SAM Teachers GuideFour Levels of Protein Structure

OverviewStudents explore the four levels of protein folding. They explore variations of surface charges of amino acids and correlate that to the structure of the proteins they form. Students interpret how the sequence and properties of amino acids relate to how proteins fold. They identify patterns of folding known as secondary structure and explore final folding patterns. Finally, students learn about how tertiary and quaternary structure relate to protein function.

Learning ObjectivesStudents will be able to:

Recognize that a protein’s three-dimensional shape allows it to perform a specific task.

Identify the primary structure of a protein as a linear sequence of amino acids.

Identify the unique side chains of amino acids that give them their properties.

Explore how amino acids interact with water and how that affects the way proteins fold.

Differentiate among the common secondary structures of a protein and identify the importance of hydrogen bonding in stabilizing these structures.

Identify tertiary structure as the final folding pattern of a protein and infer that mistakes in folding are responsible for many human diseases.

Explain that quaternary structure occurs when a protein is composed of more than one subunit, and that the subunits form a complex to achieve functionality.

Possible Student Pre/Misconceptions Proteins are a straight chain of amino acids that result from

translation as seen in previous activities and units. The three-dimensional structure is not important.

Proteins are uniform throughout rather than having different parts for various functions.

Models to Highlight and Possible Discussion QuestionsAfter completion of Part 1 of the activity:

Models to Highlight: Page 1 – Sample Proteins

o Highlight how structure relates to function.

o Explain that most protein structures do not have shapes that help us to identify their functions just by looking at them.

Page 2 – Primary Structure Model o Review the different views of the protein and focus on the

definition of primary structure. Page 3 – Model and Link to 20 Amino Acids

o Highlight that the backbone of all 20 amino acids is the same. It is the side chains that give each amino acid a different personality.

Page 4 – Electronegativity o Take time to review/reinforce the definition of

electronegativity and how bonding will affect the structure of a protein.

o Link to other SAM activities: Intermolecular Attractions and Chemical Bonds. The interactions between amino acids in a protein are affected by unequal sharing of electrons.

Page 6 – Protein Folding Starts in Water o Review polarity and link to the importance of how proteins

behave in water. Use model to review hydrophobic/hydrophilic interactions and how one protein can have regions of both. This will impact folding.

o Link to other SAM activities: Chemical Bonding. Polarity and electronegativity will influence the type of chemical bonds formed.

Possible Discussion Questions: How do charged amino acids affect the shape of a

protein? How do amino acids’ interactions with water affect the shape of

the protein? Why do you think different folding patterns happen? Give students a mystery protein and a key with the 20 amino

acids. Have students devise a folding pattern that makes sense based on their knowledge thus far of both proteins and chemical bonding/ electronegativity.

After completion of Part 2 of the activity:Models to Highlight:

Page 8 – Exploring Secondary Structures in Protein Kinase o Use bottom model to help students practice identifying

alpha helices, beta sheets, loops and turns. Use this opportunity to review polarity again. Encourage students

to rotate and zoom to get a better view of/feel for the structures.

Page 11 – Folding Creates Important Sites on Proteinso Highlight how protein folding creates specific sites on

proteins, which allow for specific functionality. Page 12 – Multi-Subunit Proteins

o Some proteins achieve their function by acting as a complex of multiple subunits (quaternary structure).

Link to other SAM activities: DNA to Proteins. Highlight the idea that proteins are encoded in the DNA.

Link to other SAM activities: Four Levels of Protein Structure. Highlight that the unique surface of each protein enables it to perform its specific function.

Possible Discussion Questions:

Why is the folded structure of a protein so important for its functionality? Can you think of any examples?

What are some specific jobs of proteins that require them to have a distinct 3D structure? (Possible answers: enzymes, roles in signal transduction, DNA synthesis, etc.)

How do proteins differ? Highlight primary, secondary, tertiary, quaternary structure.

What types of situations may impact how a protein would function? Generate ideas about temperature, whether it is surrounded by water or oil, etc.

Demonstration/Laboratory Ideas: o Construct chains or amino acids and physically show

folding patterns using beads, children’s toys, etc. o Use Toobers (inexpensive flexible foam rods) for showing

folding and how distant parts of a protein come together to form a binding site or other specialty area. For more information and clear ideas on how to use them, see http://www.umass.edu/molvis/toobers.

o Use molecular model kits to focus in on bonding within a protein.

o Use oil and water demonstration to review hydrophobic/ hydrophilic interactions. Link back to the importance of water in living systems (cell membrane review).

Connections to Other SAM Activities

The focus of this activity is for students to understand the primary, secondary, tertiary and quaternary structures of proteins.

