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                    <OTText id="f38fcdc0-008d-11de-953e-cb3d794622f6" text="&#xA;A protein that becomes a pore in a membrane:" />
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                    <OTText id="f62c98b9-008d-11de-953e-cb3d794622f6" text="&#xA;Create an image that clearly shows both ends of the string of amino acids. In the snapshot, use the text annotation tool  to mark both ends." />
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                    <OTText id="f8ee9eef-008d-11de-953e-cb3d794622f6" text="&#xA;Use the link above to open and explore the 20 rotatable 3D amino acids. Then select the &quot;Sidechain&quot; color scheme. The atoms that are colored gray are the same in every amino acid. What are they called?" />
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                        <OTText text="the sidechain atoms" />
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                    <OTText id="f8eeed15-008d-11de-953e-cb3d794622f6" text="&#xA;On the page of 3D amino acids, find glutamine and histidine. Use the different color schemes to select the true statement(s) below. (More than one statement may be true)." />
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                        <OTText id="f8ef1427-008d-11de-953e-cb3d794622f6" text="they are both polar amino acids" />
                        <OTText text="one is polar and the other is non-polar" />
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                        <OTText text="they are both non-polar" />
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                    <OTText id="fb620ffd-008d-11de-953e-cb3d794622f6" text="&#xA;Describe the distribution of electrons and polarity of an O-H bond." />
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                    <OTText id="fb623711-008d-11de-953e-cb3d794622f6" text="&#xA;Describe the distribution of electrons and polarity of a C-H bond." />
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                    <OTText id="fdd72eb5-008d-11de-953e-cb3d794622f6" text="&#xA;Snapshot of asparagine:" />
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                    <OTText id="fdd755c8-008d-11de-953e-cb3d794622f6" text="&#xA;Snapshot of leucine:" />
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                    <OTText id="fdd77cdb-008d-11de-953e-cb3d794622f6" text="&#xA;Snapshot of threonine:" />
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                    <OTText id="fdd7a3ee-008d-11de-953e-cb3d794622f6" text="&#xA;For Asparagine, which surface shows the correct charges?" />
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                        <OTText id="fdd7a3f0-008d-11de-953e-cb3d794622f6" text="surface 1" />
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                    <OTText id="fdd7cb03-008d-11de-953e-cb3d794622f6" text="&#xA;Which surface shows the correct charges for Leucine?" />
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                        <OTText text="surface 3" />
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                <OTQuestion id="fdd81927-008d-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page5.cml">
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                    <OTText id="fdd81928-008d-11de-953e-cb3d794622f6" text="&#xA;Which surface shows the correct charges for Threonine?" />
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                        <OTText id="fdd8192a-008d-11de-953e-cb3d794622f6" text="surface 5" />
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                <OTQuestion id="fdd8403c-008d-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page5.cml">
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                    <OTText id="fdd8403d-008d-11de-953e-cb3d794622f6" text="&#xA;Choose the best way to complete this sentence:&#xA;When two atoms in a bond have very different electronegativities, the surface of the molecule..." />
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                        <OTText text="has no charge." />
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                        <OTText text="has a negative charge." />
                        <OTText text="has a positive charge." />
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                    <OTText id="fdd88e64-008d-11de-953e-cb3d794622f6" text="&#xA;Explain how the colors on the surfaces of the side chains indicate whether it is polar or non-polar." />
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                <OTQuestion id="031ad6d7-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page6.cml">
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                    <OTText id="031ad6d8-008e-11de-953e-cb3d794622f6" text="&#xA;Is water a polar or non-polar molecule? Explain your answer by writing about the bonds in water." />
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                <OTQuestion id="031afdeb-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page6.cml">
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                    <OTText id="031b24fc-008e-11de-953e-cb3d794622f6" text="&#xA;Which type of amino acid is hydrophobic?" />
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                        <OTText text="neither - they both don't attract water very well" />
                        <OTText text="neither - they attract the water molecules equally" />
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                <OTQuestion id="031b4c12-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page6.cml">
