SAM Teacher’s Guide DNA to Proteins 

 Overview Students examine the structure of DNA and the processes of translation and transcription, and then explore the impact of various kinds of mutations.  Learning Objectives Students will be able to:

• Describe how DNA, consisting of four bases, can store the genetic code for proteins, which are made from a sequence of twenty different types of amino acids.

• Describe the processes of translation and transcription. • Manipulate the DNA code and predict how it will change the sequence of mRNA 

and potentially a protein. • Explain the effects of various types of mutations, including substitutions, 

insertions and deletions, on the resulting transcription and translation of a gene. • Demonstrate how substituting one nucleotide for another often makes no 

significant change in the shape of a protein, unless it occurs at a critical location.  

Possible Student Pre/Misconceptions 

• DNA and RNA are structurally identical. • Transcription and translation are somewhat random processes. • Transcription and translation both happen in the nucleus. • Information is stored somewhere within the nucleotides and not in their 

sequence.  Note: There are many animations (and simulation models) of transcription and translation found on the Web. The SAM transcription and translation models, though simplified in representation, are powerful tools and are different in the following ways:

• This interactive model allows the users to control the sequence of DNA being transcribed and then translated.

• The model has an emergent properties aspect; users can see that, when they alter the sequence, the resulting peptide chain will have a different characteristic, say, a fold, or behavior in solution. 

• Changes in the model happen almost instantaneously, reinforcing the link between the sequence of nucleotides in the gene and the structure of the protein. 

 

Models to Highlight and Possible Discussion Questions  Page 1 – The Architecture of DNA 

Model: DNA Structure • Highlight the organization of DNA, including the subunits that make up 

nucleotides, the base pairs, and especially the hydrogen bonds.  • Link to other SAM activities: Intermolecular Attractions.   

 Possible Discussion questions  

• Discuss why having weak bonds makes it easy to “unzip” the DNA, and why this is an advantage.  

Page 2 – Transcription   Model: Transcription 

• Highlight the complementary base pairing between strands. Point out which strand is the template, and that mRNA is single stranded and detaches from the DNA. Note how this model represents the RNA (red band) and that the amino acids are in a water environment. 

• Link to other SAM activities: Intermolecular Attractions.    

Possible Discussion questions  • Where does the model fall short of representing transcription accurately? ?  

(For example, incoming nucleotides are not shown.) Is there a good reason or trade‑off for the omission or simplification by the model? (Showing incoming nucleotides might overly complicate the image, making it difficult to focus on transcription itself).  

• Link to other SAM Activities: Molecular Geometry. Highlight the importance of the 3D structure of both DNA and RNA in the processes of transcription and translation.   

Pages 3‑4 – Translation  Model: Translation  

• Highlight that three nucleotides encode one amino acid in the chain. Also, review that there are available amino acids (which attach to tRNAs) in the cell.  

• Both transcription and translation can be reviewed step-by‑step.  • Transfer RNAs (tRNAs) are missing from the model; there is a link at the 

bottom that orients students towards the relationship of tRNA in the translation process.  There is one tRNA for each amino acid codon.  Highlight the complementary base‑pairing between mRNA and tRNAs. 

• What does this model show compared to the animation?  

Possible Discussion questions • Compare and contrast transcription and translation. • How does the structure of DNA play a role in its function? • Link to other SAM Activities:  Solubility and Nucleic Acids and Proteins. Review why shape is so important. Review polarity and hydrophobicity and their role in protein shape.  

Extensions:

• What is non‑coding DNA? How much of the human genome is non‑coding? (~95‑98%) What are some functions of non‑coding sequences?    

• What are some differences in transcription and translation in eukaryotic vs. prokaryotic cells? 

• Where does transcription take place in eukaryotic cells? (the nucleus). Where does translation take place? (cytoplasm). What would be the advantages of this arrangement?  

Demonstration/Laboratory Ideas:

• DNA replication kits to model transcription/translation.  • Analogy activity with other codes (Morse Code).  • Fit in with PCR or electrophoresis labs.  

 Page 6 – Substitution Mutations  

Model: Making Mutations • Point out the means of making a mutation in this model (right‑clicking on a 

DNA nucleotide). This skill is also used on the next pages of the activity. • Highlight the possible changes that can result from a substitution 

mutation.    

