protein structure
We're picking up
where we left off and this video is going
to go over the secondary through quantnary structure
of proteins that we've covered in
our first few classes. And one of the things that you need to
make sure that you remember are a couple of really key things. There are multiple
places for non covalent bonds to
form in a protein. First of all, side chain interactions
are going to be super important in
the tertiary and the quantinary
structure of proteins, and so that higher order folding of that
polypeptide chain. The non covalent
interactions can occur between
those side chains, and so you can get electrostatic interactions
like ionic bonds, like hydrogen
bonds forming from those side chains. You can also have all the hydrophobic amino acids
interacting together. It doesn't have to
just be two together. If you have a bunch
like in the bottom of the slide of non polar amino
acids, for example, those non polar
amino acids could come together and form a hydrophobic core inside of a protein,
for example. Another thing that
you're going to see, and this is going to
be important both in the tertiary and quantinary structure
of proteins, but you'll find
out it's also important in the secondary
structure as well. Is the fact that the
carbonyal oxygen from a polypeptide bond from a peptide bond as well as this hydrogen and
nitrogen from what was the amide group are going to be able to
form hydrogen bonds. Those are not, again, from the side chains, those are coming out of the peptide bond
themselves. Make sure that
you understand these key non
covalent interactions that are happening
in proteins. Also remember
our proteins, our cells are
full of water, and that's going to
shape how proteins are folding and the interactions
that they make. The exceptions
to that, think about it is going
to be in membranes. Membranes are
very hydrophobic. Proteins that are embedded in membranes are
going to have hydrophobic amino acids interacting with
the lipids. As we think about these non covalent
interactions, you're going to
see proteins depicted in different
ways in this class. In the space
filling model, they've colored the
protein from blue to red, depending on the
hydrophobicity or hydrophicity, how much it is attracted to or not attracted
to water. The more hydrophilic
the amino acids are, the bluer they are, and
the more hydrophobic, the more red they are. If you see these two
protein sub units, each one is a
polypeptide chain with an amino terminus and
a carboxy terminus, these two sub
units dock with one another, and
they dock where. We said in class.
Clearly, what's happening is a
little sticky hydrophobic spot
on the outside of each of these
sub units and those hydrophobic
interactions and Venerable attractions keep those two sub
units together. We practiced a
little bit in class. If you're not sure of
your answers to this, please talk to
other students. If you really need me
to, I can post a key. But I think you should
have been able to find a whole lot of hydrogen
bonds on the left, as well as an
ionic interaction. There were no hydrophobic interactions and
on the right, you should have had
the hydrogen bond and ionic bond forming
that salt bridge. We didn't spend a lot of time talking
about this, but again, folded
globular protein. A protein that
has some shape, but it's not a long fiber is a globular protein. And so which amino
acids would you find? And if I gave you a list, you should be
able to tell me. So if I gave you a list
of where you should find amino of
particular amino acids, you should be able to
tell me where I might find those amino
acids in terms of whether they may be more exposed on the outside of a protein were found embedded in the interior. Again, that context
will matter a little as to whether
it's a soluble protein, inside of an organel
or in the cytosol, or if it's a
protein embedded inside of a membrane,
where of course, that phospholipid bilayer, the lipids will interact with hydrophobic
amino acids. Context will matter
for those questions. Generally, if you're thinking
about soluble proteins inside of cells, either in the cytosol or inside of actual organes, or the nucleus, then those hydrophobic
amino acids are going to
form that core. That fact that cells
are full of water really dominates how
they're going to fold. As we start talking
about protein structure, there's a table
at the end of this slide deck that is basically a
primary structure, secondary tertiary
quatinary, and it talks about
bonds found in each one and which part of the amino acid
is involved, et c in those bonds
and in that structure, you should be able to know that information
backwards and forwards. You really need
to understand protein structure to do and think about
cell biology. So we will be
talking about that. I think I mentioned in the lecture that
protein size or mass is really Is determined using a
unit called a Dalton. A Dalton is about
a 12th of the mass of a neutral carbon
atom, Yeah, whatever. It's all relative.
