SAM Teachers GuideDNA to Proteins

OverviewStudents explore the structure of DNA and the processes of translation and transcription, and then continue to look at the impact of various kinds of mutations.

Learning ObjectivesStudents will be able to:

Reason how DNA, made of four different types of monomers (adenine, thymine, guanine, and cytosine), can store the genetic code: information about sequence of amino acids in proteins.

Describe the processes of translation and transcription. Manipulate the DNA code and observe how it changes the sequence of

m-RNA and proteins. Define a mutation and give examples of three different types of

mutations including substitutions, insertions and deletions. Demonstrate how substituting one nucleotide for another often makes

no significant change in the shape of a peptide chain, unless it occurs at a critical location.

Possible Student Pre/Misconceptions DNA is a linear string. DNA and RNA are the same structurally. Transcription and translation are somewhat random or magical

processes. The amino acids that make up a protein chain appear out of the blue

they are not always available in the cell.

Models to Highlight and Possible Discussion QuestionsNote:There are many animations of transcription and translation found on the Web as well as in our activity. The DNA to Protein model, though simplified in representation, is a powerful tool and is different from other animations in the following ways:

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

The model has an emergent properties component that allows the user to see that when the user alters the sequence s/he will get a new fold in the resulting peptide chain.

Moreover, it happens instantaneously, thus reinforcing the link between the sequence of nucleotides in the gene and the structure of the protein.

It is different form traditional animations of transcription/translation where the emphasis is on viewing and memorizing the steps, as well as memorizing the base pairs.

After completion of Part 1 of the activity:Models to Highlight:

Page 2 – Model of DNA o Highlight the organization of DNA, including the subunits

that make up nucleotides, the base pairs, and especially the hydrogen bonds.

o Connection to other SAM Activities: Intermolecular Attractions. Discuss why having weak bonds makes it easy to “unzip.”

Page 4 – Modeling Transcription o Review the complementary base pairs, point out which

strand is the template, and that mRNA is single stranded and detaches. Point out how this model represents the RNA (red band) and that the amino acids are in a water environment.

o 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.

Page 5 – Modeling Translation o Highlight that three nucleotides encode one amino acid in

the chain. Also, review that there are available amino acids in the cell.

o Both transcription and translation can be reviewed step by step.

o Review why shape is so important. Discuss polarity and hydrophobicity and its role in protein shape. Discuss what the model is missing, tRNA, for example, and what this model shows compared to the animation.

Possible Discussion Questions: Is all DNA essential for the production of proteins? Why or why

not? How does the 3D structure of DNA play a role in its function? What are two differences between DNA and RNA? Where does transcription take place? Where does translation

take place? Compare and contrast transcription and translation. Demonstration/Laboratory Ideas:

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

After completion of Part 2 of the activity:Models to Highlight:

Page 7 – Substitution Mutations o Highlight the possible changes that can result from a

substitution mutation. Discuss the redundancy in the DNA code.

Page 10 – Insertions / Deletions o Highlight the possibility of devastating effects from an

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

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

Possible Discussion Questions:

Can mutations be good? Think about it from an evolutionary point of view. What role can mutations play in adaptations?

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

Why can a substitution mutation be considered silent? How could environmental factors affect alterations in DNA and

cause problems such as cancer? Demonstration/Laboratory Ideas:

o Tie in with natural selection activity on mutation / evolution / adaptations.

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 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. To understand why protein-folding patterns occur, a background in electrostatics is also helpful. The Chemical Bonds unit will allow 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, Proteins and Nucleic Acids 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 have the opportunity to make connections between the protein’s physical structure and the jobs they carry out.

Activity Answer Guide

Page 1:Introduction

Page 2:

1. Take a snapshot that best shows that DNA is really two separate molecules wrapping around each other. And then follow the instruction below to drag the image in.

Sample snapshot: One chain is shown as a ribbon and the other with the specific nucleotide arrangement. DNA is clearly two separate molecules wrapping around each other. One pair of hydrogen bonds joining the two strands is also circled in red.

