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Professor Kevin Ahern: How's everybody doing?
You're doing better than I am, huh?
Okay, so we are moving our way through protein structure
and one of the things I wanted to say something about,
there's a couple of things about amino acids I didn't finish
saying something about,
so I'd like to make sure that you're aware of them.
There's some terms that I use,
and they involve some calculations as well.
One is the term PI.
You have probably seen them on one of the problem sets
and I haven't explained that to you.
So I want to say a little about what that is.
So PI is a pH.
It's a special pH.
It's a pH at which a molecule, that's any molecule,
has a charge of exactly zero.
The PI for a molecule must be calculated precisely.
It's not something that some of the estimates that I give you
will work.
Now one of the estimates that I've given in the notes,
I haven't talked about it specifically in class
but I'll mention it here also, is-
there is an estimate you can make for the charge
of a molecule based on its pH and its pKa.
And this estimate that I'm going to give you for the charge
of a molecule only works for estimating.
It does not work for calculating PI.
So here is the estimate, this estimate is one
I will not give you on an exam.
You'll need to know what I'm getting ready to tell you.
I give you formulas, I give you various things,
but I am not going to give you what im getting ready
to tell you and that is that to estimate the charge
of a molecule, if the pH is one or more units above
the pKa of the molecule or of a given group,
we have a molecule where there is more than one.
If the pH is more than one unit above the pKa of the group
then the proton is off.
If the pH is one or more units below the pka then the proton is on
and that's good for estimating charge
and we'll use that frequently.
So you're going to have to estimate charges of amino acids,
you may estimate charge of proteins and so forth,
that's very good for that estimate.
It's not good for calculating PI.
Now I'm not going to go through how you calculate
PI here because I have a video online
that shows you how to calculate PIs.
People think that the only videos in this class
are the ones that are under this column on the left.
In fact, if you look on the right
you'll see problem solving videos here and here
and there's more as you go further down.
Practice protein charge problems here.
If you watch those videos and you work through those problems
you will have some good practice.
How do you calculate the PI?
The PI is calculated as the average of the two pKa values
around where the molecule has a charge of approximately zero.
So when you look at a titration plot you'll see a place
where a molecule has a charge of approximately zero,
it's the average of the two pKa values around that.
That means that you can't just add up the pKas and average them,
you got to do a plot and figure out where
that approximate zero point is and then average
the two pKa values on either side of it.
If you watch the video it should help you
and if you have questions after that then of course come see me.
PI is a very important thing because it's the place
where a molecule has a charge of exactly zero
and we'll see later that there's sometimes when its useful first
to know when a molecule,
a protein, an amino acid or whatever,
has a charge of approximately zero.
We'll see when that occurs.
Another term I haven't used, that I've mentioned
also I think in my highlights, but I'll bring it up here,
is the term zwitterion.
Z-W-I-T-T-E-R-I-O-N
You can bet if I spell it for you its spelling must be important.
Zwitterion is a molecule who's charge is zero.
So you say well it's the same thing as PI, well no PI is the pH
at which the molecule has a charge of zero.
A zwitterion is a molecule whose charge is zero.
Two different things.
Okay, excuse me, alright.
So I wanted to make sure I got those out there because
there are some practice problems I've gotten to work,
and who knows, you might even see something like that
on an exam, so its entirely possible
that you'll have that happen.
I want to make sure that your familiar with those things.
Questions about that?
No questions, okay?
Question, Yeah!
Question was, ‘do I mean zero charge or net zero charge.'
And the answer is, same thing.
A molecule has a zero charge if its net zero charge is zero.
Alright well, let's see, so last time I got to the point
of talking about Ramachandran plots,
and I don't want to make too big of a deal
out of Ramachandran plots because students go,
‘Oh my God, what do I have to know
'about this, et cetera et cetera.'
Well what you have to know about Ramachandran plots
is first of all, they're theoretical plots
that tell us something about the structure that
a protein can have.
It tells us something about the structure.
