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Protein structure...

Discussion in 'MCAT Study Question Q&A' started by Temperature101, 04.30.12.

  1. Temperature101

    Temperature101

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    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?
  2. MedPR

    MedPR

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    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.
  3. Temperature101

    Temperature101

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    You are correct...Secondary is the answer
  4. chiddler

    chiddler

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    Why is secondary a better answer than tertiary?
  5. MedPR

    MedPR

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    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.
  6. YouNeverKnow22

    YouNeverKnow22

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    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..
  7. Temperature101

    Temperature101

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    The explanation says that...
  8. MedPR

    MedPR

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    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.
  9. YouNeverKnow22

    YouNeverKnow22

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    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).
  10. SH3

    SH3

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    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?
  11. SH3

    SH3

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    Just another way of looking at the answer choice irrespective of what was mentioned prior about membranes.
  12. pm1

    pm1

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    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
  13. MedPR

    MedPR

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

    chiddler

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

    MedPR

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

    chiddler

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    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.
  17. MedPR

    MedPR

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    :confused: 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

    [​IMG]
  18. pm1

    pm1

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

    MedPR

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    I thought disulfide bonds helped to stabilize secondary structure?
  20. chiddler

    chiddler

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    i think you're right.

    [​IMG]

    depends on context.

    on other hand, it may enable some hydrogen bonds that would not exist without the disulfide bond.
  21. pm1

    pm1

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

    chiddler

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    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?
  23. MedPR

    MedPR

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

    chiddler

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    therefore, technically disulfide bonds are only tertiary though they may contribute to secondary.
  25. pm1

    pm1

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

    chiddler

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    thank you too for the initial update.

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