[Kikko]

After reading the list provided, I'm thinking it could be hemiaminal, but that has 5 R groups.  Is it a hemiaminal?

The specific linkage in the red box is a hemiaminal - not sure where you are getting 5 R groups from:

You have in this case:


R1 = sugar ring; R2 = sugar ring; R3 = Asn residue of peptide

More specifically (also considering what is outside the red box) you could call this structure an N-acyl hemiaminal (because R3 is an acyl group).

Based on the core amide structure:



and given that R1 = glycosyl, you could call it an N-glycosyl amide. There are a lot of functional groups present, so there is more than one logical way of describing what is present.

In the PDF file you posted, with the names, there are 5 R groups, I guess thats why he is confused that its an hemiaminal.

On wiki its showing an "easier" structure:
http://en.wikipedia.org/wiki/Hemiaminal


Mod edit: Image resized. Dan

[Studentofstuff123]

After reading the list provided, I'm thinking it could be hemiaminal, but that has 5 R groups.  Is it a hemiaminal?

The specific linkage in the red box is a hemiaminal - not sure where you are getting 5 R groups from:

You have in this case:


R1 = sugar ring; R2 = sugar ring; R3 = Asn residue of peptide

More specifically (also considering what is outside the red box) you could call this structure an N-acyl hemiaminal (because R3 is an acyl group).

Based on the core amide structure:



and given that R1 = glycosyl, you could call it an N-glycosyl amide. There are a lot of functional groups present, so there is more than one logical way of describing what is present.

Hmmm...thank you Dan.  I will tell my professor on Monday. I am sure he will ask me how I figured it and will definitley tell him from here because he is way too smart to think I figured this by myself. 

He basically challenged everyone in the class to find this and he said NO one has EVER figured it out in 10+ years. I just wanted to see why that was.

I will keep you all posted, thank you.

[Kikko]

Is it a tertiary amine ?

No, look it up: example of a list I found on google.

In your original post you highlighted this fragment:

Looking back at it, I am not sure where you get your "fragment".
I can understand the R3 group.
But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R?
Isnt Arkcon his figure better?
=>

OK, so ... removing all the rest of the graphic, and drawing it out, (and converting to SMILES so it displays here,)



Is that sort of close to it -- ignoring that the rest of the sugar ring has to be called a CH₃ (I'm not very good at SMILES yet)?  Like everyone else, I see a couple of functional groups, but I don't know a name for this one by itself.  Unless the letters for the atoms spell your school's initials, or something.  Could that be it?

Also

@OP, You must make an attempt; that is a forum rule.  However, I will give you a hint.  The functional group that connects a base (purine or pyrimidine) to a ribose or deoxyribose in RNA or DNA respectively, is similar.

And I dont think the functional group that connects a base to a ribose is an hemiaminal

[Dan]

Looking back at it, I am not sure where you get your "fragment".
I can understand the R3 group.
But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R?
Isnt Arkcon his figure better?

This is what I did:

[Kikko]

Looking back at it, I am not sure where you get your "fragment".
I can understand the R3 group.
But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R?
Isnt Arkcon his figure better?

This is what I did:

Ok, I see what you did, but I am still confused about what R1 and R2 is.
Does R2 refer to the "second" sugar ? (the one attached to the "first" sugar that contains the O that is found in the red square?)

[Arkcon]

Well, R₁ and R₂ are by definition anything, since the O.P. drew a red box to exclude much of the ring.  Its a bit confusing, since in the original molecule, what ends up as R₁ and R₂ are parts of the same ring, but the question isn't about that.

[Kikko]

Well, R₁ and R₂ are by definition anything, since the O.P. drew a red box to exclude much of the ring.  Its a bit confusing, since in the original molecule, what ends up as R₁ and R₂ are parts of the same ring, but the question isn't about that.

Ok, but if I look at your drawing compared to the one Dan does.. to me those are different molecules...
Thus changing the name of the functional group?
Or?

[Arkcon]

Oh yes, 'cause mine is wrong, and doesn't describe the OP's question, I'm new to SMILES.

[AWK]

http://goldbook.iupac.org/H02775.html

[Babcock_Hall]

It is common to refer to the linkage between a base and the (deoxy)ribose in RNA or DNA as an N-glycoside.  However, this is frowned upon in some circles.  "...however the use of 'N-glycoside', although widespread in biochemical literature, is improper and not recommended here ('glycosylamine' is a perfectly acceptable term)."  One wonders whether the present group might be called a glycosylamide.  http://www.chem.qmul.ac.uk/iupac/2carb/33.html

[Kikko]

It is common to refer to the linkage between a base and the (deoxy)ribose in RNA or DNA as an N-glycoside.  However, this is frowned upon in some circles.  "...however the use of 'N-glycoside', although widespread in biochemical literature, is improper and not recommended here ('glycosylamine' is a perfectly acceptable term)."  One wonders whether the present group might be called a glycosylamide.  http://www.chem.qmul.ac.uk/iupac/2carb/33.html

Its getting a bit more complicated..

Now how do you call the structure in DNA that you described: @OP, You must make an attempt; that is a forum rule.  However, I will give you a hint.  The functional group that connects a base (purine or pyrimidine) to a ribose or deoxyribose in RNA or DNA respectively, is similar.

You would say its a hemiaminal or glycosylamide ?

 Because I justed asked around and they told me that what you describe is also called a tertiary amine...
So I am confused!

ALso: if I look up the definition of Glycosidic bond, I see it refers to having a hemiacetal group and this is not the case in DNA so I wonder where they came up with this glycosidic bond.

[Dan]

N-Acetylhemiaminal and N-glycosylamide are both, in my opinion, perfectly acceptable descriptions of the functional group (as I already said in reply #14).

They differ in their level of generality. N-Glycosylamides are a type of N-acetylhemiaminal.

[Babcock_Hall]

ALso: if I look up the definition of Glycosidic bond, I see it refers to having a hemiacetal group and this is not the case in DNA so I wonder where they came up with this glycosidic bond.

Glycosides are a form of acetal, not hemiacetal.

[Studentofstuff123]

He confirmed that it was indeed correct, hemiaminal ether more specifically

[Kikko]

He confirmed that it was indeed correct, hemiaminal ether more specifically

Pretty weird that the biochemistry majors dont know this.
Altough, I guess its more a thing for (organic) chemistry majors.