[Catalist] Chemistry: Proteins

[Leon Harris]

Hi Andrew.
Yes, that is true, (a) is true. "most likely" makes it the best answer, 
but it is kind of sneaky. Primary structure determines all structures 
above it, protein function is related to its structure. (I will avoid 
issues of folding, chaperones, metastable states etc because they are 
beyond the scope of this course).
And you can also get to the right answer from within the syllabus by 
elimination: b&d are absolute statements and thus require caution, c 
requires knowledge that there are many different proteins within a 
species, and being different, they will have different sequences.

By the way, b is close enough to be true too: many proteins with 
different primary sequences have identical secondary and tertiary 
structure, especially if they are evolutionarily conserved due to a 
critically important function. The classic example of this would be the 
variants of cytochrome c found in horse, rat, mouse, human and fish. The 
only reason for choosing a) over b) is to avoid the absolute in b): you 
may end up fighting over what is "identical" at the secondary and 
tertiary level.  (At the level of structure we teach in Y12, they are 
indistinguishably identical) a and b are both correct, but I would 
counsel my students to avoid b because it is a "well known trap" of the 
type "absolute statement", and there is too much "wiggle room" in the 
phrase "high degree of".

More on this at http://chemistry.umeche.maine.edu/CHY431/Evolve2.html


The statement you query:
"Proteins that show a high degree of similarity in their primary 
structure are most likely to have a similar function".

is correct in that it heehaws enough to let you back away from it in the 
cases of the well known exceptions.

For example, the crystallins in your eye are very similar in primary 
structure to the alcohol dehydrogenase enzyme, but are completely 
unrelated in function. In general terms, your statement is true, but 
there are so many exceptions that it doesn't have a huge amount of 
predictive power. However the "most likely" gets you out of it.


All of this just emphasises how important the primary / secondary / 
tertiary/ quaternary structure viewpoints are to understanding proteins, 
and how sequence alone is not enough.

Cheers,
Leon

On 23/08/2016 2:06 PM, Andrew Bland wrote:
> <https://www.facebook.com/secularicondesign/>
>
> Dear Chemists/ Biochemists,
>
>
> Please cast your eyes over the question taken from MC section of the 
> 2016 Chemistry WACE Sample Exam provided on SCSA website.
>
>
> 24. Proteins that show a high degree of similarity in their primary 
> structure in the Protein Data Bank are most likely to have:
>
> (a) similar function.
> (b) identical tertiary structure.
>
> (c) been isolated from the same species.
> (d) the same amino acid composition.
>
> The answer listed is (a) similar function.
>
> The only reference that I can find that supports this answer comes 
> from Lucarelli describing that lysozyme has similar functions in 
> humans and chickens, but the human version has a "slightly different 
> structure" (screen shot attached).
>
> Other readings that I have come across suggest that changing the 
> primary structure will change a protein's function, as different 
> sequences of amino acids will result in different bonding between side 
> chains, therefore resulting in a different tertiary structure.
>
> //If you have some knowledge on this please clarify if it suitable to 
> say that "Proteins that show a high degree of similarity in their 
> primary structure are most likely to have a similar function".
>
> Regards,
> Andrew.

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