SAM Teachers Guide
Nucleic Acids and Proteins (Long Version)
Overview
Students explore the structure and function of two of the four major macromolecules:
proteins and nucleic acids. On the first day they explore proteins and on the second
day, the nucleic acids making up DNA and RNA. After examining the atomic structure
of proteins, students consider linear polymers, the polarity of the monomers (amino
acids, nucleic acids) making up these polymers (proteins, DNA), and the way charged
surfaces contribute to their shape and consequent function. Students apply their
understanding of intermolecular attractions, three-dimensional structures of molecules,
and polarity to the structure and function of these two kinds of macromolecules.
Learning Objectives
Students will be able to:
• Observe that proteins and nucleic acids are made of a small subset of elements.
 Explore organic polymers and identify the monomer components of two kinds of
polymers: proteins and nucleic acids.
 Understand and construct simple monomers and polymers.
 Recognize how the side chains of amino acids vary in terms of polarity and
determine how this polarity affects the surface, relationship with water, and
consequent shape and function of the protein.
 Relate the way DNA/RNA and proteins form to the random motion of
molecules.
 Connect the information carried in DNA to the sequence of nucleotides, to RNA,
and finally to proteins.
Possible Student Pre/Misconceptions
 DNA and RNA are small molecules.
 There are no hydrogen atoms in these macromolecules.
 Organic molecules are two-dimensional and are static.
 Proteins are characterized by only one level of structure.
Models to Highlight and Possible Discussion Questions
After completion of Part 1 of the activity:
Models to Highlight:
 Page 3 – Building Polymer Chains
o Construct regular and irregular polymers and have students think
about the macromolecules they have learned about. Have students
categorize them.
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Pages 4 – The Importance of Polarity
o Discuss with students the charge distribution on the surface of the
amino acids and how this is related to the properties of the amino
acids. Look at the representation as a class and help students
interpret the representation.
Page 5 – Hydrophobicity
o The molecular concept of hydrophobicity is complex. Students
often think it means “afraid” of water. In fact, at the molecular
level hydrophobicity is the result of water molecules being more
strongly attracted to each other than to the hydrophobic molecule.
Water, therefore, excludes nonpolar molecules. This process is
important, so spend some time emphasizing this point.
o Link to other SAM activities: Intermolecular Attractions and
Solubility. Students can discuss how charges on the molecule's
surface can affect the molecule's interaction with polar water.
Page 6 – Sequence and Structure
o Use a projector to show a randomized sequences of amino acids
and have students try to predict which amino acids will be on the
outside and which will be on the inside.
Possible Discussion Questions:
 What are the most abundant elements in proteins?
 Why is polymerization important to living things?
 Describe the structure of proteins.
 How is the structure of protein similar to carbohydrates and lipids? How
do they differ?
 Why is it important to understand how amino acids interact with water?
After completion of Part 2 of the activity:
Models to Highlight:
• Page 7 – Nucleotides
o Review the nucleotides with your students. Point out what part is
similar on the 3D model and where there are differences.
• Page 8 – Hydrogen Bonds
o Point out that hydrogen bonds, represented by dashed lines, are
just another polar attraction between molecules and they are found
in biological systems.
o Link to other SAM activities: Intermolecular Attractions. Highlight
how hydrogen bonding is optimal when the shape of the two
molecules allows them to line up close together.
• Page 10 – Transcription
o Highlight how the model is showing the random motion of the
nucleotides in the cell. This is mirroring the cell in that nucleotides
are only attached in the sequence if through random motion they
are in the right place at the right time.
o Link to other SAM activities: Diffusion, Osmosis, and Active
Transport. Students can discuss what they remember about how
particles move and why.
Possible Discussion Questions:
 How are DNA and RNA similar to proteins? To carbohydrates? To lipids?
 How are nucleic acids and proteins different?
Connections to Other SAM Activities
The Nucleic Acids and Proteins activity focuses on the basic structure of protein, DNA
and RNA—the monomers, the distribution of charges and polarity, and how charged
surfaces contribute to their shape and function. Atomic Structure introduces students to
the positive and negative parts of atoms. Electrostatics explores attractions among
charged particles. Intermolecular Attractions looks at the role of these attractions in
protein folding and in the way nucleic acids act as a template for other nucleic acids.
