Protein Synthesis

DNA carries the information for the synthesis of all the proteins of an organism.
Proteins are large and complex molecules, composed of hundreds of amino acids. There
are twenty different amino acids. The sequence of the nucleotides in the DNA molecule
determines the sequence of amino acids in a protein molecule. The information
encoded in the nucleotide sequence of DNA is not used directly in protein synthesis.
Instead, the information carried in the DNA molecule is encoded, or transcribed, into a
special type of RNA, messenger RNA (mRNA). This process is called transcription. In
transcription, the nucleotide thymine is replaced by uracil, so the pairing of nucleotides
becomes A-U, while C-G remains the same. Once transcription has finished, the mRNA
passes out of the nucleus and travels to a ribosome. Here the mRNA is read, and the
correct amino acids are brought into specified places by another type of RNA, transfer
RNA (tRNA). The amino acids are then linked together by peptide bonds to form the
protein originally specified by DNA.

OBJECTIVES In this activity you will:

1. Explore GenBank and the human genome.

2. Learn how the transcription of DNA occurs during protein synthesis.
3. Become familiar with the code by which the information in mRNA is translated.
4. Use paper models to see how transcription and translation of mRNA occurs
during protein synthesis.

Part 1: Exploring the Human Genome

PROCEDURE:

1. Go to https://www.ncbi.nlm.nih.gov/genome
2. In the middle of the page you will see a link for the Human Genome, click on
the link.
3. This will take you to a page that will allow you to explore the human genome.
It is part of PubMed’s GenBank, a data base that is a bank of verified submitted
and published gene sequences.
4. You will see a diagram containing the 22 autonomic chromosomes, both the X
and Y sex chromosomes and mitochondrial DNA found in humans.
5. Explore the human genome by clicking on several chromosomes. Use the back
button to return the human genomes resources page.
a. What kinds of genes do you see? What types of molecule do the genes
code for?

b. Do all the chromosomes have genes with the same function? The same
number of genes?
 6. Once you have finished exploring the human genome return to the human
genome resources page.
7. In the “Search for Human Genes” search bar, enter in the gene’s name, for this
lab we will use the TAS2R16 gene. Press “Search.”
8. Click on the TAS2R16 gene from humans.
9. The page displayed provides researchers with a summary of the gene’s key
features. Information on the gene’s function, an outline of the gene sequences,
including mRNA and protein sequences, the species of origin, links related
publications can all be found in a full report. Based on the information found in
the summary,
a. What does this gene code for?

10. To see the gene sequence, scroll down the page to the portion called NCBI
Reference Sequences. Under Genomic click on the link for GenBank.
11. Once you are redirected to GenBank scroll down to the bottom of the page.
12. Find the nucleotide sequence for the gene. In the space provided copy down
the last 18 nucleotides in the sequence before the tata box (tataat). Copy the
sequence in order and list below. You will use this sequence for Part 2 of the
lab.
__ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __

Part 2: Protein Synthesis Simulation

PROCEEDURE:
1.) Transcription: DNA to RNA
a. Obtain one package of yellow post-it-notes. Make a strand of DNA by
sticking 19 notes together in a row. Insert an image of your DNA
sequence below.
 b. On the first note mark 3’. Assign each of the remaining notes a letter
from the sequence you obtained in Part 1.
c. As illustrated below:

d. Determine the complementary messenger RNA sequence.

i. Is RNA the same structure as DNA? If not how do the two nucleic
acids differ?

e. Write the mRNA sequence in the space below.

mRNA: __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __

f. Using pink post it notes® transcribe the coding strand to mRNA as

illustrated below.

i. What is the enzyme that performs this task in transcription?

.
g. Save the pink mRNA strand for the next exercise and dispose of your
DNA. Insert an image of your mRNA sequence below.
1. Translation: RNA to Protein
h. Place a sheet of 8.5x11 paper in landscape orientation. Using a pen,
divide the paper in thirds up and down. This is your ribosome.
i. On the left one third of the page mark the letter E this is the Exit site. The
middle third mark with the letter P. This is the peptidyl site. On the right
third of the page, mark the letter A. This is the aminoacyl site. See image
below.

E P A

j. Using the Genetic Code Table provided, determine the amino acid
sequence of your strand of mRNA.
i. How many nucleotide bases make up a codon?

k. Using the codons found in the mRNA on step e and the genetic code
below, write the amino acid sequence in the space provided using the
abbreviation for each amino acid.

______ ______ ______ ______ ______ ______

GENETIC CODE
 l. Using the mRNA sequence from step e, determine the 3-letter anticodon
(carried by the tRNA) for each codon and write it in the space provided.

Anticodon: [ __ __ __ ] [ __ __ __ ] [ __ __ __ ] [ __ __ __ ] [ __ __ __ ] [ __ __ __ ]

m. Write the abbreviation for each amino acid on a separate blue Post-it-
notes® and each anticodon for the mRNA codons on pink Post-it-notes®
n. Obtain six petri dishes. These will be your tRNAs. Each petri dish will have
an anticodon and carry an amino acid.

Amino
Acid

Anticodon

a. Place a blue Post-it-note® with the amino acid on top (north) end of each
Petri plate. Place a pink Post-it-note with the anticodon on the bottom
(south) end of each plate.
b. Now simulate elongation of translation!
i. Move the 1st mRNA codon into position on the P site of the
ribosome. Then bring the corresponding tRNA into position on
the ribosome on the P site.
ii. Move the second tRNA into the A site.
1. Which step of elongation are you simulating?

iii. Remove the amino acid (post-it-note) from the tRNA on the P site
and stick it onto the amino acid (post-it-note) on the A site.
1. Which step of elongation are you simulating?

iv. Now slide the A to the left so that the first codon and tRNA are in
the exit site, the second codon and tRNA is in the P site, and the
third codon is on the A site.
1. Which step of elongation are you simulating?

v. Move the appropriate tRNA into the A site. Remove the peptide
chain (post-its) from the P site tRNA and stick them to the A site
amino acid.
 vi. Repeat until you reach the end of your sequence. Insert a picture
of your amino acid sequence below.

REVIEW QUESTIONS:
1. What are the three phases of transcription? Give a one sentence description of each.

2. Briefly describe RNA processing. When, where and in what cell types does it occur?
Why is it necessary?

3. What are the three phases of translation? Give a one sentence description of each

4. What is a codon? What is an anti-codon?

5. How does an mRNA molecule specify where the polypeptides it encodes should
begin? How does it specify where the polypeptide should end?
6. What subcellular structure is involved in translation? Of what two types of
molecules is it composed?

7. Why can scientist create genetically modified organisms? In other words, why can
scientist insert a fire fly gene into a tobacco plant? What properties of the genetic
code and the central dogma of protein synthesis allow for this?