[SQUEAKING]
[RUSTLING]
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MATTHEW VANDER HEIDEN: So today I
want to continue our discussion of amino acid metabolism.
And before we do that, I just want
to come back for a few minutes and revisit the urea
cycle and the Krebs bicycle that we
discussed at the very end of the last lecture.
I only want to do that because it--
a lot going on with this cycle.
It can appear on the surface to be confusing,
the molecules are hard to draw.
And so I just wanted to draw it neatly here
for you one last time and go through it again.
And so remember, if we start from the amino acid arginine,
arginine can be converted into the non-proteinogenic amino
acid ornithine, and in the process, release urea.
That ornithine can then be in the mitochondria converted
to citrulline, another non-proteinogenic amino acid.
By picking up a carbon and a nitrogen
from this molecule, carbamoyl phosphate, which
is generated from CO2/bicarbonate, as well
as ammonia and to phosphorylations with ATP
to get carbamoyl carbon phosphate,
that's added to ornithine to get citrulline.
That citrulline and then combine with the amino acid aspertate
to give this molecule, argininosuccinate.
So arginine plus a succinate on it.
And then loss of fumarate leaves you with arginine.
That fumarate a can, of course, go through the TCA cycle
to regenerate malate, oxaloacetate, ultimately pick
up nitrogen on oxaloacetate is that alpha-keto acid,
is transaminated to aspertate, of course
getting that nitrogen from glutamate
to alpha-ketoglutarate.
And glutamate, of course, can get its nitrogen
either by transamination with another amino acid
to an alpha-keto acid, converting
alpha-ketoglutarate to glutamate,
or glutamate can be generated by this redox reaction
where it picks up on ammonia via the enzyme glutamate
dehydrogenase.
So, you'll notice in this cycle that ultimately the arginine,
the urea group-- what is released as urea from arginine,
comes from the carbamoyl phosphate.
So that's one of these nitrogens that
was picked up in the synthesis of carbamoyl phosphate.
And the other one comes from aspertate,
which, of course, can come from ammonia
via glutamate dehydrogenase and transamination,
or from transamination from nitrogen picked up
from any other amino acid to ultimately end up on aspertate.
You'll notice that there's redox balance
across this whole cycle.
And so there's a NAD that's required
to reconvert the malate to oxaloacetate to run
this half of the reaction.
But of course, if we pick up an ammonia,
we also have a redox reaction involved
in the glutamate dehydrogenase reaction.
You'll see that ATP is also--
quite a bit of ATP is needed.
You need 2 ATP to generate each carbamoyl phosphate,
as well as 2 ATP equivalents to generate argininosuccinate,
because remember, if you go back to your notes from last time,
you'll see that ATP to AMP plus pyrophosphate
was part of the citrulline and aspertate generating
argininosuccinate reaction.
And the last thing is that CO2 is
required to run the urea cycle.
That's where the carbon in urea comes from.
And that CO2 is, of course, picked up
in the generation of carbamoyl phosphate.
Now, I think sometimes we can fall into the misconception
when we talk about these that all cells generate urea.
That's not true.
So remember, different organisms use different strategies
to excrete nitrogen. So in us as humans, the liver
and the kidney would run the recycle as I have drawn it here
as a way to ultimately produce urea that
gets excreted in the blood--
I mean, sorry, in the urine, whereas most tissues
in our body would simply ship off
excess nitrogen from the catabolism of amino acids
to the liver and the kidney by generating either glutamate
or glutamine in the reactions that we talked about last time,
and then those organs would deal with-- use the urea cycle
to produce urea and get rid of excess nitrogen.
But of course, there's other animals
that will use other strategies secreted as ammonia directly
or produce the purine uric acid, which, of course,
we'll talk about next time, how one can interconnect
all this amino acid nitrogen metabolism with nucleic acid
nitrogen metabolism.
I just want to stress that this glutamate dehydrogenase
reaction is a really key reaction that
is necessary to get nitrogen in and out of the system.
