>> Hello and welcome to the Penguin Prof Channel.
In today's episode we're going to be talking about amino acids,
and levels of protein structure.
This is a fibro in protein, and we're going to talk
about how the structure, and the chemistry
of this protein is what accounts
for the amazing properties of silk.
These are cocoons from the larvae of the Mulberry Silkworm,
some of the most famous silk in the world.
And it is all about the chemistry
that gives us all the incredible properties of silk,
including just how strong, and also light reflective it is.
You're gonna want to stay tuned.
We're going to talk about chemistry and the four levels
of protein structure, and by the end even these really
complicated structures will make some sense to you.
So before we get into it, you know the drill.
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Let's get into proteins.
All right.
You guys know already how incredibly important proteins
are for biological organisms.
It is really all about the proteins.
But this video is about how they are built, and how we talk
about the levels of structure.
They are really complicated.
We start with the basics, monomers to polymers.
So if you forget, right, mono means one, poly means many.
If you've got two monomers, and you want
to join them together we run a reaction called
dehydration synthesis.
On the other hand, you can break a bond between two monomers
in a reaction called hydrolysis.
Okay. Now, in proteins the monomers are amino acids,
so named because they have an amine in,
and a carboxylic acid in.
We've also got a side chain,
that's the part that's going to vary.
We'll talk about it later,
and that's central carbon we call an alpha carbon.
Now, before we get any farther into this,
my students always ask me about this.
You're gonna see amino acids drawn like this,
and you will also see them drawn with charges.
I just want you to know that the ionization states
of those functional groups,
that's what that's called, right.
Whether or not they're behaving as proton donors or acceptors,
it just depends on the PH of the solution.
Okay. So it really doesn't matter how you draw them.
Okay. So don't get all caught up with that.
All right.
We're going to take two amino acids, two monomers,
and we're going to join them together
in that reaction dehydration synthesis,
and the bond we make is called a peptide bond.
You're going to see a lot of terms with that peptide in it.
Right. Di, tri, tetra.
Oligo means some.
Poly still means many.
When we use the word protein, we're usually talking about more
than 50 amino acids joined together.
Are you ready to meet them?
Okay. Here they are.
Your textbook will give you tables like this.
An alphabetized table of amino acids tells me nothing.
On the other hand, some of you may have
to memorize the essential amino acids.
These have to come from the diet,
so you may need to know those.
Here's a pneumonic for those.
But, ladies and gentlemen, this is not the way to do it.
All right.
It's all about chemical properties.
What you want to do is look
at amino acids based on their chemistry.
Are they non polar?
Which means they fear water.
Or are they polar?
Which means that they are water loving.
If they're polar, they can be either acidic basic or neutral,
and that's the key
to understanding amino acid function.
You may remember that there are other things, like hormones.
It's the same thing.
It is really all about the chemistry,
so get over your fear of chemistry.
A little bit of chemistry makes all the difference.
It's all about the side chains.
That side chain is going
to dictate what group the amino acid is in.
Here are the groups.
We've got non polar.
That is hydrophobic amino acids.
Often subdivided based
on whether they have an aromatic ring or not.
Then we've got the polar, that is the hydrophilic amino acids.
Then we've got the proton acceptors, basic,
and proton donors, acidic.
Those are the categories.
This is what's going to dictate how amino acids behave
in a protein.
So the function, and the structure
of the protein is going to be dictated by the order
of amino acids in the chain, and the properties
that those amino acids have.
That's it.
That's the secret.
So, I know it's not very sexy, right.
One, two, three, and four, primary is the order
of the amino acids in the chain.
What determines that is the DNA sequence.
All right.
So DNA to messenger RNA.
We've got transcription,
and then on the ribosomes we've got translation,
and messenger RNA into the final protein.
So if you haven't learned this yet, you will.
The dictionary of life, right.
This is how messenger RNA encodes all 20 amino acids.
How about a quick example?
Let's look at glucagon.
This is the primary structure of glucagon.
It is just the order of amino acids in the chain.
By the way, glucagon is a peptide hormone made
by alpha cells of the pancreas.
