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Primary, Secondard & Teriary Structure of Proteins

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Primary, Secondard & Teriary Structure of Proteins

Postby orbit » Fri Apr 20, 2007 5:39 am

Hi all, I am studying environmental science at uni (1st year) and am having difficulties understanding primary, secondary and tertiary structures. I have some understanding of how the structures are formed, but what do they get used for? I believe that the tertiary structure is what give the proteins there overall shape (I think, correct me if I'm wrong) and that this then means that they can perform different functions. What about primary and secondary then? Any advice (in english please :)) on the subject for a bio newbie? :)
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Postby kotoreru » Fri Apr 20, 2007 11:14 am

The primary structure is simply the sequence of amino acids as determined by the process of translation in protein synthesis.

The secondary structure is the overall 'form' this sequence takes. To keep it simple just think either alpha helices or beta 'pleated' sheet (though I think some revision of the terminology has happened since my first year in Uni).

The tertiary structure is as you say; the 'shape' of the protein. And yes this is what gives certain proteins their functions (active sites etc.) This is determined by many different functions within the cell, which I cant go into here...enzymes, 'helper' proteins, pro-protein forms...etc.

I hope that helps.
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Postby orbit » Fri Apr 20, 2007 12:24 pm

Thank for your advice, it helps :)
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Postby Darby » Fri Apr 20, 2007 3:22 pm

To add just a little -

Primary is the chain, without caring about how the links work.

Secondary deals with how different amino acids link up, producing local patterns along the chain, and bending bits back around to come by earlier bits again.

Tertiary is about those bit-to-bit connections that hold the entire things as a big, functional lump.
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Postby Knighty » Sat Apr 28, 2007 9:47 am

I have a questions that's been on my mind for a while... How exactly does the protein transform for one sturcture to another... ?? Is it by forming different kinda bonds?? Anyone got any picture illustrating that..??

Thanks for anyone willing to take the time to help... :D
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Postby kotoreru » Sat Apr 28, 2007 11:59 am

That's a little complicated, I suggest you find a good Biochem book and have a look through...every chapter :(

That just reminded of Quaternary structures though, which havent been mentioned yet. Several proteins associated to form a larger complex is the quaternary structure of a protein e.g. Haemoglobin (4 helices + haem)
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Postby Darby » Sat Apr 28, 2007 3:33 pm

Knighty, much of the shape comes from hydrogen bonds, which are affected by the slightly uneven distribution of electrons that produce partial charges.

Proteins often need help to fold up properly, since these bonds can form in a number of different ways. And when new substrates attach to the proteins, it affects the electron distribution and can change the shape, either locally (as with active sites) or overall (as in toxin denaturation). These aren't solid lumps, but dynamic, vibrating systems.
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Postby Knighty » Mon Apr 30, 2007 11:00 am

Thanks alot kotoreru & Darby... ;)

By the way, are yo'all doctors (I mean in this forum) ?
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Postby MrMistery » Mon Apr 30, 2007 12:14 pm

@Knighty
Your question is actually one of the most complex ones in proteomics.
You see, it is true that the conformation of the protein is determined by different kind of intermolecular bonds between aminoacid residues: mainly hydrogen bonds, but also ionic bonds and Wan der Wals bonds. Also hydrophobic regions cluster together to evoid the aquaeos environment - what is termend improperly by some biochemistry books as hydrophobic bonds.
However, the real question is how the protein knows how to assume the right conformation(biochem talk: how to fold properly). It is true that some proteins do misfold, but the vast majority fold properly(either spontanously or assisted by chaperones). You see, an average protein has more than 100 aminoacids, which means that there are many possible combinations of bonds that can form. But the protein always formes the bonds in the right way, and very very quickly. Prospective applications of the physiology of protein folding are numerous in nanotechnology. However, the field is only at the beginning.
And no, we are not. I, for example, am in high-school.
Regards
PS: moved the topic to molecular biology
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Postby victor » Wed May 02, 2007 3:50 pm

Knighty wrote:I have a questions that's been on my mind for a while... How exactly does the protein transform for one structure to another... ?? Is it by forming different kinda bonds?? Anyone got any picture illustrating that..??

Thanks for anyone willing to take the time to help... :D


Protein (enzyme) can transform its substrate to yield a product by several process:
- Proximity & orientation effects
This is where the enzyme speed up the reaction by orientating its active site structure into the shape of its substrate so that the substrate can easily drawn into its active site. After the substrate is bound into the enzyme, then the enzyme will form a bridge structure thus making the substrate has a high energy to react and forming a product (transition state).

- Acid-base catalyst and covalent catalyst
An enzyme may use one or both of this catalyzing pathway. In acid-base catalyst, an enzyme may act either as an acid (donating H+ ion) or a base (withdrawing H+ ion) towards its substrate. In covalent catalysis, an enzyme may affect one or more functional groups within the substrate and may alter it to yield a product.

- Strain & distortion
To cleave a substrate (ex: protein), or to do another action towards its substrate, an enzyme may need to strain or to distort some of the substrate's covalent bonds in order to change it into product.

- Changes in Environment
In order to reacting with its substrate, an enzyme need to provide a favorable microenvironment. This include some proper folding so that the active site of an enzyme remains in the 'core' of the enzyme.

Hope this helps :D
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