Most proteins are 50-2 thousand
amino acids, from about 30 to
150 kilodaltons. Of course, a kilodalton
is 1,000 Daltins. There is a really
huge protein found in your muscles
called Titan, that's 4.2 mega Daltons. And it's 38,000 amino acids and a single
protein, pretty massive. Okay Let's start off on these protein
structures. Primary structure
you should know is what kind of bond peptide and covalent. T you should be able to
draw a peptide bond, know which parts of the amino acids
are forming peptide bonds have
that down cold. That NCC NCC, making that primary chain or backbone on a protein with the side chain
sticking out. The next thing are these secondary
structures, and there's two regular
ones that form, the Alpha helix and
the Beta sheet, and we want to
think a little bit about how that
actually forms. If you think about
taking a chain of amino acids and making
a helix with it, that carbonooxygen
and that hydrogen coming off of that amide nitrogen
is going to, they're going to
form hydrogen bonds. If I look at this drying
and look carefully, I'm seeing hydrogen bonds form as they loop to the next loop
above them. As those hydrogen
bonds form, you're keeping a coil. Think about a slinky with little cross links between the different loops
of that slinky. Those hydrogen bonds
keep this structure in such shape that
the side chains are not involved in the
secondary structure, but they stick out. They stick out like
spokes on a wheel, that's looking
down the barrel of an alpha helix. When you do that, those
side chains again are going to be exposed on the outside of that helix, and And when we
were in class, I taught you a trick
for thinking about which amino acids can interact and
form an alpahlx, and awful lot of them can prolene can't
because remember it can't form this
kind of peptide this hydrogen bond based
on the peptide bond because there's
not an H on that particular
amino acid. If you have
some really big bulky branch side chains, they're not going
to be found because they are too bulky
really to fit. The other thing is if you have a bunch of
side chains that are on top of one another and they repulse
each other, that's not going
to work either. You want to think
about this in three D, and you want
to think about the side chains that are interacting on top of one another on the loops. The way to do that is
this drawing here, where you think about
amino acid number one, and then you think about amino acid number two, and then amino acid number three and draw box,
and then four. Now when you go to five, let me change colors. We'll make another loop on our little wheel
of the helix. Think about amino
acid number five. Number six, number seven. Number eight. You're
getting the idea. As you draw, always
go to the right. If we're going to do
yet another loop, I'm going to do amino
acid number nine, and number ten,
I'm running out of room because
I drew it too big. If you do that, what you see is certain
amino acids. Here we have
six, three, ten, and seven on the same face or side of the helix, and those can't be things that repulse
each other. And they can't be things
that are going to be so bulky that you can't fit them on
top of one another. So there's some
information in the module on
protein structure. It's like extra
helpful information about protein structure or something along
those lines under the extra resources. It's really helpful
to think about alpha helical
structure and how amino acids can
form those helices. Think about a protein
where you have an alpha helix
and one side of the helix is exposed to the soluble cytosol and the other side is
buried on the inside. What would you
have in terms of hydrophobic hydrophilic or polar nonpolar
amino acids? If you think about it, you would probably have then one side maybe or one face of the
helix that's very hydrophilic and
facing that cytosol. Then maybe you have
one face or side of that helix that is
very hydrophobic. Those could all be non polar amino acids
on that side. Don't just memorize this. Think about how these form and then think about
where they would be in a protein
in the context of that protein shape and function and where it's
located in the cell. There's some questions
on the practice test that have
to do with this. And that's just
another picture, kind of showing you those amino acid
side chains sticking out of
the alpahlic. Okay. And yet more
pictures of alphahalss. And there's some
good animations from your textbook too
that are embedded. If you want to use
those. So here's this wheel trick that I was talking
to you about. And this is
showing you kind of how particular
amino acids are fo that on
particular sides of of an alpha
helix, right? And so Yeah. The other secondary
structure is a Beta sheet or a
beta pleated sheet. If you think
about a helix, there's like 3.6 amino
acids in a turn. Every coil is about
3.6 amino acids. If you think
about a sheet, it's going to be every other amino acid
is up or down, so it's going to be
amino alpha carbon, x amino acid alpha
carbon down, an amino acid Alpha carbon up amino acid
Alpha carbon down, amino acid Alpha carbon, and every other
amino acid, the side chains
stick up or down, up or down, up or down. In a Beta sheet, you take one of those
chains up down up down, up, down, up down,
and you put it next to another amino
acid chain. Up down, down up down. In this case, instead
of forming a helix, that carbonyl
oxygen and that NH are going to
form hydrogen bonds between and I'm going
to go to the next slide between the
polypeptide chains. What you're going to
get, and I'm going to change my color here
just a little bit. What you're going
to get then are going to be
hydrogen bonds forming between
the chains, these peptide chains, and you can just