Possible Discussion questions • Discuss the redundancy in the DNA code.  • Discuss why some amino acid changes do not affect protein folding 

(hydrophobic to hydrophobic or hydrophilic to hydrophilic). • Highlight some of the effects that a substitution mutation can have:  for 

example, you might want to review sickle cell disease, caused by a single point mutation. (See the MW activity Hemoglobin.)   

Page 7 – Silent Mutations  Model: Making Mutations 

• Highlight that many amino acids are coded for by more than one codon.  

Possible Discussion questions • Discuss the redundancy in the DNA code.  

 Page 8 – Stop Codons  

Model: Making Mutations • Highlight that there are three codons that will cause protein synthesis to 

end.    

Possible Discussion questions • Discuss the utility of stop codons in normal cell function.  • Discuss the impact of a mutation that causes an early stop codon vs. a 

mutation that causes a delayed stop codon.  

Page 9 – Insertions and Deletions  Model:  Making Mutations 

• Review how three nucleotides encode a particular amino acid and what happens if the reading frame is shifted.   

Possible Discussion questions • Discuss different ways to make insertion and deletion mutations that do 

not shift the reading frame.  Will the proteins produced by these variations have the same number of amino acids?  (No; a series of 3 insertions will increase the length; a series of 3 deletions will decrease the length; an insertion tempered by a deletion will have the same number of amino acids.)  

• Connect to protein functions in the body and how mutations in DNA impact those functions.  

• Highlight the possibility of devastating effects from an insertion or deletion.  

Possible Summary Discussion Questions for Mutations

• Can mutations be good? Help students to think about this from an evolutionary point of view. What role can mutations play in adaptations?  (Be careful not to imply that the environment changes the DNA so that the organism can adapt.) How are mutations passed on to the next generation? 

• Why do some mutations result in small changes? Large changes? No changes?  

• Why can some substitution mutations be considered silent?  • How do environmental factors effect alterations in DNA and cause problems 

such as cancer?  

Demonstration/Laboratory Ideas:

• Tie in with natural selection activity on mutation/evolution/adaptation.    

  

Connections to Other SAM Activities

The focus of this activity is for students to explore the processes of transcription and translation. They determine how DNA’s structure encodes for proteins. The DNA to Proteins unit activity is supported by the Electrostatics activity. To predict why the base pairs (A-T, C-G) bond, students first need to appreciate the role of attraction between molecules. A background in electrostatics is also helpful in understanding protein folding. The Chemical Bonds activity allows students to reason about why amino acids might be hydrophobic or hydrophilic. Intermolecular Attractions helps students examine the concepts of base pairing and protein folding with regard to polar (and non-polar) attractions. Finally, Nucleic Acids and Proteins has students explore the basic structure of these molecules. This activity supports other biology activities including Four Levels of Protein Structure and Structure and Function of Proteins. In DNA to Proteins, students learn how proteins are generated. In Four Levels of Protein Structure, students can then explore in more detail the structure of a protein and four distinct levels of organization. When students complete Structure and Function of Proteins they will have the opportunity to make connections between the protein’s physical structure and the jobs that it does in the cell.

  Activity Answer Guide  Page 1: 1. Take a snapshot that best illustrates the bonds that hold the two strands of DNA together in a double helix.

2. A DNA nucleotide from one strand pairs with a specific nucleotide on the other strand. Take a snapshot showing which nucleotide pairs with cytosine (C). Use the annotation tools to indicate this nucleotide.

Page 2: 1. In this model, the bottom DNA strand is transcribed. Which DNA strand is most similar to the RNA strand? (a) 2. A group of three nucleotides codes for one amino acid. Notice the black tick marks above the DNA strand showing these triplet groups. How many amino acids are coded for by the strand in the model above? (c)

3. From using the model above, you should now know the “rules” for which RNA nucleotide pairs with each DNA nucleotide. RNA pairing with DNA: A pairs with T, U pairs with A, C pairs with G, G pairs with C The nucleotide T (thymine) is replaced by U (uracil) in RNA. Other than that, the base pairings are the same. 4. If six bases on the template strand of DNA are AGTAAC, what are the six bases on the complementary section of the RNA? Complementary section = UCAUUG Page 3: 1. Click the “Translate step by step” button and describe each step as the RNA is translated. mRNA leaves the DNA (and also the nucleus) and attaches to a ribosome in the cytoplasm. The nucleotide triplets code for particular amino acids. Amino acids link up in a peptide chain and then the chain detaches from the mRNA. 2. Compare the sequence and shape of both proteins that are formed. The sequence and shape of both proteins is the same because the directions (the mRNA starting material) are the same.

