Name____________________________________________________________
Four Levels of Protein Structure – Interactive Web Activity
Directions: Go to http://workbench.concord.org/database/activities/322.html. This link
can be found on the class website. Click “Go To Activity”. Follow the directions on this
handout and mark your answers on this paper. (You won’t be doing all of the activities
on the website.)
Page 1: Read the info on page 1.
1. What is meant by “primary structure”?
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Click “Play Movie”. Read the subtitles as you watch the movie.
Under “Do It Yourself”, choose “beads” under “select style”, and “amino acids”
under “select color”. Then click “Build It” to see the primary structure of the
protein and how it’s folded.
Page 2: Read the info on page 2. Click on the 20 amino acids link to help answer
these questions.
2. Use the link to open and explore the 20 rotatable 3D amino acids. Then select
the sidechain color scheme. The atoms that are colored gray are the same in
every amino acid. What are they called?
3. On the page of 3D amino acids, find glutamine and histidine. Use the polarity and
charge color schemes to select the true statement(s). (More than one statement
may be true). Write your answer here.
Page 3: Read the info on page 3. Use the animation controls to get a good look at
the alpha helix and beta sheet structures.
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Under the image of the kinase, select “cartoon” from the drop-down menu.
Then, next to “highlight 30 amino acids”, keep clicking on the up arrow to see
the helices and sheets in this protein.
Page 4: Read the info on page 4. Next to the image of Protein G, uncheck “side
chains” to more clearly see the hydrogen bonds. Then click on “alpha helix”, and “beta
sheet” to view different angles.
4. Hydrogen bonds stabilizing alpha helices and beta sheets form between the
atoms of which part(s) of the amino acids involved?
Page 5: Read the info on page 5. About halfway down the page, click “polar amino
acid” and “Run” to see an animation. Then click “nonpolar amino acid” and “Run” to see
an animation.
5. Which type of amino acid is hydrophobic?
6. Which of the following correctly describe the interactions of the amino acids with
water?
Scroll down to the section on protein folding. Choose “Water” and “Run” to see an
animation. Then choose “Oil” and “Run” to see an animation.
7. Which solvent(s) leads to folding of the protein?
8. Where do the amino acids with polar side chains end up when the protein chain
folds?
Page 6: Read the info on page 6. Next to the image, click on “hydrophobic core” to
view polar and nonpolar amino acids. Then choose “one” under disulfide bonds to see
an animation. Also choose “one” under salt bridges and side chain hydrogen bonds to
see each animation.
Page 7: Read the info on page 7. Next to the first image, click “Show NAD only”, then
click “Amino acids that create binding site” to view an animation.
9. On the left is a different small molecule than NAD. Why wouldn't this molecule
bind to alcohol dehydrogenase in place of NAD?
Scroll down to the section on proteins and heat. Under the image, click "Run" and
observe the stability of the protein shape. Then gradually raise the temperature by
clicking on the red arrowhead.
10. What would you expect to happen to the function of proteins at very high
temperatures?
Page 8: Read the info on page 8. Next to the image, click “Load Homodimer” and
“Play” to view an animation. After it’s over, click “Load Heterotrimer” and “Play” to view
an animation.
Scroll down to the next image. On the first pulldown menu, choose “ribbons”. On the
second pulldown menu, choose “subunits”.
11. Does TNF have the quaternary level of structure?
Page 9: Answer these questions.
12. The "primary structure" of a protein refers to:
13. What part of an amino acid has properties (shape, charge) that are different from
other amino acids?
14. The protein shown at right has folded in water. Which of the following statements
about it is FALSE?
15. Which of the following do hydrogen bonds help to stabilize?
16. Select the two correct choices:
A protein with quaternary structure...