And once you get nitrogen in and out of the system,
you can then use these transamination reactions
to move nitrogens around between amino acids
and alpha-keto acids using pyridoxal phosphate as we
discussed last time.
This is shown up above also as the bicycle reaction.
And again, just stresses that you sort of
are running the urea cycle on the right, this other TCA--
modified TCA cycle, if you will, on the left,
and ultimately illustrates how you pick up those nitrogens
and CO2 to generate urea.
But, of course, if we're going to talk
about how you would make amino acids, which is really
the topic of today, how you break down
and synthesize the carbon skeletons
of different amino acids, well, obviously here's
arginine metabolism.
You can imagine that you could use
the same reactions to produce or break down arginine,
and that is what happens.
But I also want to talk about the remaining amino acids.
In the remaining amino acids, it's
really about how do we deal with the carbon
skeleton, the alpha-keto acids.
And of course, these are linked via
this pyridoxal phosphate-driven transamination reaction.
Now, I don't have time to in this course
to go through how each amino acid carbon skeleton is
produced and broken down.
We'll discuss some major themes.
However, if I don't cover your favorite amino acid,
because of course, all people should
have a favorite amino acid, you can look up the pathways
to make it or break it down, and I
promise that if you paid attention
through the whole class, you have the skills to understand
that particular pathway even if we don't study it in class.
So I want to remind you that in general
for amino acid catabolism--
and this is in general.
Of course, there are exceptions.
Arginine would behave as I just described for the urea cycle.
But for most amino acids, you start with transamination.
So what does that give you?
That gives the nitrogen to alpha-ketoglutarate
to generate glutamate.
And so that glutamate can then be shipped off
to generate ammonia if you're a fish,
generate urea if you're a human, et cetera.
And what does that leave you with?
That leaves you with a alpha-keto acid related
to the amino acid that can then be oxidized to CO2 using
various pathways-- burn it and get energy, just like we've
described for carbohydrates and fatty acids, or, of course,
in some cases produce glucose or some other molecule that
can then be used to support gluconeogenesis in the liver,
keep glucose high in our blood.
And so that's generally how most amino acids are stabilized.
It's very clear how this works.
If we start with some of the more obvious ones--
so we talked last time about how alanine, the amino acid,
is related--
so transamination, get the alpha-keto acid.
That alpha-keto acid is pyruvate, aspertate.
Amino acid undergoes transamination.
The alpha-keto acid is oxaloacetate.
Glutamate undergoes transamination.
alpha-keto acid is alpha-ketoglutarate.
It's very clear how all of these can end up
in the TCA cycle or gluconeogenesis for The cell
to either oxidize for energy or to produce something
like glucose that can be used elsewhere.
Now of course, there's other amino acids
out there that we've already talked about.
So remember asparagine, very similar to aspertate.
Glutamine similar to glutamate.
So those were the ammonia group on the side chain.
We can simply remove those.
Should be clear how to then get those into the TCA
cycle or gluconeogenesis.
A little bit of metabolic trivia.
Humans, we actually don't have an enzyme
to break down asparagine.
Other organisms do.
And then the other one that we alluded to last time
was proline, which is cyclized and oxidized glutamate.
And so I'll just illustrate here quickly how
proline can be metabolized just so you can see this.
So here's the amino acid proline.
And so proline, to show you, if we
do oxidation of this carbon-nitrogen bond,
so that utilizes these an electron acceptor.
That electron acceptor happens to be
FAD being reduced to FADH2.
That generates this molecule.
We can then add water across that double bond.
Now we can open up the ring like this.
So just opened up the ring.
Now I'm going to oxidize this aldehyde to the acid.
So if I do that, something else has to be reduced.
That something else can be NAD+ or NADP+ depending
on the enzyme.
There's enzymes that use either NAD or NADP to make
NADPH or NADH respectively.
And then what I'm left with is this amino acid glutamate.
And so that's how I turn proline into glutamate.
Two additional oxidation steps generating
FADH2 and NAD or NADPH.