Page 4: 1. Paste your amino acid sequence below.

Page 5: 1. Make a prediction: which mutation types do you think will most likely cause the biggest changes in the translated protein? (Check ALL that apply.) Answers will vary. 2. Explain the reasoning behind your prediction. (In the rest of this activity, you will learn how to test this prediction.) Answers will vary. Page 6: 1. Challenge 1: Insert the snapshot image of the protein synthesis before mutation.

2. Challenge 1: Insert the snapshot image of the protein after mutation. Mutated strand - The second amino acid is now Ser instead of Phe and hydrophilic (blue) instead of hydrophobic (pink).

3. Challenge 2: Place an image of a protein here that has one of the original hydrophobic amino acids changed to another by a substitution mutation. Answers will vary.

4. Some substitution mutations result in a malfunctioning protein, but others do not. What might be the reason for this? Some substitution mutations result in the same amino acid being added, which does not change the structure of the protein at all. Some substitution mutations result in a similar type of amino acid (hydrophobic for hydrophobic or vice versa) being added. This does not greatly affect the protein folding. Some substitution mutations result in a different type of amino acid (hydrophobic for hydrophilic or vice versa) being added. This affects the protein folding as it cannot fold in the same manner as before since the amino acids with different properties don’t interact with water in the same way.

Page 7: 1. All of the following codons are used in the model below. Synthesize the protein, and then check off the ones that code for Leu. (Check ALL that apply.) (a) (b) (c) 2. Enter the original codon. Enter the mutated codon. What amino acid is specified by both codons? GGG GGC Glycine Answers will vary. The only amino acid in the protein that cannot be mutated to another synonymous codon is Methionine. All of the others have at least two codons. Page 8: 1. Drag a snapshot image that shows the mutated protein.

Student snapshots will vary. Before the stop codon UAG, a chain of only five amino acids is translated. 2. Compare the effects of a mutation that causes an amino acid change with a mutation that causes a stop codon. Which do you think would affect the protein more? Why? A protein that results from a stop codon mutation will be more affected than a substitution mutation. The protein is not able to be made so there will be zero function whereas there might be some functionality in a protein that is the result of a substitution mutation.

Page 9: 1. Drag a snapshot image that shows the original protein before mutation.

2. Take a snapshot image that shows the mutant protein resulting from the frame-shift mutation.

Student snapshots will vary. 3. Why do insertion mutations have a bigger effect on the protein than substitution mutations? Insertion mutations cause a shift in the reading frame. This means that all of the amino acids after the insertion are potentially wrong, as well as causing the stop codon to not be in the reading frame. This could mean that the stop codon comes too early or that the protein goes on for too long because the DNA and mRNA are no longer being read as they were supposed to have been read.

4. Take a snapshot image that shows the mutant protein that is not the result of a frame-shift.

Student snapshots will vary. Some proteins will be shorter than the original due to 3 deletions. Some will be longer than the original due to 3 insertions. Some will be the same length (if a stop codon was not accidentally created) due to an insertion and a deletion. 5. How did you make insertion and/or deletion mutations that did not cause a frame-shift? Student answers will vary. Valid answers are: 3 deletions (or multiples of 3), 3 insertions (or multiples of 3), or matching numbers of insertions and deletions (in a 1:1 ratio). Page 10: 1. The process by which the genetic code of DNA is copied into a strand of RNA is called: (b) 2. Which one of the following is the mRNA made from the following DNA sequence: TAGTTTAGACGATG (c) 3. Use the terms DNA, RNA, codon and protein to explain the connections between genetic information and proteins. The DNA is where the genetic information is stored. The DNA is unable to leave the nucleus. An RNA copy of the DNA is made. The RNA copy leaves the nucleus and goes to the ribosome in the cytoplasm. The RNA is read by the ribosome, where each codon, a triplet of nucleotides, codes for an amino acids. The string of amino acids makes up the protein. The directions for the protein were coded for by the DNA.

