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Topic: Sp'cefic Sp'cificity!  (Read 9026 times)

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Offline 2810713

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Sp'cefic Sp'cificity!
« on: April 21, 2006, 02:26:38 AM »
For proteins, living systems are specific for L-AAs but for carbohydrates that degree of specificity is not observed...how do we explain it in the context of evolution..?

Also please tell me what is the degree of specificity for D-sugars & L-AAs...i mean when the specificity can be violated naturally, i'm interested in knowing that...
I got that D-Alanine is a bacterial marker [ i guess due to its role in murein formation of bacterial cell wall] but i don't know if any 'polypeps' contain D-AAs , & if yes ...upto what extent & all...

Similar querries for L glucose...& alph & beta sugars...

Please help me... i'm searching the web...suggest any good links too...


Thanking in advance,



hrushikesh

Offline limpet chicken

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Re: Sp'cefic Sp'cificity!
« Reply #1 on: April 21, 2006, 03:25:24 AM »
A species of frog, Phyllomedusa Bicolor, also known as dow-kietl, produces a highly potent mu agonist opioid  peptide called dermorphin, which includes a D-alanine residue, and apparently its also found in the urine of some autistic people, probably due to microbial breakdown of dietary products of some sort.

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Offline Equi

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Re: Sp'cefic Sp'cificity!
« Reply #2 on: April 21, 2006, 08:12:34 AM »
A species of frog, Phyllomedusa Bicolor, also known as dow-kietl, produces a highly potent mu agonist opioid  peptide called dermorphin, which includes a D-alanine residue, and apparently its also found in the urine of some autistic people, probably due to microbial breakdown of dietary products of some sort.
We take up quite a lot of D-AAs as our commensal intestinal flora produces them. Most are deaminated to carbon skeletons by specific D-AA-deaminases and - if possible - re-aminated the "right" way again (otherwise they probably end up in gluconeogenesis).

For proteins, living systems are specific for L-AAs but for carbohydrates that degree of specificity is not observed...how do we explain it in the context of evolution..?
By chance. That's it. This is like explaining why our brain tells us light with a wavelength of ~400nm is blue and not green... :)
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Offline 2810713

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Random Specifity!!!
« Reply #3 on: April 23, 2006, 04:14:40 AM »
Thanks for that rare & specialized peice of info limpet chicken...

thanking  Equi 2.& one point , when one of the property/molecule is basically selected & FIXED randomly [ for L or D form, i mean] THen i think the choice for remaining properties/molecules need not remain unbiased , as it may be affected by the previous unbiased choice. Which one was first selected is imp. I heard that water molecules for some kind of paramagnetic isomers were 1st selected , that also not randomly...so that was also not the ultimate unbiased selection, if all are interdependant[ i think most are...atleast today]
  If the FIXED ness of the previously chosen property/ies will intern tell us the randomness of the selection of successive property/ies...right? If they are less fixed then the choice would be more random...

Convey your opinions...please,

hrushikesh


Offline Equi

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Re: Sp'cefic Sp'cificity!
« Reply #4 on: April 23, 2006, 04:48:43 AM »
From what I understood, you mean that random choices at the beginning have impact on any further evolution?
Well, from my point of view I agree. However, many things still have/had huge degrees of freedom and even after the first RNA "life-forms" developed, it was not sure that proteins were going to be constructed from amino acids (and definitely not those common 20 ones nowadays).
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Offline Yggdrasil

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Re: Sp'cefic Sp'cificity!
« Reply #5 on: April 23, 2006, 07:20:28 PM »
This thread might be somewhat helpful:

http://www.chemicalforums.com/index.php?topic=6319.0

Offline 2810713

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Re: Sp'cefic Sp'cificity!
« Reply #6 on: April 24, 2006, 12:49:44 AM »
Equi, so all chara need not get affected by the pre-fixment of some other character, & if its getting affected, it may also not get fixed but a range is defined, right? That was a thoughtful, thanks alot.

Yggdrasil, that topic was a great revision,
but what i want to ask in this 'new' topic is-

We observe conformational specificity for Amino Acids, My question was is such kind of stereo specificity observed for carbohydrate/ lipid/ DNA/RNA subunits i.e. is that specificity is specific for proteins or is it present in other molecules of life too? & if yes was it by chance & if yes how do we disprove the presence of any selective pressure in earlier environments..?

Also , what is the degree of specificity? I mean , what is the percentage of D-AA proteins & L-AA proteins, & how much is it for other biomolecules...Are there diff. enzymes/ pumps for them?

Intersting, quick, useful , all this for my sweet chemical forum... :)

Offline Yggdrasil

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Re: Sp'cefic Sp'cificity!
« Reply #7 on: April 24, 2006, 04:30:44 AM »
We observe conformational specificity for Amino Acids,

This is just a matter of semantics, but conformation refers to molecules with different dihedral angles (i.e. different rotations about bonds).  The word you're looking for is stereospecificity, since D- and L- amino acids are stereoisomers, not conformers.

Quote
My question was is such kind of stereo specificity observed for carbohydrate/ lipid/ DNA/RNA subunits i.e. is that specificity is specific for proteins or is it present in other molecules of life too? & if yes was it by chance & if yes how do we disprove the presence of any selective pressure in earlier environments..?

Yes.  If an organism produces a chiral molecule, almost always you will find only one enantiomer and not the other.  From a narrow perspective, this is because all biological enzymes are chiral molecules which contain three dimensional binding pockets which can accept only one enantiomer.  Even if one wanted to, it would be very difficult to have an enzyme accept both enantiomers and catalyze the reaction of each enantiomer with equal efficiency.  As for the selective pressures that produced such stereospecificity in early evolution, that is still an open question in biology.

Quote
Also , what is the degree of specificity? I mean , what is the percentage of D-AA proteins & L-AA proteins, & how much is it for other biomolecules...Are there diff. enzymes/ pumps for them?

To the best of my knowledge there are no natural D-amino acid proteins (although D-alanine is found in bacterial peptidoglycans).  The same goes with most other biological molecules.  For example, all sugars are always found in their D-form (except for fucose which is always found in its L-form).  In general, if one enantiomer of the compound is present, it is very unlikely that the other enantiomer will be present unless it racemizes by itself.
« Last Edit: April 24, 2006, 04:34:26 AM by Yggdrasil »

Offline AWK

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Re: Sp'cefic Sp'cificity!
« Reply #8 on: April 24, 2006, 04:54:35 AM »
Quote
In general, if one enantiomer of the compound is present, it is very unlikely that the other enantiomer will be present unless it racemizes by itself.
Something different is for lactic acid.
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Offline 2810713

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conclude?
« Reply #9 on: April 26, 2006, 09:00:02 AM »
thanks for correcting me,
So can we predict which [one or more] was/were stereofixed , so that others also got 'somewhat' stereofixed... Because we don't know if proteins came first or carbohydrates...

& about enzymatic & receptor/pump transport there will be high specificity for the molecule  getting transported or reacted, even if it is a carbohydrate/lipid or any other molecule.

So, the stereospecificity is not specific for proteins...right?


hrushikesh

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