Alright, So this was the Ramachandran plot
that I showed you last time
and I noted that there was an awful lot of space
on a Ramachandran plot where structures are not stable
now I'll remind you that a Ramachandran plot has a
plot of phi and psi
and there's three hundred and sixty degrees for each one,
from plus one eighty to minus one eighty,
from minus one eighty to plus one eighty.
These are rotational angles
of the two bonds around the alpha carbon.
I don't care if you memorize which one is which.
That's not an important thing.
But what is important is the fact that there's only certain
rotations around those bonds that give rise
to stable protein structures.
Anything that's colored up here
is relatively stable, the darker it is, the stabler it is.
And the whites are basically regions of
rotation around those bonds that are not stable.
Now we're going to see in a little bit that some
of those rotations correspond to very specific structures
that are commonly found inside of proteins.
Commonly found inside of proteins.
Well that's kind of nice to know.
That a theoretical plot matches up with what proteins
actually have and that not only that but we see commonality,
we see these structures over and over and over
inside of proteins and we're going to talk
something about that.
So that's the sort of jist
of a Ramachandran plot.
You're not going to draw a Ramachandran plot, okay?
You're not going to interpret a Ramachandran plot
but you should know something about what a Ramamchandran
plot tells you.
Well, I've just finished talking about
what I've been discussing so far which is primary structure.
I'll remind you that primary structure was the sequence
of amino acids within a protein
and I said that the sequence of amino acids in a protein
determine everything, ultimately about the protein.
We're going to turn our attention now from
primary structure to secondary structure.
And as we go higher levels of structure
we start thinking about interactions
between amino acids that are further and further away.
Primary structure was the sequence
and the sequence related to
the immediately adjacent amino acid.
This amino acid, this amino acid,
this amino acid in a protein, okay?
There's no distance, the very next one is the one that matters.
Well with secondary structure we expand that view
out to about ten amino acids.
So secondary structure, I'm going to give you
a definition here, secondary structure is a regular,
repeating structure that arises between amino acids,
less than ten apart.
Less than ten amino acids apart.
Is a regular, repeating structure that arises as a result
of interactions between amino acids
that are ten or fewer apart.
Now that's a definition.
In reality, what does secondary structure mean?
For our purposes we're going to talk about
two primary types of secondary structure
and we're going to see that they line up with
that Ramachandran plot pretty well.
The two primary types are known as alpha helices
and beta strands.
And these were the structures that Linus Pauling
discovered and received the Nobel Prize for.
It was his first Nobel Prize.
The structure of a protein.
Here are four depictions of an alpha helix.
An alpha helix, as its named suggests is a helix.
And you see four different ways of portraying that helix
that protein chemists frequently draw.
This one I kind of like, this is called a ribbon structure
it's sort of like a combination ribbon and atom structure
if it didn't have those atoms on there
we would just call it a ribbon structure.
But ribbon structures are really good
for giving us the shape that a structure would have.
If we wanted to be precise we would actually look
at the second structure here, and this is the depiction
of what that short section of peptide would look like
if we looked only at the atoms.
It's a little harder to look at,
but it also has an advantage that in this structure
we can see some of the forces that are stabilizing
this alpha helix.
The forces that stabilize an alpha helix are hydrogen bonds.
Hydrogen bonds stabilize an alpha helix.
You see them in this structure here
as little green dashes.
These little green dashes arise between amino acids
that are between four to seven amino acids away.
That's less than ten.
Notice that the definition I gave you said it's a regular
repeating structure.
What does that mean?
Well, a coil is a regular repeating structure.
That's what this alpha helix has,
that's what this is trying to portray.
What else can we say about an alpha helix?
Well, what we can say also shows up nicely in both C and D.
If we look at those green dots that are on there,
on each of these,
the greens correspond to the r groups.
Now if we look at this,
we see in an Alpha helical structure,
that the r groups are pointed outwards from the helix,
that's nice.
Some of you have asked me individually
and I think somebody asked in class also,
do some amino acid side chains
effect the structure of the protein?
The answer is yes they do.
