How do we make the proteins we need to live?
You may recall that DNA codes for proteins, that is, the sequence of the DNA nucleotides has the directions to make every protein we must have. In high school biology, you will be given a sequence of DNA bases and a codon chart with the instructions to predict the primary structure of the protein. The primary structure is simply the order of the amino acids.
If you have the DNA sequence of ACAGTATTC, then what sequence of amino acids will form the primary structure of the protein? This tutorial will not involve secondary or tertiary structure.
Since protein synthesis involves two steps, transcription and translation, we have two steps to reach our solution.
Transcription is the creation of the messenger RNA or mRNA. This mRNA is made from free RNA nucleotides and will travel out of the nucleus to the ribosomes. Remember, RNA nucleotides have ribose for a sugar instead of deoxyribose, and their possible bases are adenine, uracil, cytosine, and guanine. By the base pairs rules, A pairs with U, T (thymine) pairs with A, G pairs with C, and C pairs with G.
Since our DNA strand is ACAGTATTC …
This has our mRNA as UGUCAUAAG .
Double-check that you do not have any thymine in the RNA. You will never have any uracil in the DNA. Always double-check that you have paired every base correctly.
Once the mRNA strand has formed, it leaves the nucleus, and the DNA strand returns to normal.
Translation is the creation of the protein from amino acids based on the mRNA. The mRNA is read three bases at a time. This is called a codon. The order matters! If a base is missing or added or if an incorrect base is included, the amino acid sequence may be incorrect.
Look at the codon chart. On the left side of the chart, you should see “first base.” Fine the letter matching the first base of the first codon ‘UGU.’ This is a ‘U.’ You should now be on the top row.
Look above the codon chart. You should see “second base.” The second base of the first codon is ‘G.’ You should now be on the fourth column. Remember, we are still in the top row.
Look to the right of the codon chart. You should see “third base.” This is a ‘U.’ Inside the first row, this is the top base. This is the amino acid abbreviated as ‘Cys.’ This is our first amino acid for the protein. Write it down.
Now we go to the second codon. Follow the same procedure. Find the first base, the second base, and the third base. Each step brings you to a more specific part of the chart, so that you have only one amino acid for each codon. The second codon is ‘CAU.’ Find the corresponding amino acid now.
This should be ‘His.’ So far, our amino acid sequence is ‘Cys-His.’
We have one more codon for this problem. Find the last codon now (AAG).
This should be ‘Lys.’ Our amino acid sequence is ‘Cys-His-Lys.’
There are two major points you need to know now.
First, the amino acid sequence you just determined is not a complete protein. You have translated a middle portion of the protein. Translation must begin with a start codon which is AUG. Translation ends with a stop codon, which can be UGA, UAA, or UAG. If you are decoding them on a codon chart, the codon chart will include ‘stop’ or ‘start’ where the amino acid is normally listed. The codon chart provided here does not include ‘start.’
Second, codon charts can be written in a variety of ways. They may be a typical square chart or may be circular. Some will provide the complete codon for you. Others will be like our example, and only list one base at a time. Read the chart carefully. You will have enough information to answer the question.
If you have further questions, feel free to contact me. Best of luck with biology! It’s an amazing subject, and there’s a lot to learn.
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