[Aymeric]

Hello,

I'm reviewing the basics and I'm reading a chapter on carbohydrates.
In Haworth, glucopyranose has a CH2OH sticking out from C5. Does it have a name?
I see some websites refer to the whole of CH2OH as a "primary hydroxy group", but my textbook uses this terminology to refer ONLY to the -OH part, not CH2OH as a whole.
I'd be grateful if anyone could clarify these two things for me:
1/name of -OH when it is attached to a primary or a secondary carbon
2/names of CHOH and CH2OH as a whole (i.e. the hydroxy plus the carbon).

Thanks!

[wildfyr]

-CH2-OH is hydroxymethyl

https://en.wikipedia.org/wiki/Hydroxymethyl

CHOH I would call just a secondary alcohol along the lines of its IUPAC designation.

[AWK]

The official rules for naming organic compounds are very precise and extremely extensive - have you learned them all?
You ask for names that are sometimes used in conversations between chemists, which even chemists sometimes manage to smuggle for publication if the reviewers and the editor are not vigilant enough (because they also use such abbreviations). Such names are only used when they are unambiguous.
There is no point in talking about the fructose hydroxymethyl group where there are two such groups; likewise, there is no point in talking about the hydroxymethine group in fructose, where there are three such groups.
The systematic names of organic compounds are unambiguous, although the nomenclature rules allow the use of a small number of strictly defined common names for chemical compounds or functional groups.
You still have a lot of time for the usual shortcuts.

[wildfyr]

Methine! How was I blanking on that term! Yeesh. Methyl, methylene... m?

It is of note that "hydroxylmethyl" is a pretty poor term by IUPAC standards, its better described as "hydroxylmethylene"... which is itself a discrete (but short lived) carbene molecule.

Like AWK said, context is everything in a conversation between chemists where you are both on the same page, as opposed to in a classroom or a paper.

[Aymeric]

-CH2-OH is hydroxymethyl

https://en.wikipedia.org/wiki/Hydroxymethyl

CHOH I would call just a secondary alcohol along the lines of its IUPAC designation.

Thank you ! Doesn't "secondary alcohol" seem to refer only to the OH part in CHOH, without the carbon?
I'm asking because in my course about glucopyranose formation, it is said that the joining is made between the carbon with the carbonyle group, and "the carbon bearing the last secondary alcohol function", which is quite a mouthful, and since it goes on to explain that for ease of memorisation this latter part sticks out on top of C5, I thought it would be nice if it had a name.

The official rules for naming organic compounds are very precise and extremely extensive - have you learned them all?

No I haven't. I'm studying biochemistry applied to nutrition, so this is not part of the curriculum.

There is no point in talking about the fructose hydroxymethyl group where there are two such groups; likewise, there is no point in talking about the hydroxymethine group in fructose, where there are three such groups.

I'm not sure I understand your rationale, because by the same token there are many hydroxyl groups in fructose so there is no point naming them?

You still have a lot of time for the usual shortcuts.

It's hard to ignore the condescending drift, I was looking for help, not for irrelevant jugement about my current skills. I'm only trying to make my learning and memorization easier, I don't really see what's wrong with that. For example I find it much easier to memorize the fructose molecule now that I can say that is has two hydroxymethyl groups at each end, a cetone function and three hydroxymethine groups. Much easier to memorize than the semi-developed formula. But thanks anyway.

[wildfyr]

On a sugar, we number the carbons and use them as reference point. So you would say the C-5 alcohol, not the secondary alcohol. AWK does make an important point though.  This naming convention I'm using is very specific to sugars. You both need to know the "priority" naming system of a given sugar when talking to someone.

If we were talking about a benzene ring (another cyclic carbon system) we would use terms like ortho, meta, and para to describe the location of substituents.

I guess if all youre doing is working with sugars, then the issue shouldn't be too confusing, but all sorts of people come to this form to look through archives for info.

