SAM Teachers Guide
Nucleic Acids and Proteins (formerly Proteins and Nucleic Acids/PNA)
Overview
Students explore the structure and function of two of the four major macromolecules:
nucleic acids and proteins. In the first half of the activity, students explore DNA and
RNA, and in the second half, proteins. Students consider the monomers of each type of
molecule, the order of nucleotides that contains a code, and the polarity of amino acids,
which affects protein folding and function. Students apply their understanding of
intermolecular attractions, the 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:
 Identify examples of proteins in living beings and link to their function
 Identify the monomer components of nucleic acids and proteins.
 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.
 Connect the information carried in DNA to the sequence of its nucleotides.
 Recognize how changes in amino acid sequence cause changes in the folding of
the protein.
Possible Student Pre/Misconceptions
 DNA is a short molecule.
 Sometimes there are no hydrogen atoms in 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
Page 1 – Introduction to Nucleotides
Model: DNA Is Built from Nucleotide Monomers
 Use the “ball and stick model” checkbox under the DNA double helix to
help students connect the double helix structure with the four individual
nucleotides in the models below it.
Model: What’s in a Nucleotide?
 Review the nucleotides with your students. Make sure they can
point out what parts of the nucleotides are identical and what part differs
between them.
Page 2 - The Interactions of Nucleotide Bases
Model: Making a new strand of DNA
 Take a close look at the basis of complementarity. Why do the hydrogen
bonds form? Point out that some nucleotide pairs form more hydrogen
bonds than others.
Discussion question:
 What is a hydrogen bond? Why are they important in biology? Emphasize
that a hydrogen bond is just a polar attraction between molecules that
occurs very frequently in biological molecules.
 What is the advantage of complementarity? Although this activity does
not deal directly with transcription or replication, it may be useful to give
students a rough idea of the processes they will encounter later on.
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 closely together.
Page 3 – The Double Helix
Model: The double helix
 Feature different ways to represent and color DNA: different
representations emphasize or clarify different important aspects of DNA
structure.
Discussion Questions
 Ask students which representation is the best (or worst!) for seeing
specific aspects of DNA structure, such as size, two strands, shape,
complementarity. Some answers may not be the same for all students.
 How can you use the centering function in the control panel to focus in on
a certain element of the DNA? (Check the box, click on an atom and it will
move to the center; then zoom in; you may need to try a few different
atoms to get the feel of it.)
Page 4 – Introduction to Proteins: Special shapes for special jobs
Model: An Introduction to Proteins
 Point out that with each protein, the outer atoms that attach to the chain
are removed in order to reveal a chain-like nature. Make sure that
students understand that this is just a visual aid to seeing the underlying
structure, not a loss of atoms.
Page 5 - Amino Acid Chains
Model: Amino Acids Have Different “Personalities”
 Discuss with students the charge distribution on the surface of the amino
acids and how this is related to the polarity of the amino acids. Look at the
representation as a class and help students interpret the representation.
 Take this opportunity to point out the different shapes and sizes among
these three amino acids.
Discussion Questions
 Why is it important that amino acids have differing characteristics?
 Compare the fact that proteins have 20 monomers and DNA/RNA have
only four.
Page 6 - Protein Interactions in Water
Model: In Water, Proteins Have a Hydrophobic Core


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The molecular concept of hydrophobicity is complex, and quite important.
Students often think hydrophobic molecules actively avoid water. In fact,
at the molecular level hydrophobicity is the result of water molecules
being more strongly attracted to each other, due to their polarity, than to
hydrophobic molecules.
Remind students of the behavior of the water molecules in the model on
the top half of the page (since they are not shown in this model).
Encourage them to use the “Randomize amino acids” button repeatedly
and deduce what is happening when many hydrophobic amino acids are
present. Note that when there are many hydrophilic amino acids present,
the protein does not fold, because the hydrophilic side chains are
interacting with water.
Link to other SAM activities: Intermolecular Attractions and Solubility.
Students can discuss how charges on the molecule's surface affect the
molecule's interaction with water.
Discussion Questions:
 What would the water molecules look like in your snapshot of the
protein? Have students draw them in on a printout, or make a new
drawing altogether.
Wrap-up Discussion Questions:


How is the structure of protein similar to that of carbohydrates and lipids?
How do they differ?
How are DNA (and RNA) macromolecules similar to proteins?
carbohydrates? To lipids? How are they different?
Connections to Other SAM Activities
The Nucleic Acids and Proteins (formerly Proteins and Nucleic Acids) 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 Molecular Recognition
because students learn to relate the structure to the major functions of proteins.
Activity Answer Guide
Page 1:
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.
CCAATGGCCAT
2. Which components are the same in all
DNA nucleotide monomers?
(c)
Page 3:
1. The order of the nucleotides in DNA is
important - it carries a code used in making
proteins. Take a snapshot that best shows
the order of the bases in a single DNA chain.
3. Which components serve to link the DNA
nucleotide monomers together into a double
helix?
