AP Computer Visualization

When you click Submit (at the bottom of this web page) it will save your work on the server for me.

DO NOT Click submit more than once!

8/29 in class; If you are absent 9/1.

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.)

(Since you can work in pairs, put both names!)

Name:

Class Period

Click on the link below, and switching between this document and the open browser answer the questions. Most of the answers can be found through observation, but some require thought or research on the web.

This assignment will be posted on the web, and you can e-mail it to me if you want to complete it on your own time. You will NOT get additional time with the laptops. Do what you can.

If you are going to work at home use the following link.  http://c4.cabrillo.edu/projects/library/duoviewer/index.html You may need to install Chime (search Chime installer).

In school you will use a program called RASMOL which is in a folder on the desktop of the laptops. In the folder is a program file that looks like 3 linked balls. After you click on the program click on file and open one of the models. The models we will look at come in two formats. Brookhaven and MDL.

 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.

Click on ball and stick (it is easier to visualize molecules that way). (In RASMOL you change visualizations with the top menu).

 Look at the following inorganic molecules and briefly describe them (linear, polar/non-polar etc.) They can be found as "Brookhaven" files.

Question 1: Ammonia

Question 2: Water

Question 3: Carbon Dioxide

Question 4: Oxygen

Question 5: Ozone

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

Question 6: In this visualization, what does a line represent? How many electrons are in a single line?

Question 7:  In the section of alcohols, compare methanol, ethanol, n-propyl alcohol.  What makes an alcohol an alcohol?

All of the rest of the molecules are in MDL format and if you are using RASMOL you need to change the "File of type" box when you try and open the files.

Question 8:  In the section on carbohydrates look at D-Glucose, D-Fructose, lactose, and sucrose. Describe the general structure of a sugar. Is it polar/non-polar? What is a disaccharide?

Question 9:  In the section on lipids, look at oleic acid, palmitic acid, and the two triglycerides (one with 2 unsaturated fatty acids and the other all saturated fatty acids). Describe the general structure of a lipid?  Is it polar/non-polar? What is the difference between saturated and un-saturated fatty acids?

Question 10:  In the section on amino acids and proteins, look at alanine, glycine, cysteine, gly-gly, and the first choice (ala-cys-lys-asp-phe-cys) in the polypeptide sections. What is the general structure of an amino acid? What is a peptide bond? Why are proteins important?

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

Question 11:  Under nucleotide look at ribose and deoxyribose. How are they similar? Different?

Question 12:  Under nucleotide look at purine and pyrimidine. How are they similar? Different?

Question 13:  Under nucleotide look at uracil, thymidine, cytosine, guanine, adenine. How are they similar? Different? Assign each to a “category” as either a purine or a pyrimidine.

Question 14:  General conclusions: What do molecules look like? Why do we use visualizers?

Question 15: "System" conclusion. Was this easier/harder than writing by hand on a worksheet? Which would you prefer in the future, worksheets or computer forms? Why? (For me, handwriting is also an issue!)