This activity is supported by many activities that deal with the attractions between atoms and molecules. First, Electrostatics focuses on the attraction of positive and negative charges. This will play a role in understanding salt bridges, hydrogen bonding and intermolecular attractions. The Intermolecular Attractions activity highlights hydrogen bonding, which plays a role in stabilizing the alpha helices and beta sheets within proteins. In addition, this activity discusses the forces of attraction that are at work on the intramolecular level of proteins as well as the intermolecular level (in the quaternary structure of proteins). Chemical Bonds allows students to make connections between the polar and non-polar nature of bonds and how one part of a molecule could be partially positive or negative due to the uneven sharing of electrons. The Solubility activity highlights the tendencies of globular proteins that have hydrophobic and/or hydrophilic regions and how they will behave, particularly in water. Molecular Geometry explains the specific orientation of atoms within larger molecules. Finally, Proteins and Nucleic Acids introduces the structure and function of amino acids and protein molecules while DNA to Proteins explains where proteins originate.

This activity supports three other SAM activities. First, Four Levels of Protein Structure builds on student understanding of why structure is so important in protein function. This activity also supports Diffusion, Osmosis, and Active Transport and Cellular Respiration because there are references in both of these activities to larger scale protein complexes.

Activity Answer Guide

Page 1:

1. A protein that can puncture a cell wall:(b)

2. A protein that forms a cable:(a)

3. A protein that becomes a pore in a membrane:

(c)Page 2:

*Sample snapshots: Other snapshots may answer the questions.

1. Put a snapshot of the surface of the protein here.

This snapshot shows the protein's surface. (Note, alternatively, students may take a snapshot after using the “Show protein surface” checkbox.)

2. 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.

Sample snapshot:

The annotation indicates each end of the protein chain.

Page 3:

1. Look closely at the two ball & stick structures for alanine and phenylalanine. Can you pick out the atoms that make them

unique? Use the annotation tool in the snapshot to circle the atoms that make them different — that is, the atoms of each one's side chain. Sample snapshot:

2. Use the link above 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? (b)

3. 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.) (a) (c)

Page 4:

1. Describe the distribution of electrons and polarity of an O-H bond.

The O-H bond is polar. Oxygen is better at attracting the electrons, making that side of the molecule more negative.

2. Describe the distribution of electrons and polarity of a C-H bond

The C-H bond is non-polar. They share electrons evenly.

Page 5:

Sample snapshots:

Polar bonds are those from nitrogen or oxygen to carbon or hydrogen.

Non-polar amino acid – no bonds should be circled.

Polar bonds are around oxygen.

1. For Asparagine, which surface shows the correct charges? (a)

2. Which surface shows the correct charges for Leucine? (b)

3. Which surface shows the correct charges for Threonine? (a)

4. Choose the best way to complete this sentence: When two atoms in a bond have very different electronegativities, the surface of the molecule... (b)

5. Explain how the colors on the surfaces of the side chains indicate whether it is polar or non-polar.

The colors represent whether the electrons are being shared evenly or not. The blue shows areas of partial negative charge, where electrons have been pulled; red indicates a partial positive charge. Surfaces colored with blue and red are polar. The pale area shows that electrons are being shared evenly (non-polar).

Page 6:

1. Is water a polar or non-polar molecule? Explain your answer by writing about the bonds in water.

Water is a polar molecule. Oxygen is electron greedy, thus attracting electrons. This leaves oxygen slightly negative and the two hydrogen atoms slightly positive.

2. Which type of amino acid is hydrophobic?(b)

3. Use your knowledge of positive and negative charge to explain why polar molecules attract each other and water better than non-polar molecules.

The uneven charge distribution in water allows for attraction with polar molecules. Opposite charges attract while like charges repel. Because there is no net charge difference in a non-polar side chain, this same attraction to water does not occur.

4. Which solvent(s) leads to folding of the protein? (c)

5. Where do the amino acids with polar side chains end up when the protein chain folds?

(c)

Page 7: No questions.

Page 8:

1. Snapshot of an alpha helix:

Alpha Helix

2. Snapshot of a beta sheet:

Beta sheet 3. A loop between a beta sheet and an alpha helix:

Loop connecting alpha helix and beta sheet

Page 9:1. The hydrogen bonds that stabilize an alpha helix.

The above picture shows hydrogen bonds stabilizing an alpha helix. Hint: Use “Color Atoms by: Structure” to get a clear image.

2. The hydrogen bonds that stabilize a beta sheet.

The above picture shows hydrogen bonding stabilizing a beta sheet.

