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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.