Gene Expression Worksheet
Part 1: Transcription
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READ THIS: DNA is often referred to as a genetic blueprint. In the same way that blueprints contain the
instructions for construction of a building, the DNA found inside the nuclei of cells contains the
instructions for assembling a living organism. The DNA blueprint carries its instructions in the form of
genes. In most cases the genes direct the production of a polypeptide, from which other more complex
proteins, such as enzymes or hormones, may be constructed. These polypeptides and other molecules
run the organism’s metabolism and, in multicellular organisms, dictate what each cell’s job is. So, what is
the language of these instructions and how are they read and decoded by the cellular organelles? This
activity will focus on the decoding of genes in eukaryotes.
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1. Refer to Model 1.
a. What is the base-pair rule for a DNA strand matching an RNA strand?
The base pair rule for a DNA strand matching an RNA strand is that Adenine
pairs with Uracil, Thymine pairs with Adenine, Guanine pairs with Cytosine,
and Cytosine pairs with Guanine.
b. Compare this base-pair rule with that of two DNA strands.
For two DNA strands, Adenine and Thymine pair together and Cytosine and
Guanine pair together, while when DNA matches RNA, Adenine pairs with
Uracil rather than Thymine, but Thymine still pairs with Adenine.
2. Which strand of the DNA contains the “blueprint” for the pre-mRNA?
The template strand contains the "blueprint" for the pre-mRNA.
3. Consider Model 1
a. In which direction is the DNA molecule read?
The DNA molecule is read from 5' to 3'
b. The DNA template strand and pre-mRNA strand are anti-parallel. With this in mind label
the 3ʹ and 5ʹ ends of the pre-mRNA strand in Model 1.
c. In which direction is the pre-mRNA molecule constructed?
5' to 3' direction
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READ THIS: In eukaryotes the enzyme RNA polymerase joins with several transcription factor proteins
at the promoter, which is a special sequence of base pairs on the DNA template strand that signals the
beginning of a gene. The transcription factor proteins, along with the RNA polymerase, is called the
transcription initiation complex. This moves along the DNA template strand at about 40 base pairs per
second producing pre-mRNA. When the RNA polymerase reaches the terminator sequence of base pairs
on the DNA template strand, it completes the production of pre-mRNA and releases it into the
nucleoplasm.
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4. Where on the DNA strand does the transcription initiation complex form?
It forms in the promoter region.
5. Imagine the diversity of functions in which your cells participate.
a. Do you think that the cells in your big toe contain the same DNA as the neurons in your
brain?
They have the same DNA, but the express di erent genes, so the function and traits between
your big toe and neurons in your brain will be di erent
b. Will an individual cell transcribe every, or almost every, gene in its genome? Explain.
No they wont because they selectively will express di erent genes based on factors like
function or environmental conditions.
6. Compare the pre-mRNA to the mRNA leaving the nucleus in Model 1.
a. What has been removed from the pre-mRNA to make it into mRNA?
The introns were removed from the pre-mRNA to make it mRNA
b. What has been added to the mRNA that was not present in the pre-mRNA, and where
on the mRNA strand are the additional items located?
A 5' cap and a poly-A-tail to the 3' end has been added
7. Can mRNA diffuse through a membrane? Why or why not?
No, the membrane is selectively permeable. It is a large molecule, so it is harder for it to pass
through the lipid bilayer in the cell membrane.
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READ THIS: Introns are sections of pre-mRNA that are noncoding. That is, they don’t provide useful
information for the production of the polypeptide being synthesized. There is evidence that suggests
these introns allow certain sections of DNA to code for different polypeptides when different sections
are removed. The removal of specific sections is triggered by a signal response in the cell. The portions
of the pre-mRNA that remain are called exons. The methyl cap (sometimes called the GTP cap or 5ʹ cap)
helps the mRNA molecule move through the nuclear pore and attach to a ribosome, its final destination.
mRNA is a short lived molecule. Once in the cytoplasm the mRNA will be subject to exonucleases that
immediately start removing individual nucleotides from the 3ʹ end of a nucleic acid. The individual
mRNA nucleotides will then be free to be used again during the process of transcription.
