pH, pKa, pI, protein charge, and acidic vs. basic amino acids

pH: Measure of free proton availability (comes from combined effect of all acids & bases in a 
solution)  
 
pKa: Measure of acid strength (of an individual deprotonatable site); pH at which there's a 50:50 ratio of protonated & deprotonated 
 
pl: Isolectric point; pH at which a multiprotic molecule is net neutral 
 
pKR: the pka of an amino acid R-group (side chain) 
 
Something can only act as an acid in its protonated state.  
 
But the stronger the acid is, the less likely it will be to be in that state!  
 
So the more likely it is to be in the deprotonated state, where it can only act as a base!  
 
If the molecule is neutral in its protonated state (conjugate acid), it will be negatively-charged in its deprotonated state (conjugate base). 
 
But if the molecule is positively-charged in its protonated state (conjugate acid) it will be neutral in its deprotonated state (conjugate base).  
 
The happier a molecule is to be in a state, the more likely it will be in that state. Resonance and inductive effects can make molecules happy, so resonance etc. that stabilizes one state will make it favorable, even if it comes with charge.  
 
We call amino acids basic or acidic based on what their neutral form acts as - even if their predominant form acts the opposite! So, for example, you pretty much always find arginine in its protonated, acid state because its neutral form is a stronger base, so we call it basic (and show it as blue). On the other hand, you pretty much always find aspartate in its deprotonated, base state because its neutral form is a stronger acid, so we call it acidic (and show it as red) 

Note: updated and adapted from past videos of mine
 
more on pH, pKa, and the Henderson-Hasselbalch equation: http://bit.ly/phbuffers YouTube:    • Henderson-Hasselbalch equation = wher...   &    • Avoiding common problems & confusion ...     
 
more on interpreting & drawing amino acid titration curves:    • Quick guide to interpreting and drawi...    
  
more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0 or search blog: http://thebumblingbiochemist.com