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Assume you want to make and study fragments of a protein. Would you expect that any fragment of the polypeptide chain would fold the same way as it would in the int...

Question

Assume you want to make and study fragments of a protein. Would you expect that any fragment of the polypeptide chain would fold the same way as it would in the intact protein? Consider the protein shown in Figure $4-19$. Which fragments do you suppose are most likely to fold correctly?

Assume you want to make and study fragments of a protein. Would you expect that any fragment of the polypeptide chain would fold the same way as it would in the intact protein? Consider the protein shown in Figure $4-19$. Which fragments do you suppose are most likely to fold correctly?



Answers

Assume you want to make and study fragments of a protein. Would you expect that any fragment of the polypeptide chain would fold the same way as it would in the intact protein? Consider the protein shown in Figure $4-19$. Which fragments do you suppose are most likely to fold correctly?

So in this podcast we're continuing on with into molecular forces and we're going to be talking about into molecular forces that are responsible for holding protein strand in the shape. So these forces that we see hydrogen bonding. So in our protein, we have carbon. I'll group. I will hydrogen bond with our N H groups to hold the structure together. Now these C O on H functionalities exist in our amino acids that make up all proteins.

We were asked to provide four different ways in which one part of a poly peptide chain you may interact with another part. So one way that this occurs is an ionic bond forms between an acidic psyching on one segment and a basic side Cain on the other. Another example is when dia so five bridges conform between 16 side chains. Hydrogen bonds can form between some surgeons and, lastly, non polar side chance conform non polar environments. So these are also written in decreasing order, So these are the strongest, and these are the weakest.

Talking about. Amino sits here, and there are 20 common amino acids that honor and more specifically, we're gonna be looking at the properties. So if you were toe want to identify a polar hydro filic amino acid, Then you'd be looking for a head dropped him in the our group structure, where us if you were looking for a hydrophobic non polar immuno acid than the All Group should just contain hydrocarbon chains.

So here we're looking to make synthetic cuts for fragments that we might expect in Dimas Spectra off the following molecules. So fastly, just to cover a definition in spectrometry fragments is the dissociation off energetically unstable molecular irons formed when passing the molecules in the ionization chamber of a mass spectrometer. So the fragments of a molecule do cause a unique pattern in the mass spectrum. So when we're looking up fragments, we need to assign a synthetic cuts that would allow us to form are fragments. So, for example, in this first structure, while we have a a brunch hydrocarbon, where we also have a key toe we may cut here on, that would generate two different fragments. We could also cut up this site so that just two examples about we could cut in all the to generate fragments. And there are no second monkey. We have tried, he thought, Amy so obviously. But there's only really Ron sort of cut that we can make here, and that is too removed in exile group


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