DNA Transcription – A Simulation using Corticon

This Corticon rule model shows a simple simulation of the process of DNS transcription

The basic process:

  1. First the mRNA attaches itself to a ribosome.
  2. Six bases of the mRNA are exposed.
  3. A complementary tRNA molecule with its attached amino acid (EG methionine) base pairs via its anticodon UAC with the AUG on the mRNA in the first position P.
  4. Another tRNA base pairs with the other three mRNA bases in the ribosome at position A.
  5. The enzyme peptidyl transferase forms a peptide bond between the two amino acids.
  6. The first tRNA (without its amino acid) leaves the ribosome.

 

The ribosome moves along the mRNA to the next codon (three bases).

The second tRNA molecule moves into position P.

Another tRNA molecule pairs with the mRNA in position A bringing its amino acid.

A growing polypeptide is formed in this way until a stop codon is reached.

  

The Vocabulary

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Create Nucleotides

Create tRNA

All possible 3 letter combinations of the base nucleotides will be created (64 in all)

Attach Amino Acids

Attach Ribosome to mRNA Strand

 

Operate Ribosome

This is where all the work actually gets done.

If the codon at the current position of the ribosome is other than a STOP then the amino acid attached to the corresponding tRNA will be attached to the growing protein).

This process continues with the ribosome moving up the mRNA strand (in units of three) until a STOP codon is encountered

Once a STOP codon is reached then the protein that has been assembled is detached (in this example we associate it with its parent mRNA strand using the new operator) and the protein and proteinLabels are reset.

Test Case

In the first strand two proteins are created (since there is a STOP codon UGA near the beginning)

The second strand creates just one protein.

Next Steps

After the proteins are created they will fold. Modeling the rules for protein folding is left as an exercise for the reader. It’s quite a hard problem.

 

 

 

Sickle Cell Anemia:

An incorrect amino acid sequence in a protein may lead to fatal consequences. For example, the inherited disease, sickle cell anemia, results from a single incorrect amino acid at the 6th position of the beta - protein chain out of 146. Hemoglobin consists of four protein chains - two beta and two alpha.

See the graphic on the right for the sequences. This one alteration of the sequence of amino acids in hemoglobin changes its molecular geometry and hence its ability to carry oxygen and its solubility characteristics. The red blood cells change into a sickled shape instead of the normal round shape, become trapped in the small blood capillaries, and cause a great deal of pain.

Test Case for Sickle Cell Anemia

 

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