4. How many nucleotides would be needed to code for a protein with the following amino acid sequence? Ala-Ala-Met-Ile-Leu-Val-Phe-Tyr (c) 5. In cells that have a nucleus, the DNA is not able to leave the nucleus. How does the information make its way out of the nucleus so that it can be used in making proteins? The information in the DNA is transcribed into an RNA copy that can leave the nucleus. 6. How can a mutation have no effect? If it is a silent mutation, the mutation does not affect the amino acid that is coded for. There can be silent mutations because there is redundancy in the genetic code. 7. Which types of mutations, among those you created in this activity, are more likely to cause the biggest problems due to the resulting protein? Why? Insertion and deletion mutations are likely to cause the most major problems because they disrupt the reading frame. Other mutations that cause major protein problems are stop codon mutations, which can result from insertions and deletions as well as some substitution mutations. Most substitution mutations are pretty benign because the amino acid often does not change because of the redundancy in the genetic code, and even when the amino acid does change, it is more likely to be of the same type (hydrophilic or hydrophobic) than of a different type, which means that the protein folding is less likely to be disrupted.

SAM HOMEWORK QUESTIONS DNA to Proteins

Directions: After completing the unit, answer the following questions to review.  1. What is the three‑dimensional structure of a DNA molecule?  First, describe it in words.  Then, draw and label a sketch of DNA. 

 description:     sketch: 

1.

2. What happens during the process of transcription? Where does this happen in a cell? 

2.

3. The process of translation is when mRNA is read in order to create a protein chain. What are the subunits within a protein chain called? Where does the cell find these subunits? 

3. 4.

4.  How many nucleotides must have been in the mRNA chain in order to translate the protein shown on the right?  

   5. For each type of mutation listed below, describe what happens to change the DNA sequence.

 substitution – 

  insertion –  

  deletion –

6. Sickle cell disease is an example of a condition that is the result of a substitution mutation. Why do some mutations cause serious conditions while others have no effect?     

6. Career connection: The attractions of A/T and G/C bases between DNA molecules has started a new field of research called DNA nanotechnology, which creates interesting new structures from DNA that may someday be used as new materials with special properties. Find an example of a new structure made from DNA and describe it here. (Note: Computer models are used heavily in this area to predict what kinds of structures are possible before trying to assemble them.) 

SAM HOMEWORK QUESTIONS DNA to Proteins – with suggested answers for teachers

1. What is the three‑dimensional structure of a DNA molecule? First, describe it in words. Then, draw and label a sketch of DNA. 

Description: DNA is a double helix, or twisted ladder, made of four nucleotides, held together by hydrogen bonds.

Sketch: The sketch should show a double helix with hydrogen bonds connecting the two strands.

 2. What happens during the process of transcription? Where does this happen in a cell? 

Genes are copied into mRNA in the nucleus of the cell.  3. The process of translation is when mRNA is read in order to code a protein chain. What are the subunits within a protein chain called? Where does the cell find these subunits? 

Protein subunits are called amino acids. The subunits are assembled on ribosomes in the cytoplasm of the cell. The amino acids are found floating in the cytoplasm attached to specific transfer RNA molecules (tRNA).

 4.  How many nucleotides must have been in the mRNA chain in order to translate the protein shown on the right? 

30. A triplet codes for one amino acid. This protein has 10 amino acids x 3 nucleotides per triplet =30.  5. For each type of mutation listed below, describe what happens to change the DNA sequence. 

substitution – one nucleotide is replaced with another insertion – an extra nucleotide is added into the sequence deletion – a nucleotide is removed from the sequence

 6. Sickle cell disease is an example of a condition that is the result of a substitution mutation. Why do some mutations cause serious conditions while others have no effect? 

Some substitution mutations can be silent. A different nucleotide is inserted, but a codon for the same amino acid results. Other substitution mutations can be much more devastating if a change in the codon results. If an amino acid with similar properties is substituted, the results might be minor.

7. Career connection: DNA has been made into tubes, boxes, lattices and many 

other shapes. Use an image search engine with the search term “DNA nanotechnology” to find other examples.