Acid-base theory for DNA and RNA

[jackson6612]

I'm not a science student - quite a layman. So, please keep your replies simple and straightforward. Thanks.

Why are there more than one theory on acid-base? Why isn't one theory enough? Are these theories inter-compatible? Does one theory try to counter the limitations of earlier theory(ies)?

It is normally told that an acid tastes sour (something like lemon juice) and turns litmus red. Is this always true, no matter what?

Please guide me.

 

[Borek]

Does one theory try to counter the limitations of earlier theory(ies)?

You have hit the nail on the head.

Simplest theory - proposed by Arrhenius - defined acids as substances that dissociate giving off H⁺ (proton) and bases that dissociate giving off OH^-. Its limitations are obvious - ammonia is NH₃, it even doesn't contain oxygen, so in no way it can dissociate giving off OH^-, yet when it is put into water concentration of OH^- goes up. How come?

That's where the Brønsted-Lowry's theory kicks in. It defines acid as a substance able to give off H⁺, and base is substance able to accept the H⁺. Now it is clear why ammonia is a base - when put in water, it reacts with it, accepts a proton - and in effect concentration of OH^- goes up:

NH₃ + H₂O <-> NH₄⁺ + OH^-

Other theories aim to generalize the idea of acids and bases, so that more and more reactions can be classified as acid-base reaction. They are not without successes, but IMHO they sometimes go a little bit too far.

 

[jackson6612]

Thank you very much, Borek. You have really helped in a plain way.

It is normally told that an acid tastes sour (something like lemon juice) and turns litmus red. Is this always true, no matter what?

Please also let me know the answer to this one. Let me rephrase my question: Are those properties (perhaps, physical properties) always such as acid tastes sour, turns litmus red, and base turns litmus blue, always true? Do they always hold? RNA is an acid as its name tells, do those properties hold for it too?

Thanks for your guidance and time.

 

[mccoy1]

Thank you very much, Borek. You have really helped in a plain way.
Please also let me know the answer to this one. Let me rephrase my question: Are those properties (perhaps, physical properties) always such as acid tastes sour, turns litmus red, and base turns litmus blue, always true? Do they always hold? RNA is an acid as its name tells, do those properties hold for it too?

Thanks for your guidance and time.

The colour change is always true depending on the nature of the indicator or original colour of litmus paper. I think it's not true though that all acids taste sour and bases bitter. No one actually tasted them! I don't think ammonia tastes bitter (well I haven't tasted it before lol)...but it's definitely a base and have the same effect on litmus paper as other bases.

 

[jackson6612]

Thanks a lot, Mccoy.

What about DNA AND RNA which are also acids?

Which physical properties are always true for acids and bases? The one you have already stated is that they change the color of litmus.

Can all the chemical compounds be classified as acids or bases? Some, such as sodium chloride, are neutral. In organic chemistry there are many compounds which do not interact with polar solvents. To fit acid-base criteria a compound should be able to dissolve in water. Am I correct? That means those compounds which do not mix in water can never be classified as an acid or base?

Best wishes
Jack

 

[Borek]

Color change of an indicator depends on the pH, that in turn depends on the acid strength and concentration - so just because something behaves like an acid doesn't mean it will always turn litmus red. In most cases yes.

When it comes to solubility - situation is not that easy. For example some resins are not soluble, but they have plenty of acidic groups on the surface, so they can lower pH just when dropped (as granulate) into water.

When it comes to DNA - take a look here:

http://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg

Every oxygen with negative charge can be protonated. When protonated, molecule will be an acid.

 

[jackson6612]

Thank you very much, Borek. That is really helping me.

Color change of an indicator depends on the pH, that in turn depends on the acid strength and concentration - so just because something behaves like an acid doesn't mean it will always turn litmus red. In most cases yes.

But when it affects it has to be an acid or base?

When it comes to solubility - situation is not that easy. For example some resins are not soluble, but they have plenty of acidic groups on the surface, so they can lower pH just when dropped (as granulate) into water.

You mean that those resins aren't soluble in general but some of their 'molecules' or 'parts' dissociate from the parent molecule which is a resin and those dissociated 'parts' would affect pH.

When it comes to DNA - take a look here:

http://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg

Every oxygen with negative charge can be protonated. When protonated, molecule will be an acid.

Okay. Being 'protonated' means that when an H+ is added to those negative oxygen? But in standard form DNA and RNA are neutral molecules? What makes them neutral, H+? Assuming it's H+ which protonate negative oxygen, the that would mean when in solution DNA and RNA would release those H+ to affect pH. Please guide me on this.

Thanks a lot for all your help and your valuable time.

Wishing you happiness and prosperity
Jack

 

[jackson6612]

Help, please.

 

[pzona]

But when it affects it has to be an acid or base?

I assume that there are exceptions (this is chemistry, remember :), but for the vast majority of compounds, yes, if it changes the color of the paper it will be either an acid or base. Maybe a weak one, but still an acid/base.

You mean that those resins aren't soluble in general but some of their 'molecules' or 'parts' dissociate from the parent molecule which is a resin and those dissociated 'parts' would affect pH.

I'm not hugely familiar with DNA, so I feel I should leave this to someone who knows a little more about it than I do. Sorry I can't help here.

Okay. Being 'protonated' means that when an H+ is added to those negative oxygen? But in standard form DNA and RNA are neutral molecules? What makes them neutral, H+? Assuming it's H+ which protonate negative oxygen, the that would mean when in solution DNA and RNA would release those H+ to affect pH. Please guide me on this.

Yes, you're right. When in solution, the DNA/RNA would release the H+, which is what makes them acids. However, it doesn't have to be H+ that makes a particular oxygen neutral. If you look at the corresponding oxygen in each phosphate part of the backbone in the picture Borek gave, some of them are neutral because they are bonded to a carbon in deoxyribose. They can lose the negative charge by bonding to another piece in the DNA chain, so it doesn't have to be an H+ necessarily, although on the ends of the molecule it will likely be H+.