Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.
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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?
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.
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.
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...
Changing from ,to, is the history of each one of us....
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)
"What are humans if they don't learn at University? Animals, yes."
^^One of my ex-girlfriends said that. I stress the ex part.
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.
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.
PS: moved the topic to molecular biology
"As a biologist, I firmly believe that when you're dead, you're dead. Except for what you live behind in history. That's the only afterlife" - J. Craig Venter
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
Q: Why are chemists great for solving problems?
A: They have all the solutions.
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