Modeling Biological Macromolecules Each set should consist of the following parts: 16 black Carbon atoms 13 red Oxygen atoms 32 white Hydrogen atoms 5 blue Nitrogen atoms (some model Nitrogen atoms are able to pick up H+ to ionize) 58 grey single covalent bonds Flexible white covalent bonds (for double bonding) CARBOHYDRATES Carbohydrates have the generalized formula of (CH2O)n. Glucose and fructose contain six carbon atoms in the molecule. Both have the chemical formula C6H12O6 and exist in cells in the ring form. Glucose: Construct a model of glucose in the ring form. The ring will not be completely flat. In order to get the correct orientation of the hydroxyl and other groups projecting from the ring, hold the ring parallel to the floor. Save your glucose until the end of this section. When depicting structural formulas, the carbons at the corners of the ring are sometimes left out for simplicity. Fructose: Construct a model of fructose (called fructofuranose in its ring form). Save your fructose for the next step. Sucrose: Sucrose is a disaccharide found in plants such as sugar beet and sugar cane. Its structure consists of a glucose ring linked by a glycosidic linkage to a fructofuranose ring. This molecule forms by dehydration synthesis. Construct a model of sucrose by detaching the hydroxyl group from Carbon 1 of glucose and a hydrogen from the hydroxyl group attached to Carbon 5 of fructose. The result is sucrose and water. The two rings are connected to each other with an Oxygen in the middle. This is called a glycosidic linkage. When exposed to dilute acid, sucrose undergoes hydrolysis to break into its two constituent monosaccarides. Once you have finished this section, dismantle your sucrose. LIPIDS Construct a model of glycerol [C3H5(OH)3]. Save your glycerol until the end of the Lipids section. The generalized formula of a fatty acid is CH3(CH2)nCOOH. As you build these lipids, take note of how few Oxygen atoms are present compared to carbohydrates. Save all three of your fatty acid molecules for the next step. Construct a model of acetic acid: CH3COOH. Construct models of butyric acid and caproic acid. Use the molecular models of glycerol, acetic acid, butyric acid, and caproic acid to construct a triacylglycerol molecule. Remove the three hydroxyl groups (-OH) from the glycerol molecule. These open bonds are where the fatty acids will bond. Remove a hydrogen atom from each of the carboxyl ends of the three fatty acids. This oxygen will bond directly to the Carbon of glycerol. Once you have attached the three fatty acids to glycerol, you will have one fat molecule, and three water molecules. The bonds between glycerol and the fatty acids are called ester linkages. In a living cell, the order of connection would determine the shape and function of the triacylglycerol. Most fatty acids in cells are at least 16 carbons long, rather than the 2, 4, and 6-carbon fatty acids in this modeling exercise. Once you have finished this section, dismantle your triacylglycerol. PROTEINS Amino acids are the building blocks of proteins. There are 20 amino acids which occur commonly in nature, and they are all alpha-amino acids. Their general formula is NH2CHRCOOH. Construct a model of glycine. This is the simplest amino acid. Construct models of alanine and serine. Keep all three models until the end of this section. ‘ Amino acids are often present in cells in their ionized (zwitterion) form. Once you have three amino acid models, remove the hydroxyl from the carboxyl group of glycine and one hydrogen from the amino group of alanine. Join these molecules together where the open bonds exist to form a peptide bond. Two amino acids joined together form a dipeptide. Now remove the hydroxyl from the carboxyl group of alanine and one hydrogen from the amino group of serine to form another peptide bond. This molecule is called a tripeptide. Many amino acids joined together in this way will form a polypeptide. Once you have finished this section, dismantle your tripeptide. NUCLEIC ACIDS Nucleotides are the building blocks of nucleic acids. There are 4 deoxyribonucleotides, and 4 ribonucleotides, that are used in formation of DNA and RNA, respectively. REVIEW QUESTIONS 1. What chemical elements are characteristic of carbohydrates? 2. Calculate the molecular mass of glucose by counting the number of each type of atom and multiplying that number by the atomic mass of the atom. Sum these numbers to get the mass of the molecule. (Consult a periodic table as you answer this question.) 3. What does the term dehydration synthesis mean? 4. What chemical elements are characteristic of lipids? 5. Do you think that a triacylglycerol molecule is hydrophilic or hydrophobic? Explain. 6. By adding water to a molecule of fat, it can be broken down into three fatty acids and glycerol. What is this process called? 7. Can the reactions modeled in this lab take place inside living cells? 8. What other molecule(s) is/are necessary for breakdown of fat to happen inside a living cell? 9. What chemical elements are characteristic of proteins? 10. Which two functional groups are present on all amino acids? 11. What is meant by the “R group” of an amino acid? 12. What is the R group found in the amino acid alanine? 13. Name two ways in which amino acids differ from fatty acids. 14. How is protein digestion completed in living cells? 15. What chemical elements are characteristic of nucleic acids? 16. If you dissolve sugar in water, hydrogen bonding causes the sugar to dissolve. If you heat a sugar solution made up in distilled water, water evaporates as hydrogen bonds are broken. Eventually, the sugar will recrystalize. What does this experiment tell you about the relative strength of hydrogen bonds and covalent bonds?