Hi. It’s Mr. Andersen and in
this video I’m going to talk about proteins. Proteins are incredibly important because
that’s what we’re made up of. When you look at me you’re looking at my proteins. We just
completed the human genome project and we figured out the DNA in a typical human but
now we’re headed into what’s called the proteom project where we try to figure out what these
proteins made up of and what do they look like three dimensionally. This used to be
an incredibly hard process. This is John Kendrew here putting together a model for myoglobin
and he had to do it by hand. We now do a lot of this with computers. But you can help.
At the end of this video I’m going to show you a program called Foldit and you can actually
build and fold proteins that are going to be used in scientific research. And so it’s
a really cool thing. And it’s a really cool time in reference to proteins. But let’s start
by building a little bit of knowledge. Proteins are made of amino acids. And most seventh
graders understand this. They’re the building blocks of proteins. But where do we get those
amino acids? We get them in our diet. And so basically we eat proteins. We break them
down into amino acids and then we can weave those back together again into the proteins
that make us. And so when you’re looking at me, the amino acids in my skin, used to be
part of my food. And so I literally am what I eat. Now here’s five different amino acids.
There are a total of twenty that we use in life, but here’s five basic amino acids. When
I show this to my students they tend to get a little bit overwhelmed because it’s too
much chemistry here on one page. But let’s try to figure out the things that are the
same on this page. And so basically if we were to look at the middle of each of these
we find that there’s a carbon with a hydrogen attached to it. We call this carbon alpha
carbon. It’s going to sit right in the middle. What else is the same in every amino acid?
Well on the left side we have a nitrogen attached to two hydrogens. We call this an amino group.
And then if we look on the right side we have what’s called a carboxyl group. And so basically
every amino acid is going to have these three similar parts. And so the only thing that’s
going to be different is going to be what comes off the bottom. And we call that the
R group. And so all amino acids are the same except what comes off here. And that gives
it different properties. And so let’s kind of see how they’re put together. And so when
I build proteins inside my body, I’m doing that with amino acids. And we use something
called dehydration synthesis to do that. And so let me move this one over here. Basically
what we do is we position one amino acid right next to an amino acid. You can see here that
there is two hydrogens and an oxygen here and you know that in chemistry if we have
two hydrogens, H2O that’s simply a water. And so what we can do is we can lose that
water. Now it’s not as simple as that. This whole thing sits inside a ribosome. So there’s
a giant enzyme around the outside of it. But let’s attach another one. So now we bring
another one right next to it. You can see that the hydroxyl group or the carboxyl group
is attaching to the hydrogen. We’re going to lose a water and then we’re going to form
another covalent bond. And then we put another one next to it. We lose another water, we
form a covalent bond and we do that again and now we have what’s called a polypeptide.
And so each of these individually are called a peptide. But if we attach them all together
we have a polypeptide. And you can see that the strand across the top looks the same.
It looks uniform, but the only thing that’s going to be different in each of these is
going to be the R group, the trails off the bottom. So where does this occur? Well basically
these are the amino acids. This would be the ribosome in a cell and all life does this.
Basically you have these little tRNAs that will bring their amino acids in and then we
attach them together. And when you have a bunch of amino acids attached together, you
have a polypeptide. And that polypeptide will eventually fold into a protein. And so here’s
our five amino acid sequence right here. These are each going to have different chemical
properties. And so for example, this one right here, threonine is going to be polar. What
that means is it’s going to have a charge. If we look at alanine right down the way this
is going to be nonpolar. And so why is that important? Well if you’re polar then you’re
hydrophilic. That means that water is going to be attracted to you. In other words we’re
going to find threonine in the presence of water. But alanine, since it’s got this methyl
group right here, it’s not going to be attracted to the water and so it’s going to hide from
the water. Or if we look at the aspartic acid, it’s going to have a negative charge. And
if we look at the lysine over here it’s going to have a positive charge. And so these two
things or these two amino acids are found in the same polypeptide and they’re going
to try to get next to each other because the positive and the negative are going to attract.
