My misunderstandings about protein structure

[scilearner]

Ok as the title suggests I want to clear up my misunderstandings on protein structure.

 

1. When they say primary,secondary,tertiary and quarternary structure do they mean different stages of a protein. What I mean is do all proteins have a tertiary or quarternary structure and are primary,secondary structures simply stages of them before they became a protein. Or do some proteins remain in secondary or primary structure.

2. "Myoglobin is a single-chain globular protein of 153 amino acids, containing a heme (iron-containing porphyrin) prosthetic group in the center around which the remaining apoprotein folds. It has eight alpha helices and a hydrophobic core. "(wikipedia)

 

Does myoglobin have 8 different polypeptide helix chains joined or is it the same chain twisted to make 8 helixes. I thought one chain could only make one helix.

 

"Collagen contains three different polypeptide helixes joined together"

 

Does this make Collagen a quarternary structure. What is the basic difference between quaternary and tertiary structure. My understanding is that tertiary structure only has one chain twisted many ways and quaternary structure has two or more different polypeptide chains. Is this wrong?

 

Thanks a lot for taking your time to read this. If you could help me with these basics I would be very greatful. Thank you

[CharonY]

1. When they say primary,secondary,tertiary and quarternary structure do they mean different stages of a protein.

 

It does not refers to stages of a protein but to the different complexities of its structure. Every proteins has a primary structure, which is the pure amino acid sequence. If the amino acids would not interact, that would be the end of it. But essentially due to hydrogen bonds they form up secondary structures like helices or beta sheets. A long protein can have many of those. The secondary structure essentially refers to these local conformations.

But there are other forces, including ionic or hydrophobic interactions and disulfide bonds that can further determine the structure of the protein. This is then referred to as the tertiary structure.

The proteins does not got through stages but these are just different levels of complexities to describe the protein. As the amino acids alone will normally interacti with each other, native proteins will all have a tertiary structure (and implicitly also a secondary and primary) unless you denature the protein (i.e. break up all interactions either) which causes the protein to lose its tertiary and secondary structure.

The quarternary structure refers to protein complexes in which several proteins or polypeptides interact to form a superstructure.

 

Does myoglobin have 8 different polypeptide helix chains joined or is it the same chain twisted to make 8 helixes.

A single polypeptide can have any amount of helices. It only depends on the composition of it.

 

Does this make Collagen a quarternary structure.

Yes, it consists of serveral polypeptides interacting with each other.

[scilearner]

It does not refers to stages of a protein but to the different complexities of its structure. Every proteins has a primary structure, which is the pure amino acid sequence. If the amino acids would not interact, that would be the end of it. But essentially due to hydrogen bonds they form up secondary structures like helices or beta sheets. A long protein can have many of those. The secondary structure essentially refers to these local conformations.

But there are other forces, including ionic or hydrophobic interactions and disulfide bonds that can further determine the structure of the protein. This is then referred to as the tertiary structure.

The proteins does not got through stages but these are just different levels of complexities to describe the protein. As the amino acids alone will normally interacti with each other, native proteins will all have a tertiary structure (and implicitly also a secondary and primary) unless you denature the protein (i.e. break up all interactions either) which causes the protein to lose its tertiary and secondary structure.

The quarternary structure refers to protein complexes in which several proteins or polypeptides interact to form a superstructure.

 

 

A single polypeptide can have any amount of helices. It only depends on the composition of it.

 

Yes, it consists of serveral polypeptides interacting with each other.

 

Thanks a lot I'm glad I asked this question and got everything cleared up. Also while we are at it can you explain how stearic hindrance destabilizes alpha helix structures. Especially proline. My understanding is that bulky side chains in proline would inhibit other things from reacting. However side groups are perpendicular to the helix so they don't react much anyway. So how does stearic hindrance affect side chains. Thanks a lot

[CharonY]

Proline is special due to two reasons, first it lacks an amide hydrogen therefore the backbone hydrogen bonds for the carbonyl groups at positions (i−3) and (i−4) is missing. Secondly the proline ring destabilizes the backbone by increasing the helix rise in one turn (to avoid the carbonyl group at position (i−4)). Both elements destabilize the alpha helix. This is actually important for certain functions, especially of transmembrane proteins.

[jimmydasaint]

Does this make Collagen a quarternary structure.

Yes, it consists of serveral polypeptides interacting with each other.

 

But...we have taught for many years in the UK, that collagen represents a secondary structure because its structural complexity does not go far beyond an alpha helix. We have also taught that silk fibroin is a secondary structure. However, are they secondary structures or heavy in particular structural motifs? Textbooks have not helped students in this regard. Please clarify Charon Y...

 

The a-helix and the b-sheet were discovered by Linus Pauling, for which work he got the Nobel prize in 1954. There are a number of other secondary structure motifs such as the b-bend, the triple helix (only found in collagen), and the random coil.

 

http://www.biologymad.com/master.html?http://www.biologymad.com/biochemistry/biochemistry.htm

Edited October 27, 2009 by jimmydasaint

[CharonY]

Well the formal definition of quarternary structure only refers to the interplay of polypeptides but does not include any necessary complexity.

It is easier to see it if thinking hierarchically. The triple helix is a secondary structure. It is a local structure. The whole complex however, would be described as a quarternary structure. It does not matter that the whole protein complex is merely consisting of helices.

[jimmydasaint]

Well the formal definition of quarternary structure only refers to the interplay of polypeptides but does not include any necessary complexity.

It is easier to see it if thinking hierarchically. The triple helix is a secondary structure. It is a local structure. The whole complex however, would be described as a quarternary structure. It does not matter that the whole protein complex is merely consisting of helices.

 

OK, to clarify completely, so silk fibroin, collagen and haemoglobin are all quaternary but have secondary motifs (e.g. portions with alpha helices etc...). If that is the case, thank you for the answer.

[CharonY]

Essentially yes. "Motifs", however are used in again a different context, so it may not be optimal to use this term to describe it. The secondary structure tends to refer to the structure of local segments. It can also describe the totality of said structures (e.g. proteins x has so and so many alpha helices) but it does not refer to the complete interaction within, or between polypeptides and proteins.

Thus one would not normally use primary, secondary etc. structure to classify protein (e.g. protein x is a quarternary protein), as this does not really make sense, but one could state that the quarternary structure of collagen consists of three chains twisted into a helix. The secondary structure of collagen consists of a triple helix (ignoring the fact that several peptides are involved). An easier way to think of secondary structure is to refer to it as the spatial arrangement of the peptide backbone while disregarding side chain interactions. Normally a quarternary structure would be dependent on the side-chain interaction. The case for collagen is somewhat complicated due to the unusual triple helix which just does not require that (though they add to the stabilization of the fiber).