(a) (b)
Page 2:
1. What is the greatest total number of
hydrogen bonds you can form in the model?
(d)
2. Take a snapshot that best illustrates the
hydrogen bonds that attract the two DNA
strands together. Use the annotation tools to
label the hydrogen bonds.
2. Insert below the snapshot that shows how
you arranged the nucleotide bases to create
the greatest number of hydrogen bonds.
3. Using what you learned about fitting the
bases as opposite pairs, predict which bases
you will find paired with each of the four
bases in a DNA double helix.
A with T
C with G
Page 4:
1. Which protein can puncture a cell wall?
(b)
2. Which protein can form a cable?
(a)
3. Which protein can become a pore in a
membrane?
(c)
Page 5
1. Take a snapshot of an amino acid with a
non-polar side chain. Use the annotation
tools to circle the side chain of the amino
acid.
2. If there are many non-polar (hydrophobic)
amino acids in the protein, where do they
tend to end up once the protein folds?
(b)
3. Explain how interactions between water
molecules cause the hydrophobic amino
acids to fold into the center of the protein.
The attractions between the non-polar amino
acids and water (polar) are not very strong
compared to the attractions between polar
molecules. So the polar molecules attract each
other and the non-polar molecules are excluded.
Page 7:
1. What causes the two strands of DNA in a
double helix to attract and wrap around each
other?
(d)
2. What is it about the atoms in a polar side
chain that makes the side chain polar?
Explain your answer.
There is a difference in electronegativity of some
of the side chain atoms so that some are
attracting electrons more strongly than others.
This makes for a separation of positive and
negative charge.
Page 6
1. Using the "randomize" button, create a
protein with many non-polar (hydrophobic)
amino acids, and let it fold in water. Place a
snapshot of your folded protein here.
2. Which part of a DNA nucleotide carries
genetic information?
(c)
3. The side chain of an amino acid
(b)
4. A protein chain (Check all that apply.)
(a) (d)
5. How are the structures of DNA and
proteins similar to each other, and how are
they different?
Both are polymers, long chains, and
macromolecules.
They are made from different monomers.
DNA carries information, whereas proteins have
lots of different functions.
6. The protein shown to the right folded in
water. Which color represents the non-polar
(hydrophobic) amino acids, and which color
represents the polar (hydrophilic) amino
acids? Explain how you know.
The light blue represents hydrophilic and the
pink hydrophobic, because the blue are mostly
on the outside, in closer contact with water and
the pink are closer to the inside, where
hydrophobic amino acids would have folded,
away from water.
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 chain-like molecules?
2. Tryptophan, shown below, is an example of a non-polar amino acid. How do you
think a tryptophan amino acid will behave in water? Why?
3. The protein chain below is made entirely from hydrophobic amino acids.
a). Draw a picture that shows how this protein might fold in water.
b). Draw a second picture that shows the difference in folding that would occur if four
amino acids on the right end of the chain were replaced with four hydrophilic amino
acids.
c). Explain your drawings.
SAM HOMEWORK QUESTIONS
Proteins and Nucleic Acids – With Suggested Answers for Teachers
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 chain-like molecules?
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 tryptophan 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 nonpolar region will not come in contact with water. This is because its side-chain is hydrophobic.
Several problems here – “react” sounds like a reaction. “An amino acid” doesn’t fold – so
this doesn’t make sense. Is the question asking how a single amino acid will behave in
water? That is not useful. I tried with the following, but I think it is probably too difficult:
2. Tryptophan, shown below, is an example of a non-polar amino acid. How do you
think a protein chain made entirely of non-polar amino acids would behave in oil,
which is a non-polar liquid? Explain your answer.
A protein chain would remain extended in oil, because the oil molecules are just as attracted to the non-polar
amino acid as they are to other oil molecules.
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. For part a, drawings should show a compact shape formatted by all the amino acids. For
part b, the drawing should reflect their knowledge that the right end of the protein chain can now attract water
and will maximize the interaction of these amino acids with water.
RESOURCES
Associated Program: Center for BioMolecular Modeling
This excellent program, located at the Milwaukee School of Engineering, offers handson models of biomolecules for classroom use.
ADDITIONAL HOMEWORK QUESTIONS:
1. Comparing DNA and RNA:
a. Identify whether the following sequences of nucleic acid represent DNA or RNA, and
explain your reasoning.
i. ATCCATTACGTATCA
ii. AUGGUGACCAUGGA
iii. CCTAGTCAATGCAAT
b. What are two other differences between DNA and RNA?
2. DNA base-pairing:
a. Create a complementary strand of DNA for the sequence shown below, using what
you know about nucleotide base pairing.
ATTCATGATTAGAC
b. Draw a picture showing how the last two bases (A and C in the original strand) pair
with their complementary strand. What holds the two strands of DNA to each other?
(Don’t worry about getting the structures exactly right; you can use cartoons to
represent the molecules!)
c. Which pair bonds more strongly: A-T or G-C?
