Download Taken from http://www.gtac.edu.au/ 2007 EXPLORING ENZYME

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