And so that's how you would derive energy
from the catabolism of proline, by feeding it into glutamate,
which can then, of course, be transaminated
to alpha-ketoglutarate, and the rest of the carbon
enter the TCA cycle.
OK.
So that covers 1, 2, 3, 4, 5, 6 amino acids.
7 if you count arginine that we talked about
with the urea cycle.
That leaves 13 additional amino acids.
Many of them are first transaminated to the alpha-keto
acid, and then ultimately use--
the carbon skeleton can be used to generate
another intermediate that's either involved
in the TCA cycle or glycolysis.
And shown here on the slide is basically
just a figure from a textbook that
contains all of the various--
all of the 20 amino acids from protein
and what they generate either in the TCA cycle or up here.
So you can see here [INAUDIBLE] oxaloacetate, fumarate
succinyl-CoA, alpha-ketoglutarate, acetyl-CoA
pyruvate, acetyl acetate.
Which, of course, as we saw last time,
can be used to generate 2 acetyl-CoA
or be used to generate the ketone body beta-hydroxy
butyrate.
Now, obviously if you can generate any of these things,
we already know the pathways about how you can oxidize them,
or, in some cases, how you can turn them into glucose.
But now I want to return to this idea
that we've come to a bunch of different times
that really comes down to this fact of what we talked about
with the TCA cycle, how the TCA cycle can't net do anaplerosis
from two carbon units.
That is, you can't turn acetyl-CoA or acetoacetate,
because that's just two acetylcholine molecules,
into anything that can generate glucose.
that We don't have the glyoxylate cycle.
Organisms that have the glyoxylate cycle can do this,
but we as humans cannot do that.
Now, many of our amino acids can be
used to produce things like fumarate, succinyl-CoA,
oxaloacetate.
All of that stuff can easily be turned into glucose.
And so if we starve ourselves or go on a low-carbohydrate diet,
well, what happens is, our liver will break down amino acids
and use those amino acids to make glucose,
but we can only make glucose from amino acids
if those amino acids are broken down
into something that's not acetyl-CoA or acetoacetate
because we don't have a glyoxylate cycle.
Just remember I mentioned a couple lectures
ago when we talked about the ketogenic diet,
a true ketogenic diet isn't just low carbohydrates,
it's also low protein because your liver will turn
that protein back into glucose.
And so if you really want to be ketotic,
you have to limit both glucose and--
both sugars and proteins, because fat, of course,
will only be broken into two carbon units,
and you can't turn those into glucose,
so you instead turn them into ketones.
Now, not all amino acid skeletons,
though, can be used to make something
that can generate glucose.
Some can only make stuff--
acetyl-CoA, acetoacetate-- that can
be used to generate ketones.
And so this defines another way to classify amino acids,
is so-called glucogenic amino acids or ketogenic amino acids.
And this is a direct consequence of what those amino acid carbon
skeletons are broken into.
And so a glucogenic amino acid is really
any amino acid where the product of breakdown
is greater than 2 carbons that is not acetyl-CoA.
Whereas ketogenic amino acid is an amino acid
where the product of breakdown is acetyl-CoA.
And I should mention, or acetoacetate,
because acetoacetate, as we saw, is 2 acetyl-CoAs.
So acetyl-CoA, acetoacetate can be turned into the ketone body
beta-hydroxybutyrate, an alternative fuel for the brain.
If you break down an amino acid and all you
get is acetyl-CoA or acetoacetate,
you can't turn that carbon skeleton back into glucose;
therefore, it's a ketogenic amino acid.
All other amino acids that generate oxaloacetate,
succinyl-CoA, whatever, something greater
than 2 carbons, not acetyl-CoA, it can then
be turned into glucose, therefore, it's
a glucogenic amino acids.
Now if we come back over here to our slide
and you look at the various amino acids,
most of the amino acids are turned into something that
can be turned into glucose.
And so most amino acids are so-called glucogenic.
However, there's a few amino acids that are ketogenic,
and there's some amino acids that are
both glucogenic and ketogenic.