3. Comparing DNA and proteins:
a. What are the monomers in DNA called? What are the monomers in proteins called?
b. There are 20 different types of monomers in proteins. What makes each of these
monomers unique?
c. Compare the functions of DNA to the functions of proteins.
d. How are proteins and DNA similar in how they are constructed?
e. How does the construction of DNA and proteins compare to the construction of
carbohydrates and lipids?
4. Some amino acids are hydrophobic and others are hydrophilic.
a. Explain what is meant by hydrophobic and hydrophilic.
b. How do hydrophilic amino acids act in a watery environment? Draw a picture to
show the molecular interactions.
c. How do hydrophobic amino acids act in a watery environment? Draw a picture to
show the molecular interactions.
d. The picture below shows a protein composed entirely of hydrophobic amino acids in
water.
Draw a picture showing how it will fold in a watery environment, and explain why it
would fold this way.
e. If the first 4 amino acids on the right were replaced with hydrophilic amino acids, how
would this affect the protein folding? Draw a picture to show any differences.
5. Why are water molecules strongly attracted to other water molecules? What causes
them to form hydrogen bonds with each other?
ADDITIONAL HOMEWORK QUESTIONS: Answers
1. Comparing DNA and RNA:
a. Identify whether the following sequences of nucleic acid represent DNA or RNA, and
explain your reasoning.
i. ATCCATTACGTATCA DNA—presence of T
ii. AUGGUGACCAUGGA RNA—presence of U
iii. CCTAGTCAATGCAAT DNA—presence of T
b. What are two other differences between DNA and RNA?
RNA is single-stranded and uses a ribose sugar in its backbone, compared to
deoxyribose in DNA.
2. DNA base-pairing:
a. Create a complementary strand of DNA for the sequence shown below, using what
you know about nucleotide base pairing.
ATTCATGATTAGAC
TAAGTACTAATCTG
b. Draw a picture showing how the last two bases (A and C in the original strand) pair
with their complementary strand. What holds the two strands of DNA to each other?
(Don’t worry about getting the structures exactly right; you can use cartoons to
represent the molecules!)
Picture should show A pairing with T and C pairing with G. The A-T and G-C bonds
should be held together with H bonds (3 between G-C and 2 between A-T).
c. Which pair bonds more strongly: A-T or G-C?
G-C because there are more H-bonds holding them together.
3. Comparing DNA and proteins:
a. What are the monomers in DNA called? What are the monomers in proteins called?
DNA monomers are nucleotides; protein monomers are amino acids.
b. There are 20 different types of monomers in proteins. What makes each of these
monomers unique?
the R-group or sidechain
c. Compare the functions of DNA to the functions of proteins.
The function of DNA is to carry genetic information, and the job of proteins is to do all of
the work around the cell (each protein has a specific job, and there are proteins to do all
of the cell’s activities; from copying DNA to breaking down glucose to make energy for
the cell to making more proteins, proteins are involved in all of the cell’s activities.)
d. How are proteins and DNA similar in how they are constructed?
Both DNA and proteins are made from monomers that link to form long chains.
e. How does the construction of DNA and proteins compare to the construction of
carbohydrates and lipids?
DNA, proteins, and carbohydrates are composed of long chains of monomers. Lipids
are composed of monomers too, but these do not form long chains.
4. Some amino acids are hydrophobic and others are hydrophilic.
a. Explain what is meant by hydrophobic and hydrophilic.
Hydrophilic means “water loving” and hydrophobic means “water fearing” or “water
avoiding.”
b. How do hydrophilic amino acids act in a watery environment? Draw a picture to
show the molecular interactions.
Hydrophilic amino acids will interact with the water as the water forms H bonds between
the polar or charged R groups. The drawing should show that the water is clustered
around the polar side chain of the amino acid.
c. How do hydrophobic amino acids act in a watery environment? Draw a picture to
show the molecular interactions.
Hydrophobic amino acids will cluster together as the water does not interact with the
non-polar R groups. The drawing should show that the water does not interact with the
non-polar side chain of the amino acid but only interacts with other water molecules.
d. The picture below shows a protein composed entirely of hydrophobic amino acids in
water.
Draw a picture showing how it will fold in a watery environment, and explain why it
would fold this way.
The drawing should show the amino acids closely bunched together as they are pushed
away from the water by other water molecules. It would fold this way because the water
molecules have a stronger attraction to other water molecules.
e. If the first 4 amino acids on the right were replaced with hydrophilic amino acids, how
would this affect the protein folding? Draw a picture to show any differences.
The drawing should show the hydrophilic amino acids on the outside since water
molecules will be attracted to those amino acids at least as much as they are attracted
to other water molecules.
5. Why are water molecules strongly attracted to other water molecules? What causes
them to form hydrogen bonds with each other?
Water molecules are polar. The oxygen atom has a slight negative charge while the
hydrogen atoms have slight positive charges. The positive and negative charges are
attracted to each other, forming H-bonds.