We try to put two bulky side chains next to each other
that it may very well disrupt
and prevent an alpha helix from forming.
Now we can actually use computer programs
to analyze an amino acid sequence
and predict with a reasonable amount of certainty
if a given segment of a protein is present in an alpha helix.
A computer program can do that using the knowledge
that we have of the r groups and so forth.
So, that's something that a computer can do for us quite readily.
This shows some of the interactions between
hydrogens and oxygens, and oxygens and hydrogens
within an alpha helix.
And we twist these around in three dimensional space,
something that looks like its far away in primary sequence
actually ends up being pretty close
to each other in secondary structure.
So this and this are fairly close when the alpha helix forms.
If we look at the Ramachandran plot, we see Ahh!
There are two places on the Ramachandran plot
where the helices can form.
One is a right-handed helix, which is very common,
And the other is a left-handed helix which is very rare.
But, they appear right square in the middle
of predicted regions of stability by Ramachandran.
This is a nice depiction of a protein
that's full of alpha helices.
Now you'll notice that this alpha helix doesn't just go forever,
it'll have a little bend sometimes,
sometimes it will have a bigger bend
and we'll talk about those bends when we talk about
tertiary structures.
But suffice it to say that there are proteins that have almost
exclusively alpha helical structure.
Not all proteins, but some proteins have that.
Alright, another common secondary structure,
and the second one described by Linus Pauling,
are known as what some people call beta sheets.
I like to call them beta strands.
If we take beta strands
and we arrange them together we get a sheet.
So a sheet is an arrangement of a bunch of beta strands.
We'll start here with the Ramachandran, and look, oh wow!
The beta strand's structure right square in the middle
of the theoretical region of stability in the Ramachandran plot.
What is a beta strand?
Well, let's talk about that.
Here's what a beta strand looks like.
It's a little hard to tell from this figure what it looks like.
But a beta strand is like a helix in two dimensions.
A helix goes round, and round, and round,
a beta strand is like and also called pleats.
Up, down, up, down, up, down, up, down, up, down, like that.
So it's a flattened, two-dimensional version of an alpha helix.
Alright, this depicts that up, down, up, down, pretty well.
Okay, up, down, up, down, up, down, up, down, up, down, okay.
You see that the greens again are the r groups
and you remember from the structures
that we saw before the r groups
that they were on opposite sides every other one,
so here's one in the back, front, back, front,
and here's the central part with the carbonyl group,
the alpha carbon, and the carboxyl group,
up, down, up, down, up, down, up, down, up, down,
you can see like that.
Now, what this shows is interactions
between two different beta strands.
Two different beta strands interact like this,
they're going to give rise to a beta sheet,
which is a set of them.
Now when we look at this we see
that what stabilizes the beta sheet are hydrogen bonds again.
Hydrogen bonds are holding together beta sheets.
We might have a whole stack of these, we might have ten of them.
If we had ten of them stacked up like that or maybe even more,
we would have something known as silk.
Silk is full of beta sheets.
Parallel versus anti-parallel simply refers to
whether the carboxyl and the amine are like this,
or if the carboxyl and the amine ends are like this.
These are parallel, these are anti-parallel.
If this is the carboxyl end, this is the amino end,
this is the carboxyl end, this is the amino end,
anti-parallel, parallel.
That's all it is.
The overall structure doesn't matter for parallel
or anti-parallel.
Here is an enzyme that has a structure
that has beta sheets arranged
rather nicely into what we call a barrel.
You can see that this barrel and the blue parts are the strands
that are all oriented with respect to each other.
They create a barrel, and this barrel on the inside
is fairly protected from water.
Barrels like this we occasionally see
when enzymes need to have water or protection
from water for something,
or they need to have a reaction contained within a certain space
and barrels work very well for those things.
Now I showed you the alpha helix and I said,
"Alpha helix will go for a ways and then we see a bend
"or we see something else that sort of interrupts that."
So I want to say a little bit about things
that interrupt structures,
specifically things that interrupt secondary structures.
Now I've told you that there are some amino acids
that really can cause some changes.
