“As the Molecule Turns” This tutorial will walk you through how to load and complete this online lab. Follow the instructions on the following pages.

Laboratory Objectives Student will be able to: –Explain the concepts of “water-loving” and “water-hating” molecular interactions. –Identify some 3-D shapes of proteins which have had their structures solved in research laboratories. –Demonstrate how to use a computer imaging program. –Students will be able to navigate through a self guided PowerPoint

Assessment You will be evaluated by a rubric that will be used to assess the following areas: –Usage of PowerPoint –Usage of the Rasmac software –Ability to download images from the internet –Completion of the lab –Understanding of importance of both hydrophilic and hydrophobic amino acids The following object is the rubric in which will be used to assess your work.

Introduction The behavior of hydrophilic (water-loving) and hydrophobic (water-hating) molecules plays an important role in determining the structure of proteins. The structure of the protein is very critical to it’s function. As you discovered earlier in this unit proteins are simply long chains of amino acids connected by peptide bonds.

Materials To complete this lab you will have to use a program called Rasmac. Rasmac will allow you to see the 3-dimensional shape of any protein whose structure has been solved in a research lab using modern high-resolution techniques.

Using the Rasmac software. In the following pages you will be asked to open the Rasmac software. This will be represented as an icon on the following pages. By double clicking on the icon you will begin running the program. The second piece of information that you will need is the actual protein file which must be downloaded off the internet. The links for these proteins are provided for you. Simply follow the link and then click on the picture of the necessary protein to save it to your computer.

Procedure 1 (Collagen) Collagen facts: –most abundant protein in mammals. –strong fibrous protein. Click on the following link and download the Collagen pdb.file. Collagen pdb.file Once you have downloaded the collagen file simply click on the Rasmol Icon to run the program and proceed to the next slide.

Collagen Continued You now should have several different windows opened (Rasmac, PowerPoint, and Internet) By clicking on the Rasmol icon on your window bar you will see two windows available (RasMol Version 2.6 and Rasmol Command Line). Open both of these as well as your word document titled “As The Molecule Turns”. Proceed with the following directions on your Laboratory Packet by clicking on the lab title to the right. Be sure to save this document on your hard drive

Procedure 2 (Myoglobin) Myoglobin facts: –Oxygen storage protein. –Protein enzyme. Click on the following link and download the Myoglobin pdb.file. Myoglobin pdb.file Once you have downloaded the myoglobin file simply click on the Rasmol Icon to run the program and proceed to the next slide.

Myoglobin Continued You now should have several different windows opened (Rasmac, PowerPoint, Internet, and word). By clicking on the Rasmol icon on your window bar you will see two windows available (RasMol Version 2.6 and Rasmol Command Line). Open both of these as well as your word document titled “As The Molecule Turns”. Proceed with the following directions for procedure 2 on your Laboratory Packet.

Procedure 3 (Myoglobin + Amino Acids) You are now going to examine the location of water-loving and water-hating amino acids in myoglobin. If you choose to download a specific amino acid proceed to this website Amino Acids pdb.file.Amino Acids pdb.file (optional) Once you have downloaded the amino acid file simply click on the Rasmol Icon to run the program and proceed to the next slide.

Myoglobin Continued You now should have several different windows opened (Rasmac, PowerPoint, Internet, and word). By clicking on the Rasmol icon on your window bar you will see two windows available (RasMol Version 2.6 and Rasmol Command Line). Open both of these as well as your word document titled “As The Molecule Turns”.