Name Date AP Biology Unit 1, Chapters 2, 3, 4, 5 Research Question How are chemical structures visualized? Background You can represent a molecule with either a molecular formula or a structural formula. For example, the molecular formula for methane, CH 4, tells us that the gas we burn in the lab has one carbon and four hydrogens. The structural formula for methane tells us how the four hydrogens are bonded with a central carbon atom. However, neither molecular formulas nor structural formulas provide information concerning the actual arrangement of atoms in the molecule with their correct geometry. In other words, not every molecule is as flat as we draw then on paper when we determine a structural formula. Structural formulas only give some information about the real arrangement of atoms in the molecule. Since structural formulas are two-dimensional on paper, we need to understand that the actual structural molecular shapes are three-dimensional. A molecular model is far superior to a structural formula when it comes to visualizing atomic arrangement. Compared to molecular formulas and structural formulas, molecular models show much more information about the true shapes of the molecules. The most common type of chemical bond between two non-metal atoms is a covalent bond. The covalent bond consists of a pair of shared electrons; one from each atom that moves between atoms holding then together in the bond. If this pair of electrons is shared between two atoms of equal electronegativity, the bond is called a nonpolar covalent bond. However, in most cases, the pair of electrons is shared by two atoms of different electronegativity. Here, the pair of electrons is shifted toward the more electronegative element. A partial negative charge results on one side of the bond and a partial positive charge on the other side of the bond. This type of covalent bond is called a polar covalent bond. The key factor for determining the polarity of a molecule is its shape. Molecular models are helpful for determining the actual three-dimensional shape of molecules. If the polar bonds (dipoles) are symmetrical around the central atom, they offset each other and the resulting molecules are nonpolar. However, if the dipoles are not symmetrical around the central atom, the electrons will be pulled to one end of the molecule. The resulting molecule is polar. Ball and stick models are often used to demonstrate molecular shape. In this exercise you will build several covalent molecules and predict each molecule s polarity on the basis of its molecular shape.
Procedure Part 1 - The Structure of Molecules 1. Using the ball and stick model set, construct models for the following molecules. For the four molecules from chapter five you will need to combine kits with another lab bench. Include a drawing or picture of each molecule in your lab journal and have them stamped by Mr. Ballog. CHAPTER MOLECULE CHAPTER MOLECULE 2 (pg. 38) Molecular Hydrogen 4(pg. 65) Glycine 2(pg. 38) Molecular Oxygen 4(pg. 65) Cysteine 2(pg. 38) Water 5(pg. 71) Glucose Ring 2(pg. 38) Methane 5(pg. 71) Sucrose 4(pg. 64) Acetone 5(pg. 73) Starch or Cellulose 4(pg. 64) Acetic Acid 5(pg. 75) Fatty Acid 2. For each molecule listed below determine the Lewis dot structure and the molecular polarity (polar or nonpolar) for each molecule. Molecule Lewis Dot Structure Polarity Hydrogen Oxygen Water Methane Methanol Part 2 - The Structure of Amino Acids 3. At your lab table use the molecule set to build a set of amino acids to work with. Use either a text (Campbell pg. 79) or the web site; http://www.alyvea.com/biologystudyguides/buildingblocksoflife.php In the space provided draw the structural formula of your constructions. Circle the R group on each. Amino Acid Nonpolar Polar Charged Page 2 of 5
Drawing of structural formula Part 3 - The Primary Structure of Proteins Connect all of your individual amino acids into one short polypeptide chain. You will need to perform a dehydration synthesis (create water) reaction to make the peptide bond. Combine two of your polypeptides with the other groups in the class to produce a chain that is 10 amino acids in length. Make a schematic of the primary structure of the protein your class created in the space below. Include charge information on the diagram. Part 4 The Secondary Structure of Proteins Using Molecular Workbench navigate from the opening page to; Browse all Activities (Under Featured Activities)> Proteins and Nucleic Acids (Under More activities Biology)> Amino Acid Sequence and Protein Shape. Read the instructions given under Sequence and structure until you find out how to change the amino acid sequence of the polypeptide chain in the animation window. Change the default sequence to the sequence your class grouping produced in part 2 of this exercise. You may select the last sequences. Run the animation to see how your polypeptide might fold. Make a screenshot or drawing of your secondary structure polypeptide and paste below. Page 3 of 5
Common Secondary Structures Using the chenille stems (pipe cleaners) you will make the two basic shapes that a protein folds into as its secondary structure. 1) Fold one of the stems into an alpha helix taking care that the helix winds in the proper direction. Make a drawing of your helix in the space below. 2) Use two of the stems to fold a model of a beta pleated sheet. Make a drawing of your pleated sheet below. Figure 1 Alpha Helix Part 5 - The Tertiary Structure of Proteins Figure 2 Beta Sheet Using Toobers you will make a model of the tertiary structure of the polypeptide sequence your group made in part three of this lab. The Toobers represent the completed secondary protein folding. For our purposes they can be considered as representing a polypeptide folded into an alpha helix. Different colored tacks will represent the different types of amino acids along the helix. 1) Straighten the Toober 2) Insert colored tacks into the Toober spaced evenly down the length of the Toobers as well as evenly around the Toober. Rotate the Toober 90 degrees after each tack placement to represent the turn of the helix. Use Table one to determine which tack color to use. 3) Bend your Toober following the rules for amino acid folding given in the table below Use the following table to represent the different types of amino acids and how they interact. Table 1 Tack Amino Acid Folding Properties Color Properties Yellow Hydrophobic Buried on the inside surface of the protein White Hydrophilic Located on the outside surface of the protein Red Acidic (-) Located on the outside surface of the protein and away from like charges Blue Basic (+) Located on the outside surface of the protein and away from like charges Green Cysteine Always bond with another cysteine using disulfide bonds Page 4 of 5
4) Draw your completed Tertiary protein in the space below. Part 6 - The Quaternary Structure of Proteins 5) Now combine your Tertiary protein with the Tertiary protein model of someone from a group with a different amino acid sequence to produce a Quatenary Protein Structure. So! You have just folded your first protein. Easy huh? Even though the same rules apply, determining the actual folding of a full amino acid sequence is not quite as simple. Computer systems take about 30 CPU (computing) YEARS to determine the probable shape of one average length protein. Big job! Want to help? Go to; http://folding.stanford.edu/ and download Folding at Home. The program uses your computer down time (called distributed computing) to compute folding algorithms and then ships the results off to research labs at Stanford. If would rather take a more hands on approach you can compete with other protein folders from around the world in a game style system called Fold It. Warning: these guys are serious folders and the competition is stiff. If you think you are up to it go to; http://fold.it/portal/info/science Finally, if you have had enough folding just do well on the AP exam, OK? Page 5 of 5