Please help me with this question

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Biolink
Biolink's picture
Please help me with this question

Your friend has isolated a protein presnt in the cheek cells of all straight - A seniors at your university. She says that this protein helps you remember everything you read and therefore will help cut down on the number of hours needed to study for exams and calls the protein "geniuszyme". She sequences the protein and designs a probe to isolate the gene that encodes geniuszyme. to make sure she designed th eprobe correctly, she consults with the company that cloned factor Viii. They have 100% confidence that her probe will work. She also obtains a high quality liver cDNA library from the company and uses probe to try to isolate the gene for geniuszyme. Unfortunatelt, she is unable to isolate any clones.
A. What is the likely explanation for her failure?
B. Not to be discourgaed, your friends has obtained some genomic DNA isolated from the nuclei of liver cells and has made a genomic library from that DNA. Do you expect she will suceed in isolating the geniuszyme gene from this library? Why or why not?

PhilM
PhilM's picture
for part A - The mRNA for

for part A - The mRNA for geniuszyme is not transcribed highly enough or at all  in hepatocytes and so a cDNA library from liver would not contain the clone.

Biolink
Biolink's picture
Thanks a lot for your reply,

Thanks a lot for your reply, i was thinking that DNA similarity would be too low to allow hybdridization what do you say Mr Phil
 

Jason King
Jason King's picture
The expected answer: If the

The expected answer: If the protein was discovered in the mouth then why use a liver cDNA or genomic library? cDNA is derived from expressed mRNA transcripts. If they are not expressed in the liver tissue then a cDNA probe will not come up positive. The probe could come up positive on a genomic library but it would depend on how long the probe was.
Also, why assume that the protein was produced by the students at all. Perhaps it was present in something they all consumed. If the protein is small enough and has the right chemistry it could translocate into the cheek cells or associate with them.
 
Consider: Smart kids tend to eat smart (more fish, no burgers etc). Presence of fish proteins in the mouth might correlate with memory recall but doesn't necessarily cause the improved performance.
 
And, the wording of the question does not state that the protein was never found in non-straight-A students. I would expect GAPDH to be found in the cheek cells of all straight-A students too.
 
 

Ivan Delgado
Ivan Delgado's picture
 

 
This question sounds a lot like a question from an exam in an introductory molecular biology course. The concept being taught here is the connection between protein expression and mRNA expression. If you have a lot of a protein in a tissue then you expect a lot of its associated mRNA template present in that same tissue (just like PhilM and parvoman explained). The reverse is true: not enough mRNA in liver cDNA means you will not detect your gene. That is your answer to question A. For question B you can say that it will work because a genomic DNA library has all the genes in relatively equal number so the probe should pick your gene up.
As a side: it is interesting that a company that gives a 100% guarantee that a probe would work, and then sells you a liver cDNA library for this purpose, does not give any disclaimers as far as when and how this probe will work. I mean, you told them you isolated your gene from saliva...
Now I am going to go beyond what this question really requires (a little scientific humor):
1. If you isolated the protein from saliva, then trying to isolate the gene from liver sounds kind of strange (just like parvoman pointed out).
2. If I were to find a protein in saliva I would be hard pressed to make an argument that this protein is somehow associated with smarter students (or memory for that matter). Its like isolation an abundant protein from your stomach lining and saying that it is implicated with better vision. You could come up with a theory, but my guess is that it would be somewhat of a stretch.
3. Saliva is full of enzymes whose whole purpose is to degrade/digest everything that enters our mouth, including proteins. If this enzyme was isolated from saliva it must be not only very abundant but also highly stable. Few proteins found in saliva, if any, would fits that description unless their job was digesting other things. Of course it is possible that somehow amylase mutated and now is implicated in providing better memory. Somehow I find that hard to believe ;).

Biolink
Biolink's picture
Thank you Ivan for your

Thank you Ivan for your explanation, im gettign more information more than what a book or a website would teach me. As its simple i can understand and could correlate with what i have learnt. I would make it as point that i will learn this way apart from being a book worm. You opened new avenue by with your humour thoughts. Thank you once again for your reply.