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Topic: Dihydroxy without two hydroxy ?  (Read 6942 times)

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Offline abrogard

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Dihydroxy without two hydroxy ?
« on: March 29, 2014, 06:01:09 PM »

I'm not even a formal student. Just reading a little chemistry for myself.

 Using Biochemistry For Dummies.  Came across dihydroxyacetonephosphate in the glycolysis section and I couldn't see anything to apply 'di' to.

 So I googled dihydroxy and got: 'a molecule with two molecules of the  hydroxy radical (OH)'.

 But the diagram I have in that book doesn't show two should molecules.  Page 195 for those with the book (if any serious students use such a book). 

 It shows a phosphate group, a CH2, then a carbon with a double bonded Oxygen, then another CH2 and then one Hydroxy.

 How am I to understand this? There's a convention I'm not aware of perhaps?

 

Offline Archer

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Re: Dihydroxy without two hydroxy ?
« Reply #1 on: March 29, 2014, 06:19:05 PM »
Is this the molecule?

[O-]P([O-])(=O)OCC(=O)CO

If so then the "dihydroxy" indicates that the central acetone part (propanone) has two -OH groups but one has been modified to form the phosphate

This is dihydroxyacetone

OCC(=O)CO

“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

Offline abrogard

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Re: Dihydroxy without two hydroxy ?
« Reply #2 on: March 30, 2014, 06:36:11 AM »

 Yes, I guess that's it. There's two H shown on each of those C in your diagram but I see Wikipedia does it the same way you do.

 That'd be a convention, too, then?  Leave the two H out because the C will always pick them up, they can be taken for granted?





p.s.
couldn't find a way to edit that post - should be 'doesn't show two such..', not 'doesn't show two should...'  of course.

 

Offline Archer

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Re: Dihydroxy without two hydroxy ?
« Reply #3 on: March 30, 2014, 07:08:36 AM »

  There's two H shown on each of those C in your diagram but I see Wikipedia does it the same way you do.

 That'd be a convention, too, then?  Leave the two H out because the C will always pick them up, they can be taken for granted.

When nothing else is attached to a carbon atom then hydrogen atoms are always implicit.

This does not apply to heteroatoms like oxygen or nitrogen.

If a hydrogen is required to show configuration in stereochemistry in, sometimes to show stereochemistry then explicit hydrogens may be drawn in.

In the molecular structures I have drawn there are no explicit hydrogens. The terminal groups are hydroxyl groups, if you look closer you will see these are 'O' and not 'C'
“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

Offline abrogard

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Re: Dihydroxy without two hydroxy ?
« Reply #4 on: March 30, 2014, 09:33:35 PM »

 Woops... you really think I thought the OH was CH?

 We're a bit mixed up here I think, or I am.

 I was referring to the 'implied' Carbons in the angles of the diagram.

 I learned about that kind of diagram just a few days ago and knew that the Carbons were implied but didn't realise the Hydrogens on them were also implied. 

 Because I'm so new I didn't know that's what happens in nature.

 You've cleared it all up for me.  Thanks.

 :)

Offline Archer

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Re: Dihydroxy without two hydroxy ?
« Reply #5 on: March 30, 2014, 10:05:58 PM »

 Woops... you really think I thought the OH was CH?



No, but one should never assume prior knowledge.

This freeware may be of some use to you

http://www.acdlabs.com/download/
“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

Offline abrogard

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Re: Dihydroxy without two hydroxy ?
« Reply #6 on: March 31, 2014, 12:12:59 AM »

 Yes, thanks for that.  By a coincidence I found the same software yesterday after seeing your diagrams.  I thought I got to be able to do that, what a cool thing (as they say these days), so I went googling and found it.

 So far I've opened and gaped open mouthed at the plethora of options, tools and abilities...

 Powerful piece of software, looks like to me. Another example of the unprecedented riches spread before these days on the web.

 But there's going to be a little learning curve attached,  I think.

 I couldn't even find where to begin, assuming I wanted to replicate either or both of your diagrams, say.