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                    <OTText id="031b4c13-008e-11de-953e-cb3d794622f6" text="&#xA;Use your knowledge of positive and negative charge to explain why polar molecules attract each other and water better than non-polar molecules." />
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                <OTQuestion id="031b7326-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page6.cml">
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                    <OTText id="031b7327-008e-11de-953e-cb3d794622f6" text="&#xA;Which solvent(s) leads to folding of the protein?" />
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                        <OTText text="both water and oil" />
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                <OTQuestion id="031bc14d-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page6.cml">
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                    <OTText id="031bc14e-008e-11de-953e-cb3d794622f6" text="&#xA;Where do the amino acids with polar side chains end up when the protein chain folds?" />
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                        <OTText text="evenly throughout the folded protein" />
                        <OTText text="mostly inside the folded protein" />
                        <OTText id="031bc152-008e-11de-953e-cb3d794622f6" text="mostly on the outside of the folded protein" />
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                <OTQuestion id="09e6a593-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page8.cml">
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                    <OTText id="09e6cca4-008e-11de-953e-cb3d794622f6" text="&#xA;Snapshot of an alpha helix:" />
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                <OTQuestion id="09e6cca6-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page8.cml">
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                    <OTText id="09e6f3b7-008e-11de-953e-cb3d794622f6" text="&#xA;Snapshot of a beta sheet:" />
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                    <OTImage id="09e6f3b8-008e-11de-953e-cb3d794622f6" />
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                <OTQuestion id="09e6f3b9-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page8.cml">
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                    <OTText id="09e71aca-008e-11de-953e-cb3d794622f6" text="&#xA;A loop between a beta sheet and an alpha helix:" />
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                    <OTText id="0d4d5043-008e-11de-953e-cb3d794622f6" text="&#xA;Hydrogen bonds stabilizing alpha helices and beta sheets form between the atoms of which part(s) of the amino acids involved?" />
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                        <OTText text="the side chains" />
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                <OTQuestion id="11ac8bbb-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page10.cml">
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                    <OTText id="11ac8bbc-008e-11de-953e-cb3d794622f6" text="&#xA;Show an interaction that stabilizes an alpha helix and a loop:" />
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                    <OTText id="11acd9df-008e-11de-953e-cb3d794622f6" text="&#xA;Show an interaction that stabilizes two alpha helices:" />
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                <OTQuestion id="11ad00f1-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page10.cml">
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                    <OTText id="11ad2802-008e-11de-953e-cb3d794622f6" text="&#xA;Show an interaction that stabilizes a loop and a beta sheet:" />
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                <OTQuestion id="11ad4f14-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page10.cml">
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                    <OTText id="11ad4f15-008e-11de-953e-cb3d794622f6" text="&#xA;Show the hydrophobic core:" />
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                <OTQuestion id="16893497-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page11.cml">
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                    <OTText id="16893498-008e-11de-953e-cb3d794622f6" text="&#xA;On the left is a different small molecule than NAD. Why wouldn't this molecule bind to alcohol dehydrogenase in place of NAD? (Choose the BEST answer below)." />
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                        <OTText id="1689349a-008e-11de-953e-cb3d794622f6" text="it is not the same as NAD" />
                        <OTText text="it is smaller than NAD" />
                        <OTText text="it is too large to fit in the NAD site" />
                        <OTText text="it's the wrong shape, and will not form attractions with the site" />
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                <OTQuestion id="168982be-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page11.cml">
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                    <OTText id="168982bf-008e-11de-953e-cb3d794622f6" text="&#xA;What would you expect to happen to the function of proteins at very high temperatures?" />
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                        <OTText id="168982c1-008e-11de-953e-cb3d794622f6" text="the functions would not be affected" />
                        <OTText text="the proteins would not be able to function anymore" />
                        <OTText text="the functions would happen faster" />
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                <OTQuestion id="1689a8d4-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page11.cml">
