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
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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:
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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:
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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
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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?
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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:
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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.
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:
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.
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 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)
Page 4:
1. Paste your amino acid sequence below.
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).
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.)
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.
Answers will vary.
Page 6:
1. Challenge 1: Insert the snapshot image of
the protein synthesis before mutation.
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.)
Page 9:
1. Drag a snapshot image that shows the
original protein before mutation.
(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.
2. Take a snapshot image that shows the
mutant protein resulting from the frame-shift
mutation.
Page 8:
1. Drag a snapshot image that shows the
mutated protein.
Student snapshots will vary.
3. Why do insertion mutations have a bigger
effect on the protein than substitution
mutations?
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.
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.
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?
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.
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.