One was as I said, things that have very bulky r groups.
If you put two of them together, they may not fit very well
and that may cause a bend
if we had an alpha helix going on for example, or a beta strand.
Other things that I've said can disrupt protein structure
is proline.
Because proline, you may remember, was the amino acid
that had the r group that came back around and attached
to the alpha amino group and I said it was less flexible.
Well what you see on the screen is something
that arises very commonly as a result of the appearance
of proline with in a polypeptide sequence.
"I” here refers to one amino acid, "i+1” is the next amino acid,
"i+2” is the next, "i +3” is the next amino acid.
So here's a series of four amino acids
and what you see on the screen is a depiction of a bend.
Instead of going off in a helical nature or on a pleated nature,
this bend is happening right here.
And the bend is happening because something
is not consistent with that regular structure
that we saw for an alpha helix
or something that we saw for a beta strand.
As I said, most commonly bends will arise
in a structure like this because of proline.
Proline is not flexible,
and also commonly we will see in a structure like this, glycine.
Glycine, you may remember,
was the amino acid that had the smallest r group.
and its glycine that allows for the most flexibility,
the most options that are there
and glycine may often times also be in a structure like this.
Now bends are important for us to consider
when we start considering the next level of protein structure
and that's tertiary structure.
So I'm leading up to getting into tertiary structure.
I'm not going to talk about tertiary structure at the moment,
I'm going to save that for a few minutes from now,
but suffice it to say that tertiary structure
really has a lot of bends in it.
Yah question.
Student: [inaudible]
Professor Kevin Ahern: Yeah, what depicts it
or what amino acids would favor it?
So it's a good question.
So what will tend to favor
an alpha helix versus a beta helix strand?
I think I have a link on here I will show you
that some one's compiled a list of all the different amino acids
and their tendency to be in a structure that's alpha helical
or a beta strand.
There is no absolute rule first of all.
There's no rule that says tryptophan can't be in an alpha helix
because tryptophan can be in an alpha helix.
Its likelihood may be low
depending upon the amino acids surrounding it,
and we start thinking about amino acids surrounding it,
that is what makes our predictive abilities
a little bit harder to do.
So I can say for example, tryptophan is not in an alpha helix,
you would say, ‘Okay well I'll mark that one off.'
But it can be.
So but I'll show you a table
that shows a preference for one versus the other
and then you'll get a bit of an idea of it.
Is that okay?
Yah another question.
Student: [inaudible]
Professor Kevin Ahern: Do you ever see
a hydrogen bonding occurring with something in the amino group.
Let me think about that one for a second.
You will not get with in the backbone
because in the backbone the only things
that can hydrogen bond there
are those that are linked to the amin
because you have to have a partial positive charge
and there is nothing in the backbone
that would have a partial positive charge,
except for that.
If we think about r groups,
yes we can have that because r groups can have a variety
of things inside of them but not inside the backbone, okay?
Good question.
Alright, now I didn't want to talk about tertiary structure yet
because I wanted to talk about a special class of proteins
that are interesting because they only have
primary and secondary structure.
Most proteins have at least primary, secondary and tertiary,
some will have quaternary, some wont, we'll see.
Most proteins have at least primary, secondary, tertiary.
But there is a group that has almost exclusively primary,
secondary and very very little if any tertiary.
This group of proteins that has only primary secondary structure
known as fibrous proteins.
And as their name would suggest, they're fibers.
So we can imagine something that has an alpha helix
that just keeps going and going and going
and going and going and going
and your hair would be a really good example.
So your hair is full of alpha helices
that just go on and on and on and on and on.
Now in individual hair is comprised of, of course,
many individual alpha helices all meshed up and intertwined,
and so on and so forth, so it's a little complicated
but the important point is that they don't fold,
they don't have much in the way of tertiary structure.
If you have curly hair, you may have some slight bends
that happen as a result of some disulfide bonds that happened
that caused some bending to happen within
that overall bigger structure.