And so if you look here through the slide, what you'll
find is that tyrosine and isoleucine-- so there's
isoleucine, here's tyrosine.
So they're turned into ketones, but they can also be--
here's tyrosine, here's isoleucine--
can also be turned into something
that can be used to make glucose,
and so they're referred to as both glucogenic and ketogenic.
Now, as I said before, we don't have time
to go through how to break down all of the amino acids,
but I will take you through how you break down the three
branched chain amino acids.
And I will do that because, first of all,
it will illustrate that you already
know a lot about metabolism.
You'll see that how these are broken down
is just variations on pathways that we've already discussed.
And so it really drives home the fact
that the complexity of metabolism
is really just nature repurposing relatively
few reactions over and over and over again
in a way that ultimately builds complexity and diversity,
but in the end, is actually quite
consistent across the whole thing.
And you'll also see examples of how amino acid skeleton
breakdown can end up either as glucogenic or ketogenic,
and that's because of the various branched chain
amino acids.
So there's, of course, leucine, valine, and isoleucine.
So those are the three branched chain amino acids.
You'll see the leucine is ketogenic,
valine is glucogenic, and isoleucine, as I just said,
is both ketogenic and glucogenic.
So three very amino acids.
In genetic terms, very conservative
substitutions within a protein.
Very related structures.
However, the way they're broken down, in the case of leucine,
generates only things that are ketogenic;
valine generates things that are glucogenic;
and isoleucine generates both.
And so we'll go through each of these and see how that happens.
So let's start with leucine.
So leucine is a--
I said above is a ketogenic amino acid.
And so leucine, like many amino acids,
starts break down by transamination.
So this transamination will, of course, take the nitrogen
from leucine, an alpha-keto acid, alpha-ketoglutarate,
generate glutamate, as well as the alpha-keto acid of leucine,
which, just to remind you leucine looks like,
looks like this.
So this is the side chain over here of leucine.
Here's the alpha-keto acid related to leucine.
If I take this alpha-keto group, turn it
into an amino group, that's leucine.
So this is the alpha-keto acid related to leucine.
So the next step of leucine breakdown
involves oxidative decarboxylation
of this alpha-keto acid.
So if you remember, we've seen this reaction before.
We did it in pyruvate to generate acetaldehyde,
an ethanol metabolism.
We did it in--
well, we did alpha decarboxylation there,
and then we did oxidative alpha decarboxylation
when we turn pyruvate into acetyl-CoA.
And we turned alpha-ketoglutarate
into succinyl-CoA.
Well, that exact reaction, which we
saw with pyruvate decarboxylation,
as well as what we saw with alpha-ketoglutarate
dehydrogenase generating acetyl-CoA and succinyl-CoA
is what happens here for the alpha-keto acids produced
from breakdown of leucine and other branched chain
amino acids.
And so if you look back in your notes,
we went through the mechanism of this in detail.
Remember, this involved edition of CoA, loss of CO2,
it's an oxidation reaction.
So remember, the electrons needed to go somewhere,
and so they ended up going to NADH.
So that's oxidized.
NAD+ is reduced to NADH.
And remember, this involved that mini-electron transport chain
with FAD, lipoic acid, and TPP+.
And in the end, that releases the CO2
and you end up with this branched chain acyl-CoA.
So same reaction is PDH, alpha-ketoglutarate,
dehydrogenase.
Just like those two reactions, remember,
that had an E1, an E2, and an E3 subunit.
So this actually uses the exact same E2 and E3
subunit as those reactions.
The E1 subunit is, of course, different
because it's unique to the branched chain amino acids,
whereas in pyruvate dehydrogenase,
to be unique to pyruvate and alpha-ketoglutarate
dehydrogenase, you need the alpha-ketoglutarate.
In this case, this enzyme is called BCKDH for Branched Chain
Keto Acid Dehydrogenase, and allows
the oxidative decarboxylation to generate this branched chain
acyl-CoA.
Now this branched chain acyl-CoA looks a lot like a fatty acid,
and in fact, it's metabolized very much like we
would do fatty acid oxidation.
