HEMOGLOBIN: PHYSIOLOGICAL EXPRESSION AND EVOLUTION OF GENE CLUSTER

Transcription

1 HEMOGLOBIN: PHYSIOLOGICAL EXPRESSION AND EVOLUTION OF GENE CLUSTER I. Physiological Expression: HOW DO WE GET OXYGEN TO OUR BODY TISSUES? Oxygen has a low solubility in blood. During the course of animal evolution, respiratory pigments have evolved that bind oxygen and transport it to the tissues for its use in cellular respiration. Vertebrate animals contain both myoglobin, which is used to store oxygen in muscle tissue, and hemoglobin, which is used to transport oxygen to the body tissues. Myoglobin consists of a single polypeptide chain, while hemoglobin consists of 4 polypeptide chains functioning together as a tetramer. Each polypeptide chain is complexed with a heme group that contains a porphyrin ring with an iron (Fe + ) atom in the center to which the oxygen binds. A variety of different versions of these subunits exist including two types of alpha globins, alpha (!) and zeta ("). There are also three types of beta globins, beta (#), epsilon ($), gamma (%). ACTIVTY ONE: BACKGROUND INFORMATION Use available resources (e.g. internet or text) to collect background information on the various polypeptides of hemoglobin by answering the following questions. Several of these questions can be answered by accessing information from Wikipedia although there is much more information at this site than will be needed. 1. Gather information to complete the following table. When in the stages of human life history are the various types of hemoglobin polypeptide chains expressed? (Hint: think embryo, fetus, adult) Take your information and enter it into the table below: Life Stage alpha (!) zeta (") beta (#) epsilon ($) gamma (%) Embryo Fetus Adult 2. Do all of the different versions of hemoglobin polypeptides have the same ability to bind (affinity for) oxygen? Explain the relative binding affinity of each type of chain. BioQUEST Summer Bucher, Pape-Lindstrom and Tran

2 3. Why do you think the different polypeptides have different binding affinities? 4. Think carefully about human development and explain what you think might be the physiological significance of different oxygen binding affinity for the various hemoglobin chains. II. Evolution of Gene Hemoglobin Gene Cluster Now you are going to study the hemoglobin polypeptide chains from an evolutionary perspective. To do this we are going to use a tool called BIOLOGY WORKBENCH. This is a real tool used by scientists to perform authentic research.! Next, your lab group needs to decide which hypothesis you wish to investigate. o o o Hypothesis One: an evolutionary tree based on amino acid sequences of the hemoglobin chains will accurately reflect the evolutionary relationships of the major vertebrate classes. Hypothesis Two: an evolutionary tree based on amino acid sequences of the hemoglobin chains will accurately reflect the evolutionary relationships within the mammalian order, primates. Alternatively, your group can create its own hypothesis regarding evolutionary relationships reflected by amino acid sequences of hemoglobin chains. Record your group s hypothesis here: BioQUEST Summer Bucher, Pape-Lindstrom and Tran

3 ! Look at the picture above. Using your computer, go to the URL listed above. Click on register for a free account. You will only need one account per lab group. At this point, please MAKE SURE TO WRITE DOWN YOUR USER NAME AND PASSWORD. username: password: BioQUEST Summer Bucher, Pape-Lindstrom and Tran

4 Once you have logged into the workbench site, you should see the logo above.! Scroll down and click on Session Tools.! Click on Start New Session and then Run.! Session Description: This is where you create a name for your session that you will remember and is related to the topic, because you will be able to return to this session later. After you have typed in a name click Start New Session.! Write down the name of your session. A list of all sessions will come up (you will only have one). Click Run. BioQUEST Summer Bucher, Pape-Lindstrom and Tran

5 ! After starting a new session, choose Protein Tools.! Once you have clicked on Protein Tools you need to click on Ndjinn Multiple Database Search and then click on Run.! Once when you are in Ndjinn, you will need to enter your search term (starting with hemoglobin is a good idea) and also check the box of the database that you wish to use. Generally, a good database to choose to begin with is Swissprot which is in the alphabetized list and has a red box. I also recommend that you set the Hits per page at 50 per page. After you have done this click on Search. BioQUEST Summer Bucher, Pape-Lindstrom and Tran

6 ! At this point your lab group should select about 7-9 proteins that you think will help you address the hypothesis that you identified earlier in the session.! After checking the boxes of the relevant proteins scroll to the bottom of the screen click Import Sequences. BioQUEST Summer Bucher, Pape-Lindstrom and Tran

7 Now you should see a list of the various proteins which you have chosen to import.! Now, check the proteins and then the CLUSTALW tool and click Run. BioQUEST Summer Bucher, Pape-Lindstrom and Tran

8 ! Now, with the proteins checked and the CLUSTALW highlighted use arrowns on the guide tree display to choose Rooted and Unrooted Trees. Then click Submit. Your output should look similar to what you see below.! Continue to scroll down and you should see both a rooted tree and an unrooted tree that have been built using your selected protein sequences. BioQUEST Summer Bucher, Pape-Lindstrom and Tran

9 Below are examples of both the rooted and the unrooted trees. Your trees will not look exactly like these, as you selected different proteins to generate your trees.! Examine both of your trees, the rooted vs. the unrooted and talk in your group about which you think might be more accurate and why. Sketch your graph in the space provided below. BioQUEST Summer Bucher, Pape-Lindstrom and Tran

10 1. Interpret your tree diagram. Discuss with your group the major relationships illustrated within your tree. Write 2-3 sentences summarizing your results and interpretation. 2. Do the results from your tree agree with current consensus regarding the evolutionary relationships within the group you chose to study, e.g. primates or vertebrates (or something else if you formed an original hypothesis)? Use your text or a web resource if you are uninformed of evolutionary relationships within your research area. Write 2-3 sentences explaining why or why not your tree illustrates current understanding. 3. What would your group like to investigate next using these techniques? If you found anomalies in your tree, you may wish to further investigate this by importing additional protein sequences or eliminating others. If your tree is similar to current consensus regarding evolutionary relationships, think of another set of relationships to investigate. After discussing with your group, write an original hypothesis and describe how you would go about testing it using information that already exists in online data bases. In the space provided below, write a paragraph describing this that begins with your hypothesis. BioQUEST Summer Bucher, Pape-Lindstrom and Tran