[Catalist] Chemistry: Proteins

Wed Aug 24 10:31:10 AEST 2016

>From the syllabus..

"The Protein Data Bank (PDB) houses an international repository of
structural data of proteins. The information is accessed and contributed to
by scientists worldwide. The function of a protein is closely linked to its
structure."

and..

"the tertiary structure of a protein (the overall three-dimensional shape)
is a result of folding due to interactions between the side chains of the
α-amino acid in the polypeptide, including disulfide bridges, hydrogen
bonding, dipole-dipole interactions, dispersion forces and ionic
interactions" 

and..

"enzymes are protein molecules which are biological catalysts and can be
used on an industrial scale to produce chemicals that would otherwise
require high pressure or temperature conditions to achieve an economically
viable rate, including fermentation to produce ethanol versus hydrolysis of
ethene"

On the back of these statements, the only ones I can find that may pertain
to this, such a sneaky and nuanced question requiring the knowledge that
Leon has brought to bear upon it, is a possible ATAR exam question? 

How long is a piece of string?

Craig.

From: Catalist [mailto:catalist-bounces at lists.stawa.net] On Behalf Of Leon
Harris
Sent: Tuesday, August 23, 2016 5:55 PM
To: catalist at lists.stawa.net
Subject: Re: [Catalist] Chemistry: Proteins

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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