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8. The human genome contains about 25,000 genes and yet produces about 100,000 different
polypeptides. Propose an explanation of how this is possible.
A singular pre-mRNA sequence has the ability to produce a variety of mRNA sequences which
can then be produced based on which introns are removed
9. Using the information in Read This section, develop a hypothesis to explain the advantage of the
poly-A tail added to the 3’ end of the mRNA.
The advantage of the poly-A-tail being added to the 3' end of the mRNA is that it prevents the
information-carrying part of the mRNA from being destroyed by the exonucleases before the
polypeptides can even be formed.
10. Different mRNA molecules can have poly-A tails of different lengths. Considering the purpose of
adding the poly-A tail (from the previous question), why are some tails longer than others?
Justify your answer.
The length of a poly-A-tail helps regulate the mRNA translation and stability. The length can also
vary by things like environmental conditions, the cell type, and regulatory signals.
11. Summarize the steps of transcription.
Transcription occurs in the nucleus and transcribes information in DNA to mRNA. It includes 3
steps: initiation, elongation, and termination. Initiation is where RNA polymerase binds to the
recognition sites, and it unwinds and unzips the part of the DNA strand that is to be transcribed.
Elongation is when one strand of the DNA acts as the template for transcription. new
nucleotides are added only to the 3’ end of the growing strand, RNA polymerase adds
nucleotides to form the mRNA (messenger RNA) strand, and new nucleotides are added only to
the 3’ end of the growing strand. Termination is where transcription continues until the RNA
polymerase encounters a sequence known as a terminator, RNA polymerase separates from
DNA, the transcript is released, and DNA forms the double helix
Part 2: Translation
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READ THIS: The message in your DNA of who you are and how your body works is carried out by cells
through gene expression. In most cases this means synthesizing a specific protein to do a specific job.
First, mRNA is transcribed from the DNA code. Then, the mRNA sequence is translated into a
polypeptide sequence.
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12. Model 1 defines the code scientists have discovered that relates the nucleotide sequence of
mRNA to the amino acid sequence of polypeptides. The language of mRNA is often described as
a “triplet code.” Explain the significance of this reference.
The "triplet code" is also known as a codon and is the framework for translating genetic
information from mRNA into the proteins
13. If an mRNA molecule had 300 nucleotides in the coding region of the strand, how many amino
acids would be in the polypeptide that was synthesized? Show mathematical work to support
your answer. there would be 100 amino acids because the total # of
nucleotides was divided by 3 (for a codon) and we get
308 100 100.
14. Consider the information in Model 1.
a. Compare all of the codons for Proline. What are the similarities and differences?
A similarity is that the rst 2 nucleotides are the same for all the codons (CC), and of
course all the codons code for the same amino acid. A di erence are the third
nucleotide are all di erent for the codons.
b. Considering that mistakes can occur during transcription and DNA replication, what
advantage is there for an organism to have multiple mRNA sequences code for the same
amino acid?
Some advantages are things like reducing the impact of mutations due to there being more
than one mRNA sequence, or having the ability to adapt to speci c environments easier.
15. Use the mRNA codon chart in Model 1 to complete the table below:
5’ or 3’? 1st 2nd 3rd position 4th position 5th position 6th position 5’ or 3’
(for mRNA) position position (for mRNA)
DNA 3’ TAC CTT CGG ATG GTC ACT 5’
mRNA 5' AUG GAA GCC UAC CAG UGA 3'
protein N-terminus Met Glu Ala Tyr Gln Stop C-terminus
16. According to the table in Model 1, what amino acid is at the beginning of every polypeptide?
Methionine is at the beginning of every polypeptide.
17. Describe why the 3 stages of translation are named as they are. (Hint: What do these terms
mean in standard English?)
Initiation is the beginning of translation, elongation is when amino acids are added making the polypeptide
chain longer, and termination is the ending of translation
18. According to Model 2, when the mRNA leaves the nucleus, to which cellular complex does it
attach?
It attaches to a ribosome in the cytoplasm
19. The mRNA attaches to the complex at the sequence AUG. What is the significance of this
sequence of nucleotides?
AUG signi es the starting codon in mRNA and helps initiate protein synthesis
20. Describe the movement of the ribosome as translation occurs.
The ribosome binds to the mRNA at the start codon in initiation, then it moves along the 5' to
3' direction in elongation, and nally continues until it reaches the stop codon in termination.
