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Following are the three different answers to this question that I reached by googling. Which of them is right?

  1. The covalent bond between the 3' C and the O, and the covalent bond between the 5' C and the O:
    enter image description here



2. The covalent bond between the P and the O that is bonded to the 5' C, and the covalent bond between the P and the O that is bonded to the 3' C (deduced from the following image):
enter image description here



3. The -O- (two covalent bonds with an O) that link between the P and the 5' C, and the -O- that link between the P and the 3' C (deduced from the following image):
enter image description here



Maybe my confusion stems from a more general misunderstanding:
When two alcohols are linked through an ester linkage (i.e., both OH groups are replaced with an -O-), we get R1-O-R2. In this case, do we say that each of the covalent bonds with the O is an ester bond? Or is the whole -O- considered a single ester bond?


(Note that I am not asking what exactly a phosphodiester bond is, which is (if I understand correctly) everything that connects the 5' C and the 3' C of adjacent nucleotides.)

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    $\begingroup$ There's no such thing as "ester bond", there's ester group. $\endgroup$ – Mithoron Oct 26 '20 at 13:51
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    $\begingroup$ @Mithoron That's very helpful. Thank you! Could you provide a reference? The internet seems to be full of people that think that "ester bond" is a thing... $\endgroup$ – Oren Milman Oct 26 '20 at 21:12
  • $\begingroup$ @Mithoron: By the group, you mean O atom, right ? Like in $\ce{CH3-O-SO2-O-CH3}$. IMHO, $\ce{COO}$ is a group, $-\ce{COO}-$ is a bond, $\ce{O}$ in $\ce{R-O-X}$ is a group, $-\ce{O}-$ is a bond. $\endgroup$ – Poutnik Oct 27 '20 at 8:35
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    $\begingroup$ @Poutnik Biochemists may call that "a bond", but from chemical point of view it's not correct. $\endgroup$ – Mithoron Oct 27 '20 at 18:32
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    $\begingroup$ I.e. the scope of bond meanings goes from as small as gluons to as big as galaxy clusters. I would limit it to the interatomic bond only if we speak about interatomic bonds. In this case, it is the bond of molecular structures. $\endgroup$ – Poutnik Oct 27 '20 at 19:21
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All of them are right, regarding ester bonds themselves. But only one of them is right, regarding DNA context. AMP/ADP/ATP/GMP are based on ribose ( see RNA ), not on deoxyribose ( DNA ).

Phosphoric acid has 2 ester bonds in DNA.

You have somehow confused an ester and an ether bond.

$\ce{R_1-O-R_2}$ is an ether bond,

$\ce{R-O-X}$ is an ester bond, where $\ce{X}$ is a carbonyl ( from carboxylic acids or carbonic acid ) or some nonmetal like $\ce{S}$ or $\ce{P}$ for esters of inorganic acids like $\ce{(CH3O)2SO2}$.

If we are to consider it as a bond or a group depends on the point of view. It is both.

It is a group, if we focus on the $\ce{CO-O}$ atom group of esters of organic acids or $\ce{O}$ for mineral acid esters.

It is a bond ( or a bridge ), if we focus on what the group connects.

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  • $\begingroup$ Thank you. What about the general misunderstanding I mentioned in the end? Would you say in this case we have a single ester bond or two ester bonds? Or are both acceptable? $\endgroup$ – Oren Milman Oct 26 '20 at 8:26
  • $\begingroup$ "R−O−X is an ester bond" - so are you saying that the ester bond is the -O- that links between the R and the X? (by the way, a comment to my question says there is no such thing as "ester bond"..) $\endgroup$ – Oren Milman Oct 27 '20 at 7:18
  • $\begingroup$ @OrenMilman The answer has been updated. $\endgroup$ – Poutnik Oct 27 '20 at 7:43
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I will first talk about peptide bonds and ether linkages before circling back to the question. All of these (and the ester group) can be synthesized by a condensation reaction, and the compounds containing these can be split in two by hydrolysis.

Peptide bonds

Peptide bonds are a clearly defined term in biochemistry. The peptide bond is the bond between the carbonyl carbon of one amino acid and the main chain nitrogen of the next amino acid in the protein sequence. When you hydrolyze the peptide bond, you end up with a carboxylic acid group (or carboxylate, depending on solvent and pH) on the one hand, and an amino group (or ammonium depending on solvent and pH) on the other hand.

Ether linkages

In contrast to the amide functional group in proteins, which are hydrolyzed into two different functional groups, ethers are symmetric in the sense that hydrolysis yields two alcohols. Which bond breaks (or where the bridging oxygen ends up) depends on the specifics of the ether and the reaction conditions. Therefor, it is hard to call one or the other bond of the bridging oxygen the "ether bond", it could be either (pun intended).

The situation is different for glycosidic bonds (often incorrectly described as ethers). If you hydrolyze them, you get a hemiacetal and a hydroxyl group (for e.g. a 1,6 linkage in cellulose or starch). In some cases, like sucrose, both sugars use the hemiacetal group in the condensation reaction, and you could describe the linkage as containing two glycosidic bonds.

"Ester bonds"

If you want to be exact in describing the functional group called ester, you should give the name of the acid that is obtained after hydrolysis. For example, there are carboxylic acid esters (like in triacyl glycerides) and phosphoric acid esters (like in nucleic acids). When ester hydrolize, both products carry an oxygen, so like with esters, you have to figure out where the bridging oxygen goes. This depends, again, on mechanism influenced by reaction conditions and the nature of the ester, but mostly it stays with the alcohol product.

So even though ester bond is not a technical term, you will find it used (even on this site), and for a phosphate ester, it would typically be used to talk about the pond between phosphate and the bridging oxygen atom. By that logic, a phosphodiester would have two ester bonds. For the three possibilities the OP offered, number 2 would be the best one because it describes which atoms end up with which hydrolysis product (for the typical hydrolysis mechanism).

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