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I'm a Chemistry student learning about periodic trends. I know that in (many organisms') cellular respiration, oxygen serves as the final electron acceptor due to its high electronegativity.

However, applying the periodic trends, fluorine is more electronegative than oxygen, and the noble gas neon even more so than fluorine. Why aren't either of these the final electron acceptor? I know that in some organisms, the final electron acceptor is sulfur. But I've never heard of it being fluorine or neon. Why?

One of the main reasons that modern(!) biology uses oxygen as an electron acceptor is availability.

Around 2.45 billion years ago, oxygen (O$_2$) started being built up in the atmosphere (which actually killed off a lot of the lifeforms/bacteria at that point). Since then, oxygen consuming lifeforms were able to establish themselves. Before that, most organisms probably used mainly (elemental) hydrogen as electron acceptors.

Apart from not really being available in the atmosphere, there are other reasons why fluorine or neon don't make for good biological electron acceptors:

• While elemental fluorine (F$_2$) is indeed extremely electronegative, this makes it so reactive that it:
  
  a) could not be controlled by biology [the reactivity of oxygen is why it killed so many bacteria in the first place] and
  
  b) just does not occur (or at least remain in) in the elemental state in nature (there is no measurable F$_2$ in our atmosphere).


• Neon (and other noble gases) are in theory also quite electronegative, actually so much so, that they never* occur without their electrons and therefore don't react at all.

*It's somehow possible to form noble-gas compounds, but it requires very specific chemical reaction conditions, that mostly occur under controlled man-made conditions (and are not good for biological life forms).

Availability and applicability.

Availability.

In the beginning, there was CO2. It was abundant in the atmosphere, and later, the oceans.

Fluorine and neon weren't, and so respiration evolved around what was (and is) available.

Ref.: Paeloclimatology / History of the Atmosphere.

Applicability.

The other point about oxygen is that it works rather beautifully both ways. Chloroplasts can easily split up CO2 and H2O into glucose and O2 with a bit of sunlight. Hemoglobin can combine both O2 and CO2 with just a little difference in partial pressure. Mitochondria can run through the citric acid cycle without getting destroyed in the process.

Once fluorine has taken hold of another atom and formed a molecule, it will be pretty hard for an organism to make it let go again, and if it does the fluorine will want to react with something, anything really, whether that's good for the organism or not.

On the other end, neon doesn't want to react with anything.

So while chemically there's a point to be made for the more energetic oxidizer, evolution / an organism is not "interested" in the energy content alone. The substance must be available, and the process must be somewhat sustainable. Oxygen ticked those boxes, fluorine and neon didn't.

Even rocket scientists, who are really looking for the most energetic compounds they can get their hands on, dropped the idea of fluorine as a propellant because it's not safe to handle in uncombined form. There's a lesson in there.

The atomic radius of fluorine is just slightly larger than that of carbon. When a fluorine atom bonds to a carbon atom that is part of a carbon backbone, the fluorine atom covers up not only the C-F bond but also the adjoining C-C bonds. This makes it impossible for biological enzymes to access these bonds to break them, and is why fluorinated compounds are biologically inert.

This is the reason why we fluoridate water and toothpaste; bacteria have no enzymes that can break down enamel that is formed with fluorine! It is also why teflon (repeating units of -CF$_2$-) is not biodegraded yet saturated fatty acids (repeating units of -CH$_2$-) are easily biodegraded.

All elements that are used biologically have ecological cycles where they are reused for other purposes. Because fluorinated compounds can't be broken down, such an ecological cycle would rapidily come to a halt. Therefore, fluorine has an evolutionary disadvantage over other elements.

I agree with the other answers that neon can't be an electron acceptor because it won't form into compounds. I disagree with their "oxygen first" argument; evolution doesn't care which mechanisms evolve first. If a fluorine metabolic pathway had been more effective than oxygen's, its pathway would eventually surpass the earlier-evolved pathway. Furthermore, there are plenty of trace minerals (e.g. selenium) that are used by life.

Neon just does not work as an electron acceptor. It is that inert that there are currently no known Neon compounds at all.

Fluorine would work in principle, but it is rare compared to oxygen and its strong reactivity makes it a very dangerous substance in elementary form. So it seems very natural that life chooses Oxygen and not Fluorine.

The reason is, free Fluorine does not exist in nature and Neon is a noble gas. I would make the assumption, that oxygen is the only free and abundant electron acceptor in our biosphere.

1) Fluorine reacts with every element with only a few exceptions (some noble gases) and will thus be bound instantly even if it is constantly produced somewhere.

2) Because of its electronegativity the energy to free Fluorine from complexes is very high, so efficiency of photosyntheses will be shitty.

3) Under the assumption there would be an atmosphere of fluorine gas, carbon based life could not exist, because fluorine reacts with carbon already below room temperature.

The comment below stating that fluorine is rare is plain wrong. It is not as common as oxygen, but doesn't need to be. E.g. carbon is also rare in comparison to oxygen. The main problem is lack of accessibility due to stability and high energy necessary to free it, connected with the fact that it would destroy every protein. A suitable electron acceptor must be metastable and be able to co-exist with carbon based life.