MOLECULAR VISUALIZATION &

THE ELEMENTS OF ORGANIC MOLECULES

Name: ______

Background

Subatomic electrons, protons, and neutrons form atoms, and atoms bind to form compounds. In high school chemistry compounds, are commonly represented by their chemical formulas (example: H20). The molecules unique to living organisms categorized as carbohydrates, lipids, nucleic acids, or proteins can also be represented by their chemical formulas. Since these organic molecule are so large in size though other means of representing molecules have been developed. Initially, representations included two-dimensional drawings of bound atoms in spacefill and other such diagrams. Later, representations have taken advantage of the computer to display molecules and their component atoms and bonds. More recently, some of the visualization software has become available freely via the internet so that anybody that takes the time can come to a deeper and more realistic understand of molecules. In the following activity, you will first download a software package, and then you will begin to explore selected organic molecules to learn minor capabilities of the software, as well as about the most common elements found in life.

Procedure

1. Watch as your teacher shows how to access the software RasMol and the following molecule files.

phospholipid.pdb

cholesterol.pdb

glucose.pdb

sucrose.pdb

cellulose.pdb

hemoglobin.pdb

potassiumchannel.pdb

dna.pd

2. In the RasMol display window, open the “phospholipid.pdb” file using the “File”, and “Open” categories in the menu. After browsing to the molecule file and selecting OK, you will observe a wireframe representation of the molecule in the display window.

3. Once the molecule is displayed use the pull down “Display” menu to view the difference between the “Wireframe”, “Ball and Stick”, and “Spacefill” molecular representations, and answer the first question.

4. To identify a particular atom in the spacefilled representation, you can click on that atom and information about it will appear in the command window. Determine and record the color of the major atoms in the data table as you proceed. In some of the large molecules viewed in spacefilll, you will notice red spheres unattached to the molecule being represented. These are the oxygen atoms of water molecules. To make them disappear complete the following “RasMol> select water”, then “RasMol> spacefill off”.

5. Then, use the following commands to determine the number of each major type of atom composing the phospholipid. When you have identified the number of all the atoms composing the molecule determine the percentage of each atoms composition in the molecule.

RasMol Commands / Function of Command
RasMol>select all / This will return information on the total number of atoms in the molecule
RasMol>select carbon / This will return information on the total number of carbon atoms in the molecule (you can select different atoms)
RasMol> color yellow / If used after selecting particular atoms, this will color those atoms yellow (you can color other colors)
Zoom in and out / Hold the shift key while dragging the mouse. This often crashes the software.

Data Table

Molecules

/ Carbon
Atoms / Oxygen
Atoms / Nitrogen
Atoms / Sulfur
Atoms / Phosphorous
Atoms / Other
Atoms ______
spacefill color
# / % / # / % / # / % / # / % / # / % / # / %
phospholipid
cholesterol
glucose
sucrose
cellulose
hemoglobin
potassium channel
DNA
Percentage / __ / __ / __ / __ / __ / __

Questions

1. Sketch each representation for a molecule of your choice. How do the three types of molecular representations differ? What is each molecular representation best at representing about the molecule?

2. Use the ball-and-stick display and zoom (in the larger molecules) to look for specific covalent bonding involving each of the following atoms. For each atom observed not the atoms that it is bound to and sketch a representation of that particular bonding pattern. Also, use your knowledge of the atom’s number of outer electrons determine if the bonding pattern you are observing makes sense. If it doesn’t, could double bonds resolve the issue?

Hydrogen

Oxygen

Carbon

Nitrogen

Phosphorus

Sulfur

3. Did you find any of the functional groups that are shown on page 93 in your textbook? Name the ones you did and diagram and name those that you didn’t.

4. What appears to be missing from the carbon and oxygen atoms in the hemoglobin, potassium channel, and DNA molecules? What atom may be missing that would help solve this apparent problem?

5. Which atom appears to be most important in composing the basic shape of most of these organic molecules? Explain making sure to explain your logic from an atomic perspective.

6. Can you find representations of the three carbon bonding patterns shown at the bottom of page 92? Name and diagram those you didn’t, and name and identify the particular molecule for those that you did.

7. Identify the four categories of organic molecules (there in the background) and place each of the viewed molecules into its appropriate category (use textbook or internet).

8. List the atoms found in these molecules from most common to least common. Do your overall percentages of these molecules represent the known percentages these atoms in the human body (textbook page 72)? Explain.

9. Some atoms are rather uncommon in organic molecules and are called minerals in your diet. List the most common elements besides H, O, N, and C using their atomic symbol. Which of these rarer elements are found in organic molecules? Which organic molecules?

10. What are trace elements? List the trace elements using their atomic symbol. Then, label and identify some of the more important trace elements. Where any of these found in the organic molecules observed? Explain.