognized by having lots of hydrocarbons, which contain non-polar covalent bonds. Lipids may have a few polar bonds associated with oxygen, depending on the specific molecule, but on the whole lipids consist mostly of hydrocarbons. Lipids vary widely in both form and function and include things like waxes and pigments. In this activity we’ll focus on fats, phospholipids, and steroids. First, ensure you have all of the lipid cards – there are 8 of them. Look for molecules that have long chains or rings of hydrocarbons. List the lipids here: 33 35 36 37 38 40 42 44 Steroids Steroids are one type of molecule in the class of compounds known as lipids. Cholesterol, shown at the right, is a steroid, and plays an important role in membrane formation. Steroids can be recognized by their multiple rings of carbon atoms connected together. Find the 3 steroids in your stack of cards. Identify them here: 40 42 44 It’s useful to keep in mind that, similar to proteins, molecules can have regions that are nonpolar and regions that are polar. This is incredibly important in cell membrane functions. Re-examine the cholesterol molecule. Circle the region of the molecule that is polar. Fats and Fatty Acids Among your cards you should have some long hydrocarbon chains with a carboxyl group at one end. One of the defining features of these hydrocarbon chains is the absence of oxygen except in one carboxyl group at one end of the molecule. Draw a carboxyl group here: Is a carboxyl group polar or non-polar? The presence of which element tells you this? Polar. Oxygen. Fatty acids can exist alone as a single chain of hydrocarbons, or can join a glycerol molecule to form larger molecules with multiple chains. The chains themselves can vary in terms of the presence or absence of double bonds between the carbon molecules. Fatty acids that contain no double bonds are considered saturated. Fatty acids that contain at least one double bond are considered unsaturated. Saturated fats are solid at room temperature because the chains pack together more densely than do unsaturated fats, which are liquid at room temperature and less dense. Saturated fats tend to be found in land animals; unsaturated fats tend to be found in plants and fish. Identify the three cards that show individual fatty acid chains. 33 35 36 Look more closely at these three cards. Which chains are saturated? How can you tell? 33 35 There are no double bonds. Which chain is unsaturated? How can you tell? 36 There are double bonds present. You should now have two larger molecules remaining, each with multiple fatty acid chains attached to a glycerol. Fats, as you consume them in your food, are formed by joining three fatty acids to a glycerol molecule. In addition to the number of double bonds, the length of the fatty acid chains can also vary. Which card shows a molecule that is a fat? 38. This fat is known as a triacylglycerol, or a triglyceride. This is one of the molecules that is found in your blood. Doctors track the amount of triglycerides found in blood. Too much triglyceride in your blood is a possible indicator of heart disease. The last remaining lipid is a phospholipid. Look closely to see that there are two fatty acid chains attached to a glycerol. The third carbon on the glycerol molecule has a phosphate attached to it. Which card is the phospholipid? 37 Is a phosphate group polar or nonpolar? Polar Are the fatty acid chains polar or nonpolar? Nonpolar This molecule is “amphipathic,” meaning that is has both hydrophilic and hydrophobic regions. On this simplified diagram of a phospholipid, label the polar region and the nonpolar region of the molecule. Phospholipids are essential for cells because they are major constituents of cell membranes. In this diagram of a cross-section of a cell membrane, label the region that is nonpolar and the two regions that are polar. Nucleic Acids Nucleic Acids store, transmit, and help express hereditary information. You should have 12 cards remaining. The monomer of nucleic acids are nucleotides, which themselves contain a nitrogenous base, a sugar, and anywhere from 1 to 3 phosphate groups. Five of your cards contain only the nitrogenous bases: a single or double-ring structure that contains nitrogen. Identify the five nitrogenous bases. Ensure the cards you select do not contain a pentose sugars, as shown here: Which cards contain nitrogenous bases? 4 7 8 11 19 Nitrogenous bases are either pyrimidines (single ring structures) or purines (double ring structures). Which of the five cards are pyrimidines? 8 11 19 Which of the five cards are purines? 4 7 The nitrogenous base connects directly to a pentose sugar, either ribose in RNA or deoxyribose in DNA. In the diagram above, circle the Oxygen that is present on ribose that is absent on deoxyribose. You have four cards that show a nitrogenous base attached to a pentose sugar. When molecules are in this state, they care called nucleosides. Which cards are these? 39 41 43 45 Look closely at the sugars on each card. Do these molecules contain ribose or deoxyribose? Ribose When nucleosides combine with one, two, or three phosphates they are then nucleotides. The more phosphates that are present, the more energy contained in the molecule. Adenosine triphosphate (ATP) is not only a major subunit of DNA and RNA, but also a major energy carrier in living systems. How many phosphate groups should you expect to find in adenosine triphosphate? 3 Which of your cards contains ATP? 32 When ATP is used for cellular energy, water hydrolyzes the terminal phosphate group from the ATP, leaving only two phosphates behind – a molecule called adenosine diphosphate. Which of your cards contains ADP? 31 Through a process called cellular respiration, glucose is broken down and the terminal phosphates that were removed are added back on to ADP, so these molecules are continuously recycled by the cell. While nucleotides that are free floating in the cell’s cytoplasm typically consist of three phosphate groups, when each is added to a growing molecule of DNA or RNA, the end two phosphate groups are removed by dehydration synthesis, leaving only one phosphate group. Which of your cards contains a molecule that looks like this? 30 On the molecule of a different nucleotide to the right, label the phosphate, pentose, and nitrogenous base. The single pentose sugar and the single phosphate group on each nucleotide join with others so as to form a sugarphosphate backbone of a molecule, with the nitrogenous bases on the interior of the molecule. Now examine the molecule below. Which letter represents the phosphate group? Z Which letter represents the pentose sugar? Y Which letter represents a purine? W Which letter represents a pyrimidine? X