SAM Teachers Guide
Four Levels of Protein Structure
Overview
Students 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 Objectives
Students 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 Questions
After 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.
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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 Proteins
o Highlight how protein folding creates specific sites on proteins,
which allow for specific functionality.
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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
Sample snapshot:
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.
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:
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
mark both ends.
to
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)
Non-polar amino acid – no bonds should be
circled.
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:
Polar bonds are around oxygen.
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:
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).
Polar bonds are those from nitrogen or oxygen
to carbon or hydrogen.
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.
Beta sheet
3. A loop between a beta sheet and an alpha
helix:
Page 8:
1. Snapshot of an alpha helix:
Loop connecting alpha helix and beta sheet
Alpha Helix
2. Snapshot of a beta sheet:
Page 9:
1. The hydrogen bonds that stabilize an
alpha helix.
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.
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.
This picture has the side chains removed and
shows just the hydrogen bonding in the
backbone of the protein.
Page 10:
*Sample snapshots*
3. Show an interaction that stabilizes a loop
and a beta sheet:
1. Show an interaction that stabilizes an
alpha helix and a loop:
Disulfide bond stabilizing alpha helix and loop.
Side chain hydrogen bonds stabilizing a loop
and a beta sheet.
2. Show an interaction that stabilizes two
alpha helices:
4. Show the hydrophobic core:
Salt bridge stabilizing two alpha helices.
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 QUESTIONS
Four 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 QUESTIONS
Four 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.