2. Take a snapshot that best illustrates the hydrogen bonds, which attract the two strands together. And then follow the instruction below to drag an image in.

Sample snapshot: Hydrogen bonds attracting the two strands are shown in white.

Page 3:No Responses.

Page 4:

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? (b)

3. List two ways in which the RNA strand in the model above is different than the DNA strand from which it was copied (the template strand).

RNA is single stranded. RNA replaces Thymine with Uracil.

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 5:

1. Describe each step as the RNA is translated.

mRNA leaves the DNA (and also the nucleus) and attaches to a ribosome. 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 6:No responses.

Page 7: 1. Drag a snapshot image that shows the synthesized protein before mutation.

Translation with no mutation.

2. Drag a snapshot image that shows the synthesized protein after mutation.

Mutated strand - The second amino acid is now S instead of F and hydrophilic (blue) instead of hydrophobic (pink).

3. Some substitution mutations result in a malfunctioning protein, but others do not. Why is this?You can substitute a nucleotide yet still end up with the same amino acid; you can substitute a nucleotide and end up with a different amino acid yet the amino acid will have similar properties to the one it replaced and therefore not affect the protein; or you can substitute a nucleotide which in turns means the amino acid that replaces it has changed. This change can cause a change in the structure and in the function of the protein. It is dependent upon how/if the substitution affects the properties of the amino acid created. In this case, it changed its interaction with water.

Page 8:

1. How did you create a silent mutation? Explain, giving the code for the triplet where you made your substitution, before and after the mutation.

A guanine was substituted for the last thymine in the DNA nucleotide sequence so the code was CTT and becomes CTG. Even though a G was substituted, a leucine was still bonded to the final protein and the product looks identical.

Page 9:

1. Drag a snapshot image that shows the mutated protein.

Before the stop codon UAG, a protein of only four amino acids is translated.

2. Why do mutations that create a stop codon have a bigger effect on the protein than other mutations?

If a stop codon is present, translation will end. The protein synthesis will be cut short and a different protein chain is made.

Page 10:

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

Protein before insertion mutation.

2. Drag a snapshot image that shows the mutant protein.

Shortened protein synthesized after insertion caused frame shift. Stop codon was now read.

3. Why do insertion mutations have a bigger effect on the protein than substitution mutations?

The entire reading frame is shifted. Each group of three nucleotides is then affected and a new peptide chain is formed.

4. Drag a snapshot image that shows the mutant protein.

No frame shift mutation occurred because three insertions in a row kept the rest of the reading frame the same.

5. How did you make an insertion or deletion mutation that did not cause a frame shift?

Three insertions or deletions in a row would not cause a frame shift. Either a new codon was added or an entire one was removed.

Page 11:

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 place where genetic information is stored in the cell: (c)

3. How can a mutation have no effect?

Mutations can be neutral if they do not affect the amino acid that is added to the protein chain.

4. What is the connection between the DNA sequence of a gene and the amino acid sequence of the protein that is produced from that gene?

DNA is copied or transcribed into RNA. The RNA is read in groups of three called codons. Each codon codes for one amino acid. Therefore the sequence of nucleotides in DNA determines the sequence of amino acids.

5. How many nucleotides would you need to code for a protein with the following amino acid sequence: (24 amino acids) AAMILVFYYWWHKKKRQAPPRRGG (c)

6. Which types of mutation, among those you created in this activity, are more likely to be lethal? Why?

The most lethal would be insertions or deletions because they may impact the entire reading frame and, therefore, the structure and function of the protein.

SAM HOMEWORK QUESTIONSDNA 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:

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

3. The process of translation is when RNA is “reread” in order to code a protein chain. What are the subunits within a protein chain called? Where does the cell find these subunits?

4. How many nucleotides must have been in the RNA chain in order to translate the protein below?

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

a) substitution –

b) insertion –

c) 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?