SAM Teachers Guide
Nucleic Acids and Proteins (short version)
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, they explore 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.
Note: This activity assumes you have done the Introduction to Macromolecules activity
first, a short (three page) activity that is intended to be paired with either the Lipids and
Carbohydrates activity or the Nucleic Acids and Proteins activity. There are long
versions of both of those activities that eliminate the need for the Intro to
Macromolecules activity.
Learning Objectives
Students will be able to:
 Identify examples of proteins and their functions.
 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 static.
 Proteins are characterized by only one level of structure.
Models to Highlight and Possible Discussion Questions
Page 1 – Introduction to Nucleic Acids
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 the parts of the nucleotides that are identical and the parts that
are different.
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.
 Link to other SAM activities: Intermolecular Attractions. Highlight that
hydrogen bonding is optimal when the shapes of the two molecules allow
them to line up closely together.
Possible Discussion Question:
 What is a hydrogen bond? Why is it 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.
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, or
complementarity. 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
Model: An Introduction to Proteins
 Point out that with each protein, the outer atoms are removed in order to
reveal the protein’s chain-like structure. Make sure that students
understand that this is just a visual aid to show 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. Emphasize that there are twenty amino acids.
Discussion Questions
 Why is it important that amino acids have differing characteristics?
 What are the implications of the fact that proteins are made from twenty
different monomers, and DNA/RNA from only four?
Page 6 - Protein Interactions in Water
Model: In Water, Proteins Have a Hydrophobic Core
 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 students 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 on a printout, or make a new drawing
that includes them.
Wrap-up Discussion Questions:
 How is the structure of protein similar to that of carbohydrates and lipids?
How is it different?
 How are DNA (and RNA) macromolecules similar to proteins? How are
they different?
Connections to Other SAM Activities
The Nucleic Acids and Proteins activity focuses on the basic structure of protein, DNA,
and RNA, as well as their 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, Nucleic Acids and Proteins supports Protein
Partnering and Function 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 above DNA
fragment in sequence, from #1 to #11, in the
space below.
CCAATGGCCAT
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.
2. Which components are the same in all
DNA nucleotide monomers? (Check all that
apply.) (c)
3. Which components serve to link the DNA
nucleotide monomers together into a
polymer? (Check all that apply.) (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.
Page 4:
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
1. Which protein can puncture a cell wall? (b)
2. Which protein forms a cable? (a)
3. Which protein becomes 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 with 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 attract
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 DNA and proteins are polymers, long
chains, and macromolecules. However, 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 amino
acids, and the pink represents hydrophobic
amino acids. This is because the blue amino
acids 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. Comparing DNA and RNA:
a. Identify whether the following sequences of nucleic acid represent DNA or RNA, and
explain your reasoning.
1) ATCCATTACGTATCA
2) AUGGUGACCAUGGA
3) 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 in the original strand (A and C) 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. How are proteins and DNA similar in how they are constructed?
4. Some amino acids are hydrophobic, and others are hydrophilic.
a. Explain what is meant by “hydrophobic” and “hydrophilic.”
b. The picture below shows a protein composed entirely of hydrophobic amino acids in
water. Draw a picture showing how it would fold in a watery environment, and explain
why it would fold this way.
c. If the first four 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?
6. 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
Directions: After completing the unit, answer the following questions for review.
1. Comparing DNA and RNA:
a. Identify whether the following sequences of nucleic acid represent DNA or RNA, and
explain your reasoning.
1) ATCCATTACGTATCA DNA—presence of T
2) AUGGUGACCAUGGA RNA—presence of U
3) CCTAGTCAATGCAAT DNA—presence of T
b. What are two other differences between DNA and RNA?
RNA is single-stranded, and its sugar has an extra oxygen atom compared with 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 in the original strand (A and C) 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 called “nucleotides”; protein monomers are called “amino acids.”
b. There are 20 different types of monomers in proteins. What makes each of these
monomers unique?
the R-group, or sidechain
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.
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 avoiding.”
b. The picture below shows a protein composed entirely of hydrophobic amino acids in
water. Draw a picture showing how it would 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.
c. If the first four 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, because 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.
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.
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.