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SAM Teacher’s Guide
Four Levels of Protein Structure
Overview
Students explore how protein folding creates distinct, functional proteins by examining
each of the four different levels of protein structure. Students interpret how the
sequence and properties of amino acids relate to how proteins fold. They identify the
characteristic patterns of folding known as secondary structure, final folding of the
entire protein chain (tertiary structure), and the coming together of more than one chain
to form a functional unit (quaternary structure). 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 protein chain (subunit), and that the subunits come together to achieve
the protein’s function.
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 of proteins is less important than the amino acid
sequence.
 Proteins are uniform throughout rather than having different parts for various
functions.
Models to Highlight and Possible Discussion Questions
Page 1 – Form and Function
Model: Parvalbumin
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Highlight that the protein is made up of one long amino acid chain that is
folded into a specific shape.
Emphasize that representing a protein’s structure in different styles and
colors can illustrate the different, important aspects of its structure.
Students will likely need help and feedback on choosing the views for the
snapshots of this model.
Link to other SAM activities: DNA to Proteins. Remind students that the
sequence of amino acids is encoded in the sequence of nucleotides in DNA.
Possible Discussion Question:
 How might a mutation in DNA affect the primary structure of a protein?
Page 2 – Twenty Amino Acids
Model: Twenty Rotatable Amino Acids
 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. The backbone
connects to the backbones of other amino acids to form the peptide chain
that makes up the protein.
 Emphasize that each amino acid has a side chain (or R group) that is
different and that these side chains determine the polarity of the amino
acid.
 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.
Possible Discussion Question:
 What is the difference between polar and non-polar amino acids?
 What is the difference between a polar amino acid and one that is charged?
Page 3 – Secondary Structure
Model: Protein Kinase
 Point out the use of the menu to change the way the model is drawn,
which is essential for identifying the secondary structures.
 Highlight that alpha helices and beta sheets are present in the folded
protein and ask how they can be identified.
Possible Discussion Question:
 Why do you think different folding patterns happen?
Page 4 – The “Glue” in Secondary Structures
Model: Protein G
 Highlight that helices and sheets are stabilized by hydrogen bonds
between the backbone atoms common to all amino acids – not the side
chain atoms.
 Highlight the use the checkboxes and radio buttons to arrive at images that
display different aspects of the secondary structures.
Possible Discussion Question:
 Why are beta sheets and alpha helices common in proteins?
Page 5 – Water Helps Shape Proteins
Model: Protein Folding in Water or Oil
 Review polarity and link to the importance of how proteins behave
(folding, solubility) in water.
 Emphasize hydrophobic/hydrophilic interactions and how one protein can
have regions of both. This will impact folding.
 Link to other SAM activities: Chemical Bonding. Polarity and
electronegativity will influence the type of chemical bonds formed.
Possible Discussion Question:
 How do amino acids’ interactions with water affect the shape of the
protein?
 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.
Page 6 – Tertiary Structure
Model: Lysozyme
 Note that tertiary structure is the coming together of distinct secondary
structures.
 Emphasize that the stabilizing interactions between (not within) alpha
helices and beta sheets (salt bridges, disulfide bonds, and additional side
chain interactions) results in the protein having a very specific shape.
Possible Discussion Questions:
 Why is the folded structure of a protein so important for its functionality?
Can students think of any examples?
Page 7 – Protein Function
Model: Alcohol Dehydrogenase
 Highlight how the folds of the protein come together from different parts
of the chain to create this site, which will bind only with NAD or a
molecule extremely similar to NAD.
 Highlight that all proteins are very specific in their recognition of partner
molecules.
Model: Can Proteins Take the Heat?
 Proteins are destabilized by heat because of the increased molecular
motion. Relate the change in the egg whites to the destabilization and
unfolding of the secondary and tertiary structures of the protein.
Possible Discussion Questions:
 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.)
 What types of situations may impact how a protein would function?
Generate ideas about temperature, whether it is surrounded by water or
oil, etc.
 Denaturation of proteins happens when proteins are heated, but it also
happens when proteins are in acidic or basic environments. How do all of
these things cause the same end result? What does denaturation look like
at the molecular level?
Page 8 – Quaternary Structure
Model: Homodimer (Alcohol Dehydrogenase) and Heterotrimer (G Protein)
 Some proteins achieve their function by acting as a complex of multiple
subunits (quaternary structure).
 Highlight that the unique surface of each protein enables it to perform its
specific function.
Possible Discussion Questions:
 How do proteins differ? Highlight the differences at primary, secondary,
tertiary, quaternary structure.
 Why is the folded structure of a protein so important for its functionality?
Demonstration/Laboratory Ideas:
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Construct chains or amino acids and physically show folding patterns using
beads, children’s toys, etc.
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.
Use molecular model kits to focus in on bonding within a protein.
Use oil and water demonstration to review hydrophobic/ hydrophilic
interactions. Link back to the importance of water in living systems (cell
membrane review).
Use an overhead projector and Petri dish to demonstrate that acid can cause
denaturation of egg white proteins. Relate this demonstration to what happens
in digestion in the stomach.
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,
Nucleic Acids and Proteins 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, Protein Partnering and
Function 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 snapshots: Other snapshots may
answer the questions.