So people who go, and people used to go do this
and get permanents and things like that to get their hair styled
and curled and so on and so forth
would come out of the hairdresser smelling like stinky
because the hair dresser had to break those disulfide bonds,
those are sulfur bonds,
they had to use sulfur compounds to do that
and that's why your hair stinks after a permanent.
Those bonds aren't permanent though,
as you discover if you have one of those,
so they will come apart
and they will go back to its original shape.
So even if you get your hair curled,
it doesn't stay curled forever.
If you have curly hair,
your hair has already assumed those structures
in its most native form,
and it's hard to change that, but again,
that's what a permanent does.
Let's look at some of these arrangements.
So these are coils of coils.
Here's an alpha helix,
and here's an alpha helix coiled with another one.
We can imagine that hair might have many of these guys,
many of these bundles that come together
to ultimately make a hair that we can see.
I'll talk about that another time.
Let's talk about - don't do that to me.
One of the most interesting of the fibrous proteins
is the most abundant protein in your body.
One of the most interesting of the fibrous proteins
is the most abundant protein in your body.
And the most abundant protein in your body is known as collagen.
Collagen is a very odd fibrous protein,
I'll tell you why in a second.
But it is a fibrous protein,
it has very little tertiary structure.
And it too is a coil of coils.
It's three coils coiled together.
So that was actually, here it is.
That's one depiction of it.
We see three coils coiled together.
We see one strand in blue, one strand in red,
and one strand in yellow.
Collagen in the glue that holds us together.
It attaches cells to each other, it attaches, bones to muscle,
and a variety of things.
So collagen is really an important glue for us
and that's why we have so much of it.
It's very very important for us to have that glue
that holds us together.
I'm going to tell you something that's kind of cool
and has medical implications about collagen.
Collagen as you saw, was in fact, a coiled structure
and we can imagine that we have one coiled structure now
that bundles with another coiled structure
and we get sort of super order of these coiled structures.
It turns out that there is a reaction
that occurs to modify some of the amino acids in collagen.
We haven't talked about modifying amino acids,
it's appropriate now that we talk about that.
Some amino acids in proteins get modified after
they're put into a protein.
They're modified after they get put into a protein.
In collagen, the two most common are lysine and proline.
After they are made into the collagen structure,
they are modified by putting a hydroxyl group onto them.
Modified by putting a hydroxyl group onto them.
That reaction requires vitamin C.
One of the reasons you have to have vitamin C in your body
is so that you can make collagen
that has those modified prolines and lysine residues there.
I'm going to tell you why they are important in a second,
but you need to understand what they are first.
Now you're probably sitting there scratching your head going,
‘But Kevin, you said that proline disrupted-‘
I'll tell you what it's disrupting right here is the collagen...
If proline is so disruptive,
what's it doing inside of this helical structure?
Well it turns out it's everywhere in this helical structure.
And what's interesting about it is wherever we see a proline,
we almost always see a glycine.
Pro, Gly, Pro.
This is a little bit of a clue as to what's going on.
Proline being very inflexible, glycine being very flexible,
put the two together, helical structure become possible,
very very possible.
So this is one of the reasons it's an odd fibrous protein.
Now proline, as I said, gets modified.
It gets hydroxide groups put onto it as does lysine
and it turns out that those hydroxide groups are
reactive towards each other.
Hydroxyl of a proline on this strand over here
or this bundle over here may react with a hydroxyl on a proline
on this bundle over here and when they do that,
they split out water and make a covalent bond.
Covalent bonds, as we remember, are very very strong.
Why is that important?
I'll tell you why it's important.
I see several people on here with long hair.
If you braid your hair or you've braided somebody's hair,
you know that you can take it
and you can make beautiful braids with the hair,
but if you don't tie it off at the bottom with a rubber band,
what happens?
It will all come out.
The equivalent of the rubber band are these covalent bonds
that form in between these hydroxyl groups
in the individual bundles or strands
that I am describing for collagen.
What these bonds give to collagen is great strength
and when we talk about holding our bodies together as a glue,
we want great strength.
