Name: ________________________________________ Period: ______ Date: ______________
Learning about Protein Structure Using Beads:
Amino Acids, Polypeptides, Multi-polypeptide Proteins
Part 1: Amino Acids
Examine your bag of beads. Your beads represent amino acids.
Pour your beads onto a large plate.
1. How are your beads different? Describe the differences between three beads.
2. How are the beads similar?
Each type of amino acid has a particular structure. Look at the amino acid structure chart provided by your
teacher and answer the following questions.
Central Carbon
Hydrogen
On the right, there is a general structure diagram of an amino
acid.
3. What does each amino acid have in common?
Amine Group
4. What makes different amino acids different?
Carboxylic Acid
Group
5. How do you think “amino acid” got its name?
6. Bonds between carbon and carbon atoms store a lot of energy. When broken, they release a lot of energy.
How many carbon-carbon bonds are in each amino acid?
________________
7. Which should a cell “burn” for energy, monosaccharide or amino acid? Why?
© Bethany Lau 2012
1
Part 2: Polypeptide
Two amino acids bonded together are called a dipeptide.
8. What is the reaction that takes place between 2 smaller biological molecules
to form 1 larger biological molecule?
_______________________
9. Finish the chemical equation for the reaction below:
Amino Acid + Amino Acid  ____________________ + ____________________________
The bond between two amino acids in a chain is
called a peptide bond.
A polymer chain of amino acids, strung together
with covalent bonds, is called a polypeptide.
Each person should fill a pipe cleaner with
beads of different colors, shapes, and sizes.
Make sure you use the letter beads to form a
short word (3-8 letters) long within your pipe
cleaner polypeptide.
A. Sequence of Amino Acids
10. Describe the first 6 beads on your polypeptide. (Example: yellow turtle, pink letter B, red round bead…)
The sequence of your amino acids in your polypeptide is called the primary structure of your polypeptide.
11. Is your polypeptide sequence different from your partners? How?
Polypeptides are produced from “blueprint instructions” stored in the cell’s DNA. Each type of polypeptide is
different, just as different machines built from different instructions are different. The structure and function of
a polypeptide is determined by its sequence.
© Bethany Lau 2012
2
B. 3-Dimensional Structures
Bend your polypeptide to form a helix, like the one on the right.
Amino acids within a helix attract each other, to keep the polypeptide in the
shape. For example, bead 1 in the diagram is attracted to bead 2, causing the
polypeptide to stay a helix. The dotted line represents an attraction between
the two beads. Bead 3 is attracted to bead 4.
1
12. In the space below, draw a similar diagram using a rough sketch of your own
peptide. Draw imaginary bonds between “attracting” beads in your
polypeptide.
2
3
4
When your polypeptide is twisted into a helix or other simple structures called beta strands, scientists say it has
a secondary structure.
13. Take your helical polypeptide and fold it into an even more complex folding shape. Draw a rough picture of
your protein below.
When your polypeptide has a helix or beta strand and is folded over itself into a more complex structure,
scientists say it has a tertiary structure.
© Bethany Lau 2012
3
Part 3: Multi-polypeptide Proteins
Cells often use proteins to do jobs around the inside and surface of the cell. Each protein has a specific function.
Sometimes proteins only need one polypeptide chain to function properly. Often proteins need more than one
polypeptide chain to work properly.
Pick up two polypeptides your group built. Fold them over each other, twisting them so they stay together. You
have now formed a functional protein that has two polypeptide subunits.
14. Draw a rough sketch of your functional protein below. Just as in your individual helix, there are beads that
(you can imagine) “attract” each other to keep the two polypeptides together. Draw at least two of these
attractions in your sketch.
When a protein has more than one polypeptide that stick together and function together, this protein is
described as having a quaternary structure.
© Bethany Lau 2012
4
Name: ________________________________________ Period: ______ Date: ______________
Additional Questions:
15. As you folded your pipe cleaner, you may have discovered that certain beads promote folding near them or
make folding near them easier. Look at your amino acid chart again. Which amino acids are represented by
these beads? Why?
