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Proteins, the Essence of Life
Proteins, the Essence of Life
Simulating the Process of Protein Synthesis
Proteins are the molecules that carry out the “business of living”. Humans can synthesize over 50,000
different proteins. How does a cell synthesize so many different proteins? The blueprint for the
synthesis of these proteins is found in molecules of DNA. DNA contains the genetic information
needed for protein synthesis. DNA is restricted to the nucleus in eukaryotic cells yet the actual synthesis
of proteins occurs on ribosomes found in the cytoplasm of cell. This implies that there must be some
sort of intermediate molecule that is responsible for moving the information from the nucleus out to the
cytoplasm. That intermediate is RNA.
There are two parts to protein synthesis, transcription and translation. Transcription is the process of
converting the information encoded in the DNA molecule into a messenger RNA molecule. This occurs
in the nucleus. Translation is the actual synthesis of a protein or polypeptide chain. This occurs in the
cytoplasm and requires several components. The ribosome serves as the workbench for this process by
bringing together the mRNA instructions with the tRNA carrier of the amino acid.
PURPOSE
In this activity you will simulate the process of transcription and translation. These processes will lead
to the formation of a protein from a DNA gene.
MATERIALS
copy of a portion of a double helix DNA molecule
scissors
kits to simulate protein synthesis
copy of mRNA codons
clear tape
PROCEDURE
Transcription
1. The following should be cut prior to class: DNA strand and mRNA codons. Tape the two strands of
the DNA molecule together to form one long DNA strand. Obtain a kit that contains the models
needed for this simulation. Answer questions 1-3 on the student answer sheet.
2. To begin transcription, enzymes break the weak hydrogen bonds between the base pairs of the two
DNA strands. To simulate this use scissors to cut the double stranded DNA into two single strands.
This demonstrates how the DNA molecule unwinds. Answer questions 4-6 on the student answer
page.
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3. Notice that many of the DNA nucleotides are in groups of three nucleotides. This grouping
represents a codon. A DNA codon is a group of three nucleotides that will determine which amino
acid will be placed in the polypeptide chain. Answer question 7 on the student answer page.
4. Transcription occurs when mRNA nucleotides base pair with DNA nucleotides. The enzyme, RNA
polymerase, is responsible for base pairing the correct RNA nucleotides to the correct DNA
nucleotides. Only one side of the DNA molecule is transcribed. Transcribe the top side of the DNA
molecule by base pairing the appropriate mRNA base pairs using RNA polymerase. Tape the RNA
nucleotides together to make one long mRNA strand. Answer questions 8 and 9.
5. Remove the mRNA from the DNA gene and “zip” the DNA gene back together with tape. At this
point the mRNA is an immature mRNA molecule and must be processed. In eukaryotic genes, there
are nucleotides that are not used or expressed. One might view these DNA nucleotides as “junk
DNA”. They are called introns because they are intervening sequences. RNA polymerase can not
tell the difference between these intron (intervening) and exon (expressed) regions. Therefore these
introns are also found on the mRNA. Look at the mRNA. Notice a sequence that is not grouped in
three nucleotides. This represents an intron. In reality, a eukaryotic gene has many introns and
introns are much longer than four nucleotides. The intron must be removed, and a structure called a
spliceosome is responsible for removing the intron. Place the mRNA on the paper spliceosome.
Using scissors, remove the intron. The mRNA nucleotides that remain are called exons because they
will be expressed. The spliceosome will splice the remaining exons together. Tape the exons
together using tape. Answer questions 10-12.
6. The next thing that occurs is the addition of a 5’ cap, which is composed of a number of RNA
nucleotides. The purpose of the 5’ cap is to protect the RNA molecule from being degraded in the
cytoplasm and also aids in recognition between the ribosome and mRNA. Cut out the 5’ cap and
add it to the mRNA. Answer question 13.
7. At the 3’ end, a series of adenine nucleotides, called a poly-A-tail, are added. The function of the
poly-A-tail seems to also aid in protecting the mRNA from being degraded and plays a role in
determining how many times the mRNA can be translated. The tail can average between 100 and
200 adenines long. Answer question 14.
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8. After splicing and adding the 5’ cap and 3’ tail, this mature piece of mRNA is ready for the actual
synthesis of a protein. The process of synthesizing a protein is called translation. The sequence of
the mRNA nucleotides determines the order of the amino acids in the protein. Notice that the RNA
nucleotides are in groups of three nucleotides. This grouping represents a codon. The RNA codon
is a group of three nucleotides that will determine what amino acid will be placed in the polypeptide
chain. Remember the RNA codon has it sequence determined by the original DNA codon. Below is
the genetic code based RNA codons. For example if an mRNA codon is UUU, this is the code for
the amino acid, phenylalanine. Answer questions 15 and 16.
9. Determine sequence of amino acids encoded in your mRNA and record them on your student answer
page under question 17.
Translation
1. Translation is the actual synthesis of a polypeptide chain. Move your mRNA from the hypothetical
nucleus to the hypothetical cytoplasm on your desk. There are three necessary components for
translation to take place. They are:
a. MRNA — This will determine the sequence of the amino acids
b. tRNA charged with an appropriate amino acid — This molecule brings the appropriate amino
acid to the correct codon on the mRNA
c. Ribosome — This is a workbench where the actual synthesis of the polypeptide will occur.