But the order, and the individual amino acids makes a
big difference.
These are diseases, which are caused
by a single amino acid change.
A single mutation.
Let's look at sickle cell anemia as an example,
where the red blood cells take on a sickle shape.
This happens because of one amino acid switch
from glutamic acid to valine.
So, yeah, the order makes a big difference.
Next level of protein structure we call secondary.
These are regions of regular folding due to hydrogen bonds
between amino acids that are close to each other,
and specifically we're talking about bonds
between atoms in the backbone.
So we're not talking about the side chain.
We're talking about the amine, and the carboxylic acid groups.
Two different types of secondary structures.
We call them alpha helices, and beta sheets,
and both of these structures make a huge impact
on protein function, and structure.
I've got some demos here.
So we're gonna look at an alpha helix first.
So if this represents the primary structure
of amino acids, it's kind of like a wet noodle, right.
It's just a chain of amino acids, no shape.
Look what happens when I roll it up into an alpha helix.
Now I've got something [bell sound] that's really rigid,
and strong.
Alpha helices provide tremendous structure to proteins.
This is a G protein coupled receptor.
You actually saw this guy in the signal transduction video.
The alpha helices represent membranes spanning regions.
Let's look at them here, where every ball is an amino acid,
and you see there are seven places
where this protein crosses the membrane.
How does it stay there?
You know, how does this protein stay in the lipid by layer?
Well, it's chemistry.
The non polar amino acids are inside the lipid bilayer.
The polar amino acids are in the extracellular,
and intracellular fluids.
So the properties, and sequence
of the amino acids are what keep the receptor anchored
in a fluid lipid bilayer.
It is all about structure.
Here's an example.
In another way we're going to look at hemoglobin.
The alpha helices here actually keep the shape
of this protein hemoglobin bines for up to four molecules
of oxygen gas, and it is mainly alpha helices
that hold the thing together.
All right.
Let's look at beta sheets.
I had some fun in the kitchen.
Again, just the primary structure.
I try and use it to hold up another penguin.
No, but if I fold the paper into a beta sheet,
same size paper, a lot more structure.
[Bell sound] A lot more rigidity.
Beta sheets are what accounts for the strength
of that [inaudible] protein that I showed you
in the beginning that makes up silk.
Not only do all these beta sheets give it the tensile
strength that silk has, it's because of the shape
of the beta sheets that accounts for the way light reflects off
of silk, and gives it that beautiful luminous quality.
All right.
We're up to the third level of protein structure.
The third level is all about the side chains.
Those R groups, and the chemical interactions
that they have with each other.
That can be either close by
or across great distances in the protein.
Four different types of interaction.
And basically in the tertiary structure we see the complete
three dimensional shape of the polypeptide chain.
So across great distances
or right nearby you see all different types
of chemical reactions between those side groups.
This is also where we get into denaturing agents, right.
So these denaturing agents can cause those tertiary structures
to break down.
Sometimes they're reversible, sometimes they're not.
You've probably fried an egg.
That is the denaturing of the egg white protein, albumin.
Finally, quaternary structure.
This happens when you have two or more polypeptide units.
So di, meaning two.
Tri, tetramer, right.
This just refers to the number of units that have
to be assembled for the final protein to work.
We generally categorize them as fibrous or globular.
Let's look at hemoglobin again,
but it's colored in a different way.
So now each of the four subunits are shown in a different color,
and you see how all four are assembled
to make the final functional protein.
All right.
So hopefully what you've seen is that the interactions
of amino acids are the key.
Primary level of structure is the sequence dictated
by the DNA.
Secondary regions of regular folding, these are between atoms
in the backbone itself, not the side chains,
and we form alpha helices and beta sheets.
Really the structural sort of framework of all proteins.
Tertiary, we get into four different types of bonds,
and those are between side groups, right.
Those side chains are interacting,
and forming a complex three dimensional shape.
Quaternary, you've got two or more polypeptide chains
that are assembled into a single functional unit.
Ladies and gentlemen, that's it.
As always, I hope that was helpful.
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