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Computer Molecular Models

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8/30-In class

TAB OR USE THE MOUSE Between the fields....

Answer the questions as best you can. The boxes will expand as you type if you need more space. (Don't worry if it is a one word answer. The box size is standard.)

Name: (Include all the names in your group. Maximum group size = 3.

Class Period

1 2 3 4 5 6 7 8

Open the folder called "Rasmol." For each of the molecules listed in the questions below double click on the molecule in the folder. It will open in Internet Explorer. It will probably give you security warnings. Click to allow the page to open. You can right click to access the viewing options.

Spend a couple of minutes “playing” with the program so that you can easily call up molecules and compare them. You should be able to rotate molecules, zoom in on them etc.

Right click and choose display. Choose  ball and stick (it is easier to visualize molecules that way).

 

Question 1: Look at the following inorganic molecules and briefly describe them (linear, polar/non-polar etc.)

Ammonia, water, carbon dioxide, oxygen, ozone.

Question 2: What does a line represent in these molecules? What are the color conventions in the computer models and how are they different from the color conventions in the plastic models?

Question 3: Compare methanol, ethanol, 1-propanol. What makes an alcohol an alcohol?

Question 4: Look at D-Glucose, D-Fructose, lactose, and sucrose. Are sugars polar or non-polar? What is a disaccharide?

Question 5: Look at oleic acid, palmitic acid and the two triglycerides (one with 2 unsaturated fatty acids and the other with all saturated fatty acids.

What is the general structure of a lipid? Is is polar or non-polar? What is the difference between saturated and unsaturated fatty acids?

Remember, the boxes will expand as you type if you need more space.

Question 6: Look at glycine, alanine, cysteine, gly-gly and the hexapeptide (ala-cys-lys-asp-phe-cys).

What is the general structure of an amino acid? What is a peptide bond? Why are proteins important?

Question 7: Look at ribose and deoxyribose. How are they similar? How are they different?

Question 8: Look at purine and pyrimidine? How are they similar? How are they different?

Question 9: Look at uricil, thymidine, cytosine, guanine, and adenine. How are they similar? Different? Assign each of them to a category as either a purine or pyrimidine.

Question 10: Why would we use computer visualizers rather than plastic models

      
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