Chemistry 3B Lecture 25

Chemistry 3B Lecture 25 - Chemistry 3B Lecture 25 Tuesday...

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Chemistry 3B Lecture 25 Tuesday April 28 th , 2009 Complex amino acids: Amino=amino group, and acid = carboxy group in the same molecule. Amino groups don’t have to be on the alpha carbon. They pertain to biological systems; the alpha amino acids are more prevalent in alpha amino acids. Amino acids is a generic term for alpha amino acids. Beta amino acids and gamma amino acids are also talked about. There are 22 “DNA” encoded amino acids: DNA recognizes what these 22 amino acids are. 19 of the 20 common amino acids are chiral. The amino group is always to the left, so that’s why we call them the L-amino acids. The vast majority of sugars are D-sugars like D-glyceraldehyde. All of the 20 common amino acids all have 3 letter codes, as well as 1 letter codes. Everything is in table 26.1 including pka values, and the codes. The only achiral of the DNA encoded amino acids is Glycine becauses it has a CH2 group. Lets examine Alanine (Ala): It has a methyl group in it. Lets look at the acid base characteristics of this amino acid. We are going to examine the acid base characteristics starting with fully protonated alanine. The fully protonated means the carboxy group and the amino group is protonated. The structure of alanine would be like this at low pH. The amine is a base and put in acidic solution will get protonated. if we increase pH, then what we find is that we will pull of a proton. What is the first proton to come off? The carboxy proton or the ammonium ion? The carboxy proton because the pka values are lower for the carboxy proton. The next proton to come off is the ammonium ion proton. But there are other protons. We have alpha hydrogens, etc… but we are only interested in amino acids. The pH range we are considering is 0-12. We’re not interested in the pKa of the hydrogen group out at 40, etc… The alpha hydrogens (if it was an ester) it would be about 22, but since it’s a carboxylate they will be at 30. Hydroxide ion will not pull these protons off. The overall charge of the molecule shown is +1, the next one has a charge state of 0 and the last one has a charge state of -1. There must be a counterion associated with these. But we are interested with the charge on the amino acid itself. The ion with a 0 charge is called the zwitterions and it has a neutral
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charge. The – and + balance each other out. Let’s plot this out on a graph. The pH is on the x axis and the percent composition of the solution is on the y axis which is how much of each of these various forms are going to be present. At a low pH, we are starting with the species of charge state +1 (blue) at 100%. As the pH increases, the concentration of the +1 ion will decrease and the zwitterion concentration will increase. As the +1 ion decreases, the 0 ion amount increases and where the cross is at 50% abundance. But since we are plotting pH, right at 2.3 we have 50% of both the +1 ion and the 0 charged ions. We have all seen this equation: pH= pka +log ((A-)/(HA))
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Chemistry 3B Lecture 25 - Chemistry 3B Lecture 25 Tuesday...

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