 So I closed it up and marked it down for attention later, as soon as possible...

 

Offline Archer

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Re: Dihydroxy without two hydroxy ?
« Reply #7 on: March 31, 2014, 03:30:48 AM »
On this forum we use SMILES

So to get

OCC(=O)CO

We type
[ SMILES]OCC(=O)CO[/SMILES]
(Without the space at the beggining

You can generate SMILES from ACD or many online resources such as Wikipedia. Alternatively you could learn how convert a molecule into SMILES
“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

Offline abrogard

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Re: Dihydroxy without two hydroxy ?
« Reply #8 on: March 31, 2014, 04:47:35 AM »
wonderful.  thanks for that.  I get what you're telling me - look, here's your pic:

OCC(=O)CO

 this is great. i better go learn something about smiles.  i hope it doesn't distract me from learning something about chemistry...

 :)

Offline Borek

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ChemBuddy chemical calculators - stoichiometry, pH, concentration, buffer preparation, titrations.info, pH-meter.info

Offline Babcock_Hall

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Re: Dihydroxy without two hydroxy ?
« Reply #10 on: March 31, 2014, 11:28:27 AM »
I realize that you said that you are not a chemistry student, but it might help to think of it this way:  dihydroxyacetone phosphate is an ester.  An ester and one water molecule are the products of the reaction between an acid and an alcohol.  Which alcohol and which acid can form dihydroxyacetone phosphate.

Offline abrogard

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Re: Dihydroxy without two hydroxy ?
« Reply #11 on: March 31, 2014, 09:40:46 PM »
Didn't help me a bit right now.  What's that last line?  A question?

Jeez I'll be glad when I can understand....

 :)

Offline Babcock_Hall

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Re: Dihydroxy without two hydroxy ?
« Reply #12 on: April 01, 2014, 09:15:31 AM »
Yes, it was a question to help you understand dihydroxyacetone phosphate better.

Offline abrogard

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Re: Dihydroxy without two hydroxy ?
« Reply #13 on: April 01, 2014, 07:11:16 PM »

 Good grief.  I don't know.  Don't know how to begin figuring it out.  Couldn't even Google it.

 'Understand it better' ?  When it comes to understanding I'd like to know just why the glucose molecule takes the form it does in the first place.

 I don't even understand that.

 Why is the OH on the third carbon show 'upwards' where all the other OH are shown 'down' ?

 Because that's the form. I know. But I mean why did the molecule take that form?

 And a quote "..when a glucose molecule enters the cell phosphorylation is immediate.."   But I've been led to believe the cell is a crowded area. Very crowded. Totally crowded.

 How can phosphor groups find the glucose molecule 'immediately' ?

 Similar thought when I think of tiny pills ingested by us that effect the whole organism, the whole 200lb of meat or whatever.  How can that tiny amount of chemical spread throughout the organism so quickly, permeate everywhere?

 My understanding of the molecular, atomic world is miniscule. It only started a couple of weeks ago.

 And as I say, I'm not formally a student.

 So if you find my questions, observations, understandings annoyingly obtuse, immature, ignorant then please ignore them... I don't mean to pollute the waters...

:)

Offline Archer

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Re: Dihydroxy without two hydroxy ?
« Reply #14 on: April 02, 2014, 03:36:37 AM »

 'Understand it better' ?  When it comes to understanding I'd like to know just why the glucose molecule takes the form it does in the first place.

 I don't even understand that.

 Why is the OH on the third carbon show 'upwards' where all the other OH are shown 'down' ?


All natural products are made by enzymes, enzymes are large proteins which fold up in a specific way when in water. There are spaces in the folds which hold the molecule a certain way up and way around as this is the best fit. Imagine a left shoe, out of your  hands and feet only your left foot will fit.

So when the -OH groups are incorporated in the molecule the enzyme holds it in the right way to have them in the right place and coming up or down.

This is a complex system but I hope this simplification helps towards your understanding.
“ I love him. He's hops. He's barley. He's protein. He's a meal. ”

Denis Leary.

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