[Aymeric]

Thanks wildfyr, yes all we need to know is restricted to the molecules found in food-related metabolic pathways (glycolysis, Krebs, Wakil and the like) so they basically only teach us the main functional groups (carboxylic acid, hydroxy, ester, carbonyl, amine, amid, thiol, thioester, and off we go). However we are also required to be able to draw the molecules in question, and that's where breaking them down into recurring subunits (and naming said subunits) comes in handy for better recall. We do have to learn aminoacids and fatty acids, but thank God we are not required to memorize larger molecules such as cholesterol, sphingosine or eicosanoids for example. I guess we're doing an extremely simplified version of actual biochemistry.

[wildfyr]

just FYI, by IUPAC naming, the hydroxy methyl would probably by written as (methyl-1-ol)... however sugars are pretty weird in that since they often exist in both cyclic and linear forms, and we use the linear form to do the naming (Fischer projection), the methyl is often part of the "longest carbon chain" and therefore isn't written as a substituent branch.

[AWK]

The basic principles of biochemical naming of sugars are found in practically every biochemistry textbook. If they are not there, it is the professor's duty to indicate supplementary materials. In biochemistry, the terms primary, secondary, and tertiary are irrelevant for sugars, as opposed to organic chemistry. Biochemical reactions are performed by specialized enzymes dedicated to specific molecules or functional groups. Sometimes we are very happy to find gaps in the specialization of enzymes and use them practically (e.g. synthesis of vitamin C, semi-synthetic penicillins and cephalosporins).
For the student, the Fischer, Haworth and conformational projections (basically for glucose and fructose and ribose) are important. The -CH2OH groups (they can be called as such and it is a unique name) are only relevant for the assessment of conformational stability. Enzymes "like" to put phosphate groups on them.
https://www.khanacademy.org/test-prep/mcat/chemical-processes/aldehydes-and-ketones/a/cyclic-hemiacetals-and-hemiketals
https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Book%3A_Organic_Chemistry_with_a_Biological_Emphasis_v2.0_(Soderberg)/10%3A_Nucleophilic_Carbonyl_Addition_Reactions/10.03%3A_Hemiacetals_Hemiketals_and_Hydrates

[Aymeric]

In biochemistry, the terms primary, secondary, and tertiary are irrelevant for sugars, as opposed to organic chemistry.

I think the idea was to make us understand which -OH becomes joined with the carbonyl-group carbon when the linear molecule becomes a pyrane (the secondary alcohol farthest to the carbonyl group) and also which -OH determines the series of the sugar. Other than that, I admit that after going over our entire biochemistry course, I don't really see the point of learning about this, or about asymetric carbons and epimers which are also in the chapter on sugar, even though these concepts never reappear in subsequent chapters about the various metabolic pathways, unless I've missed something.

Thank you for the links. I don't think we need to delve into such details but it will be fun reading all this once I'm done with the basics.

[amphotericinb]

HydroxyMethyl

[Babcock_Hall]

https://pubmed.ncbi.nlm.nih.gov/8647345/

There is an enzyme in the Leloir pathway to metabolize galactose that interconverts uridinediphosphoglucose and UDP-galactose.  The reaction is an epimerization; therefore, there is some value in knowing what epimers are.  Likewise, epimerizations occur in what is sometimes called stage III of carbon fixation in plants.  Stage III is the regeneration of the molecule that accepts (fixes) carbon dioxide, starting from glyceraldehyde 3-phosphate.  Other kinds of isomerizations (aldoses interconverting with ketoses) also occur at this stage.

When I use the term "hydroxyl group," I don't intend to suggest that the oxygen atom attaches to any one kind of atom, but when I use the term alcohol, I mean that the oxygen atom is attached to a carbon atom.  I am not 100% certain that this is universal.  If one were to use the term "hydroxymethylene group," the word group differentiates it from a carbene, in my opinion.

[Aymeric]

When I use the term "hydroxyl group," I don't intend to suggest that the oxygen atom attaches to any one kind of atom, but when I use the term alcohol, I mean that the oxygen atom is attached to a carbon atom.  I am not 100% certain that this is universal.  If one were to use the term "hydroxymethylene group," the word group differentiates it from a carbene, in my opinion.

Thank you, I’ve re-read the whole chapter in my course and indeed the authors actually refer to the carbon+OH combination when talking about primary/secondary alcoholc not just the -OH.