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In the diagram of ATP below this paragraph there are no lines between the atoms in the $\ce{NH2}$ molecule or in the $\ce{OH}$ molecules; however, there are lines between all the other atoms. Does the omission of those lines represent some facts about $\ce{NH2}$ and $\ce{OH}$ in the ATP molecule, or did the illustrator omit them in order to emphasize the rest of the molecule?

ATP

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    $\begingroup$ This is a common convention in order to make things clearer. Also, note the fact that not even all atoms are shown. $\endgroup$ – Ivan Neretin Dec 27 '15 at 16:45
  • $\begingroup$ What atoms are missing? It's hard for me (a first year science student) to imagine an atom being so inconsequential that an illustrator could just as well omit it from the diagram. $\endgroup$ – Hal Dec 27 '15 at 17:03
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    $\begingroup$ Look at the ball-and-stick structure (second image from the top) and find that out for yourself. Now, it's not that these atoms are irrelevant and could just as well be absent; no, they must be there, but we simply draw the whole thing this way as a shorthand, much like we say "won't" instead of "will not", or like you just said "ATP" instead of "Adenosine triphosphate". $\endgroup$ – Ivan Neretin Dec 27 '15 at 17:16
  • $\begingroup$ @IvanNeretin It seems to me that the point of a diagram is to show what the molecule is. When we say won't, we know that the listener knows that the meaning of won't is 'will not'. If we have to show someone what a molecule is, then they don't know what it is. A diagram might also be used (instead of "ATP") to aid communication to an audience familiar with the molecule, but in those cases, the depicted portions would only be the parts relevant to the topic. So I should have asked why do diagrams of ATP typically depict the atoms depicted in the diagram above instead of other atoms? $\endgroup$ – Hal Dec 27 '15 at 17:35
  • $\begingroup$ What you have shown is a variant of a structural formula. I use the word variant as there can be more than one way of showing a structural formula. What you seem to allude to in your question about showing all the bonds relates to a displayed formula. $\endgroup$ – Beerhunter Dec 27 '15 at 20:46
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Your example is one of a variety of shorthands that exist because every chemist after the third year of studies knows what is meant so they are too lazy to draw.

In a nutshell, the $\ce{NH2}$ group will always be a nitrogen with a lone pair, two single bonds (one to each hydrogen) and one bond to the molecular skeleton. Much like $\ce{-OH}$ will always be $\ce{-O-H}$. It is also common practice to omit any insignificant hydrogen atoms in organic molecules; in the image above, a total of eight hydrogens has been omitted because every chemist will know where they are (and that they are there).

In principle, the phosphate chain could also be shortened to $\ce{HO3P-PO2H-PO2H-{}}$ rather than writing out all of it. Any chemist will mentally ‘expand’ the molecule in the same (correct) way.

As you continue to study, you will notice when which groups are generally shortened, which rules to observe while doing so and which hydrogens are so superfluous that they are not drawn — and, most importantly maybe, how atoms are labelled that actually are missing hydrogens. it is beyond the scope of a single answer to note them all.

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  • $\begingroup$ I see. So then, just as we omit the hydrogens attached to carbons because carbons give us reason to count on hydrogens being there, there are other constituents, x, that justify us in believing that if y is there. Thank you. $\endgroup$ – Hal Dec 27 '15 at 17:55
  • $\begingroup$ Third year chemist? Really I thought this was like second-third year high school stuff? $\endgroup$ – DRF Dec 27 '15 at 21:45
  • $\begingroup$ @DRF Take that as at the very, very, very latest, even if they stay in phys chem or comp chem. $\endgroup$ – Jan Dec 27 '15 at 21:46
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Essentially scientists have better things to do than draw (an look at) every single atom. This is a skeletal diagram of the molecule. It is meant as a quick and efficient way to convey the structure of the molecule. In fact if you look closely you'll notice that hydrogens bonded to carbons are not even shown. This is done because chemists know they are there, but showing them would take time, clutter the molecule and obscure the functional groups that are more important to the properties of the molecule. The $\ce{OH}$ and $\ce{NH2}$ groups lack lines because they are functional groups and again scientists know but have better things to do. Occasionally functional groups get even more short-handed. the phenyl group which is a bonded benzene ring is often abbreviated $\ce{Ph}$ to conserve space on a paper and save time. Hydrogen atoms will often be shown if they are bonded to a chiral center, but even they may be omitted and assumes to be opposite a show stereo group.

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