My Personal Science Nerd

OK, just as a heads up, it is CRUCIAL that you learn this. I’ve found that for most people, it either seems really easy and unnecessary or it seems really complicated and overwhelming. Either way, you won’t hear the end of protein structure… that is, unless you’ve decided to go into law and removed yourself from biology forever. So, let’s explore.

EACH “LEVEL” OF PROTEIN STRUCTURE DESCRIBES SOME PART OF THE PROTEIN… and “PROTEIN”=”POLYPEPTIDE”… remember that. Keep them in your mind as you read the rest of the article.

A.) There are four levels of protein structure: Primary (first), Secondary (second), Tertiary (third), and Quaternary (fourth). Think about this like a stack of books: you can’t get to the third book without there being two books underneath, but you can have a stack of only two books without the need of a third or fourth.

Likewise, you can have primary structure without having secondary, or you can have tertiary structure without quaternary. If, at this point, you’re still unsure about exactly WHAT each of those are, it’s ok. Just make sure that you know that you must start at the bottom and work your way up and that every protein won’t have all four.

B.) The first level of protein structure DESCRIBES the order of amino acids in the protein. It has NOTHING to do with shape at this point. Eventually, these amino acids will effect the shape of the protein, but for now don’t worry about that.

When you think of Primary Structure, think back to kindergarten, when you were forced to stand in line between the same two people everywhere your class went. The primary structure of a protein is similar to the kindergarten line in that it focuses on the ORDER of the CERTAIN amino acids that make up that polypeptide. These lines of amino acids, bound to one another by peptide bonds, are the building blocks of the next level of structure…

C.) The second level of protein structure DESCRIBES the ways that the primary structure of the protein interacts with itself. This is the first instance of 3D shape that you see in polypeptides.

There are two major configurations that you need to know at this point, Aplha Helix and Beta Pleated Sheet. Actually, just to make things simpler, we’ll just call them helix and pleated sheet. The “alpha” and “beta” are just “the man” trying to keep you down. A helix is shaped like a tube and a pleated sheet is has ridges like a “Ruffle’s” potato chip.

In schematic representations of proteins, like these pictured here, flat ribbons are the accepted representation of beta sheets. Although they look flat, you’re just supposed to know that they are actually ridged.

In the examples given, the red alpha helices are shown in a bacterial potassium pump that is composed of only alpha helices, and the bets sheets are shown in the fhuA transport protein that is composed of only beta sheets. I’ll show in another post why these structures make them the best for their function.

Some amino acids will interact with each other to form shapes (helices or sheets). Remember concept A? It applies here. THERE IS NOTHING THAT SAYS THAT ALL AMINO ACIDS IN A PROTEIN HAVE TO FORM INTO HELICES OR SHEETS. Some just remain as strings of amino acids.

C.)  Tertiary structure is one of the easiest ones to remember. It DESCRIBES the way that the secondary structures interact… (there goes that “building blocks” thing again).

Blob. There you go. That’s tertiary structure. If you take your polypeptide “string” (primary), with all of its helix and pleated sheet “beads” (secondary), and you drop it on the floor, you’ll likely find that it falls into a bunch. Or maybe if you put the whole thing in your hand so that none of the strings hang off your palm, you’ll notice that you have to ball it up in order to get it all into your palm.

Tertiary structure is the EXACT SAME THING… kinda. it describes the way that the secondary structures interact with each other. Blob. Simple, huh? Theoretically, yes, but it’s at this point that proteins really begin to take on the shapes that they need to carry out functions in the cell.

Remember proteins are tools that the cell uses to do jobs. They aren’t the only tools, but they make up a whopping majority. The jobs that proteins can do depend COMPLETELY on their shape. You cant screw a screw with a hammer because it doesn’t have the correct shape.

D.) Finally… lets speed this up a little… Make four of those blobs from concept C and glue them together somehow. That’s quaternary structure. It describes the way that those tertiary structure blobs interact to form new and novel proteins that can do NEW JOBS. If you glue a hammer to a screwdriver… well, there’s probably not a lot that you can do with that, BUT THEORETICALLY, the possibilities are endless!

So, that’s it. Protein structure really gets more hype than it  deserves. But for your memory, here’s the condensed version:

• Primary – Kindergarten Line – certain arrangement of amino acids
• Secondary – Pringle’s tubes and Ruffle’s chips – alpha helices and beta pleated sheets
• Tertiary – Blob – interactions between primary and secondary structures
• Quaternary – BIG Blob – interactions between different polypeptide chains to form new shapes.

Here are some more links that may come in handy:

http://webhost.bridgew.edu/fgorga/proteins/proteins.htm#Primary

http://themedicalbiochemistrypage.org/protein-structure.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DenaturingProtein.html

http://wiz2.pharm.wayne.edu/biochem/prot.html

Images courtesy of

Best of Luck,
Grey

Trackback URL

polypeptide, primary, protein, quaternary, seconndary, structure, tertiary