Finally, Chemical Bonds helps students visualize charge distribution around bonds and
Molecular Geometry explores the resulting 3D structures that result from charge
distribution. Finally, Solubility is important for students to understand that the
interactions of the amino acids with water are critical for protein folding.
The Nucleic Acids and Proteins activity supports the DNA to Proteins activity, which
focuses on how proteins are made from DNA and what their structures are. Four Levels
of Protein Structure builds on the basics and goes into a more detailed understanding
of the structure of proteins. Finally, this activity supports Protein Partnering and
Function because students learn to relate the structure to the major functions of
proteins.
Activity Answer Guide
Page 1:
Introduction, no questions.
Page 2:
1. Which atoms are found in all of the
proteins?
(a) (b) (c) (d)
2. Which element is found in some, but not
all proteins?
(e)
Page 3:
1. Is polyethylene (above) a homo- or
heteropolymer? Explain your answer.
Polyethylene is a homopolymer because it is
made of the same type of monomers.
2. Take a snapshot of your homopolymer and
drag it in to the box below.
Pictures will vary. The snapshot should include
only one type of monomer.
3. Take a snapshot of your heteropolymer
and drag it in to the box below.
Pictures will vary. The snapshot should include
three different monomers.
4. Why do scientists call proteins
heteropolymers?
Because proteins are made of 20 different types
of monomers.
Page 4:
Note: snapshots will vary. The ones included
are examples.
1. Large side chain:
2. Polar side chain:
If the hydrogen bonds could not form, the protein
chain would not be able to maintain its folded
shape.
2. Place the snapshot of the protein with half
hydrophobic and half hydrophilic amino
acids. Point out how the amino acids help
determine the shape of the folded protein.
3. Nonpolar side chain:
The hydrophilic amino acids are being
straightened as they extend into water and the
hydrophobic are being shaped into a ball.
4. Charged side chain:
2. Run the model and imagine you are one of
the hydrophobic amino acids. What do you
experience as the chain folds in water?
Describe your interactions with other amino
acids and with water molecules.
I stay increasingly close to other hydrophobic
molecules, while I observe water molecules
surrounding the hydrophilic amino acids.
Page 6:
1. Place the snapshot of the unaltered
protein after it has folded in the box below.
Page 5:
1. If the hydrogen bonds could not form
within the oval area, how would that affect
the function of the protein?
2. Create a protein with a different shape by
changing a single amino acid. Take a
snapshot and drag it here.
3. Place the snapshot of your arrangement of
the molecules that shows the new strand is
created:
Sample snapshot.
Pictures will vary. The amino acid on the middle
of the chain was changed.
Page 7:
1. The order of the nucleotide monomers in
DNA carries genetic information. Write the
letters of the nucleotides in the DNA
fragment above in sequence, from #1 to #12,
below.
C,G,C,G,A,A,T,T,C,G,C,G
2. Which components are the same in all the
DNA nucleotide monomers? (a) (b)
3. Which components serve to link the DNA
nucleotide monomers together into a
copolymer? (a) (b)
Page 8:
1. What is the largest total number of
hydrogen bonds you can form? (Count the
dotted lines.) (b)
2. Place the snapshot of your arrangement of
the molecules that shows the maximal
number of dotted lines (representing
hydrogen bonds):
Sample snapshot.
4. Recall the definitions of homopolymer and
heteropolymer on Page 3. A DNA molecule is
(b)
Page 9:
1. Which of the following is NOT a factor in
complementary base pairing? (b)
2. Are there equal amounts of thymine (T)
and adenine (A) in a DNA double helix?
Explain your answer.
Yes, for every T in a DNA double helix there is a
complementary A. They are always paired. So
in DNA you cannot have an unequal number of
As and Ts.
Page 10:
1. Is photocopying a document similar to
making an RNA strand? Explain your
answer.
No, it is different. When an RNA strand is
created the materials are complementary,
though not identical to the original DNA strand.
Photocopying makes identical images.