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                    <OTText id="1689a8d5-008e-11de-953e-cb3d794622f6" text="&#xA;Explain how protein folding fits in to your answer to the previous question." />
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                <OTQuestion id="1b218078-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page12.cml">
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                    <OTText id="1b218079-008e-11de-953e-cb3d794622f6" text="&#xA;Does TNF have the quaternary level of structure? Make sure to try different color schemes on the model of TNF above)." />
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                        <OTText id="1b21807b-008e-11de-953e-cb3d794622f6" text="yes" />
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                        <OTText text="it's impossible to tell." />
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                <OTQuestion id="1b21ce9e-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page12.cml">
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                    <OTText id="1b21ce9f-008e-11de-953e-cb3d794622f6" text="&#xA;Explain your answer to the previous question:" />
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                <OTQuestion id="1eb94d42-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page13.cml">
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                    <OTText id="1eb94d43-008e-11de-953e-cb3d794622f6" text="&#xA;The &quot;primary structure&quot; of a protein refers to:" />
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                        <OTText text="the folds of the protein" />
                        <OTText text="the alpha helix and beta sheet structures" />
                        <OTText id="1eb94d47-008e-11de-953e-cb3d794622f6" text="the sequence of amino acids in the protein" />
                        <OTText text="two proteins that function as a unit" />
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                <OTQuestion id="1eb99b69-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page13.cml">
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                    <OTText id="1eb99b6a-008e-11de-953e-cb3d794622f6" text="&#xA;What part of an amino acid has properties (shape, charge) that are different from other amino acids?" />
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                        <OTText id="1eb99b6c-008e-11de-953e-cb3d794622f6" text="the side chain" />
                        <OTText text="the backbone atoms" />
                        <OTText text="the secondary structure" />
                        <OTText text="none of the above" />
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                <OTQuestion id="1eb9c280-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page13.cml">
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                    <OTText id="1eb9c281-008e-11de-953e-cb3d794622f6" text="&#xA;The bond between two atoms of equal electronegativity is:" />
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                        <OTText text="polar" />
                        <OTText text="hydrophilic" />
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                <OTQuestion id="1eba10a6-008e-11de-953e-cb3d794622f6" name="http://ri-itest.concord.org/SAMActivities/FourLevelsOfProteinStruct/FourLevelsOfProteinStruct_v2/page13.cml">
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                    <OTText id="1eba10a7-008e-11de-953e-cb3d794622f6" text="&#xA;The protein shown at right has folded in water. Which of the following statements about it is FALSE?" />
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                        <OTText text="amino acid 14 is most likely hydrophobic" />
                        <OTText text="amino acid 17 is most likely polar" />
                        <OTText id="1eba10ab-008e-11de-953e-cb3d794622f6" text="amino acid 22 is most likely polar" />
                        <OTText text="amino acid 20 is most likely hydrophilic" />
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                    <OTText id="1eba5ece-008e-11de-953e-cb3d794622f6" text="&#xA;Which of the following do hydrogen bonds help to stabilize?" />
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                        <OTText text="primary structure" />
                        <OTText text="secondary structure" />
                        <OTText text="tertiary structure" />
                        <OTText text="quaternary structure" />
                        <OTText id="1eba5ed4-008e-11de-953e-cb3d794622f6" text="B, C, and D are correct" />
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                    <OTText id="1eba85e6-008e-11de-953e-cb3d794622f6" text="&#xA;Select two correct choices:&#xA;A protein with quaternary structure..." />
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                        <OTText id="1ebaacf8-008e-11de-953e-cb3d794622f6" text="is made of two or more strings of amino acids" />
                        <OTText text="is always composed of identical subunits" />
                        <OTText text="is always composed of different subunits" />
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                    <OTText id="1ebad40e-008e-11de-953e-cb3d794622f6" text="&#xA;Two amino acids that are far apart from each other in the primary structure of a protein can be touching each other in the tertiary structure of the same protein. Explain how this happens." />
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                    <OTText id="1ebb2232-008e-11de-953e-cb3d794622f6" text="&#xA;Why do defects in protein folding cause disease?" />
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