>> Welcome to Proteins and Enzymes Part 4.
On this video tutorial we are going to focus
on the primary structure of proteins.
Let's get started.
So as we know, a peptide is two
or more amino acids bonded together.
So we'll do it in words and then we'll see it
as an actual reaction.
All right.
So the amine group of one amino acid and the acid group
of the other amino acid undergo an acyl transfer reaction
to form an amide bond, but now that we're talking
about amino acids, we're going to call it a peptide bond.
So the new molecule is a dipeptide,
and then we can keep adding amino acids to build
up our peptide chain to 3, 4, to many peptides.
When we're writing a polypeptide, we're always going
to write it with the N-terminus on the left
and the C-terminus on the right.
So here we have the acyl transfer reaction.
And when you get to biology, they're going
to call it synthetic dehydration.
And so we have two amino acids here.
This first amino acids is threonine,
and then we have valine.
And so they have three-letter abbreviations.
And so what's going to happen is we'll have the bond formation
occurs here, and so it's always helpful to look
at the carboxylic acid and the carboneal carbon
of the carboxylic acid; that gives us a landmark.
And then we can see here is the peptide bond that formed
to link the two amino acids.
So we can -- but to help you see this,
before we go too much further, let's draw the neutral forms
of the amino acids to help us see the reaction pathway.
So remember, with carboxylic acids and amines we always need
to be able to overlay our acid base chemistry,
so let's do the neutral form to help us.
So we'll make everything, and we'll go here.
Let's see.
We can put that there.
There's our R-group.
So there's the threonine.
And now we'll have the valine.
All right.
So here's our landmark, the carbonyl carbon,
and so we call this synthetic dehydration.
It will always be the alcohol group --
remember everything you learned
from our functional group reactivity --
so we call it synthetic dehydration
because we're taking two small amino acids
and linking them together to form a dipeptide,
and water will be produced as a byproduct.
So now to finish this up -- so then let's put this together.
So here's our first amino acid,
and then we'll bring in the second amino acid,
and we kind of naturally get this flipping
of the R-groups up and down.
And then there's the OH.
So here is our carbonyl carbon, here is our peptide bond,
and so when we look at this dipeptide, we look, right,
to the left of the peptide bond, we have our threonine,
and to the right of the peptide bond, we have valine.
All right.
So I think if we look at the bottom,
what was our to-do list here?
So we've drawn an arrow
to the peptide bond connecting the two amino acids,
and we've circled each
of the amino acid components creating the dipeptide.
And then just for a brief review,
what is the term we would use to describe the relationship
between valine, threonine, the dipeptide; or threonine valine?
All right.
Well, they're going to have the same chemical formula; however,
right, the connections are different -- different bonding,
different connection between atoms --
and so when two molecules, two dipeptides, if this applies,
right, they're structural isomers,
or constitutional isomers.
All righty.
So the main thing here is to recognize
that when we're talking about the primary structure,
we're talking about the amino acids sequence.
So here we've practiced putting the amino acids together
to create peptides.
Now we'll practice in the reverse direction.
So on the next page, we will look at a tripeptide,
and now we will go in reverse;
we'll do the hydrolysis reaction.
So we'll use all your understanding of amid hydrolysis
to do our peptide hydrolysis.
So when we're looking at an amino acid sequence,
or tripeptide, for me the first thing I like to do is I find all
of the carbonyl carbons.
That helps me get my bearings.
And then we know, right, that this bond linking the carbonyl
to the nitrogen, those are the peptide bonds Part 1.
Now let's make sure that we can distinguish the R-groups.
So here is our first side chain, our R-group;
and then here is our second R-group
or side chain; and our third.
So let's practice what we've been learning
about amino acids and classify these.
So this first R-group, hydrocarbons;
very straight forward, nonpolar.
Here we do have a heteroatom sulfur but there --
it's not bonded to hydrogen, it's sandwiched
between two R-groups, so it's also nonpolar.
And then with this third R-group, right,
we see the carboxylate so we recognize
that as an acidic R-group.
All righty.
So now, the N-terminus and the C-terminus, right.
So we're always going to write our peptides with our N-terminus
on the left and our C-terminus on the right.
And then last but not least,
let's write the amino acid sequence, and so we're going
to have to look back through our amino acids --
and I'm scrambling to find my amino acid list,
so let's look at that, right.
So based off the R-groups, we look here --
so this benzene ring is really handy, it's a good handle --
and so we can recognize that our first amino acid is
phenylalanine, and that's symbolized Phe.
And then our second, the sulfur's very handy,
and so we can see that's methionine so that's Met.
And then our last R-group we see -- oh, look, there's two carbons
with a carboxylic acid, so we look at our amino acid list, oh,
and that's glutamic acid.
So the peptide sequence would be -- is written like this.
So that's the last part.
So these -- so this was good practice of all the skills
that you would need for amino acids
and their primary structure.
You want to be able to recognize the N-terminus
and the C-terminus, the R-groups, the peptide bonds,
and then use the R-groups to determine the peptide sequence.
So now let's have you practice that.
So here we have a tripeptide sequence with --
I think that's -- yeah -- glutamine, serine, and cysteine;
and we want to look at them at physiological pH. So for me,
I think it's easier to the start with the amino acids
in their neutral form because that's how we learned the
reactions originally.
So we look our amino acid list, which you'll always have
for quizzes and tests, and we draw the first one.
Yep. So there's glutamic acid right there; so there's our Glu.
And now we'll bring in the serine, so always drawing
with the N-terminus to the C-terminus.
And then we'll bring in cysteine, the last amino acid,
and that has the thiol.
Okay. So Step 1, look on our amino acid list and write
out the amino acids in the correct orientation
with the nitrogen on the left, the carboxylic acid
on the right, and then it really helps with the R-groups
to flip them down, up, down, it's a pattern.
And so then we know with our synthetic dehydration,
our acyl derivative formation, that carboxylic acids react
with amines to form amides.
So here is the water that gets produced,
and then that leads us to our products.
Okay. So we'll rewrite them,
but now we'll have the peptide bonds.
To keep our bearings, let's focus on those carbonyl carbons.
And -- yeah, so I think that's enough for there.
Okay. So now we bring in the second amino acid.
Maybe this should be in red, right.
So there's a peptide bond from the carboxylic acid
of the first amino acid to the amine of the second.
So then we have that, and then that will form our peptide bond,
and then we have our third amino acid right there
Okay. So now we have created our tripeptide.
And then the last piece, then, is to redraw it
at physiological pH, right, which is 7.4.
So now we're going to at pH 7.4,
so this is where we overlay our acid base chemistry.
So any time we have an amine, we want to show it protonated.
And then this carboxylic acid here, we know -- that fit?
Oh, yeah. Just fits --
right, carboxylic acids get deprotonated.
Now, of course, this is an amide, right,
so nothing happens there.
There's our amide bond.
And the NH tends to get written up like that.
Now we're on to our second amino acid, and there's going
to be the second peptide bond, and then there's the nitrogen,
and then that will be there -- whoops -- and there's the SH.
Okay. So we have it.
So remembering to deprotonate all carboxylic acids protonating
the amines.
Remember, right, alcohols are neutral and thiols are neutral
so there's no acid-based chemistry there.
All righty.
So that concludes our primary sequence of proteins
which is all about the amino acid sequence.
You want to be able to bring together amino acids
to form peptides or hydrolyze them to bring them back
down to their original amino acid form,
being aware of the acid-base chemistry.
Please reinforce your understanding
with a few homework problems now.