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Transcript
Taken from http://www.gtac.edu.au/ 2007 EXPLORING ENZYME STRUCTURE AND FUNCTION STUDENT WORKSHEET Follow the student instructions (in boxes) and answer the questions in this worksheet as you progress through each activity. Exploring amylase Exploring Amylase Open the Cn3D file named 'amylase l' found on your desktop Open the Cn3D file named ‘Amylase’ by going to the following website and downloading Cn3D 4.1 http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml 1.1 Move your mouse cursor onto the amylase structure shown. Click and drag the structure around to take a close look at it. The alpha helices are green, the beta sheets are brown and the random loops are blue. 1. How many alpha helices are there in this polypeptide? 2. How many beta sheets are there in this polypeptide? 1.2 Amylase catalyses the hydrolysis of starch molecules. It does this by removing one disaccharide at a time. The enzyme you are looking at has an inhibitor molecule blocking its active site. The active site is composed of a ring of beta sheets with a CI- ion near its centre. Locate the active site and zoom in by clicking the 'z' key on your keyboard. 3. What parts of the enzyme appear to be making up (a) the entrance to the active site and (b) the active site? 4. Charged ions are often required to assist an enzyme to do its job. These ions are cofactors. What cofactors are involved in the functioning of amylase? 5. What do you observe about their location in this enzyme? 1.3 Go to Show/Hide on the toolbar and select Show Aligned Domains. 6. How many sugar units are there in the larger carbohydrate molecule seen? Centralian Senior Secondary College – Alice Springs \ Taken from http://www.gtac.edu.au/ 2007 1.4 Go to Show/Hide on the toolbar and select Show Everything. Let's look at a 3D view of the molecule. Go to Style on the toolbar and select Rendering Shortcuts and then Space Fill. Zoom out using the 'x' key on your keyboard. 1.5 Now lets look at the hydrophobic (water 'hating') areas of the molecule. Go to Style on the toolbar and select Coloring Shortcuts and select Hydrophobicity. You can now see the carbohydrate molecule nestled in the enzymes active site. 7. Do the hydrophobic amino acids (in brown) appear to be projecting into or out of this molecule for the most part? Suggest a reason for this observation. 1.6 Now select Mouse Mode on the Sequence/Alignment Viewer toolbar and select Rectangle. Move your cursor along the amino acid sequence until you find amino acids 162 -164. Highlight these by clicking and dragging with your mouse cursor. Hint: the amino acid location is shown at the bottom of the box. 8. What is interesting about the location of the amino acids 162, 163 and 164? 1.7 Now highlight amino acids 233 -237. 9. What is interesting about the location of amino acids 233 -237? Centralian Senior Secondary College – Alice Springs Taken from http://www.gtac.edu.au/ 2007 10. How can all of these amino acids be associated with the carbohydrate molecule when they are so far apart in the primary structure (amino acid sequence) of this protein? 1.8 Move your cursor to sit over the lXDl_A in the Sequence/Alignment Viewer box. 11. What is the total number of amino acids making up this enzyme? 12. What organism was this enzyme found in, and what part of the organism? 13. The large carbohydrate in this molecule is an inhibitor molecule. It stops the enzyme from breaking down starch. Looking at the location of the inhibitor, how might it be exerting its effect? 1.9 Open the Cn3D file called "amylase 2" found on your desktop 14. What organism does this enzyme come from? 15. Give two similarities and two differences you observe between this enzyme and the human pancreatic alpha amylase enzyme? Centralian Senior Secondary College – Alice Springs Taken from http://www.gtac.edu.au/ Similarities Centralian Senior Secondary College – Alice Springs 2007 Differences Taken from http://www.gtac.edu.au/ 2007 EXTENSION QUESTIONS 16. Many plants have a natural inhibitor of this enzyme. For example, beans contain the inhibitor phaseolin. Why would they contain this inhibitor? 17.-Use the information you have learned about this enzyme to recommend a method of making a diet pill for humans to use. 18. Amylase relies on the cofactors calcium and chloride to function efficiently. What parts of your diet could supply these ions? 19. Many organisms utilise the amylase enzyme to break down starch. While there are some differences in enzyme shape, there is one part of the enzyme that is generally conserved between species (the primary structure is the same). What region of the enzyme do you think would be conserved? Explain. Centralian Senior Secondary College – Alice Springs