Additionally, RNA has an alternative nucleic
acid, Uracil, instead of Thymine.
2. Place the snapshot of your completed
RNA strand.
3. Explain the relationship between
monomers and polymers using a protein
chain as an example.
Monomers, such as amino acids, are discrete
units that are linked together into a chain. The
polymer is the protein, which is made of many
monomers.
4. Explain the relationship between the
sequence of DNA and the primary structure
(the sequence) of proteins.
Page 11:
The sequence of DNA determines the sequence
of RNA. RNA codons in turn code for and
determine the sequence of amino acids in the
protein.
1. The information in the first three
nucleotides codes for the following amino
acid:
(c)
5. Which of the following best describes
what the two amino acids F (phenylalanine)
in the center of the molecule in the picture to
the right is experiencing.
(d)
2. The function of RNA is to create a protein
chain. How is an RNA's structure related to
its function?
6. The function of a protein is determined by
all of the following EXCEPT: (c)
Each triplet codes for one amino acid (or stop
codon) of a protein chain.
7. Nucleic acids carry information for making
proteins in:
(b)
Page 12:
8. How does random motion of molecules
play a role in the way RNA and proteins
form?
1. The side chain gives an amino acid its
property. Which of the following could affect
how it interacts with other amino acids and
its environment? (Check all that apply.)
(a) (b) (c) (d) (e)
2. Proteins and nucleic acids are: (c)
In both cases, the nucleotides and amino acids
are moving randomly around in the cell nucleus
and cytoplasm. It is only when, by random
collisions, they find themselves near the location
where the RNA or protein chains are forming do
they get incorporated in the chain. It is not
directed as often it is depicted in animations
SAM HOMEWORK QUESTIONS
Proteins and Nucleic Acids
Directions: After completing the unit, answer the following questions for review.
1. Proteins and nucleic acids are built from smaller units. What are the monomers that link
together to form these two chains?
2. Tryptophan, shown below, is an example of a non-polar amino acid. How do you think a
non-polar amino acid will react in water? Why?
3. The protein chain below is made entirely from hydrophobic amino acids in water. Draw a
picture that shows what might happen to this protein chain if four amino acids on the right
end of the chain were replaced with four hydrophilic amino acids. Explain your drawing.
4. Describe how the sequence of a DNA strand is related to the sequence of the protein strand
it codes for.
5. Career connection: One of the most active areas of computer modeling in biology is
related to the interactions between genes (DNA) and/or proteins. Describe in one or two
sentences a biomodel that you found at http://biomodels.caltech.edu/
SAM HOMEWORK QUESTIONS
Proteins and Nucleic Acids – With Suggested Answers for Teachers
1. Proteins and nucleic acids are built from smaller units. What are the monomers that link
together to form these two chains?
Amino acids link together to form proteins and nucleotides link together to form nucleic acids.
2. Tryptophan, shown below, is an example of a non-polar amino acid. How do you think a
non-polar amino acid will react in water? Why?
Non-polar amino acids are not water soluble. Tryptophan will probably fold or
arrange itself so that its non-polar region will not come in contact with water. This
is because its side-chain is hydrophobic.
3. The protein chain below is made entirely from hydrophobic amino acids in water. Draw a
picture that shows what might happen to this protein chain if four amino acids on the right
end of the chain were replaced with four hydrophilic amino acids. Explain your drawing.
Pictures may vary. Student drawings should reflect their knowledge that the right part of the protein chain is now
water-loving. Folding will maximize the interaction of these amino acids with water.
4. Describe how the sequence of a DNA strand is related to the sequence of the protein strand
it codes for.
DNA is first reread or transcribed into mRNA in the nucleus. The mRNA is then translated on ribosomes in the
cytoplasm. This means that the code is read in groups of three (triplets) that encode the specific amino acids in a
protein chain. DNA’s message, in another form, tells the cell which amino acids need to be present and their order.
6. Career connection: The best way for students to find something in the biomodel databse is to
click on the “curated models” link and then just browse around by clicking on various IDs (the
links on the left). Much of what they will find will be over their heads, but some of the models
have simpler descriptions than others and they should be able to select one of the ones that could
more easily be understood.