3. Hydrogen bonds stabilizing alpha helices and beta sheets form between the atoms of which part(s) of the amino acids involved?

(c)

4. Place a snapshot here that illustrates your answer to the previous question.

This picture has the side chains removed and shows just the hydrogen bonding in the backbone of the protein.

Page 10:*Sample snapshots*

1. Show an interaction that stabilizes an alpha helix and a loop:

Disulfide bond stabilizing alpha helix and loop.

2. Show an interaction that stabilizes two alpha helices:

Salt bridge stabilizing two alpha helices.

3. Show an interaction that stabilizes a loop and a beta sheet:

Side chain hydrogen bonds stabilizing a loop and a beta sheet.

4. Show the hydrophobic core:

Hydrophobic core is translucent and polar amino acids on the outside are shown in blue.

Page 11:

1. 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.) (d)

2. What would you expect to happen to the function of proteins at very high temperatures? (b)

3. Explain how protein folding fits into your answer to the previous question.

As seen in the model above, at higher temperatures the folding pattern of the protein breaks apart. Since the folding pattern is linked to its functionality, the protein would no longer be able to do its job.

Page 12:

1. Does TNF have the quaternary level of structure? Make sure to try different color schemes on the model of TNF above. (a)

2. Explain your answer to the previous question:

Using the subunit color scheme is the easiest way to identify the quaternary structure of TNF. It shows the structure has three different subunits.

Page 13:

1. The "primary structure" of a protein refers to: (c)

2. What part of an amino acid has properties (shape, charge) that are different from other amino acids? (a)

3. The bond between two atoms of equal electronegativity is: (c)

4. The protein shown at right has folded in water. Which of the following statements about it is FALSE? (c)

5. Which of the following do hydrogen bonds help to stabilize? (e)

6. Select two correct choices: A protein with quaternary structure... (a) (d)

7. 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.

As proteins fold into their distinct patterns, amino acids that are far away in their linear sequence may end up close together.

8. Why do defects in protein folding cause disease?

Protein folding patterns play a major role in the protein's functionality. If there are defects in the folding the protein may not be able to do its job, such as bonding to the correct substrate.

SAM HOMEWORK QUESTIONSFour Levels of Protein Structure

Directions: After completing the unit, answer the following questions to review.

1. Below is a picture of a folded protein. A protein is a chain of amino acids. Use an arrow to label the amino acid subunits shown in this picture.

2. Which part of an amino acid gives it its unique personality?

3. Define the term electronegativity. What effect does electronegativity have on the bonds in a particular amino acid? What effect does it have on an entire protein?

4. Describe the secondary structures seen in the picture to the left. Be specific.

5. The way a protein is folded determines its functionality. How might the exposure of a protein to higher than normal temperatures affect its function?

6. A particular protein has both hydrophobic (water-fearing) and hydrophilic (water-loving) regions. If this protein folded in water spontaneously, which regions would you guess would be on the outside? Why? Which regions would you guess would be on the inside? Why?

SAM HOMEWORK QUESTIONSFour Levels of Protein Structure – With Suggested Answers for Teachers

Directions: After completing the unit, answer the following questions to review. 1. Below is a picture of a folded protein. A protein is a chain of amino acids. Use an arrow to label the amino acid subunits shown in this picture. Sample arrow shown.

2. Which part of an amino acid gives it its unique personality? All amino acids have a part that is unique, called the side chain.

3. Define the term electronegativity. What effect does electronegativity have on the bonds in a particular amino acid? What effect does it have on an entire protein?

Electronegativity refers to the ability of an atom to attract another atom’s electrons. This can cause specific bonds to be polar and can also cause different side chains of a protein to be polar. Polarity affects protein folding in

different environments.

4. Describe the secondary structures seen next to the arrow in the picture to the left. Be specific.

Picture shows an alpha helix (pink) connected by a loop (white) to an beta sheet (yellow). Students may not have color version but should describe The alpha helix by the shape.

5. The way a protein is folded determines its functionality. How might the exposure of a protein to higher than normal temperatures affect its function? Higher temperatures can cause proteins to denature or unfold. This can alter the shape, and, thus, the functionality of a protein.

6. A particular protein has both hydrophobic (water-fearing) and hydrophilic (water-loving) regions. If this protein folded spontaneously in water, which regions would you guess would be on the outside? Why? Which regions would you guess would be on the inside? Why? Surrounding water molecules attract polar amino acids to the outside of the protein because they are hydrophilic. Non-polar amino acids are hydrophobic — less attracted to the polar water molecules — and they tend to move into the interior of the folded protein, forming its core.