Sp'cefic Sp'cificity!

[2810712]

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 you in advance,

 

 

 

hrushikesh

[Nashyboyo]

proteins synthesis can't make a polypeptide with a mixture of both isomers of amino acids. evolution chose one and stuck with it.

 

carbohydrate moieties, found on proteins, are attached using a different method, and are not directly determined by DNA sequences. therefore the limitations in protein synthesis are not apparent in post-translational modifications (carbohydrate moiety attachment) and what not. The construction of the moiety results from a series of biochemical reactions and therefore the formation of isomers.

 

an example of the presence of alpha and beta sugars is starch and cellulose.

 

i don't really know if this answers your question, and i don't really know what your asking about

[2810712]

First of all thanks for ur reply & the info, no body helped me abt it otherplaces.

 

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?

See , this required a biochem geek, which i'm not yet...i don't get these %s from anywhere, the option was to screen data bases on http://WWW...if i do that these days, i'm sure that i'll fail in my regular class exams, if anybody knows then its too nice...& if not i'll go for it but i'll not overdo it, right sir?

 

 

hrushikesh

[2810712]

First of all thanks for ur reply & the info, no body helped me abt it otherplaces.

 

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?

See , this required a biochem geek, which i'm not yet...i don't get these %s from anywhere, the option was to screen data bases on http://WWW...if i do that these days, i'm sure that i'll fail in my regular class exams, if anybody knows then its too nice...& if not i'll go for it but i'll not overdo it, right sir?

 

Thanks again,

 

hrushikesh

[Nashyboyo]

There are different isoforms of carbohydrate/lipid. The diversity of molecules between carbohydrate molecules is much higher than diversity between protein molecules. It is thought that protein was chosen as the product of the central dogma (DNA-->RNA-->Protein) because of its appropriate properties compared to the properties inherent in carbohydrate polymers.

 

A protein only contains one isoform of amino acid per polymer. Humans are multicellular organisms derived from a zygote. Assuming you know about mitosis the cells we are composed from thus come from a single cell. Therefore every nucleated cell in our body contains the same DNA sequence and generates the same protein molecules all consisting of one isoform of amino acid.

 

You said:

"how much is it for other biomolecules...Are there diff. enzymes/ pumps for them?"

 

My answer:

???????????????????????????

 

I think i've answered something...

[2810712]

Thanks,

Now, i meant how much is the specificity [ i.e. strictly D or 70% D etc etc] for other molecules...

For given molecule , its very likely that the system accepts a single stereo as all enzymezes receptors have L-AAs only, but for another molecule of same class[ eg. carbohydrates] it may accept another stereo! So, the stereospecificity is for the given molecule definitely, but don't know if is it for all of the same class as in proteins...

help...

 

 

 

& Yes,it answers something... nice style by the way!

 

hrushikesh

[Nashyboyo]

You said:

"enzymezes receptors have L-AAs only, but for another molecule of same class[ eg. carbohydrates]"

 

What class would that be ?

[2810712]

Sorry for late reply, here i've furthered some of my brain-kinks!

 

See for a given enzyme, if it acts on n substrates & carrying out a given process in a given specific way, if all of substrates except one & the enzymes are both chemo- & stereofixed, then the remaining molecule will also

be fixed. We can just say that it is fixed, eg. if an enzyme catalyses degradation of a sugar, then for that enzyme & that process etc etc. the sugar will be stereofixed. Say its a D-carbohydrate. But for enzyme-process set of some other kind , L-carbohydrates may be being stereofixed.

In brief, i mean, for a given enzyme & process D or L is fixed, but we may not have the 'same' [ i.e. either D or L] stereofixation even if the molecule is of carbohydrate class.

 

Hope u get what i'm asking...

 

hrushikesh

[BioWizard]

I think it has to do with ramachandran allowed angles in secondary structures. The beloved right handed alpha helices cannot form with D-aminoacids, as the side chains would stick in to the inside and disrupt hydrogen bond and VdW packing. But I suppose if all amino acids were D-, you would just have left handed helices. My opinion is that it all depends on initial conditions of the evolution of the enzymes that processes these biomolecules. Once some efficiency was established with the L-isomers, it would be very difficult for other systems to outcompete them, and then everything else would build on L-forms, since they are the currency now. As to why we dont have a mixture of L and D, I would speculate that proteins structures containing such mixtures would not be as stable, for the aforementioned reason, and thus stereoselectivity for either the L or the R would reign, in this case, the L.

[2810712]

Thanks, now it's clear abt proteins...but i's reffering to stereoselectivity in case of groups other than proteins...So the q was is this stereospecificity specific for class proteins or its everywhere.

For carbohydrates as a class there may or may not be just D or just L sugars as 'natural' ones... for some reactions D wd be natural & for others the Ls...m i correct?

 

 

 

hrushikesh

[Yggdrasil]

Whenever a biological enzyme recognizes or acts upon glucose, it will almost always be selective for D-glucose and not interact with L-glucose. Similarly, an enzyme acting on fucose will almost always be selective for L-fucose and inactive toward D-fucose. So, yes, some enzymes act on D carbohydrates and some act on L carbohydrates, but in essentially all cases, enzymes are specific for one enantiomer of each species of monosaccharide.

 

Now, you may ask, why are all amino acids (except for glycine) D while some monosaccharides are D and others L? Amino acids gain their stereochemistry from essentially the same reactions (transaminations) while carbohydrates are synthesized from a variety of different reactions, generating a greater diversity of carbohydrate monomers. Why is it significant that all amino acids are D while some monosaccharides are D and others are L? It is not. The D/L nomenclature system is completely artificial, and by themselves, the D and L designations carry no biological or chemical relevance. It would be very interesting if all biological molecules were (+) or (-) since these stereochemical designations carry physical signficance (the dirrection the molecules rotate plane polarized light), but the D/L designations carry no such physical meaning.

[2810712]

Thanks its really helpful...

Now due to different given production methods u have both + & - types...but there will be a % stereospecificity resulting out of this. NOw all this specificity is induced by the stereospecificity of proteins...But in proteins stability of its structure induces almost 100% stereospecificity for AAs in them...which i think i'll call self-induced stereospecificity for proteins...isn't anysuch thing there for carbohydrates...lipids etc.?

Waiting for ur help...

 

 

hrushikesh

[Yggdrasil]

The proximate origin of stereospecificity in protein amino acids is not that protein structure causes all of the amino acids in the protein to take on the L-configuration. Amino acids are incapable of converting between the L- and D- forms in solution at physiological conditions. Only D-amino acids are present because the body produces only D-amino acids. The enzymes which catalyze the synthesis of protein amino acids in the human body do not produce a mixture of D- and L- amino acids, they produce only D-amino acids. The percent stereospecificity is 100%. It has nothing to do with protein structures inducing stereospecificity of their amino acids. A protein containing an L-amino acid would not be able to convert this amino acid into a D-amino acid. The stereospecificity is not self-induced but induced by the biosynthetic pathways.

 

Similarly, all other biological molecules have stereospecificity because the enzymes which produce these biological molecules catalyze reactions which are 100% stereospecific. The pathway for production of glucose creates 100% pure D-glucose and does not produce any L-glucose. The pathway for the production of fucose produces 100% pure L-fuccose and does not produce any D-fucose.