The Naked Scientists

The Naked Scientists Forum

Author Topic: Amino acids - left handed and right handed  (Read 22025 times)

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Amino acids - left handed and right handed
« on: 05/01/2004 19:27:21 »
Amino acids come in two types, left-handed and right-handed (called chirality).  Almost all life on earth is based on left-handed amino acids.  

My question is:  Can the two co-exist in a life form, or are they mutually exclusive.  In other words, could a simple life form (bacteria?) utilize both forms of amino acids.  Could it "eat" another bacteria that was composed of the other form of amino acids, or would it find it to be non-nutritive (or even poison)?


----
John


 

Offline chris

  • Neilep Level Member
  • ******
  • Posts: 5339
  • Thanked: 65 times
  • The Naked Scientist
    • View Profile
    • The Naked Scientists
Re: Amino acids - left handed and right handed
« Reply #1 on: 05/01/2004 23:07:21 »
Hi John

D amino acids do crop up in L- amino dependent organisms, but usually in a pathological context.

Chris McManus discusses this in his book - right hand left hand - http://www.thenakedscientists.com/html/books/psychology.htm

There is an association between the accumulation of certain D-amino acids and neurodegeneration (alzheimers) and the kidney also has an enzyme that deals with certain D-forms.

Obviously an L-based enzyme designed to work on L-based protein substrates will not work with D-amino acids. But if the same enzyme is made (artificially) using D amino acids, it will readily digest its usual substrate, provided this is also composed of D (rahter than L aminos). Amazing eh ?

Chris

"I never forget a face, but in your case I'll make an exception"
 - Groucho Marx
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #2 on: 06/01/2004 21:56:34 »
That makes sense.  So, organisms (on earth) are composed of L-amino acids, but there are trace amounts of D-forms.  And the D-forms cause problems for the organisms, even in trace amounts.

So, a bacteria composed of L-amino acids could not "eat" a bacteria composed of D-amino acids - it would find it to be poisonous.  Right?


----
John
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #3 on: 06/01/2004 23:20:09 »
well, there's "being present in an organism" and "eating."  Eating implies the material is being exposed to digestive enzymes and such, and since enzymes are very shape specific, the protein material being ingested probably wouldn't be broken down into component amino acids.  In fact, I don't even know for sure if D-amino acids are capable of the same protein polymerization.  Maybe Chris can jump on that one.  

The fact that D-amino acids are present in the cases of certain diseases doesn't necessarily mean they are the cause, by they could be a by-prodyct of a runaway biochemical process.  Much like the discussion in the alternative medicines forum about alzheimers and heavy metals.



This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline chris

  • Neilep Level Member
  • ******
  • Posts: 5339
  • Thanked: 65 times
  • The Naked Scientist
    • View Profile
    • The Naked Scientists
Re: Amino acids - left handed and right handed
« Reply #4 on: 07/01/2004 00:10:26 »
D forms occur naturally in all of us. Although the L form is the only biologically active one, amino acids spontaneously racemise to their oppsite optical isomer over time. One way to 'date' tissue is to look at how much D-hydroxyproline there is in collagen for instance.

What is absolutely true is that D forms cannot be metabolised by proteins (enzymes) constructed to metabolise L forms because the configuration of the protein prevents the right groups in the active site of the enzyme interacting in the correct way for catalysis to occur.

chris

"I never forget a face, but in your case I'll make an exception"
 - Groucho Marx
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #5 on: 07/01/2004 03:11:07 »
I've read that it may have been an accident that life started with L-amino acids and has flourished that way ever since, implying that the D-form could have been the dominant form just as easily.  Do you think that is true?

Is there a reason that only one form has come to dominate?  In other words, why don't we have organisms that are based on D-forms co-existing with organisms that are based on L-forms?  Or do we and I just don't know it?


----
John
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #6 on: 07/01/2004 05:47:56 »
Yeah, from what I know, it's pretty much random chance that we are L-amino life forms.  (and carbohydrates that are biologically active for us are D isomers, btw)  When ammonia and carbon dioxide got boiled up in a nice hot irradiated soup, it just worked out that way.  I'm sure both types of amino acids formed, it just so happened that the first biological molecules came from the L-isomers.