We don't want to fall apart.
Now I tell you that because, vitamin C,
I told you, was necessary to make those hydroxyl groups.
If we don't have vitamin C, if we are deficient in vitamin C
we develop a condition known as scurvy
and scurvy is not something you want to experience
because what happens is you literally fall apart.
Your collagen is very weak.
The rubber band at the end of your hair,
or at the end of our collagen isn't holding stuff together,
you're in bad shape.
Scurvy was discovered first among the pirates
who went off on long voyages with no fruits and vegetables
etcetera etcetera, those silly pirates.
And they went out as big, honking, ugly, mean, old pirates
and they came back a bunch of wimps.
They fell apart.
Vitamin C is important for that reaction.
It's important for making a strong collagen.
Questions about that?
Yes?
So vitamin C strengthens collagens
because vitamin C is necessary for adding the hydroxyl groups
to the lysine and proline residues
and those lysine hydroxyl groups react between
the individual strands to help hold them together
and make them stronger.
Just like if we made a braid, like for a rope,
the braid is going to be stronger than the individual strands
will be by themselves, make sense?
I'm sorry?
It's not a catalyst, no. It's a necessary sub straight
for the reaction.
Okay good questions.
So that's what I want to say about secondary structure.
Let's turn our attention to tertiary structure.
Now as I said earlier, the higher the level of structure,
the further apart the interactions are.
This is a structure of a protein
that we are going to talk a fair amount about next week,
it's called myoglobin.
Myoglobin is a protein that is not fibrous.
If a protein is not fibrous, we refer to it as globular.
Most proteins in nature are globular.
Fibrous proteins are not very common in terms of number,
they are common in terms of abundance,
like we have a lot of collagen,
but collagen is only one protein.
Most proteins are globular.
What does it mean to say something is globular?
Well I like to just be silly and say
if we were to actually look at this protein
sitting on the stage right here it would look like a glob.
It would not look very regular in structure.
It would't have nice pretty coils
going forever and ever and ever,
but it would have little coils that would go for a ways,
and then we would get a bend, and now you know how bends happen.
Mercedes-Bendz, ha ha.
Bad joke.
You guys want a joke?
You ready for a joke?
I tell this one in my class all the time,
I love this joke, it's my favorite joke in the world.
If you've ever watched my videos you probably have heard this joke
so don't give away my punch line.
This is about the hit man known as Arty.
How many people have ever heard the joke?
A couple, okay not too many.
So there's this little guy, he's a hit man, and his name is Arty.
He decides he wants to make it big in the hit man business.
If you want to be big in anything these days,
what you have to do is you have to advertise.
So he take a little business card and he puts on there,
"Will kill somebody for cheap,”
and he posts it all over his neighborhood.
So he's sitting at home one night and he gets this phone call,
and somebody's gotten his business card and they call up and say,
"Hello are you Arty?”
And he says, "Yes, yes.”
And he said, "Well I've got somebody I'd like you to kill.”
He says, "Okay.”
And he says, "But how much do you charge?”
He said, "Well I'm just getting started, I'll do it for a buck.”
This guy says, "Okay, yah yah.”
So Arty says, "Who do you want me to kill?”
And he says, "Well, I want you to kill my wife.”
It's always the wife, right?
It could be the wife wants to kill the husband, doesn't matter.
I want you to kill my spouse.
"Alright well I can do that,
"is there any way you'd like me to kill them or anything?”
He says "Yah, I'd like you to strangle them.”
He said, "Okay,” and he writes this all down.
"And where can I find them?”
"Well my spouse is down at the grocery store right now,
"could you go down and do that?”
Arty says, "Sure, why not?”
Arty goes trucking down to the grocery store and he looks,
and he sees in the grocery store,
he sees this person that meets the description.
"Ahh, my career is starting right here,
"right here in the produce section.”
So he goes up and he grabs the spouse and he starts strangling
and kills the spouse right there in the grocery store.
Yes, he's done it, right?
Oh no, somebody saw him.
Somebody saw him so he's got to do something.