Page 1:
1. Use the Do It Yourself controls above to
create a view that shows how the protein is
folded. Use the text tool
end of the folded chain.
Page 2:
1. Label the ball and stick amino acid
models as indicated in the “What to do”
section.
to label each
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?
2. Create a view that you think best shows
the primary structure of parvalbumin. Use
the text tool
to explain why you chose
this way of representing primary structure.
(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 3:
1. Take a snapshot of an alpha helix that
shows how it folds.
There are many alpha helices in the protein.
They are easy to recognize using the cartoon or
string of beads representations.
1. Hydrogen bonds stabilizing an alpha
helix. Use the arrow tool to point out the
hydrogen bonds.
2. Hydrogen bonds stabilizing a beta sheet.
Use the arrow tool to point out the hydrogen
bonds.
2. Take a snapshot of a beta sheet that
shows how much space it occupies within
the protein. Hint.
3. Hydrogen bonds stabilizing alpha helices
and beta sheets form between the atoms of
which part(s) of the amino acids involved?
(c)
There are two beta sheets in the protein, the one
above (encompassing approximately amino
acids 29-59) and from about 92-105. Students
can find the beta sheets using the cartoon
representation, then change to spacefill to show
the amount of space occupied by the sheet. This
exemplifies the advantages of two different
representations.
Page 4:
4. Place a snapshot here that illustrates your
answer to the previous question.
to other polar molecules. The opposite charges
on the polar molecules attract each other. There
is less attraction between non-polar molecules
and water because there is no opposing charge
on the non-polar molecules to attract the water.
5. Which solvent(s) leads to folding of the
protein?
(c)
6. Where do the amino acids with polar side
chains end up when the protein chain folds?
(c)
Page 6:
This image shows a backbone trace of the
protein with the hydrogen bonds (purple dotted
lines) stabilizing the alpha helix and beta sheet.
The side chains are omitted for clarity of view.
Page 5:
1. Is water a polar or non-polar molecule?
Explain your answer by writing about the
bonds in water.
The bonds in water are polar covalent bonds.
The oxygen pulls the electrons more strongly
than the hydrogens do, so the oxygen is slightly
negative while the hydrogens are slightly
positive. Because the electrons are not evenly
shared across the molecule, the molecule is
polar.
2. Which type of amino acid is hydrophobic?
(b)
3. Which of the following correctly describe
the interactions of the amino acids with
water? (Check ALL that apply.)
(b)(c)
4. Use your knowledge of positive and
negative charge to explain why polar
molecules attract each other better than nonpolar molecules.
Because polar molecules have charge
differences on their surfaces, they are attracted
1. Show an interaction that stabilizes two
alpha helices to each other. Use the
annotation tool to label the type of
interaction you are showing.
2. Create a view that shows both the amino
acids at the surface and those that fold into
the inside of the protein. Use the annotation
tools to label the part that is more attracted
to water.
Page 8:
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:
TNF is made up of three protein chains. This
can be seen using the color by subunits
selection next to the image of TNF.
Page 9:
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)
Page 7:
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?
3. The protein shown at right has folded in
water. Which of the following statements
about it is FALSE?
(c)
4. Which of the following do hydrogen
bonds help to stabilize? (Check ALL that
apply.)
(b)(c)(d)
(b)
5. Select the two correct choices:
A protein with quaternary structure…
3. Explain your answer to the previous
question.
(a)(d)
If the protein unfolds, it will lose its shape and
will be unable to perform its function(s).
Proteins are folded into specific shapes that
allow them to do their jobs.
6. 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 units shown in this picture.
2. Which part of an amino acid gives it its unique personality?
3. Identify and describe the secondary structure
indicated by the arrow in the picture to the left. Be
specific. What keeps this secondary structure in this
particular shape?
4. The way a protein is folded determines its functionality. How might the exposure of a
protein to higher than normal temperatures affect its function?
5. A particular protein has both hydrophobic (water-fearing) and hydrophilic (waterloving) regions. If this protein folded spontaneously in water, which regions would be
on the inside and which on the outside? Why?
6. Career connection: One of the most important problems scientists are trying to solve
is how to predict the shape of protein molecules produced by the genes in our cells.
Check out the Folding at Home project - http://folding.stanford.edu/ - and describe why
this is important. (You can install free modeling software to help them work on protein
folding.)
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 units shown in this picture.
Sample arrow shown. Each arrow should point to one of the beads, which represent the amino acids in the
protein.
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 or R group.
3. Identify and describe the secondary structure indicated
by the arrow in the picture to the left. Be specific. What
keeps this secondary structure in this particular shape?
Picture shows an alpha helix (pink) connected by a loop (white) to a
beta sheet (yellow). (Students may not have color version but should be able to
identify the alpha helix by the shape.) The arrow points to the alpha helix. An
alpha helix is shaped like a long spiral. It is held in this shape by hydrogen
bonds that form between the atoms of peptide backbone.
4. 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.
5. A particular protein has both hydrophobic (water-fearing) and hydrophilic (waterloving) regions. If this protein folded spontaneously in water, which regions would be
on the inside and which on the outside? 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 molecule and
they tend to move into the interior of the folded protein, forming its core.
6. Career connection: The nature of many genetic diseases is related to the form and
function of proteins. By understanding how proteins fold new drugs could be
developed and provide a better understanding of how living things function.