SAM Teachers Guide  Proteins and Nucleic Acids      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 more generally, 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 the 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: amino acids 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.   • 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 moleculeʹs  surface can affect the moleculeʹs interaction with polar water.  • Page 6 – Sequence and Structure  o Use a projector to show 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 with your students the nucleotides. 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  only are attached in the sequence if through random motion they  are in the right place at the right time.  o Link to SAM activity: 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 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 bounds  and Molecular Geometry explores the resulting 3D structures that result from charge  distribution. Finally, Solubility is important because when learning about how proteins  fold, the interactions of the amino acids with water is critical.     The Proteins and Nucleic Acids 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 Structure and Function of  Proteins because students can build on the structure and determine how it relates to the  major functions of proteins.  

  Activity Answer Guide 

Pictures will vary. The picture should include three different monomers.

Page 1: Introduction, no questions

Page 2:

4. Why do scientists call proteins heteropolymers? Because proteins are made of 20 different types of monomers.

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 4: Note: snapshots will vary. The ones included are examples.

Page 3:

1. Large side chain:

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.

2. Polar side chain:

Pictures will vary. The picture should include only one type of monomer. 3. Take a snapshot of your heteropolymer and drag it in to the box below.

3. Nonpolar side chain:

4. Charged side chain:

The hydrophilic amino acids are being straightened as they extend into water and the hydrophobic are being shaped into a ball. 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: Page 5: 1. If the hydrogen bonds could not form within the oval area, how would that affect the function of the protein? If the hydrogen bonds could not form the protein chain would not be able to maintain its folded shape..

1. Place the snapshot of the unaltered protein after it has folded in the box below.

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.

Sample snapshot.

2. Create a protein with a different shape by changing a single amino acid. Take a snapshot and drag it here.

Sample snapshot. 3. Place the snapshot of your arrangement of the molecules that shows the new strand is created: Pictures will vary. The amino acid on the right side 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 uneven number.

Page 10: 1. Is photocopying a document similar to making an RNA strand? Explain how the two processes are alike and how they are different. 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 affects 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?

1. Describe how you think the nonpolar amino acid shown below will interact with water. Explain why.

3. The protein chain below is made entirely from hydrophobic amino acids. 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.

4. Describe how the sequence of a DNA strand is related to the sequence of the protein strand it codes for.