have two of them interacting with each
other or you can stack a whole bunch
of them so that they're forming a lot
of interactions among these sheets of
amino acids. The way to think
about this is you're thinking
about amino acids and then that carbonyl oxygen and that NH are forming hydrogen bonds
between these chains, these polypeptide chains. Again, your textbook has a nice animation
that shows this, and these can be parallel
or anti parallel. When I say that, remember that proteins start
with an amino terminus. Let's put an n n here and then
this will be a C N. This would be the n n. This would be the N N, this would be C and C. In a parallel
Beta sheet, all of the peptide
strands are going in the same
direction and to C. In an anti parallel, if that was the
amino terminus, then this is the carboxy
terminus for each of these little chains,
they're antiparallel. They're going from the amino
terminus and then looping like that in an anti parallel
direction. In these cases, those
hydrogen bonds are forming between two
polypeptide chains, but the side chains
are sticking up or down from this sheet
from these flat ribbons, if you want to think
about it that way. That's what that little
animated gift at the bottom of the page
was to post to show you in three D. It's hard to wrap
your head around this until you start
seeing a lot of other a lot of protein structures
that incorporate this. Again, there's
some questions on the practice test that have you thinking
about Beta sheets and And the context
of beta sheets in the overall
structure of proteins. This is just
showing a diagram. Beta sheets are almost always shown as
a flat ribbon, as opposed to helices, which are shown as a hex, a flat curl c. It's a
ribbon that's coiled, or sometimes they're shown Alpha helices are
shown as a cylinder. Beta sheets are almost
always shown as a flat ribbon and from the end of
C direction, the tip of the
arrow always being the carboxy end of
that particular chain. These secondary
structures are part of the
tertiary structure, the next higher
order structure. But some proteins
are really dominated by their
secondary structures like these amyloid
proteins that are found in plaques
and Alzheimer's shown on the right
where you have just these massive
numbers of Beta Beta sheets
and there's a little bit of structure regions that loop each one of the Beta
strands together, but the structure
itself is really compact dense
structure with all of these beta sheets together and then hydrogen bonding between or among all of those between every
pair of them, making that really strong. Same thing with silk is almost all beta sheets, whereas some proteins
like alpha keratins or almost all phahlass, so it really depends
on the protein. We want over this
question in class. It's actually in your textbook
in the margins, and this is a
good point to point out that the
answers to all of the questions in
the margins on the textbook are in
the back of the book. Even if you go in through an assignment for a
particular chapter, you should be able to see the table of contents, and if you go to the
table of contents, you'll see at the
end of the book or the answers to all of the margin
questions in the textbook. We talked about
these in class. If you have any questions, please let me know. Once you get a
secondary structure, Alpha helix beta sheet, and some of these
unstructured regions, you can form a
larger structure. And those larger
structures each have, if you want to
think about the way that they made, they each have a
carboxy terminus and they have an
amino terminus. You've got a
carboxy terminus and amino terminus
together, and they are 11nn
and one C N, and they come together to form helices and sheets, and then those fold
up together to make a higher order structure called a tertiary
structure. In all cases, this is a single
polypeptide chain, and coming together to form particular regions that do particular jobs, those are called
domains and to form the overall
structure, higher order folding
structure of a protein. The tertiary structure, one chain, folding up, With its Alpha helices
and beta sheets, you see a couple of
examples of this in these animations
and drawings. You should be able to tell from these drawings which are sheets and
which are helices. Hopefully, you can see
the flat ribbons or sheets and the helices
are there as well. T tertiary
structure is almost completely dominated by side chain
interactions, and those side chains are going to be
super important and it's almost all
non covalent with the exception of
Remember cysteine. Two cystines across
from one another, C in an oxidation
reduction or an oxidation reaction, form a disulfide bond. That is a covalent bond. It takes an enzyme
to do this. This is only found
in some proteins. Most tertiary structure is held together by non covalent side
chain interactions. Again, they can be
hydrogen bonds, ionic bonds, so
electrostatic interactions. They can be hydrophobic interactions and Vander walls attractions of
non polar amino acids. And that is
really going to dominate that
tertiary structure and that's taking
those helices and beta sheets and structured regions
and putting them into a big structure together, and proteins will form the most stable
energetic state based on those
interactions. Again, if there's
two cystines across from one
another and in the interior
of a protein, they can interact
with each other and form the
disulfide bond, and enzyme is
needed to do that. If a cystines on
the outside of a protein and that hydro group is facing the hydrophilic cytosol, that cystine sulfhydro
group is available to react and is reactive in many enzymes
in many proteins. So again, combination of
Alpha helices beta sheets.
