SAM Teachers Guide
DNA to Proteins
Overview
Students 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 Objectives
Students 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 Questions
Note:
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 / translation
o 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:
Page 3:
Introduction
No Responses.
Page 2:
Page 4:
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.
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.
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.
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.
Sample snapshot: Hydrogen bonds attracting
the two strands are shown in white.
Page 7:
1. Drag a snapshot image that shows the
synthesized protein before 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.
Translation with no mutation.
2. Drag a snapshot image that shows the
synthesized protein after mutation.
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?
Mutated strand - The second amino acid is now
S instead of F and hydrophilic (blue) instead of
hydrophobic (pink).
If a stop codon is present, translation will end.
The protein synthesis will be cut short and a
different protein chain is made.
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 10:
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.
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.
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?
Shortened protein synthesized after insertion
caused frame shift. Stop codon was now read.
Mutations can be neutral if they do not affect the
amino acid that is added to the protein chain.
3. Why do insertion mutations have a bigger
effect on the protein than substitution
mutations?
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?
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.
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?
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.
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 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:
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?