A) A peptide with the primary structure Lys-Arg-Pro-Leu-Ile-As...

Question

A) A peptide with the primary structure Lys-Arg-Pro-Leu-Ile-Asp-Gly-Ala is sequenced by the Edman degradation procedure. If each Edman cycle is 93% efficient, what percentage of the PTH-amino acids in the fourth Edman cycle will be PTH-Leu?

B) What percentage of the PTH-amino acids in the eighth Edman cycle will be PTH-Ala?

B) What percentage of the PTH-amino acids in the eighth Edman cycle will be PTH-Ala?

Accepted Answer

Alright. So here's a 2 part practice problem broken up into part a up above and part b down below. And part a says a peptide with the primary structure shown here is sequenced by the Edmond degradation procedure. If each Edmond cycle is 93% efficient, what percentage of the PTH amino acids in the 4th Edmond degradation cycle will be PTH Leucine? And we know the 4th Edmond degradation cycle will reveal the 4th amino acid residue from the end terminal end, which is leucine. And so although this practice problem here might seem like it's asking something different than our previous practice problem, really, it's asking the same exact thing, just worded a little bit differently. And so this percentage of the correct PTH amino acid in that Edmond cycle is really just asking us for the cumulative yield. And we know that our equation, where we take the reaction efficiency per cycle and raise it to the number of Edmond cycles will reveal the cumulative yield. So all we need to do is plug into this equation. And we're told that the reaction efficiency per cycle is 93%, and 93% as a decimal is 0.93. And then we can raise that to the number of Edmond cycles, which will be 4. And so if you take your calculators and you do 0.9 3 raised to the power of 4, you'll get an answer of 0.748. And this is our cumulative yield in a decimal format. But if we want to convert it into a percentage, we just multiply it by a 100%, and that gives us 74.8%. And this is the cumulative yield and the answer to part a. And so recall from our previous lessons that a cumulative yield above 60% allows for accurate protein sequencing. And so because 74.8 is greater than 60%, that means that we'll get accurate protein sequencing up through the 4th Edmonds cycle and sequencing up through leucine. Now, now that we've got part a, let's move on to part b. And part b says, what percentage of the PTH amino acids in the 8th Edmonds cycle will be PTH alanine? And looking at at our peptide, notice that the 8th residue here is alanine. So, we're looking for the percentage of the correct PTH amino acid. And so essentially, all we need to do is use our formula up above again, except change out the number of Edmond cycles. So we're still working with a reaction efficiency of 93%, which is 0.93 in decimal format. The number of Edmond cycles is now changed to 8, so we can put 8 here. And so if we take our calculators and we do 0.93 raised to the power of 8, that gives us an answer of about 0.56. And this is our cumulative yield in a decimal format. So if we want a percentage, multiply it by a 100%, and that gives us 56%. And so this is the answer for part b, the percentage of the correct PTH amino acid. And so because this cumulative yield is less than 60%, that's saying that accurate protein sequencing through the 8th Edmond cycle up, sequencing through the 8th residue here is not going to be very accurate. And so essentially, what you guys may have noticed is that this 93% efficiency, reaction efficiency, seems really, really low, especially since we said in our previous lesson videos that 99% was already low. But through this practice problem, one of the major takeaways is that we're able to sacrifice reaction efficiency if we limit the number of Edmond degradation cycles. So when we only had 4 Edmond degradation cycles, we were able to get accurate protein sequencing with a high cumulative yield above 60%. But once we increase the number of Edmond cycles, notice that we had to sacrifice our cumulative yield and sacrifice accurate protein sequencing. So that's something important to keep in mind, the fact that not only reaction efficiency, but also the number of Edmonds Cycles, will affect the cumulative yield and accurate protein sequencing. So that concludes this practice problem, and I'll see you guys in our next video.

Struggling with Biochemistry?

Watch next

Edman Degradation Reaction Efficiency practice set