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 moleculeʹs surface affect the 

moleculeʹs 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 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. 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 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. 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.

Page 4: 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. 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. 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. 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

AssociatedProgram:CenterforBioMolecularModeling

Thisexcellentprogram,locatedattheMilwaukeeSchoolofEngineering,offershands-onmodelsofbiomoleculesforclassroomuse.