Tertiary structure. There's a word that
you guys should know there's lots of
jargon to learn. A pro protein, if you hear that
see that word, a pro protein like pro insulin is a
protein that in order to be biologically
active needs to be proteolytically. When I say that,
you're actually taking the primary structure and cleaving peptide bonds, and then the final tertiary structure
is only going to be In its final shape after that
cleavage reaction. Pro protein means there's proteolytic
cleavage of peptide bonds required for the final structure
of the protein. Here, they're showing
you pro insulin. There's a lot of
self hydro groups. Some disulphide bonds
get made, again, a single chain
here and we've got a disulphide bond in the interior, a couple here. We've got three
disulphide bonds, and then In the processing
of this protein, there's a proteolytic
cleavage reaction that's removing this
entire gray part. Here's the final
tertiary structure of that particular
insulin peptide that needed
proteolytic cleavage. This is a really unusual tertiary structure here. If those disulphide
bonds aren't there, that insulin is
not functional. Vocab hint, understand that jargon,
pro, whatever. Here's a whole bunch
of tertiary structures or proteins that are
single sub units again, they're called globular proteins
because they're not in any kind
of regular shape. They're, they're globs. A lot of times you see
these side chains like this is a protein
bound to some DNA. You'll see the
side chains from the proteins
tertiary shape able now to interact
with other molecules or other proteins,
including other proteins. In some tertiary
structures, you have the
same structure repeated over and over again into long fibers, those are called
fibrous proteins. Here's tropomyosin
from your muscles, and you see it going
back and forth between different ways to depict the structure. In one of them, you can easily
tell that these are just long palpaliss, that are interacting
with each other. Okay. More than
one sub unit, it is quantnary structure. If you have two sub
units coming together to interact to make a final functional
protein, That means two
polypeptide chains, each with an
amino terminus and carboxy terminus, then you have
quantinary structure. If you have
three sub units, if you have four sub
units five, six, 7,000, that is
quantinary structure. The highest order
structure that makes a functional protein is called quantinary
structure, and you bring together
multiple sub units. It's all side
chain interactions from those sub units. It's all non covalent that is holding those
sub units together. Remember that, that's
super important. If I heated a protein, what am I going
to break apart? Just my non covalence. If I heat up a protein
and D naturate, I'm breaking up and getting rid of my
quantinary structure, my tertiary structure, my secondary structure. The only thing
that would remain are covalent bonds, so the peptide bonds, and if there are any
disulphide bonds that disulphide bonds from
the tertiary structure. Qantinary structure is
higher order structure where there's more
than one sub unit, each subunit has an amino and a carboxy terminus. That's quantinary
structure. And this is showing a
bunch of examples of quatinary structure
with different numbers of sub units together. Quantinary
structure is often dominated by
prosthetic groups, an organic but non
protein component of a protein that's essential to its function, like a heme group
and hemoclobin. In this case, this is
an example of hemoclobd has four sub units that are called the
Alpha sub units, and two that are beta,
slightly different in sequence of amino acids. Each one of those
sub units shape is dominated by holding this hem group inside that is not made
out of amino acids, but it's where the iron is that carries the oxygen. Very important
to the shape of these sub units. And, just a great example of Qantary
structure, you'll learn
more in biochem. Again, remember, the side chains
are held together the side chains are
interacting non covalently to
hold together this higher
order structure. Hemocloba has two
conformations with and without oxygen, and you see the little
red ball come in, as the oxygen binding
to the heme group. You see the whole shape of that protein shifts
when that oxygen is found in that
prosthetic group inside of each of
the four sub units. It's all again side
chain interactions holding together all
of those sub units. Please do not
think because almost every class in almost every textbook uses hemoglobin as
an example of quantinary structure
