In this activity you
will explore the relationship between the codons and the shape
of the protein. It is important to think about what this model
shows, as well as what of the translation and transcription process
it is not representing when answering the questions.
1. Open the From
Genetic Code to Protein Structure model. [http://xeon.concord.org:8080/modeler/webstart/protein/dna1.jnlp]
2. Explore the model by clicking on any of the amino acids (beads
in the chain); you will see its respective nucleotide tripled
(codon) flashing yellow in the table below the model. Notice
that every triplet (codon) is written as three neighboring letters,
while each letter is a shortcut (nickname) for a nucleotide.
3. Find the triplet (codon) for the first amino acid in the protein
fragment (as you would read from left to right) and write its
genetic code (for example, ATA).
4. One important difference between this model and the previous
models is that here you can change the amino acid sequence by
substituting one nucleotide for another, there by changing the
codons and the amino acids for which they code.
Find the codon you would like to change and try changing it.
A. Choose, within the
codon, a nucleotide you want to substitute, and point the cursor
to it. Then Press the left button of the mouse
to open a pull-down menu with the choice of nucleotides.
B. Select a new nucleotide by pointing the cursor on it, and
press the left button.
C. You will observe that sometime a substitution of a nucleotide
leads to the replacement of the amino acid. To find out the property
of the replacement amino acid, place the cursor on it and press
the right button on the computer mouse.
5. The following is a
DNA sequence. Put the correct nucleotide sequence for each codon
into the model:
CCA-CAA-AAT-AAT-GTT-AAA-ACC-CCA-CAA-GGA-TCT-ATG-TTC-GTT-AAA-ACC-CCA-TAT-GGT-GGG
6. Record the final protein (amino acid) sequence below.
P-Q-N-N-V-K-T-P-Q-G-S-M-F-V-K-T-H-Y-G-G
Proline-Glutamine-Asparagine-Asaragine-Valine-Lysine-Threonine-Proline-Glutamine-Glycine-Serine-Methionine-Phenylalanine-Valine-Lysine-Threonine-Histidine-Tryosine-Glycine-Glycine
7. Find all the amino
acids that occur more than once in the chain. Record the location
of the amino acid, the type of amino acid and the codon (nucleotide
triplet) for that amino acid. (For example, the sixth amino acid
from the left, proline, CCA)
The last two glycines are GGT and GGG. The prolines are 1st
and 8th, and the codon for both is CCA. The lysines are 6th and
15th and the codon for both is GTT.
8. Run the model.
Draw the shape of the protein below:
9. Explain how the sequence
of nucleotides can affect the shape of the protein. Describe
the forces acting on the proteins.
10. What is missing in
this model? The model only shows the DNA sequence and the protein
fragment, but it may be better to include more steps between
DNA and the formation of the protein shape. What should a revised
model include?
The intermediate model might include the formation of messenger
RNA. Additionally a second model might represent a Ribosome translating
the RNA.
Index
