Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

Nomenclature of carbohydrates


  • Please log in to reply
10 replies to this topic

#1 robvleugel

robvleugel

    member

  • Members
  • Pip
  • 2 posts
1
Neutral

Posted 07 December 2011 - 12:03 PM

Hi all,

I have some questions about the 'ring' structures. Please look at
http://en.wikipedia....,6-bisphosphate
and
http://en.wikipedia....,6-bisphosphate

Where do you find all carbons, is simply every corner a carbon atom?
If so, what carbon is the "first" carbon? In Fructose 1,6-bisP they count from right to left, while on the 2,6 version they count from left to right if I'm not mistaken.
I mean, why is it 2,6-bisphosphate and not 1,5-bisphosphate?

And what does the --==|||||| shaped bounds shown in the picture actually mean?
I can't realy find a good answer to these questions. Can anyone provide me with some information about this matter?

Greetings,
Rob

#2 pito

pito

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 1,332 posts
81
Excellent

Posted 07 December 2011 - 12:34 PM

take a look at the wikipages , but the dutch ones (I think you speak dutch?) Then you might understand where the 1, 6 and 1, 2 come from?
THey start counting at the right right, starting from the first C (the CH2OH)

And the "dashed" lines ("het zeprapad") means the molecule is "above" the "central molecule" , while the full line means its underneath the central molecule.
I hope you understand wht I mean?

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#3 robvleugel

robvleugel

    member

  • Members
  • Pip
  • 2 posts
1
Neutral

Posted 07 December 2011 - 01:15 PM

Yes I am Dutch, I looked at the pages like you told me to. I already figured out where they started counting, I just don't understand why they start counting at that position rather than on other side, which would give 1,5 instead of 2,6.

About the dashed lines, what exactly do you mean by "above" and what exactly is the 'central molecule'?

Thanks for the help!

Greetings,
Rob

#4 pito

pito

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 1,332 posts
81
Excellent

Posted 07 December 2011 - 01:51 PM

Yes I am Dutch, I looked at the pages like you told me to. I already figured out where they started counting, I just don't understand why they start counting at that position rather than on other side, which would give 1,5 instead of 2,6.

About the dashed lines, what exactly do you mean by "above" and what exactly is the 'central molecule'?

Thanks for the help!

Greetings,
Rob


check the dutch website... do you see where you find dashed lines and where "full" lines?
If the molecule is above the central "sugar molecule" they use a dashed line... if its below the central molecule its a full line...

(in dutch: de centrale molecule is de "suikermolecule" , die met de C's rond de O, en kijk naar waar de fosforgroepen liggen in vergelijking met de ringstructuur... erboven of eronder... en kijk nu naar de gestreepte lijn en de volle lijn.. je zal zien dat de volle lijn gebruikt wordt als de fosforgroep boven de ringstructuur ligt en de volle als het eronder ligt..gebruik de nederlandse wiki voor de tekeningen te zien, daar is duidelijk aanegeven of de OH groepen of fosforgroepen boven of onder liggen.)


And why they start counting there? Its just an agreement (I think, not sure really... but there is no real reason to start counting on the left/right/middle...)

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#5 phage434

phage434

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 2,468 posts
247
Excellent

Posted 07 December 2011 - 06:43 PM

It's confusing because the 2,6 bisphosphate diagram is turned upside down and left/right reversed. Position 1 is defined as the start of the chain leading to the smallest numbered modifications to the chain. Position 2 has both a hydroxy modification and a link to the ring oxygen. Position 5, on the other hand, has only the ring oxygen. They conveniently left off the numbers, to further your confusion. If you're motivated, perhaps you could fix the diagram by putting it in the same orientation and adding numbers.

#6 neuron

neuron

    Veteran

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 187 posts
5
Neutral

Posted 08 December 2011 - 02:24 AM

I have a doubt on the counting partPosted Image ..is this not because in nomenclature the priority is given to hydroxyl group that should be in plane. What I mean here is, if you see structure of 1,6 bisphosphate...then according to this counting hydroxyl group that is in plane comes at 3rd position whereas if you count from the other side, it will come at 4th position that is why first one is preferredPosted Image ....same with 2,6 bisphosphate...I may be wrong, this was just an observation.....Just wanted to confirm can this be a reason too??Posted Image

#7 pito

pito

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 1,332 posts
81
Excellent

Posted 08 December 2011 - 07:01 AM

It's confusing because the 2,6 bisphosphate diagram is turned upside down and left/right reversed. Position 1 is defined as the start of the chain leading to the smallest numbered modifications to the chain. Position 2 has both a hydroxy modification and a link to the ring oxygen. Position 5, on the other hand, has only the ring oxygen. They conveniently left off the numbers, to further your confusion. If you're motivated, perhaps you could fix the diagram by putting it in the same orientation and adding numbers.


I have never heard of that rule...

I was always told that it doesnt matter: you either start counting from the left or right and start at the first carbon.. (and most start at the right).

Anyway, the following links might help you understand how it works.

http://www.chemguide...ions/names.html (here you see how the counting works and why sometimes molecules are "reversed or upside down" )
http://www.chemguide...s/draw.html#top (check this for your question about the dashed lines and full lines..)

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#8 phage434

phage434

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 2,468 posts
247
Excellent

Posted 08 December 2011 - 07:14 AM

Well, consider the molecule 2-methyl pentane. If you could start numbering at either end, then it might also be called 4-methyl pentane. This would make it difficult to realize it was the same molecule (of course non-systematic names make this a problem in any case). SMILES descriptions are pretty good.

#9 pito

pito

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 1,332 posts
81
Excellent

Posted 08 December 2011 - 07:54 AM

Well, consider the molecule 2-methyl pentane. If you could start numbering at either end, then it might also be called 4-methyl pentane. This would make it difficult to realize it was the same molecule (of course non-systematic names make this a problem in any case). SMILES descriptions are pretty good.

I see your point, however I have learned that 2-methyl pentane is indeed the same as 4-methyl pentane

Take for example 1-bromo-4-methylpentane as a substance... following your rule (about leading to the lowest modificatio), this is not correct, right? Or maybe I misunderstood the rule.

Edited by pito, 08 December 2011 - 01:33 PM.

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#10 phage434

phage434

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 2,468 posts
247
Excellent

Posted 08 December 2011 - 07:44 PM

Here's a reasonably coherent set of the rules. The alternative to your example is 5-bromo-2-methylpentane, which has higher numbers, so your version is correct.
http://en.wikipedia....ganic_chemistry

#11 pito

pito

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 1,332 posts
81
Excellent

Posted 09 December 2011 - 05:19 AM

Here's a reasonably coherent set of the rules. The alternative to your example is 5-bromo-2-methylpentane, which has higher numbers, so your version is correct.
http://en.wikipedia....ganic_chemistry


Its a really a confusing "science", the naming of the molecues lol
ANd then they start using different non systematic names and just for the fun of it they start drawing mirror images etc...
I think chemists just like to irritate non chemists with it.
Posted Image

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.





Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.