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Unformatted text preview: Chemistry 3B Lecture 26 Thursday April 30 th , 2009 • Of the 20 amino acids in Table 26.1, we will only classify a few. The 3 categories we place them in are: non polar, polar/uncharged at physiological pH, and polar/charged at physiological pH. We typically deal with physiological pH. The non polar ones are easiest to identify: we have valine with an isopropyl group, we have leucine, and we have phenyl alanine. Polar uncharged at physiological pH molecules include: serine, tyrosine, and glutamine. The hydroxyl group will not be charged at physiological pH. If you put an alcohol in water, it won’t get deprotonated. Glutamine is simply the amide analog of glutamic acid. How do we know it won’t be charged at physiological ph? We haven’t protonated amides unless thrown into acids. If you lok at table 26.1, under the heading pk of acidic function in R (the side chain) and you find glutamine, you will see there is no pka associated with it. If there is no pka associated with it, it can’t be charged at physiological pH. If you look at the column for serine, you won’t find a pka either. Tyrosine has one at 10. These are all polar side chains with polar side chains; they have amides, etc… The other category is polar charged at physiological pH: lysine and if you use the Henderson Hasselbach equation, it is pH=7. The pka of the side cahin is 10.5 so we need this to be -3 (the log). We need to decide what is HA and A-. HA is the ammonium ion, and A- is the neutral NH2 group. We are mainly going to have very little of the NH2, and a fair amount of NH2+ at physiological pH. We have aspartic acid: it’s pka is about 4 so at physiological pH it will be substantially deprotonated. It would be a carboxylate at physiological pH. We can’t focus on the carboxy or amino groups by looking at these. The focus is the side chain. The NH2 is focues on as an amino group but it is not the only one. The amide function is different from the amino group. The amide function doesn’t behave like an amino function. An amino group is an NH2 or NR2 with a lone pair of electrons where the lone pair cannot resonate to the R group. When the NH2 is attached to a carbonyl, it is the amide function. • Reactions: we will show 2 reactions with real amino acids. We will take valine under acidic conditions, that’s why it is charged. We’ll throw it in methanol and HCl which protonates the amino group. What we get is the ester. Carboxylic acids thrown in an alcohol and an acid catalyst will give the ester. We just get out the ester and the amine isn’t doing anything. Methianine is shown: we want to take methianine’s zwitterion form and if we take methiane or any amino acids that have a carboxy group and alpha amino group only (like if you just buy methianine) it will come as the zwitterion form. We have an NH2 and a carboxy group: base and acid exist next to each other. When you throw it into water and change the pH, then the charge state can change but we will stop...
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