SAM Teachers Guide Nucleic Acids and Proteins (Long Version) Overview Learning Objectives Possible Student Pre/Misconceptions

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1 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.

2 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 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.

3 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?

4 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.

5 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 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: 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.

6 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?

7 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): 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. Sample snapshot.

8 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: 1. The information in the first three nucleotides codes for the following amino acid: (c) 2. The function of RNA is to create a protein chain. How is an RNA's structure related to its function? Each triplet codes for one amino acid (or stop codon) of a protein chain. Page 12: 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) 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. 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) 6. The function of a protein is determined by all of the following EXCEPT: (c) 7. Nucleic acids carry information for making proteins in: (b) 8. How does random motion of molecules play a role in the way RNA and proteins form? 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

9 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

10 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.