Which carbon?

[seancassell]

Hi everyone;

I'm in grade 12 chemistry, and am trying to teach myself more advanced chemistry (frankly, I find the subject matter we're looking at in class too boring and too easy). I've started reading about organic chemistry, and it quite intrigues me.

I can't seem to figure out how, in a chemical reaction, it can be predicted which carbon will be affected. I mean, let's say you have ribose (a 5 cabron sugar) and you want to make it into deoxyribose (derived from ribose by the repacement of the hydroxyl group at the 2 position with hydrogen, leading to the net loss of an oxygen). How do you know that carbon-2 will be affected and not, say, carbon-3 or carbon-1?


Thanks!

[john500]

I am not a sugar chemistry expert and I don't remember much of the organic chemistry of them. Furthermore, I don't have access to an organic chemistry textbook or Jerry March's book either. Thus, I am winging it. I suspect that you can not selectively reduce the 2'-hydroxyl group in one step with any known reducing agents. Most likely, if you were do to this in a lab, you would have to use protecting groups and several synthetic steps and get your product in low yield. Biologically, an enzyme in living organisms is probably responsible for the conversion.

[RobJim]

In organisms, this deoxygenation is catalyzed by an enzyme called ribonucleotide reductase. The substrates are ribonucleoside diphosphates.

NDP => (ribonucleotide reductase) => dNDP

N = A, C, G, T or U

The chemical details should be in any biochemisty textbook. You can probably find them with Google too. NADPH, thioredoxin, thioredoxin reductase, glutaredoxin, glutaredoxin reductase, FADH2/FAD, and GSSG/GSH are some of the other molecules involved in the reaction.

As with all or most enzymes, the enzyme's structure is specifically designed to fit the substrate in one orientation only, and the parts of the enzyme which catalyze the reaction are specifically oriented to catalyze the reaction only for the 2' OH group.

The basic idea is that the NDP fits into a cavity in the enzyme in a specific orientation. A tyrosine radical group is in a location such that it specifically takes the 3' H, leaving a single radical electron in that position. Then an SH group donates a hydrogen ion to the 2' OH group, leaving an S(-) group, and the resulting water molecule just drifts away. The resulting cation is stabilized by the radical electron on the 3' carbon. Then a second SH group gets attacked by the S(-) group and a hydride ion gets displaced in the process. As it's getting displaced the H(-) ion is attacking the 2' carbon. Then the 2' carbon takes it's H back from the tyrosine group, and the reaction is done. Then one of the two redoxins regenerates the two SH groups for the next deoxygenation of an NDP.

Now if you're talking about a nonbiological mechanism, I'd like to know what method is being used to do the reaction before I comment on which carbons get deoxygenated.

Does that answer the question?

[seancassell]

Yes, it does, thank you.