But I wonder if a particular amino acid conformation necessarily requires the opposide conformation for carbohydrates...Chris?  



This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline chris

  • Neilep Level Member
  • ******
  • Posts: 5339
  • Thanked: 65 times
  • The Naked Scientist
    • View Profile
    • The Naked Scientists
Re: Amino acids - left handed and right handed
« Reply #7 on: 07/01/2004 13:51:51 »
The consensus of opinion is that it is down to chance. When early life began on earth it had a choice between D and L forms of everything. Reliance on L-amino acids was thus subsequently inherited by all descendents of the first life. The same is true of DNA. All DNA spirals the same way, and uses the same sugars because the enzymes that make it are set up to handle D-deoxyribose.

One factor that might have influenced the choice of amino acids we use, is the relative abundance each. Analysis of material retrieved from space shows that whilst forms are present, L amino acids are slightly more prevalent. If these findings are representative of those on the early earth, the relative greater abundance of L over D might account for subsequent use of the L form.

I don't think there is any evidence that L aminos have been utilised to accommodate D sugars, however.

chris

"I never forget a face, but in your case I'll make an exception"
 - Groucho Marx
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #8 on: 09/01/2004 03:48:17 »
But why can't the two forms of life co-exist?


----
John
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #9 on: 09/01/2004 06:48:43 »
Well,  the theory of evolution states that all life on this planet began from the same origins.  Assuming this is correct, then the reliance on L aminos would be inherited from ancestral species.  Since life feeds upon life, the ability to incorporate the L aminos is only accomplished by an organism that is based on L aminos themselves.  

Chris, so you're saying then that D sugars are crucial the the L amino configuration?



This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #10 on: 09/01/2004 06:54:13 »
Oh and to further answer your question John, they could theoretically coexist (its not like they'd annhilate each other or anything) but the D amino life forms would need their own food chain with life forms all derived from D amino acids....I mean what else would they eat?  Unless of course they developed an enzyme that would isomerize the L amino to the D amino form.

This whole thing got me thinking though...I'm working on a research project currently that is using quantum mechanical computations to determine the most energetically stable spatial arrangements of organic molecules.  Maybe for my next run I'll compare L and D isomers of a simple amino acid to see which configuration is the most stable.  Would you be interested in seeing my results?





This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline chris

  • Neilep Level Member
  • ******
  • Posts: 5339
  • Thanked: 65 times
  • The Naked Scientist
    • View Profile
    • The Naked Scientists
Re: Amino acids - left handed and right handed
« Reply #11 on: 09/01/2004 11:28:51 »
The question of D / L amino acids is not quite as mutually exclusive as you might think.

D amino acids do crop up in nature, and bacteria exploit them to their advantage. For instance bacterial cell walls contain proteins which incorporate D-amino acids and which our 'standard' proteases cannot digest.

Human kidneys contain enzymes that can break down D-amino acids, essentially removing them from the body to prevent them having a deleterious effect, and in alzheimer's disease the amyloid plaques that accumulate in the brains of sufferers are relatively enriched for D-serine. The resistance of D-serine to proteolysis might explain the pathological stability of the amyloid plaques, and their neuro-toxic effects.

The use of L-amino acids and D sugars probably stems from life-s origins. The slight over-abundance of L versus D amino acids probably explains the use of the L form by early life which subsequently gave rise to other forms of life. If you assume that kick-starting life is not a simple thing to achieve, then it is easy to understand why once life had got started, and was using one set of 'rules' which it passed on to all subsequent generations, no other life forms arose spontaneously with their metabolism revolving around the mirror image.

Also, bear in mind that all life of earth relies on other forms of life on earth. The ecosystem is a tight web linking every aspect of life on earth. How would an organism that has mirror-image chemistry fit into that - not without difficulty !

Chris

"I never forget a face, but in your case I'll make an exception"
 - Groucho Marx
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #12 on: 09/01/2004 18:31:02 »
I guess it would be difficult for two separate ecosystems to co-exist.  But it's an interesting idea.

Jay, I would be very interested in seeing your research on quantum mechanical analysis.  However, it will be way over my head.  I'd probably be more interested in the modelling programs you are using.  I love modelling and simulation.


