2. You are studying zebrafish and comparing the proteins found in zebrafish reti

Question

2. You are studying zebrafish and comparing the proteins found in zebrafish retina versus zebrafish heart (libraries were obtained by mass spectrometry). You find one protein called CRYPTIC that is 200 amino acids in the retina library but 300 amino acids in the heart, * A. Briefly explain an experiment that you could do (include the steps) to determine if these two variants of CRYPTIC are from the same mRNAs B. Unfortunately, the results from your proposed experiment above are ambiguous and you are unsure if it is a difference in the DNA, mRNA, or other factors that leads to the different CRYPTIC variants. There are a few possible explanations for what is going on. For each provided explanation: (i) briefly explain how it could make sense & (ii) if you would expect the mRNA in the retina and heart to be the same or different for the CRYPTIC variants (think size & identity). The first answer is provided for you as an example

Explanation / Answer

The CRYPTIC gene in heart and retina have a difference of 100 amino acids. This can be from the same mRNA or from different. To find out, we can isolate mRNA and carry out microarray experiment. The probe can be synthesized which will bind to CRYPTIC mRNA of one of the organ. If the probe binds to mRNA of both the organ then it might be possible that they are from the same mRNA.
However, it is not clear, whether they have minor differences, or they come from different DNA sequence with some modifications.

B. RNA editing enzyme:
i. The enzyme can alter the U to C change point mutations. This can add a stop codon or remove a stop codon.
ii. This will change the mRNA in a cell where the editing is active. The mRNA length would be same but protein will be of different length.

Post-translational processing:
i. The protein can be edited after it is translated and the signal sequences and other leader sequences can be removed. This can change the length of the protein.
ii. The mRNA will be of the same length, but the protein in retina will be trimmed to give smaller protein

Mutation in the DNA that results in a longer protein
i. This can change the DNA which might add new bases to the protein. The DNA in the heart can contain this mutation which results in longer protein in the heart
ii. The mRNA in heart and retina will have different lengths and so is the protein.

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