16. As you folded your pipe cleaner, you may have discovered that certain beads inhibit folding near them or
make it difficult to fold near them. Look at the amino acid chart in the back of this packet. Which amino acids
might be represented by these beads? Why?
17. Are the terms protein and polypeptide synonymous terms? Explain.
18. As you view your folded polypeptide, are all beads equally important to the structure or the message you
placed in your polypeptide? Explain your answer. How do you think this relates to real polypeptide sequences
and structures? Do you think all amino acids in a sequence are equally important?
© Bethany Lau 2012
5
Name: ____ANSWERS!_____________________________
Period: ______ Date: ______________
Learning about Protein Structure Using Beads:
Amino Acids, Polypeptides, Multi-polypeptide Proteins
Part 1: Amino Acids
Examine your bag of beads. Your beads represent amino acids.
Pour your beads onto a large plate.
1. How are your beads different? Describe the differences between three beads.
Student answers may vary (“AMV”). Size, color, shape…
2. How are the beads similar?
all have holes through them, AMV
Each type of amino acid has a particular structure. Look at the amino acid structure chart provided by your
teacher and answer the following questions.
Central Carbon
Hydrogen
On the right, there is a general structure diagram of an amino
acid.
3. What does each amino acid have in common?
central carbon, amine group, carboxylic acid group
Amine Group
4. What makes different amino acids different?
R group
Carboxylic Acid
Group
5. How do you think “amino acid” got its name?
amine group plus acid group
6. Bonds between carbon and carbon atoms store a lot of energy. When broken, they release a lot of energy.
How many carbon-carbon bonds are in each amino acid?
__1______________
7. Which should a cell “burn” for energy, monosaccharide or amino acid? Why?
Monosaccharides have 5 carbon-carbon bonds. Amino acids only have 1. Monosaccharides are better to
burn for more energy.
© Bethany Lau 2012
6
Part 2: Polypeptide
Two amino acids bonded together are called a dipeptide.
8. What is the reaction that takes place between 2 smaller biological molecules
to form 1 larger biological molecule?
___dehydration synthesis____________
9. Finish the chemical equation for the reaction below:
Amino Acid + Amino Acid  ___dipeptide_________________ + ___water_________________________
The bond between two amino acids in a chain is
called a peptide bond.
A polymer chain of amino acids, strung together
with covalent bonds, is called a polypeptide.
Each person should fill a pipe cleaner with
beads of different colors, shapes, and sizes.
Make sure you use the letter beads to form a
short word (3-8 letters) long within your pipe
cleaner polypeptide.
C. Sequence of Amino Acids
10. Describe the first 6 beads on your polypeptide. (Example: yellow turtle, pink letter B, red round bead…)
Student answers will vary
The sequence of your amino acids in your polypeptide is called the primary structure of your polypeptide.
11. Is your polypeptide sequence different from your partners? How?
Yes, different sequence, different amino acids, different patterns.
Polypeptides are produced from “blueprint instructions” stored in the cell’s DNA. Each type of polypeptide is
different, just as different machines built from different instructions are different. The structure and function of
a polypeptide is determined by its sequence.
© Bethany Lau 2012
7
D. 3-Dimensional Structures
Bend your polypeptide to form a helix, like the one on the right.
Amino acids within a helix attract each other, to keep the polypeptide in the
shape. For example, bead 1 in the diagram is attracted to bead 2, causing the
polypeptide to stay a helix. The dotted line represents an attraction between
the two beads. Bead 3 is attracted to bead 4.
1
12. In the space below, draw a similar diagram using a rough sketch of your own
peptide. Draw imaginary bonds between “attracting” beads in your
polypeptide.
2
3
student drawing will vary
4
When your polypeptide is twisted into a helix or other simple structures called beta strands, scientists say it has
a secondary structure.
13. Take your helical polypeptide and fold it into an even more complex folding shape. Draw a rough picture of
your protein below.
student drawing will vary
When your polypeptide has a helix or beta strand and is folded over itself into a more complex structure,
scientists say it has a tertiary structure.
© Bethany Lau 2012
8
Part 3: Multi-polypeptide Proteins
Cells often use proteins to do jobs around the inside and surface of the cell. Each protein has a specific function.
