EK Bio 1 - EK 30min lecture 1 exam Q3

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Nov 15, 2014
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Question is:

Chaperones assist in the formation of a protein's:
a) primary structure
b) secondary structure
c) tertiary structure
d) quaternary structure.

Answer is C), tertiary structure. Most relevant info in the passage states that chaperones are 'proteins that provide assistance in the folding process by stabilizing partially folded intermediates'.

Originally I chose B), but while I was doing the exam I was torn between b, c, and d because I thought all of these structures were produced by protein folding. The solution states that only the tertiary structure corresponds to 'protein folding'.

Is this true? Does the formation of alpha helices and B-pleated sheets (secondary structure) not count as protein folding? And what about quaternary structure? Is that not folding as well?


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I think you meant quaternary structure at the end. I think about it like:

amino acid sequence (primary structure) after translation -> secondary structure (H-bonding of the peptide backbone) forming alpha helixes and / or beta sheets -> R groups starting to interact with one another and even the backbone (folding - may be assisted by chaperones).

Multiple units combining for quaternary structure likely results in shape changes but the proteins will at least be mostly "folded" by that point.
Yup! I just caught the mistake and fixed it. Thanks!

I agree with your reasoning for quaternary structure, but I still don't get your reasoning for secondary structure; I feel like the hydrogen bonding of the polypeptide backbone still counts as folding because these attractive forces cause the interacting parts to come closer together, thus 'folding' it. I mean, what is the exact definition of folding? Am I thinking about this wrong? Or are the EK test writers defining 'protein folding' as the folding due to hydrophobic forces?
You're not thinking about it wrong :) I think they are defining folding in terms of the process in which chaperones help out. They won't have to help out in the secondary structure formation.
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  • Primary protein structure is the linear sequence of amino acids.
  • Secondary structure is the alpha helices and beta sheets
  • Tertiary structure is the folding the alpha helices and beta sheets into a larger 3 dimensional shape.
  • Quaternary structure is how a multi-subunit protein, or multiple proteins, fit together.

Even though alpha helices and beta sheets do have some three dimensional nature to them, when we talk about "protein folding" we generally mean the larger 3 dimensional structure made up of alpha helices/beta sheets - or of a helix/sheet folded into a certain shape.

You could think of alpha helices as pipe cleaners, and beta sheets as matrices of pipe cleaners. Sure the pipe cleaner has a shape deep down with many atoms in the pipe cleaner "folded" on each other - but we're more interested in the folds of the pipe cleaner macroscopically. Your hands need to help the pipe cleaner get into the right shape, just like a chaperon protein may be needed.

See the image below. A normal beta sheet would just be flat, ready to be folded. This one is curved in on itself to create a cylindrical shape (this is a porin). Chaperons sometimes are needed to guide the beta sheet into the proper folded structure.