Answer question 19.
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2. Another important RNA molecule used in the process of translation is transfer RNA or tRNA. For
each mRNA codon in this model, there is a specific tRNA. tRNA is a single stranded molecule that
folds and base pairs with itself to form a clover-leaf shaped structure. At the bottom of the tRNA is
series of 3 nucleotides. These nucleotides are complementary to the mRNA codon (A-U and G-C)
and are called the anti-codons. For example if an mRNA codon is UUU, then the tRNA anticodon
found on the bottom of the tRNA is AAA. Look at the tRNA models in the kit and notice the
anticodon found at the bottom. For each mRNA codon you listed in question 17, list the anticodon
in question 18.
3. The function of the tRNA is to bring the appropriate amino acid to the appropriate mRNA codon.
This is works because there is a charging enzyme responsible for bonding the correct tRNA with the
correct amino acid. This bonding requires ATP. Find the charging enzyme. Notice that the active
site fits a tRNA and an amino acid.
4. Find an amino acid. The Styrofoam ball represents the central carbon. Notice that hydrogen is
attached as are an amine group, and a carboxyl group. Also notice there is a jumbo craft stick
representing the variable R group. On the jumbo stick is a drawing of the variable R group. Each
amino acid has a different colored stick and a different variable R group. Answer question 20.
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5. Now, using the charging enzyme, combine each tRNA with its correct amino acid. This is done by
using a paper clip to attach the amino acid (on the jumbo stick) to the tRNA (at the top end of the
pipe cleaner). The correct amino acid is bonded to the correct tRNA by a sequence of nucleotides on
the anticodon and the codon of mRNA. The charging enzyme will release the charged tRNA once
the amino acid is bonded to it. Look at the answers for questions 17 and 18 to make sure that the
correct amino acid is bonded to the correct tRNA. At this point every tRNA should have an amino
acid attached to it.
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6. Find the ribosome. Notice that it is composed of two subunits, one that is large and one that is small.
There are three places for the tRNA’s and one place for the mRNA. Now simulate the process of
making the polypeptide chain, using your mRNA and your tRNA that have been “charged” with
amino acids. Put the start codon (AUG) on the mRNA under the P site. Now find the tRNA with
the complementary anticodon and place it on the P site. Once this is done, notice that a second
mRNA codon is positioned under the A site. Find the tRNA with the complementary anticodon and
place it on the A site. This should bring two amino acids (found at the top of the tRNA) next to one
another.
7. Join the two together amino acids together by joining the carboxyl group on the first amino acid to
the amine group on the second amino acid. Fasten the two together with a paper clip at their amine
and carboxyl sites. The paperclip simulates the covalent bond that will form between these two
functional groups. It is called a peptide bond. Notice which atoms are no longer visible. This
means that a water molecule has been removed from the chemical reaction.
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8. Remove the tRNA on the P site over to the E site leaving the amino acid behind. This tRNA then
will leave the ribosome altogether. Move the mRNA down one codon and begin the process again.
The tRNA at the A site moves over to the P site. The A site is now open to receive the next tRNA
that is complementary to the mRNA below. This is called translocation. Continue this process until
the stop codon is reached.
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9. When the stop codon is reached, a release factor binds with the mRNA stop codon. This causes the
ribosome to disengage, releasing the polypeptide chain and the mRNA. This process is called
termination. At this point you should have synthesized a model of a polypeptide chain.
10. Answer the remaining questions on your student answer page.
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Name______________________________________
Period _____________________________________
Proteins, the Essence of Life
Simulating the Process of Protein Synthesis
SIMULATION QUESTIONS
1. Where is DNA located in the cell? Describe the structure of the DNA molecule.
2. DNA is a long polymer made of many subunits. What are those subunits called and what parts do
they have?
3. Write out both the top and bottom portion of the DNA molecule in the space below.
4. Define the term gene and explain exactly what a gene does.
5. How many genes are found on a chromosome?
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6. What biological molecule do the scissors represent?
7. What is a DNA codon?
8. What enzyme is responsible for base pairing the RNA nucleotides to the DNA gene?
9. Fill in the chart below for the base pairing of DNA to RNA nucleotides
DNA
RNA
Adenine
___________
__________
Guanine
Thymine
____________
__________
Cytosine
10. What are introns and exons?
11. What molecule is responsible for removing introns and rejoining exons?
12. Write out the RNA codons that remain after the intron has been removed.
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13. What are two purposes of a 5’ cap?
14. What are two purposes of poly-A-tail?
15. How is mature mRNA different from immature mRNA? How does mRNA determine the sequence
of a polypeptide chain?
16. What is an mRNA codon?
17. Determine the amino acid sequence using the mRNA codon chart below.
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18. List the complementary anticodons that will be found on the tRNA for the mRNA in question 17.
19. What is translation and where does it occur? What four items are needed for translation to occur?
20. What is the structure of an amino acid?
21. What type of bond is made when amino acids are joined?
22. How many water molecules were removed from the polypeptide chain?
23. Write in the space provided the amino acids were used to make this protein and what molecule was
removed.
24. Describe the process of termination.
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