----
John
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #13 on: 09/01/2004 18:51:37 »
The modeling software is GAMESS, it's available at http://www.msg.ameslab.gov/

Let me know if you have trouble getting them to give you access.

This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #14 on: 10/01/2004 04:32:10 »
That's a cool package.  I wish I had the time and energy to dig in to it right now, but I've written about 1000 lines of code in the last two weeks and my head already hurts.  More code is not the way to fix that.


----
John
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #15 on: 10/01/2004 04:39:42 »
Such a well educated scientist relegated to the role of a simple bit pusher  =/

This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #16 on: 13/01/2004 17:06:01 »
The worst thing I ever did was learn how to use a computer.  It's been downhill ever since.


----
John
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #17 on: 13/01/2004 23:50:20 »
Computers are great....as tools.  As a living, well, I've been down that road too and I'm glad I left it.  



This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline Donnah

  • Ma-Donnah
  • Neilep Level Member
  • ******
  • Posts: 1756
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #18 on: 15/01/2004 01:05:39 »
When I started at DeVry I didn't know how to turn a computer on.  Three years later I had a B.Sc. and heaps of debt.  It was tough with a brain full of mercury, but I enjoyed working with computers; it was the office politics I didn't like.  Now I use the acquired skills for things like developing forms and a database for my businesses.
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #19 on: 15/01/2004 02:41:20 »
Jay,
I sometimes envy you being able to get a fresh start.  I have a family and way too much debt to go back to school full time.  I don't think I have the drive to do it all at once.

I'd love to have my own business also, but the same reasons apply.  Much of the debt is because of a failed business attempt a few years ago, so I just need to be patient.  Besides, the job I have now is great; It's not terribly demanding and pays really well.  

So, what am I complaining about????


----
John
 

Offline Ylide

  • Moderator
  • Hero Member
  • *****
  • Posts: 905
    • View Profile
    • http://clem.mscd.edu/~mogavero
Re: Amino acids - left handed and right handed
« Reply #20 on: 15/01/2004 08:14:58 »
I know, I'm quite lucky to have a woman at home who is willing to pay most of the bills while I'm in school.  Luckily, once I hit grad school and am collecting a teaching and/or research stipend, I won't feel like such a mooch.  =P  I wouldn't have the drive to start fresh later in life if it weren't for the fact that I absolutely love what I'm doing.  I'm going to be pushing 40 by the time I finish grad/med school.  (your typical combo md/phd program is 7-9 years and I won't be starting one until I'm 30)

I hear you on the failed business attempt...that was my last straw before going back to college.  I tried getting a gunsmithing business off the ground with a buddy of mine, but licensing and zoning were a nightmare in Denver.  (which I found out AFTER putting thousands into training and inventory)



This message brought to you by The Council of People Who Are Sick of Seeing More People
 

Offline Donnah

  • Ma-Donnah
  • Neilep Level Member
  • ******
  • Posts: 1756
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #21 on: 15/01/2004 19:46:20 »
Well there's more than one way to learn, and an education is usually costly.  I think we can learn from our failures and our successes.  At least you two had the balls to get out there and try a business.
 

Offline tweener

  • Moderator
  • Neilep Level Member
  • *****
  • Posts: 1144
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #22 on: 16/01/2004 03:20:10 »
I learned a lot from my failures.  If I didn't, I wouldn't ever have learned half what I've learned so far. :)


----
John
 

Offline C-guy

  • Jr. Member
  • **
  • Posts: 28
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #23 on: 16/01/2004 07:16:11 »
I'm new here. I want to know how is left and right handedness defined.
 

Offline Quantumcat

  • The Kitty Down Under
  • Hero Member
  • *****
  • Posts: 894
    • View Profile
Re: Amino acids - left handed and right handed
« Reply #24 on: 16/01/2004 07:20:58 »
the hand that you have the best control with.

Hey, does anyone know why it is that I'm right handed but I do archery with a left handed bow?

Am I dead? Am I alive? I'm both!
 

The Naked Scientists Forum

Re: Amino acids - left handed and right handed
« Reply #24 on: 16/01/2004 07:20:58 »

 

SMF 2.0.10 | SMF © 2015, Simple Machines
SMFAds for Free Forums