And so what you end up getting is a three dimensional protein. The middle part, so this
brownish tan part in the middle is going to be the back bone. And that’s going to be again
made up of all of the parts of the amino acid that are the same so the amino, the alpha
and the carboxyl group over and over and over again, but all of these things on the outside
that are trailing off are going to be the R groups. These are going to be these residue
groups that kind of fold off the end. And so this right here would be a polypeptide.
This would be a number of different amino acids attached together and these usually
have thousands of amino acids in a typical protein like hemoglobin would be an example
of one that’s found in your blood. And so basically this will fold into a three dimensional
shape. And what I tell students is a polypeptide is just going to be this sequence of those
amino acids and once it’s folded into a specific shape then we can call it a protein. And so
the first, maybe you have read it, there are four levels of structure in a protein. And
so let me talk you through that first and then I’ve got a little model that will hopefully
help. And so the primary structure is going to be the order that those amino acids are
bonded together. The next thing we have are what are called alpha helixes and beta pleated
sheets. And we call that the secondary structure. And so a helix looks like this. A beta pleated
sheet is going to be two sides that are attached to each other and these little dots in the
middle are going to be hydrogen bonding between adjacent sides of that polypeptide. And so
this is the structure that comes out first. It’s going to be linear. Next we have the
alpha helixes or the beta pleated sheets. And then we have the tertiary structure. The
tertiary are the third level of structure, is going to be all of those R groups interacting
and so maybe we have one that’s hydrophobic. It’ll hide to the middle or hydrophilic on
the outside. We’ll have disulfide bonds. We’ll have positive attracting to negative. This
is the third level of structure. And then finally we have quaternary structure. Maybe
we have this one polypeptide together or this protein together with another protein. So
hemoglobin’s an example of that made of a number of different subunits. And so here’s
my little model. And so if you look at this model you can think of this being a polypeptide.
So it’s made up of amino acid after amino acid and then it’s going to have all the R
groups on the underside. Those are going to be the only things that are different, all
these R groups coming off the bottom. And so basically, primary structure like this.
Secondary structure is going to be the alpha helixes and the beta pleated sheets. And so
an alpha helix will look like this. What’s holding that in place is simply going to be
the hydrogen bonds. And then we’re going to have a beta pleated sheet. A beta pleated
sheet might look like something like that. So there’s going to be hydrogen bonds between
here and here. But maybe this right here is a real hydrophobic R group, and it’s going
to fold right to the middle and then this might be hydrophilic. It’s going to fold to
the outside. We might have positive attracted to negative then we eventually have a three
dimensional shape of a protein. Now this may combine with other proteins. But what’s cool
about proteins is their structure fits their function. If it doesn’t have this structure,
if we heat it up, if we cool it, if we change the acidity, basically it will fold apart.
We call that denature and then it doesn’t work anymore. And so I said at the end you
could help in science. So there’s a program called Foldit. I’m going to launch it and
I’ll be back in just a second. And so in this program what you’re given is a simple polypeptide.
So we have two amino acids and then this is going to be the R group. And what you do in
this video game is you try to make the R groups happy. So I’ve already cleared level one.
So let’s go on to level 2. You can download this for Mac, Lynx and Windows. Let me quickly
turn this one around. You can see here that we have a couple of, let me get the help out
of the way, you have a couple of different amino acids and then their R groups. I can
pull those apart and they’re going to be a little bit happier and then I can clear the
level. And so what are you really doing. As I play this game I can talk, basically what
you’re doing is you’re learning the rules of protein folding, but these problems are
going to get harder and harder and harder. You can see an alpha helix here. And so what
you can do is you can get really good at folding these proteins. And what’s neat about this
is people are playing Foldit hour and hour after hour. And it hit the news last year
where a couple of protein folders, probably a team of protein folders decoded the shape
of a really important enzyme in HIV infection. And so it’s plausible that in the future gamers
are going to win a Nobel prize for the work they do on protein folding. Because we know
the primary structure of proteins, but we don’t have any idea of how the three dimensional
shape is put together. And computers are good at this but it turns out that humans are maybe
a little bit better. And so those are proteins and I hope that was helpful.