So he goes over, what else is left to do?
You can't have any witnesses.
So he goes over and he grabs this person and he strangles them!
That was close.
Oh no, over here, right?
"My lucky day, right?
"I'm starting my career as a hit man and I get a witness.”
So he goes over and he grabs this other person
and strangles them right there,
and he looks around and there's nobody.
"Yes!"
So he goes running out the door, but the police catch him.
And the headline in the newspaper the next day says,
"Arty Chokes Three for a Dollar at the Grocery Store.”
[laughing and clapping]
Thank you!
[laughing]
You see why that's my favorite joke.
"Arty Chokes Three for a Dollar...”
It takes a while to set that one up, but it's a good joke.
Don't tell your friends,
that way when they take this class next year,
they won't have heard the joke, that'll be good.
Okay, back to tertiary structure.
So tertiary structure arises because of Mercedes-Bendz.
The joke still doesn't work I guess, after that joke.
But what we have are alpha helices that go for a ways
and then they turn, they go for a ways and then they turn,
they go for a ways and then they turn.
Those turns give rise to a three dimensional structure.
When we think about the three dimensional structure of a protein,
the turns are really critical
because slight changes in those turns
point the helix in a very different kind of direction.
What matters is the overall three dimensional nature,
the tree dimensional structure of that protein,
and this protein when it's in its proper three dimensional form
carries oxygen.
That little thing right here is known as a "Heme group”
that we'll talk about later that caries oxygen.
So globular proteins have a three dimensionality to them,
they have more than just a fibrous nature to them,
and they also have some bias when we talk about
what amino acids that they have with in them.
Notice here blue is charged,
yellow is hydrophobic, and white is other.
Blue charged, yellow hydrophobic, and white other.
Blue charged, yellow hydyrophobic, white other.
What you see on the screen for this particular globular protein
is that there's a bias in the amino acids
in this overall structure.
Polar or charged things tend to be on the outside of the protein.
Non-polar, uncharged things tend to be on the inside
of the protein.
That makes really good sense.
Most proteins are dissolved in water in the cell,
and for them to dissolver in water,
you want to have the polar and charged groups
interacting with water,
and the things that don't like water will fold unto themselves
and avoid the water.
There's no water on the inside of this protein
because these hydrophobic groups have squeezed it out.
They've squeezed it out.
Not all proteins are dissolved in water,
we'll see some exceptions later,
and when we see those exceptions
we'll see that they're reflected also
in the location of amino acids with in them.
In fact, I said later, here's one right here.
Here's one called "porin.”
Porin is a protein that is found in membranes of cells.
Membranes of cells are fairly non polar.
So we see the outside of this guy,
the part that's interacting with the membrane,
it's fairly non polar.
On the inside, porin, what it does,
is it allows water to pass through it.
It's a pore.
And we see on the inside of this guy, here are the hydrophilics,
or the polar charged groups, that allow water to interact
and come in through there.
These last two figures I've shown you
are probably the best examples I can give you
of structure and function.
Now, I did bring up a song,
so I think we'll finish today with a song
and then we will talk more about his next time.
Another easy song to sing.
It's called, "Oh Little Protein Molecule.”
Professor Kevin Ahern and Students: Oh little protein molecule
you're lovely and serene.
With twenty zwitterions like
cysteine and alanine.
Your secondary structure
has pitches and repeats,
arranged in alpha helices
and beta pleated sheets.
The Ramachadran plots are
predictions made to try
to tell the structures you can have
for angles phi and psi.
And tertiary structure
gives polypeptides zing
because of magic that occurs
in protein folding.
A folded enzyme's active
and starts to catalyze
when activators bind into
its allosteric sites.
Some other mechanisms
control the enzyme rates,
by regulating synthesis
and placement of phosphates.
And all the regulation
that's found inside of cells
reminds the students learning it
of pathways straight from hell.
So here's how to remember
the phosphate strategies.
They turn the GPb's to a's
and GSa's to b's.
Professor Kevin Ahern: Well talk more about those later.