C/P SB re gel electrophoresis spoiler for #69

[Doctor_Strange]

Why is HP considered "more compact", wouldn't that imply it is heavier? I thought lighter molecules during native gel electrophoresis (or any kind of gel electrophoresis) travel farther because of molecular weight and the electrical field established? I dont know what that arrow means as well.

THanks

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[theonlytycrane]

The arrow is the direction that the molecules are moving down the gel. Lighter molecules will move farther, but it depends on what the question is asking and the answer choices. HPmutant being more compact and more easily able to move through the porous gel would be one explanation for why it moved farther (assuming it is of similar weight and charge as MBmutant).

 

[Doctor_Strange]

The arrow is the direction that the molecules are moving down the gel. Lighter molecules will move farther, but it depends on what the question is asking and the answer choices. HPmutant being more compact and more easily able to move through the porous gel would be one explanation for why it moved farther (assuming it is of similar weight and charge as MBmutant).

Would this change your response?

 

[Doctor_Strange]

The arrow is the direction that the molecules are moving down the gel. Lighter molecules will move farther, but it depends on what the question is asking and the answer choices. HPmutant being more compact and more easily able to move through the porous gel would be one explanation for why it moved farther (assuming it is of similar weight and charge as MBmutant).

And yes I believe they are similar in both those aspects, I guess I interpreted more compact as meaning it is heavier? Isn't that the definition lol

 

[theonlytycrane]

^My response correlates with answer choice B.

Compactness is more about the shape than weight. If it's more spread out, it won't move through the gel as well.

 

[Doctor_Strange]

^My response correlates with answer choice B.

Compactness is more about the shape than weight. If it's more spread out, it won't move through the gel as well.

Thank you so much! I had a feeling as much, but wanted to confirm with some smarter people out there lol

 

[aldol16]

Why is HP considered "more compact", wouldn't that imply it is heavier? I thought lighter molecules during native gel electrophoresis (or any kind of gel electrophoresis) travel farther because of molecular weight and the electrical field established? I dont know what that arrow means as well.

It depends on whether you're talking about native gels or reducing SDS gels. If the former, compactness is a factor. If the latter, compactness is not a factor.

 

[Doctor_Strange]

It depends on whether you're talking about native gels or reducing SDS gels. If the former, compactness is a factor. If the latter, compactness is not a factor.

It is in regards to native gels. But to your point, molecular weight (as i interpret "compactness" to mean) would be a factor in either native or SDS since both use molecular weight as a method of identification right? I mean, I know there is non denaturing (i.e. native) SDS and reducing SDS (which yields primary sequences), but at the end of the day, they all have their own weights and so maybe compactness is not the right word but weight is certainly a factor in both I would imagine...

EDIT: I think I clarified it with specifically in regards to various PAGES, (although the aamc question was between native gel and denaturing gel only )below:

 

[aldol16]

It is in regards to native gels. But to your point, molecular weight (as i interpret "compactness" to mean) would be a factor in either native or SDS since both use molecular weight as a method of identification right? I mean, I know there is non denaturing (i.e. native) SDS and reducing SDS (which yields primary sequences), but at the end of the day, they all have their own weights and so maybe compactness is not the right word but weight is certainly a factor in both I would imagine...

Molecular weight is indeed a factor in both but weight is distinct from compactness. Compactness refers to how well a protein folds - globular proteins are more compact than extended structures. So say you have a 100 kDa and 125 kDa protein. In terms of weight, the second one is heavier and you would expect it to migrate slower. However, say the second one is a globular protein whereas the first has a lot of extended beta sheets. The second is thus more compact and in a native gel, it may well be that the second one migrates farther than the first. In a native gel, this so-called "apparent" molecular weight is misleading as to the actual molecular weight and you can't identify a protein using only a molecular weight ladder.

 

[Doctor_Strange]

Molecular weight is indeed a factor in both but weight is distinct from compactness. Compactness refers to how well a protein folds - globular proteins are more compact than extended structures. So say you have a 100 kDa and 125 kDa protein. In terms of weight, the second one is heavier and you would expect it to migrate slower. However, say the second one is a globular protein whereas the first has a lot of extended beta sheets. The second is thus more compact and in a native gel, it may well be that the second one migrates farther than the first. In a native gel, this so-called "apparent" molecular weight is misleading as to the actual molecular weight and you can't identify a protein using only a molecular weight ladder.

Damn, totally did not know any of this. Thank you, I am gonna have to really consider the nuanced differences between the two more carefully before may 6th comes around!

 

[663697]

The passage stated that the RNA was single stranded, so does this imply there was intramolecular H-bonding which lead to the folded conformations prior to denaturation? In other words, did the denaturation cause the ssRNA to linearize?

 

[Doctor_Strange]

wow i got ptsd reading this thread again lol

 

[theonlytycrane]

wow i got ptsd reading this thread again lol

More trauma coming soon for us both.