that quantinary structures for sub units. Again, anything more than one sub unit is quantinary structure, two sub units, 1,000
sub units. Okay? Here are some
examples with more than two spies. You'll see that proteins, sometimes functional
proteins actually act as molecular machines to
do things in the cell, and it's really,
really cool. We're going to be
talking about these as the semester goes on. That's why it's just
so fundamentally important that you have protein structure down as we go on in this
class and you really get it at a deeper level and
no ur amino acids. Spend some time learning that if you
haven't already. I will tell you
that folding is a complex process. Proteins fold into their energetically
most stable state spontaneously for
the most part. But particularly
for larger, more complex proteins. Often, there's
proteins called chaperone proteins
that will help mask particular amino
acids until the protein is ready to fold into its
final shape. That's mainly because
as the protein is made, you're thinking
about a peptgin emerging from ribosome. The amino terminus
comes out first. But maybe some
of the amino acids that are
going to interact with the amino acids
at that end terminus. Maybe there are 20
amino acids in, and so it's going
to take a while before that comes out
of that ribosome. The chaperones help mask those regions
on the protein as it's polypeptiis, it's being made and then help fold it
into its final shape. I keep I realize I'm realizing as
I'm recording this that I need
to be precise with my language and
you need to be precise with
your language. If we say the
word protein, we're implying that
it is functional. If I say the word
peptide or polypeptide, meaning there's more
than one amino acid, if I say polypeptide, I can just be
talking about a chain of amino acids, but it's not necessarily functionally functional. If I talk about a sub unit of a protein that has
quatnary structure. It is a single
polypeptide chain. It is a polypeptide, but it is not yet a
protein because it might not be functional is
an individual subunit. Careful with your jargon, careful with being precise with
your language, matters on tests, it matters when you're talking about the science, and you're going into healthcare and you
need to start to learn to be incredibly precise with your
language when you're communicating
so that people understand exactly
what you mean. And so because not being clear has real
implications, right? If I say the word protein, the implication is
it's fully folded and functional unless
we're talking about a denatured protein, in which case I've broken all the non covalent
bonds and I'm down to just that
polypeptide chain. Okay. Yeah. Si chains are not only allowing for protein suben
to interact, but also allowing for proteins to interact
with other molecules. The more non polar
interactions you have, sorry, the more non covalent
interactions you have, the more tightly things
are held together. Think molecular Velcro.
Lots of little loops, a big patch of Velcro, very hard to pull apart. Only a couple of
little loops. Maybe you've got some
fuzz on your velcro and only a couple are
working much looser, much more easy
to pull apart. That's how cells
are going to manage some of
those interactions. Things you want tightly bound and never
coming apart, you're going to put a lot of non covalent
interactions in or the cell is. The proteins that
are going to come together only
for a little amount of time or things that
you might need to only stick together a
little bit and then pull off for
another function, those are going
to have far fewer non covalent
interactions from those side chains. Makes sense. When I say something's
really stable, it usually means
there's a lot of side chain
interactions that are forming lots of
non covalent bonds, less stable, not so many. We already talked
about this and then think again about the fact that your cells are filled with water. If you were a cytosolic soluble protein
dissolved in that liquid inside of the cell or inside
of a organal, you are going
to be dominated by hydrophilic
amino acids, do polar charge on the outside of
the protein and the non covalent
interactions in the inside are going to be hydrophobic
interactions and Vanders attractions. It becomes soluble. Notice the waters interacting with
the protein. It is dissolved
in the cytosol. I gave you some
practice on this. I might put up a key if anybody really
wants me to. You should be able to do this pretty darn easily and recognize the amino acids that are part
of this chain. If you want me to
put up the key for this, I'll be
happy to do so. Say the word. We already