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Teacher/Instructor Patrick Roisen
Patrick Roisen

M.Ed., Stanford University
Winner of multiple teaching awards

Patrick has been teaching AP Biology for 14 years and is the winner of multiple teaching awards.

Proteins, also known as polypeptide chains, are macromolecules of linked amino acids. Proteins are types of organic compounds that, among other things, store energy and form enzymes. Proteins have several levels of structure. On their primary structural level, they resemble neat chains, while on their tertiary level they resemble tangled messes.

Proteins are one of the four basic kinds of organic molecules. Now when I teach them in my class kids will ask me "so what do proteins do?" And it's actually a lot easier for me to explain but they don't do because proteins are used for so many different things in your body. For example, they form a lot of different structures. A protein called keratin for example makes up your hair. A protein called collagen makes up your ligments and tendons and lips.

There's lots of different things made up of proteins. Antibodies, one of the main weapons of your immune system against foreign invaders, they're made out of, you guess it proteins. Hormones such as insulin are made of proteins and then enzymes, the chemical workers of your cells, those are yes again proteins. So they pretty much do anything and everything you'd like to do in the cell.

The monomers that make up proteins are called amino acids. And they get joined together to form long chains called polypeptides. Now these long chains of amino acids wind up folding together in very complex ways and that complex structure gave scientists problems for quite sometime. But let's begin by looking closer at what an amino acid is. Now, all amino acids and there is about twenty used in nature have four basic parts to them. The central part is called the alpha carbon which has a hydrogen attached to it and then all the other side groups. This group over here is called the amino group and it's made up of a nitrogen with a couple of hydrogens. Some textbooks depending on the PH that it's drawn at will show three but I had chose to just do two. Over here we have the carboxyl group which gives the acidic quality to an amino acid because this C double bond OOH that's a carboxylic acid. And like all acids that you learned about in Chemistry, sometimes that hydrogen will have fallen off, so you may occasionally see this oxygen written with a little negative symbol next to it. Up here you see the R group. That doesn't mean that it's a pirate R. That instead is just a place holder used to represent the different side groups that give each amino acid its individual qualities. For example here we see the amino acid called alanine and you'll see that its R group is a methyl group, a carbon with three hydrogens attached to it while over here cysteine has the same amino, amino, carboxyl, carboxyl group but instead of the methyl group it's got a C, double H and then a sulphur over the hydrogen attached to it. That gives it very different chemical and structural properties than the methyl group here. Phenylalanine and glutamic acid also share very different qualities based on their R group.

Now when scientists first started studying proteins, a protein basically will have this kind of structure and if I explain, asked you "so go ahead and describe this to me." You'll sit there go "what! It just looks like a tangled mess" and some respects that's what proteins are, tangled masses. And it's too hard for early scientists to figure it out. It's much like if you hand a kindergartner a big novel and say "so, tell me, what are the themes that run through The Lord of the Rings?" They'll throw up their hands up in failure. So instead scientists started off at the most basic level and they came up with something called "primary structure" and then once they started understanding that, they went to secondary structure and tertiary structure, the third level of structure. Now we're getting much better and much able, much more able to understand the structure of proteins. We even learnt about something called quaternary structure which is how multiple proteins work together.

But let's take a look at this YouTube video and let's see how it shows all these different levels put together. So I'll go ahead and go to full screen on this. So here we see a bunch of amino acids. Now they get joined together and it's the sequence of amino acids in this that it's called primary structure. Now because of their R groups, they all start interacting with each other so our long chain will start to form into these weird little bendy parts here and twisty parts there. Now scientists don't like calling things bendy parts and twisty parts so they named it alpha helix and beta pleated sheet. I'm going to go ahead and pause the video right here and show you some models that help show this. This right here shows an alpha helix and again it's just a long chain of amino acids joined to each other but due to hydrogen bonding between the R groups and other parts of the amino acid chain, it started to form up into this twisted structure. You've heard of the helix before if you've ever studied DNA, cause it has a double stranded twisty shape called the double helix.

Now in the video you saw these bendy parts that were running in parallel. That's called a "beta pleated sheet" and that's what we see. So we have again one long chain but it gets bent up because of the structural properties of carbon to form this up and down up and down sheet shape called a beta pleated sheet. The pleated part refers to the, how it buckles up and down like that, kind of like pleats on a pair of pants. So both of those qualities are determined by primarily the hydrogen bonding of the various R groups in the amino acid chain. So let's restart up the video and see now how we take these small regions of structure, the secondary structure and we have all sorts of other interactions, more hydrogen bonding and covalent bonding between different parts of the chain to form the three dimensional shape. Now, a lot of proteins are done then but some proteins have additional chains attached to them and in very specific ways which is called the "quaternary" or fourth level of structure and that's a protein.