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Topic: presence of only L-amino acids in natural proteins  (Read 12417 times)

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Offline 2810713

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presence of only L-amino acids in natural proteins
« on: December 31, 2005, 05:24:56 AM »
Why r only L-AA present in the natural proteins?
Why not a mixed composition i.e. both Ls and Ds.
or just Ds???
I have tried making something with the molecular mekano, i feel that mixed one is quite unstable or envolving non-uniform stability... But why not just D???
 or its just by chance that  only Ls are selected and not only Ds???

help me out, please.


hrushikesh

Offline Albert

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Re:presence of only L-amino acids in natural proteins
« Reply #1 on: December 31, 2005, 06:37:53 AM »
Maybe it's because of a supreme design :angel1:

There isn't any known reason for it...for the moment.
« Last Edit: December 31, 2005, 06:39:21 AM by Albert »

Offline Yggdrasil

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Re:presence of only L-amino acids in natural proteins
« Reply #2 on: December 31, 2005, 06:23:14 PM »
Basically, the reason is that the biosynthetic enzymes which produce amino acids evolved to produce only the L form.  It is an advantage to organisms to produce only one stereoisomer since utilizing both forms of the amino acid would require two enzymes, one recognizing the L-form and one recognizing the D-form, for each biochemical process involving the amino acid.  Plus, by producing enzymes which are composed of only L-amino acids, these enzymes are able to catalyze reactions with very high stereoselectivity and stereospecificity, which is an essential feature of many biological reactions.

However, as to why all L as opposed to all D, biologists are still debating.  Some claim that asymmetric crystals in clay may have lead to an overabundace of L-amino acids in the "primordial soup".  Others believe that polarized light may have had an effect on the relative ratios of D- and L- amino acids.  There is also the possibility life forms based on D- and L- amino acids evolving separately, then the L-amino acid-based life forms outcompeting the D-amino acid-based lifeforms (by chance or by genetic drift).  Still, there is only the possibility of random chance.  Maybe the first lifeform arbitrarily incorporated L-amino acids only, so life evolved using only L-amino acids.  So the ultimate origin of chirality in biological systems still remains unknown.

Offline 2810713

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Re:presence of only L-amino acids in natural proteins
« Reply #3 on: January 01, 2006, 10:04:28 AM »
 I think followed much of what u said Yggdrasil, and am really thankful for that.
I couldn't understand the mechanisms behind these 2 possibilities -
Some claim that asymmetric crystals in clay may have lead to an overabundace of L-amino acids in the "primordial soup".  Others believe that polarized light may have had an effect on the relative ratios of D- and L- amino acids.  
 By what mechanism did the assymetric crystals would lead to over abundance of Ls and not Ds, same thing. For that polarized light possibility, it says that light polarity will affect molecule stability , am i right???

 Please explain a bit.

Albert, good way of telling that no scientific explanation exsists today.
 
hrushikesh
« Last Edit: January 01, 2006, 10:05:21 AM by 2810713 »

Offline Borek

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Re:presence of only L-amino acids in natural proteins
« Reply #4 on: January 01, 2006, 10:50:04 AM »
It will be enough for the assymetric crystals to catalyze some organic reaction faster for L-particles than for D-particles, to create initial abundance of some L-particles. Once there is some inequity in amounts it can easily propagate in a self-amplifying process. This explanation assumes assymetry was external so one may ask why the crystals were assymetric in the first place and we are back in the same place.

However, there are many mechanisms that - while not necesarilly have any chemical meaning - can be used to explain how it may happened without any initial assymetry.

Assume racemic 50/50 mixture of D and L. Imagine some process requiring three particles. If they are randomly selected they can be all the same (DDD or LLL) or one can be different (DDL and DLL). Now imagine the process is such that if initial particles are DDD or LLL nothing happens, but DDL gets converted to DDD and DLL gets converted to LLL. Let it go for a long time. At first nothing happens, but the equilibrium is unstable, so sooner or later all particles get converted to D (or L) - and it is not possible to predict which way the system will move.

It is pretty easy to program such simulation and play with it. While it not necesarilly gives an answer, it shows that the natural process of conversion is possible.
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Offline Yggdrasil

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Re:presence of only L-amino acids in natural proteins
« Reply #5 on: January 01, 2006, 03:31:54 PM »
Unfortunately, I don't know the mechanisms of such processes, but the principle is that they create a chiral environment in which the properties of enantiomers can be differentiated.  I have just heard them as theories explaining the origin of biological chirality.

Offline 2810713

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Re:presence of only L-amino acids in natural proteins
« Reply #6 on: January 03, 2006, 06:11:22 AM »
 Thanks Borek, Yggdrasil.
I'm trying to tell you what i've understood, now-
After fixing L or D , i think due to stability differences those purely L or D are selected. I've also thought about some example now-
 If there are 100 spots[surface of crystals..] where a process occurs, such that 50 are D and 50 are L. We add equal amounts of D and L reactant  at  each spot. Lets assume that at D spots only D-type reactant can react , while for all L spots only L-type reactant can react.Now the process requires somany other things without which it will not lead to complition.The probability of getting all of these at the same time at the same spotis very less , so only very few of these 100 [ say only 1] spot happens to have them all. So even if there are Ds available to D spots and Ls available to L spots due to less probability of  presence of all required factors is less the process will complete only at 1 spot which might be D or L.  So,  the probability of occurence of subprocess with L is 50 out of 100 i.e.1/2 and the same for D .The probability of complete process[life...] occuring with L or D  can't be difined with only examining 100 spots, as  complete process occurs only at 1 spot. So, if we examine large no. of completely occured processes we might find that the probability of   complete process[life...] occuring with L or D is 1/2. Here it means if we examine many  lives we can define the probability for random selection mode as 1/2 each L and D. i.e. 1/2 would have Ls and 1/2 would have Ds.

Till yet, when 2 choises are given & only one is randomly selected, i was more tending to say that probability of getting selected is 1/2 each. But these
probability laws are applicable for large statistical data and random mode of selection. Here, there is absense of large statistical data.

 
Now, why only 1 of L or D is fixed is still remains to be confirmed by me. So, please help.

Hope that was not so bad way of telling this...

yours always endoknowledgic,
hrushikesh

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