Any Lab Folks Out There

[flyfish4l]

Hello,

 

It is my first time post, and its nice to be on the forum.

 

I'm having trouble with a certain biochemistry problem from one of my practice tests. It pertains to a laboratory problem in which a target enzyme that needs to be expressed and crystallized is not being synthesized for some reason. A number of expression vectors have been utilized, but to no result. However, we do have the sequence of the N-terminal tryptic peptide to work from, which is as follows:

 

Asp-Val-Met-Ile-Lys-Arg

 

which corresponds to an mRNA sequence of:

 

GA(U or C)- GU(V)- UAG- AU(U,C or A)- AA(A or G)- (A or C)G(V)

 

where (V) relates to a fully degenerate portion of the codon.

 

 

 

The question then asks what is inhibiting the synthesis of this protein and how to correct for the problem.

 

 

As of now, my best guess is that somehow the initial pattern is being interpreted as an intron due to the GU of the Val codon and the possible AG in the Lys and Arg codons, which represent the most common elements in the consensus sequence of splice sites. The A residues of a number of the codons in between these sites could then serve as a branch site for the formation of an intron lariat. This process could then be inhibiting protein synthesis.

 

I haven't started my lab work yet, so I'm not big on biochemistry lab procedure or even common problems. This might just be a dumbed down version of a real world problem, so don't take the conditions too literally as I think it is only supposed to test for knowledge of the underlying principle.

 

Anyways, if someone could tell me if I'm working in the right direction or if I've got it completely wrong, it would be greatly appreciated. Thanks.