Sometimes proteins only need one polypeptide chain to function properly. Often proteins need more than one
polypeptide chain to work properly.
Pick up two polypeptides your group built. Fold them over each other, twisting them so they stay together. You
have now formed a functional protein that has two polypeptide subunits.
14. Draw a rough sketch of your functional protein below. Just as in your individual helix, there are beads that
(you can imagine) “attract” each other to keep the two polypeptides together. Draw at least two of these
attractions in your sketch.
student drawing will vary
When a protein has more than one polypeptide that stick together and function together, this protein is
described as having a quaternary structure.
© Bethany Lau 2012
9
Name: ________________________________________ Period: ______ Date: ______________
Additional Questions:
15. As you folded your pipe cleaner, you may have discovered that certain beads promote folding near them or
make folding near them easier. Look at your amino acid chart again. Which amino acids are represented by
these beads? Why?
smaller beads are easier to fold near them. glycine is a small amino acid that makes it easy to fold near it.
(other answers possible)
16. As you folded your pipe cleaner, you may have discovered that certain beads inhibit folding near them or
make it difficult to fold near them. Look at the amino acid chart in the back of this packet. Which amino acids
might be represented by these beads? Why?
large beads may make it harder to fold near them. tryptophan or lysine or other similarly large amino acids
may inhibit or reduce folding near them.
17. Are the terms protein and polypeptide synonymous terms? Explain.
“Protein” can mean more than one polypeptide, so they are not synonymous terms. A polypeptide might be
one protein, but one protein may hold more than one polypeptide.
18. As you view your folded polypeptide, are all beads equally important to the structure or the message you
placed in your polypeptide? Explain your answer. How do you think this relates to real polypeptide sequences
and structures? Do you think all amino acids in a sequence are equally important?
Some of the beads in your strand spelled a particular word you chose. If you replace one of those “essential”
beads, the meaning of your word would change and might spell something very different. If you replace
another random bead that does not matter to your message, it may not change your bead
sequence/structure/message that much.
This is the same with amino acids in a polypeptide chain. Some amino acids are more essential to the function
and structure of a polypeptide than others. A “mutation” occurs when an amino acid is replaced with another
one. Sometimes this mutation is harmful to the structure/function of the polypeptide and can cause a disease.
Some mutations may be “harmless”.
© Bethany Lau 2012
10
Learning about Protein Structure Using Beads:
Amino Acids, Polypeptides, Multi-polypeptide Proteins
by Bethany Lau
Teacher Instructions for Learning about Protein Structure with Beads:
**Before performing this activity, students should have a basic background in
chemistry. Single bonds, simple molecular structure recognition, and an
understanding of dehydration synthesis and hydrolysis reactions are necessary to complete the activity. Also,
there is one question that refers to a monosaccharide, so it will help if your students have learned about
carbohydrates already. This activity could directly follow my “Learning about Carbohydrate Structure with
Beads”. Performing both of these activities will greatly increase student understanding of molecular
structure, carbohydrates, proteins, and the differences between the two polymers.**
This activity is best performed by small groups of students (2-3). Before class, you will need to collect and
prepare the following materials for each student group, bagged in a larger Ziploc bag for easy pass out and
cleanup:
Each group of 2-3 students will need a set of the following in a Ziploc bag:
- 1 pipe cleaner per person in the group
- a large paper plate
- Approximately 75-100 Assorted beads of different shapes and sizes, including some beads with
alphabet letters.
- A separate sheet with an amino acid structure chart for each student. I recommend the one found on
the following website: http://www.geneinfinity.org/images/aminoacids.jpg (Due to copyright, I cannot
provide you a copy as a part of this download, but I highly recommend this one! It has an excellent
highlight of the R groups and shows the differences clearly.)
See the next page for pictures of setup and a sample result!
Depending on the ability of your group, you can be as teacher-led or as student-led as you want with this
activity. With my honors classes, I can usually hand these out and just monitor the room. With my lower level
classes, I might need to lead them through each step. The answer key is included!
The last page of additional questions could be used as a homework assignment to take home.
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© Bethany Lau 2012
11
© Bethany Lau 2012
12
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