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Protein structure

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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Protein structure

Postby ccBiologist » Thu Sep 29, 2011 8:15 am

i dont understand the difference between primary,secondary, Tertiary and Quaternary so far this is what i understand by the following terms

ok so far i know the primary structure is linear arrange of the amino acids in a peptide chain to show the sequence and number of amino acids in the chain

The secondary structure is the arrangement of a peptide chain into either of two definite structures:- 1 the alpha helix and beta pleated sheet

The tertiary structure is a 3d representation of a peptide chain to show how non-covalent bonds i.e ionic bonds , hydrophobic interactions , disulphide bridges and hydrogen bonds hold the 3d shape together

The Quaternary structure is a 3d model that shows how non-convalent bonds hold together 2 or more polypeptide chain

My question is what is the difference between secondary and primary, secondary and tertiary and are any of the above definitions wrong
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Re: Protein structure

Postby JackBean » Thu Sep 29, 2011 8:51 am

the definitions seem fine to me.

The primary structure is like Asp-Gly-Glu-His-Gly-Phe blah, blah
the secondary structure is like:
DGEHGF (the sequence from above in 1-letter code)
HH..EE (where H means helix and E means the beta sheet, I think it's marked E)
However, there are more secondary structures, than just alpha-helix and beta-sheet. There are several helices (e.g. pi-helix, left-handed helix etc.), also several turns etc.
Anyway, the primary structure says only the sequence, as above.The secondary structure tells you the local structure. The tertiary structure is overall structure (that is, helix 1 is in close proximity with helix 3 and both are covered with beta-sheets 4-6)
To my knowledge, the quaternary structure applies only for the multi-subunit proteins and shows, how exactly they bind (what's the interface etc.).
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: Protein structure

Postby merv » Sun Oct 02, 2011 3:29 pm

Question asker: I think from you're understanding you are correct. Not sure what you don't understand. the first explanation also is correct.
If it helps, I understand it as follows:

1 The primary structure gives no information on folding; it is order of the linked amino acids come out of the machine (ribosome).

2 the secondary structure identifies if the amino acid in question is in a region of helix/sheet etc (many are not),

(3)
the tertiary is the single (monomer) structure - although this relates to the gene and protein sequence, and is typically what one sees when one sees a ribbon structure picture.

4. (Quaternary) - many many proteins do not function without dimerisation, (trimerisation, and maybe more also occur), and this is dealt with here. As there is no defined 5th level, protein complexes with and without their substrates and co-factors tends to come under this category as well. Also many proteins only fold properly in association with a membrane insertion, and this should therefore perhaps be considered as part of their structure- this would have to come into this category as well, perhaps as a folding co-factor. Many encoded polypeptides (often termed proteins, not incorrectly) are merely components for supercomplexes - which are dependent upon each other for the complex to function - although many components function in isolation, they are far more efficient and/or controlled by the supercomplex they are a part of.
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Postby akatalitha » Thu Sep 20, 2012 5:22 am

Here an analogy to help you understand: Take your name signature (cursive) for both last and first name.


First level: straighten the signature and you get two lines, which would be the polypeptide (peptide chain).

Second level: take the line and start arranging it by bending and folding it to your signature. The individual bends and folds are the second level.

Third level: The first name and the last name individually as individual structures. Alone they make the two third levels.

Fourth level: Put your first and last name together.


I hope that this helped you. I left out the actual comparison to the protein structure because what you write above is correct. This should be used as an analogy.
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Postby CindyHang » Mon Oct 08, 2012 10:01 pm

Hello friends,

Proteins are polymers of amino acids covalently linked through peptide bonds into a chain. Within and outside of cells, proteins serve a myriad of functions, including structural roles (cytoskeleton), as catalysts (enzymes), transporter to ferry ions and molecules across membranes, and hormones to name just a few.

With few exceptions, biotechnology is about understanding, modifying and ultimately exploiting proteins for new and useful purposes. To accomplish these goals, one would like to have a firm grasp of protein structure and how structure relates to function. This goal is, of course, much easier to articulate than to realize! The objective of this brief review is to summarize only the fundamental concepts of protein structure.

Best regards
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