Protein structure...

[Temperature101]

Taking a protein from a lipid environment and placing it into an aqueous environment would most likely affect which of the following?

A. Primary structure
B. Secondary structure
C. Tertiary structure
D. Quaternary structure


Can someone help me visualize that stuff?

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[MedPR]

Taking a protein from a lipid environment and placing it into an aqueous environment would most likely affect which of the following?

A. Primary structure
B. Secondary structure
C. Tertiary structure
D. Quaternary structure


Can someone help me visualize that stuff?

It will fold differently since the solution has changed. I always had a problem with these since secondary will change, but so will tertiary. Secondary is probably the answer though, correct?

You can think of the protein the same way as the lipid bilayer. It projects its non-polar parts to the non-polar solution, and its polar parts to the polar solution. So in the lipid environment, its non-polars are pointing out toward solution and polar inward away from solution and vice versa for an aqueous environment.

 

[Temperature101]

It will fold differently since the solution has changed. I always had a problem with these since secondary will change, but so will tertiary. Secondary is probably the answer though, correct?

You can think of the protein the same way as the lipid bilayer. It projects its non-polar parts to the non-polar solution, and its polar parts to the polar solution. So in the lipid environment, its non-polars are pointing out toward solution and polar inward away from solution and vice versa for an aqueous environment.

You are correct...Secondary is the answer

 

[chiddler]

Why is secondary a better answer than tertiary?

 

[MedPR]

You are correct...Secondary is the answer

Ok so secondary structure is basically the alpha helices and beta sheets. These help to determine the tertiary structure (how the protein folds). Whenever the environment changes, the protein will fold differently.

Does that make sense?


I still don't know why secondary is a better answer than tertiary, but I got these types of questions wrong so many times (I always picked tertiary) that I now have an intuition about when the answer they want is secondary.

 

[YouNeverKnow22]

It will fold differently since the solution has changed. I always had a problem with these since secondary will change, but so will tertiary. Secondary is probably the answer though, correct?

You can think of the protein the same way as the lipid bilayer. It projects its non-polar parts to the non-polar solution, and its polar parts to the polar solution. So in the lipid environment, its non-polars are pointing out toward solution and polar inward away from solution and vice versa for an aqueous environment.

I agree with MedPR, badly worded question because technically all structures can "change" except primary. Though a secondary structure is most likely present in the membrane..

 

[Temperature101]

I agree with MedPR, badly worded question because technically all structures can "change" except primary. Though a secondary structure is most likely present in the membrane..

The explanation says that...

 

[MedPR]

I guess the reasoning is that you can't change tertiary structure without first changing secondary structure... But that makes it seem like tertiary structure will never be the answer to "which structure changes..." type questions so idk.

 

[YouNeverKnow22]

The explanation says that...

I wouldn't stress too much over these things, just know the basic definitions of all the basic protein structures, and know all of them can be affected when stressed except the primary structure (i.e. denaturation).

 

[SH3]

Taking a protein from a lipid environment and placing it into an aqueous environment would most likely affect which of the following?

A. Primary structure
B. Secondary structure
C. Tertiary structure
D. Quaternary structure


Can someone help me visualize that stuff?

The determining factor I believe is that all the other structures are derived upon the secondary structure. Therefore, if you simply said quaternary or tertiary, you assume that the tertiary and secondary are not affected. By selecting Secondary as the answer choice you are undoubtedly selecting all further structures that rely on its presence. Make sense?

 

[SH3]

Just another way of looking at the answer choice irrespective of what was mentioned prior about membranes.

 

[pm1]

Ok so secondary structure is basically the alpha helices and beta sheets. These help to determine the tertiary structure (how the protein folds). Whenever the environment changes, the protein will fold differently.

Does that make sense?


I still don't know why secondary is a better answer than tertiary, but I got these types of questions wrong so many times (I always picked tertiary) that I now have an intuition about when the answer they want is secondary.

I just ran into something that might explain why secondary is a better answer than tertiary.

Because tertiary involves covalent bonds (disulfide bonds), which are more stable, and secondary don't. Thus upon exposing proteins to denaturing factors such as temperature or pH change would actually disturb the secondary structure before the tertiary, but since tertiary is build up on the secondary tertiary consequently would also be affect.

But then does that mean that if tertiary structure is affected then secondary must be as well? Does this reasoning make sense?

This is the question that made me thing about this: (From EK 30' in class exam)

Which of the following bonds in a protein is likely to be LEAST stable in the presence of heat?
A. a disulfide bond
B. a hydrogen bond
C. a polypeptide bond
D. the double bond of a carbonyl

Answer: B

 

[MedPR]

I just ran into something that might explain why secondary is a better answer than tertiary.

