CLASS SET. Modeling Life s Important Compounds. AP Biology

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1 Modeling Life s Important Compounds AP Biology CLASS SET OBJECTIVES: Upon completion of this activity, you will be able to: Explain the connection between the sequence and the subcomponents of a biological polymer and its properties. Refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. Use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. This is a cut-and-tape paper exercise to emphasize the process of dehydration synthesis. You will also be constructing models of each biochemical structure so that you have an understanding of how the structure helps the molecule perform certain functions. Although this may seem elementary for an AP level class, sometimes it is difficult to visualize chemical reactions, especially biochemical ones. So we will be using paper models of the various organic polymers important to living things to demonstrate how they are made and broken apart for use by living organisms. To perform this activity, you will need: Glucose papers Fatty acid papers: saturated and unsaturated Glycerol papers Amino acid papers Water papers Nucleotide papers Introduction Organic molecules contain atoms of carbon bonded to hydrogen atoms. Compounds considered to be organic present in living organisms are things such as carbohydrates, lipids, proteins and nucleic acids all also called biomolecules. These are known as polymers, and are generally large molecules composed of smaller repeating subunits known as monomers. These monomers are assembled into polymers using a chemical reaction known as dehydration synthesis (condensation). An example is given below: In the figure above, notice how a glucose molecule and a fructose molecule are being joined together to make a molecule of sucrose. Notice that a water molecule is formed from the removal of a hydrogen ion and a hydroxide ion, and a glycosidic linkage forms between the two individual sugars. Page 1 of 5

2 The reverse of this process is known as hydrolysis, and in living systems, involves enzymatic activity that results in adding a water molecule back in to hydrolyze the bond that formed to join the individual monomers together in the first place. Notice how the figure above shows that a glucose molecule and a fructose molecule are being split apart from one another with the help of the enzyme invertase. Water is used to hydrolyze the glycosidic linkage that initially joins the monomers together. You will model both of these processes using paper models of the monomers used to construct biomolecules. Part One: Molecules for Cell Energy and Structure Carbohydrates and Lipids Directions for Assembly: Carbohydrates 1. To build carbohydrates, monosaccharides are needed. Obtain two glucose monomer papers and number the carbons like this: Numbering the carbon atoms is important so that you can determine where the bonding of monomers will take place. Paste down a single glucose into your BILL. 2. Now you will form a disaccharide. Join (bond) the two glucoses together by cutting off an H from one molecule and an OH from another and taping the 2 molecules together forming a glycosidic bond. Give your disaccharide a name, bearing in mind that sugar names end in ose (i.e. glucose, fructose). Affix your completed model into your BILL, labeling the glycosidic bond. 3. Then take the trimmed H-O-H, affix it to the water drop, and tape/glue the water drop onto the glycosidic bond. Your finished product may look something like this: 4. Now, take the disaccharide you have created, and bond it in the same manner with another pair of students and their disaccharide using the same paper dehydration synthesis process. Give your polysaccharide a new name, remembering that it too must end in ose. Directions for Assembly: Lipids Page 2 of 5

3 1. To build lipids, glycerol and fatty acid chains are needed. You have two choices of fatty acid chains: a. Saturated: these fatty acids have no double bonds along the carbon backbone b. Unsaturated: these fatty acids have at least one double bond along the carbon backbone Obtain a glycerol paper and three different saturated fatty acid papers. You will first build a saturated fat, and then an unsaturated fat. 2. Take one glycerol molecule and three differently colored saturated fatty acid molecules and join them by cutting off an H from one molecule and an OH from another and taping the two molecules together forming an ester bond. Label this bond. 3. Then take the trimmed H-O-H, affix it to the water drop, and tape the water drop onto each ester bond. 4. Repeat this process to build an unsaturated fat, except use an unsaturated fatty acid paper in place of one of the saturated fat papers. Part Two: Molecules For Cell Structure, Transport and Regulation Proteins (polypeptides) Directions for Assembly: Proteins 1. To build a protein, use at least 5 of the amino acid papers your teacher gives you. 2. Once you ve got your amino acids selected, you will need to use your textbook to find out whether or not the amino acids you have been assigned are charged or uncharged, polar or nonpolar. Then, write the name and the chemical characteristic on each amino acid paper. This will help you to determine how the amino acid will behave once it is assembled into a protein. 3. Now, join your amino acids together by cutting off an H from one molecule and an OH from another and taping the two amino acid molecules together to form a peptide bond. In your lab notebook, sketch a dipeptide built from two of the amino acids you were assigned. Be sure to label each amino acid and the peptide bond that forms between them. 4. Then, take the trimmed H-O-H, affix it to the water drop, and tape the water drop onto the peptide bond. Your finished product may look like this: Note: This is a very short polypeptide and that proteins in biological systems can be hundreds or even thousands of amino acids long. 5. Now that you know how proteins are formed, it s time to fold them based on the chemical properties of their constituent amino acids. Remember that polar amino acids will orient themselves to the outside of the molecule so that they interact with the aqueous environment of the cell, while nonpolar amino acids will orient themselves toward the inside of the molecule to avoid contact with the aqueous environment of the cell. If your protein has sulfur atoms, disulfide bridges may form. If your protein has amino acids with positively charged and negatively charged regions, then you may have ionic bonding taking place as well. This will cause the amino acids with opposite charges to be attracted to one another. 6. Give your newly formed protein a name. The naming convention for proteins is such that protein names typically end in the suffix in. Page 3 of 5

4 Part Three: Molecules for Cell Information Storage Nucleic Acids Directions for Assembly: Nucleic Acids 1. To build nucleic acids, you will need nucleic acid papers. 2. You will first need to locate the carbons on the deoxyribose sugars of your template strand. In particular, make note of where the 3 and 5 carbons are located. This is significant because DNA can only replicate itself in one direction, and replication begins at the 3 end of the molecule. 3. Now, build the complementary strand to the template you have by matching your complementary bases to one another, taking care to repre sent dehydration synthesis. 4. Note the orientation of the molecule, and sketch a section of your resultant nucleic acid in your notebook, being careful to label the nucleotides and bonds that hold them to each other. Page 4 of 5

5 Lab Questions: Answer these in your BILL. 1. Describe the process of dehydration synthesis. 2. Give a biological function for each of the following molecules, with a named example of each: a. Proteins b. Carbohydrates c. Lipids d. Nucleic Acids 3. Where in a cell would long-chain carbohydrates be synthesized, and by what organelle? During what cellular process would this occur? 4. How does putting a double bond in the carbon chain of a lipid affect the structure of the fatty acid? 5. Based on what you have observed about lipid structure, could a lipid be considered a polymer? Why or why not? 6. What organelle in a cell is responsible for lipid synthesis? 7. Based on the structure of carbohydrates and lipids you have observed, explain which molecule is better suited for long-term energy storage and why you think this. 8. What effect on protein structure do the following have: a. Nonpolar amino acids b. Polar amino acids c. Negatively charged amino acids d. Positively charged amino acids 9. What do you notice about the orientation of the nucleotides in a DNA molecule? 10. How do the following bonds in a DNA molecule make it a good information storage and transfer molecule: a. Polar covalent bonds (phosphodiester bonds) b. Hydrogen bonds c. Complementary base pairing of nucleotides 11. Based on their structures, why do you think that nucleic acids are better for storing and transmitting genetic information than proteins? Page 5 of 5