They help grow the polypeptide chain until translation is nished.
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READ THIS: The ribosome is a large complex of ribosomal RNA (rRNA) and proteins. It consists of two
subunits. The smaller subunit binds to the mRNA strand and the larger subunit holds the tRNA molecules
in place while the covalent peptide bond is formed between the amino acids. Several ribosomes can
attach to an mRNA molecule simultaneously. This allows for many polypeptide chains to be synthesized
at once. _____________________________________________________________________________
21. The tRNA molecules in a cell are short sequences of nucleotides (about 80 bases) that contain an
anticodon and carry a specific amino acid.
a. Find the tRNA in Model 2 that is carrying the Histidine (His). What sequence of
nucleotides makes the anticodon on this tRNA molecule?
GUA
b. What codon on mRNA would match this anticodon?
CAU
c. Verify that the codon you wrote in part b codes to Histidine by looking at the table in
Model 1. d. What anticodon would be found on a tRNA molecule carrying Glycine (Gly)?
(Note: There are several correct answers here.)
CCA, CCG, CCU
22. The “t” in tRNAs is short for transfer. In a complete sentence, explain why this molecule is called
transfer RNA.
It is call tRNA because it helps transfer speci c amino acids to the ribosome during protein synthesis
23. Describe two things that occur during termination as illustrated in Model 2.
The ribosome encounters the stop codon and proteins bind to the ribosome, and there is
also the release of the polypeptide
Part 3: Extension Questions
24. Consider the hypothetical protein represented by triple letter amino acid designations:
a. Propose one RNA sequence that could encode this sequence (be sure to include start
and stop codons and indicate 5’ and 3’ ends).
5' - AUG GCU UCU UAC GGU UAA - 3'
b. Propose the Template DNA strand sequence that could be transcribed into your RNA
sequence (be sure to include start and stop codons and indicate 5’ and 3’ ends).
3' - TAC CGA AGA AUG CCA ATT - 5'
25. Here is the beginning of a protein-encoding gene sequence. Assume the bottom strand is the
template strand.
5’-ATGAAGTTTGGCACTTAA-3’
3’-TACTTCAAACCGTGAATT-5’
a. Give the RNA transcript that would be transcribed from this DNA sequence.
5’-AUG UUC AAA GCC UGA UUA-3’
b. Translate the mRNA sequence into a protein sequence.
Met - Phe - Lys - Ala
c. What would be the effect on the final protein product if a mutation caused the
following single base-pair insertion:
5’-ATGAAGATTTGGCACTTAA-3’
3’-TACTTCTAAACCGTGAATT-5’
d. What would be the effect on the final protein product if a mutation caused the
following single base-pair substitution:
5’-ATGAAGTTCGGCACTTAA-3’
3’-TACTTCAAGCCGTGAATT-5’
there would be a loss of function and shortened protein
e. What would be the effect on the final protein product if a mutation caused the
following single base-pair substitution:
5’-ATGAAGTTTCGCACTTAA-3’
3’-TACTTCAAAGCGTGAATT-5’
Some e ects would be an amino acid change and a possibility of loss of function.
f. What would be the effect on the final protein product if a mutation caused the
following single base-pair substitution:
5’-ATGTAGTTTGGCACTTAA-3’
3’-TACATCAAACCGTGAATT-5’
It could mess with the function and stability.
g. Using your knowledge from class, predict which of the above mutation(s)
you would expect to be the most severe in terms of the overall effect on the
person carrying such a mutation? Justify your answer.
UUC to UAC could a ect the stability of its function, and GGC to GCA would also
a ect function and stability, but both of these would not be as severe as a frameshift
mutation, which usually makes proteins fully loose function.
26. A mutation is a change in the DNA sequence which can then propagate to the mRNA and
protein. A silent mutation is one that does not affect protein structure. Write a code for an
original DNA strand containing at least 12 bases, and then mutate the original DNA so that the
final protein is unaffected.
original DNA sequence
5’-ATGCCGTTAGC-3’
mutated DNA sequence
5’-ATGCCGTTAGT-3’
