Biochemistry More Examples with Amino Acids & Peptides

This lecture covers four in-depth examples of amino acid reactions. The first example explains how to find the isoelectric point of serine, its structure at different pHs, how to manipulate pH using sodium hydroxide, titration curves, and the buffer range of serine. Example two discusses quantitative analysis, molar mass, and finding tyrosine residues of an unknown protein. The third gives several procedures and tests and explains how to find the structure of methionine encephalin from the results. The final example talks about the Merrifield synthesis of a particular tripeptide including glycine, phenylalanine, and leucine, giving an overview of the synthetic process.

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How to Draw the structure of lysine that predominates at PH =5.5 and PH= 12.7 ?

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Post by Torrey Poonon January 28, 2014

Thank you Prof. Hovasapian, that explanation helped!

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Last reply by: Professor HovasapianMon Jan 27, 2014 3:30 PM

Post by Torrey Poonon January 27, 2014

How did you get the value 27,166 g/mol on Example 2, part b?

More Examples with Amino Acids & Peptides

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Transcription: More Examples with Amino Acids & Peptides

Hello and welcome back to Educator.com, and welcome back to Biochemistry.0000

We just finished discussing amino acids and peptides, and what I thought we would do is just do some more example problems with amino acids and peptides just to make sure we have a complete understanding, give us a little bit of review of the things that we have done before, and just get familiar with it.0004

First of all, we want to know how many moles of serine there is in there because it is going to depend on how many moles of ionizable groups that we have to titrate because that is what the hydroxide is doing.0374

The hydroxide is going in there, and it is pulling off the hydrogen from the carboxyl group; and when that is done, that is going to be the isoelectric point, and then it is going to go and start pulling off the hydrogens from the amino group until it's done.0386

That is the second plateau on the titration curve, which we will draw in just a minute.0402

Well, since we have 0.02mol of ionizable group that have been ionized, that means, and it's a 1 to 1 ratio, 1 hydroxide per 1 ionizable group, right, is pulling off 1 hydrogen, that means there are 0.02mol of the hydroxide that I have to use.0533

Because if it were fully ionized, it would carry a charge of -1, but at the pK1 - remember we said that's when half of the groups are ionized - the protonated and deprotonated form are in equal concentration.0740

If you are given a titration curve with numbers on it, you should be able to say this happens here, this happens here, this happens here; or if you are given a numerical data, you should be able to produce the titration curve.1044

So, the first question we want to ask you is...and this is the process that you will use.1511

Assuming the protein contains only 1 tyrosine residue, calculate the minimum molar mass of the protein.1520

What we are going to be doing by assuming that we actually have just 1 tyrosine residue, we have the percentage, if we assume just 1 tyrosine residue, we can place a lower limit on the molar mass; and then from there, given this other bit of information, the 135,800, then we can go ahead and find out a little bit more about it.1557

Well, we take the 163g/mol, divided by the total protein mass, times 100, and they already told us that this is equal to 0.60, because it’s 0.60%m/m tyrosine, part over the whole, tyrosine over the whole; and when I solve for the mass, I end up with 27,166g/mol.1663

It reacts with the last one first, and then if you have any other free acids, then that tells you how many that you have, but in this case, there was only 1 DNB-Tyr that was detected, but there were no free tyrosines, which means there is only 1 tyrosine, so this 2:1 to 1:1 is not just a ratio, it is exactly how much we have.2202

We have 2 glycines; we have 1 methionine, 1 phenylalanine, and we have 1 tyrosine.2221

Now, pepsin cleaves, like we said, pepsin cleaves the phenylalanine, the tyrosine and tryptophan, but we don't have to worry about tryptophan on the left.2245

When it cleaves it on the left, that means, in other words, if you have, OK, if this is either phenylalanine or tyrosine, it is going to break it right there.2260

So, one of your fragments is going to have a phenylalanine or a tyrosine on the left.2277

One of the dipeptides, they said, contains phenylalanine and methionine.2282

Well, we know that that dipeptide has to have a phenylalanine on the left.2286

So, we know that we are looking at Phe and Met- that is our dipeptide.2291

Well, we also know that tyrosine...there is also a tyrosine and a glycine on a 1:2 ratio.2297

Well, I have already accounted for the phenylalanine and the methionine.2307

I know that tyrosine is on the left, so that I know that I'm looking at this- Gly and Gly.2310

I know there is nothing to the left of the tyrosine because that is the N-terminal amino, therefore, all of this information points to the following: Tyr, Gly, Gly, Phe, Met- tyrosine, glycine, glycine, phenylalanine and methionine.2318

Hopefully I can do it, so let's start off with our leucine, and I'm going to react it with our Fmoc-chloride, and that is going to give me Fmoc-leucine; and then, I'm going to react this with a bead, those polymer beads.3024

What I end up with is Fmoc-leucine, and then the bead; and then I'm going to subject this to trifluoroacetic acid or mild base to deprotect that leucine, get rid of the Fmoc.3050

We have got Phe; we've got Leu, and we've got a bead, and we want to go ahead and subject that to trifluoroacetic acid, and we end up with glycine, phenylalanine, leucine, still attached to a bead, and then we wash this with some hydrofluoric acid.3210

We end up releasing that; we end up breaking this bond, the leucine and bead bond, and we end up with our final glycine, phenylalanine and leucine.3236

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