Because tertiary involves covalent bonds (disulfide bonds), which are more stable, and secondary don't. Thus upon exposing proteins to denaturing factors such as temperature or pH change would actually disturb the secondary structure before the tertiary, but since tertiary is build up on the secondary tertiary consequently would also be affect.

But then does that mean that if tertiary structure is affected then secondary must be as well? Does this reasoning make sense?

This is the question that made me thing about this: (From EK 30' in class exam)

Which of the following bonds in a protein is likely to be LEAST stable in the presence of heat?
A. a disulfide bond
B. a hydrogen bond
C. a polypeptide bond
D. the double bond of a carbonyl

Answer: B

Well, A, C and D are all covalent, so B is the answer. What you're saying does make sense though!

 

[chiddler]

Is it accurate to say that tertiary structure of a protein does not refer to any non-covalent interactions?

 

[MedPR]

Is it accurate to say that tertiary structure of a protein does not refer to any non-covalent interactions?

No. H-bonds, nonpolar interactions, and ionic interactions contribute to the tertiary structure.

 

[chiddler]

No. H-bonds, nonpolar interactions, and ionic interactions contribute to the tertiary structure.

then how can it be said that a disulfide bond is a tertiary structure? it can stabilize regions of a protein just as an alpha helix does.

 

[MedPR]

then how can it be said that a disulfide bond is a tertiary structure? it can stabilize regions of a protein just as an alpha helix does.

Tertiary structure has covalent and non-covalent interactions. Whether a particular disulfide bond is considered secondary or tertiary depends on where it is.

Remember there are 5 forces that contribute to tertiary structure:

H-bond
disulfide
nonpolar
ionic
van der waal

 

[pm1]

Tertiary structure has covalent and non-covalent interactions. Whether a particular disulfide bond is considered secondary or tertiary depends on where it is.

wait so disulfide can be considered secondary? I thought it was only tertiary.. isn't secondary only H bonds?

 

[MedPR]

wait so disulfide can be considered secondary? I thought it was only tertiary.. isn't secondary only H bonds?

I thought disulfide bonds helped to stabilize secondary structure?

 

[chiddler]

Tertiary structure has covalent and non-covalent interactions. Whether a particular disulfide bond is considered secondary or tertiary depends on where it is.

i think you're right.

depends on context.

on other hand, it may enable some hydrogen bonds that would not exist without the disulfide bond.

 

[pm1]

I thought disulfide bonds helped to stabilize secondary structure?

ha! okay! good to know, thanks!
EK doesn't talk about it...

 

[chiddler]

from my physio book:

As a polypeptide chain forms, a secondary structure, its spacial arrangement or shape, forms. The secondary structure is stabilized by hydrogen bonding between different parts of the molecule.

Ok so secondary refers ONLY to hydrogen bonding it seems. Then it lists the three most common shapes, the helix, pleated sheets, and a B-turn.

"Three dimensional shape of a protein is tertiary structure.... The tertiary structure of globular proteins arises partyly from the angles of covalent bonds between amino acids and partyly from hydrogen bonds, van der waals, and ionic bonds that stabilize the tertiary structure."

Ok here is a point of interest:

"Two cysteines can covalently bond to each other pulling different sections of the chain together".

And this is under tertiary structure paragraph. So disulfide I think refers only to tertiary though it contributes to secondary?

 

[MedPR]

from my physio book:

As a polypeptide chain forms, a secondary structure, its spacial arrangement or shape, forms. The secondary structure is stabilized by hydrogen bonding between different parts of the molecule.

Ok so secondary refers ONLY to hydrogen bonding it seems. Then it lists the three most common shapes, the helix, pleated sheets, and a B-turn.

"Three dimensional shape of a protein is tertiary structure.... The tertiary structure of globular proteins arises partyly from the angles of covalent bonds between amino acids and partyly from hydrogen bonds, van der waals, and ionic bonds that stabilize the tertiary structure."

Ok here is a point of interest:

"Two cysteines can covalently bond to each other pulling different sections of the chain together".

And this is under tertiary structure paragraph. So disulfide I think refers only to tertiary though it contributes to secondary?

I guess hydrogen bonds form the secondary structure and the disulfide bonds in the tertiary structure help to stabilize any nearby secondary structures.

 

[chiddler]

therefore, technically disulfide bonds are only tertiary though they may contribute to secondary.

 

[pm1]

therefore, technically disulfide bonds are only tertiary though they may contribute to secondary.

okay, I thought so. EK wasn't misleading after all.
Thank you guys!

 

[chiddler]

okay, I thought so. EK wasn't misleading after all.
Thank you guys!

thank you too for the initial update.