Secondary Structure
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Secondary Structure

Once the primary structure has been created, a secondary structure of some sort evolves.

Alpha Helix

Here we have representation of a primary structure. It consists of a sequence of amino acid residues. In this case I have left out the hydrogen and the side group from the alpha carbon. I just want to ignore those for a moment.

Bare primary structure of protein. [68032.jpg]

One of the most common types of secondary structure is referred to as an alpha helix. Essentially what is involved in an alpha helix is that the primary structure of the protein twists around upon itself in such a way, somewhat like rolling up this paper model, to form a recurring pattern that is very important.

Bare primary structure of protein rolled into an alpha helix. [68034.jpg]

The hydrogen from the amino group lines up with the oxygen from a carbonyl group. That happens over and over again in this structure. So you can see that hydrogen bonding can occur with this arrangement of amino acids in an alpha helix.

Bare primary structure of protein rolled into an alpha helix, pointing to hydrogen bond. [68035.jpg]

If we were to build a model of this alpha helix and consider bond angles, you would find that it doesn't work out quite as smoothly as what is shown here.
Also, if you consider the side chains that I originally chose to ignore, you would see that they tend to stick out on the outsides of the helix.

Bare primary structure of protein rolled into an alpha helix with side groups attached. [68036.jpg]

The type and location of these side groups is very important in determining the ultimate structure and also the function of a particular protein.

Bare primary structure of protein rolled into an alpha helix with side groups attached, viewed from the top. [68037.jpg]

 

Beta Sheet

It is also possible for the protein's strands to line up side by side with one another and form hydrogen bonds in this way. When that happens with the strands both running  in the same direction it is called parallel.

Parallel beta sheet structure of protein. [68038.jpg]

When that happens with the strands running in the opposite direction it's called antiparallel.

Anti-parallel beta sheet structure of protein. [68039.jpg]

Parallel or antiparallel, this particular kind of secondary structure is referred to as beta sheet structure. These strands, of course, are not completely flat as shown on this screen. The amide bond portion is flat but the molecules bend on both sides of the alpha-carbon with tetrahedral angles. Consequently they fold up and down and these structures are quite often called beta pleated sheets.

Collagen Helix

A third type of secondary structure involves three strands of protein bonded together between the chains with hydrogen bonds and then twisted into a helix that is referred to as a collagen helix. That occurs primarily (perhaps exclusively) in protein known as collagen.

Three peptide strands in the collagen helix. [68040.jpg]

Secondary Structure Mixes

Proteins generally have a mix of different kinds of secondary structure. They are rarely, to my knowledge, all of a particular type. One part of a particular protein may have an alpha helix, whereas another part can be folded back in the beta sheet arrangement.

Whatever type of secondary structure is involved in a particular protein, the secondary structure is held in place by hydrogen bonding interactions between the amino group of the amino acid residue and the carbonyl group of another amino acid residue.

Secondary struture results in the side groups of the amino acid chain of the protein chain sticking out to the side. Certain kinds of side groups will enhance the formation of alpha helix, others will enhance the formation of beta sheet and so on. But whatever the secondary structure happens to be, the side groups are going to be sticking out.

Next we'll take a look at the tertiary structure of proteins which involves the interaction between the side groups.

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