Amino Acids- Acid Base Chemistry

Continuing on from yesterday's post about amino acids, today I'm going to go into a bit more detail about their properties.

Understand the pH scale and know the definition of of pH. Be able to calculate pH from [H+] and [H+] from pH. Understand that H+, H3O+ and H+(aq) are used interchangeably.

Know that high pH is alkaline and low pH is acidic, neutral pH is about pH 7.

Nice easy dot points to start off with :) The pH scale is, in a nutshell, a measure of how acidic or basic a substance is. It runs on a scale of 1-14, with lower pHs indicative of acidity and higher pHs indicative of basicity. A pH of 7 is neutral (neither acidic or basic).

pH is related to the concentration of hydrogen ions in solution. pH is equal to the negative log of the concentration of H+ ions in solution. Hence:

pH = -log [H+] and [H+] = 10^(-pH).

As for the last point, if I remember correctly from year 12 chemistry, hydrogen ions tend not to exist by themselves in solution, but rather associate with water molecules to form hydronium ions (H3O+). Hence H3O+ and H+ can be used interchangeably. (As for the H+(aq)... well that's just the same as H+ except it also has the state symbol.)

Know the difference between strong and weak acids and bases and understand the relationship between a conjugate acid and a conjugate base. 

The strength of an acid or base depends on how readily it dissociates into ions in solution. An acid or base that dissociates more fully in solution is considered to be a strong acid/base, whereas an acid or base that does not dissociate very much is considered to be a weak acid/base.

A conjugate acid is simply a base with a proton added, whereas a conjugate base is simply an acid with a proton removed.

Know the definition of pKa and be able to calculate it from Ka. Understand the relationship between pKa and acid strength. 

Ka is basically the equilibrium constant of the acid/base dissociation equation. If that doesn't make sense, let me try and explain with an equation. Let's say that you have an acid HA (where A is any anion). Its dissociation equation is this:

HA <--> H+ + A-

Equilibrium constants are basically the product of the concentration of the products divided by the product of the concentration of the reactants. Hence the Ka, or the equilibrium constant of this equation, is as follows:

([H+][A-])/[HA]

pKa is the negative log of Ka:

pKa = -log(([H+][A-])/[HA])

Lower pKas are indicative of stronger acids, whereas higher pKas are indicative of weaker acids. Let me try and explain why:

In a strong acid, there is a much higher concentration of products than reactants. Hence Ka is high. When taking a log, you'll also end up with a relatively high number, but this will then be reversed by the negative sign. (So for example if Ka was 10^3 you'd end up with a pKa of -3 by the end of it.) In a weak acid, on the other hand, the ratio between products and reactants is much smaller and hence Ka will be smaller. After taking a negative log you'll end up with a larger number. For example, if Ka was 10^(-6) the pKa would be 6.

That was a pretty terrible explanation, but moving on...

Know the derivation of the Henderson-Hasselbalch equation and the equation itself. Know that when the pH = pKa the concentrations of A- or conjugate base and HA or conjugate acid are equal. Be able to use the Henderson-Hasselbalch equation to calculate pH or pKa or concentrations of conjugate acid and conjugate base or net average charges. 

The Henderson-Hasselbalch equation is, simply put, a way of relating pH and pKa. This equation can be derived from the pKa equation (given above) and the knowledge that pH = -log[H+].

pKa = -log(([H+][A-])/[HA])
pKa = -(log([A-]/[HA]) + log[H+])
pKa = -log[H+]) - log([A-]/[HA])
pKa = pH - log([A-]/[HA])

This can be rearranged to give pH = pKa + log([A-]/[HA])

A neat feature of this equation is that it makes it easy to work out the isoelectric point- that is, the pH at which the concentration of A- is equal to the concentration of HA. You see, when pH is equal to pKa, they cancel out on both sides, giving log([A-]/[HA]) = 0. Now log 1 = 0, so ([A-]/[HA]) = 1. Hence A- must be equal to HA (since a number divided by itself gives 1).

Average net charges can be found by looking at the pKa of each ionisable group. Firstly you need to find the ratio of conjugate base (A-) to conjugate acid (HA). To do this simply plug in the pH and pKa given into the equation. If the ratio of conjugate base to conjugate acid is high, then assume that nearly all of the substance is in the base form, and calculate the charge accordingly. (This will depend on the substance- for example if you have NH3+/NH2, the deprotonated form will be neutral, whereas if you have COOH/COO-, the deprotonated form is negatively charged.) You can use similar logic if the ratio is very low, but in this case you would assume nearly all of the substance is in the acid form. If the substance is at its isoelectric point and half of it is protonated and the other half deprotonated, use the average of the charges of the two forms. For example if you had half NH3+ and half NH2, the average would be +0.5. From there, you can add up all of the charges to get an average net charge.

Be aware of the approximate pKas of the α-amino and α-carboxyl groups of amino acids. 

This one'll be quick to answer. The approximate pKa of the alpha-amino group is 9.0 while the approximate pKa of the alpha-carboxyl group is 2.0.

Know the structures of the ionisable groups of amino acid side chains e.g. Asp/Glu: –COOH <--> COO- + H+, Lys: -NH3 + <--> - NH2 + H+, Cys: -SH <--> S- + H+ and hence know the charge on the conjugate acid and conjugate base forms of the ionisable groups. 

Generally, for polar acidic amino acids, the protonated form is uncharged while the deprotonated form is negatively charged. For polar basic amino acids, and other polar uncharged amino acids with -NH2 groups, the protonated form is positively charged while the deprotonated form is uncharged. Finally, for cysteine, the protonated form is uncharged while the deprotonated form is negatively charged.