So what's the first step in beta oxidation of fatty acids?
Well, we would introduce a double bond here.
And so that's exactly what happens next.
So this would be a membrane-bound FAD
containing enzyme, part of the electron transport chain.
Going to oxidize that carbon-carbon bond.
There's that generate.
All right.
Now, if we are doing fatty acid oxidation,
we would, of course, add water across the bond.
We'll do that in a minute.
Before that happens, the next step, though,
is that to facilitate ultimately break down of this,
we're going to end up adding our carboxyl group
to the end of the molecule.
So if we're going to add CO2 to the end of the molecule,
how would we do that?
Well, we've seen that reaction many times before as well.
So if we're going to add a CO2 group,
that's going to come from biotin.
So the next enzyme would have biotin in the active site that
can pick up a CO2.
How does it pick up the CO2?
Well, it picks up the CO2 via bicarbonate plus ATP,
and that's going to go to--
that's going to phosphorylate the bicarbonate.
And then when we transfer that phosphorylated bicarbonate
onto biotin, we'll release the PI, then the CO2 from biotin
can be added to carboxylate.
That molecule, just like we've saw before
with other carboxylation reactions,
and that will generate this intermediate.
This intermediate here.
OK.
So no new chemistry.
You've seen all this many times before.
Now we're going to continue with--
what we would do is if we were breaking this down--
oxidizing it as a fatty acid.
And so now we're going to add water across that double bond.
OK.
Now we added water across that double bond.
And then now we're just going to do this reaction, which
will generate from this side of the molecule an acetyl-CoA.
And if you look on the other side of the molecule, what we
are left with is acetoacetate.
Acetoacetate can be broken down into two acetyl-CoAs.
If I break it in half, add CoA to each one of them
by reactions I showed you before as well, or, of course,
we can reduce this ketone to the alcohol
and make the ketone body beta-hydroxy butyrate.
You can look that up from the end of the last lecture.
But in the end, this is how one can break down
the leucine skeleton.
You get a acetyl-CoA or acetoacetate.
Can't generate glucose from any of those molecules as humans
because we don't have a glyoxylate cycle.
Therefore, leucine is a ketogenic amino acid.
All right.
Valine.
Let's look at valine.
So valine is glucogenic despite the fact
that it's very similar to leucine
and broken down in a way that's very similar to leucine.
So, how do we break it down?
So first step, transamination.
Nitrogen from valine to alpha-ketoglutarate
to generate glutamate, and as well as the branched
chain alpha-keto acid that's related to valine.
So that's the alpha-keto acid related to valine.
One carbon shorter than side chain, one
carbon shorter than leucine.
Just like we did with leucine, we're
going to metabolize the alpha-keto acid
with the branched chain keto acid dehydrogenase.
Same reaction.
Oxidative decarboxylation here.
That releases CO2, adds CoA.
Reaction involves also NAD+ to NADH.
Requires lipoic acid, TPP+, FAD, just like we described before.
I'm not going to draw out all the pieces of it again,
but we're going to end up with the branched chain acyl-CoA.
Metabolize this branched chain acyl-CoA
as if it's a fatty acid.
And so first step, oxidize this carbon-carbon bond.
That electrons go to FAD, make FADH2.
This product, add water across that double bond.
Water across that double bond.
Next, if we oxidize this alcohol twice--
so oxidize it once, we'll get the aldehyde.
Oxidize it again, we can get the carboxylic acid.
And so oxidizing twice means NAD+ times 2 and NADH times 2.
And now that becomes the acid.
OK.
So same molecule, but now this alcohol becomes an acid.
I drew it that way on purpose.
If you look back in your notes, this
is methyl methylmalonyl-CoA, which
we saw before in our discussion of odd chain fatty acid
metabolism.
And you'll remember that there was this B12-dependent reaction
where I can basically swap the positions of this proton
and this thioester group here.
This is not aero-pushing.
This B12-dependent reaction that I described
before where I can rearrange methylmalonyl-CoA
to make this molecule, which is succinyl-CoA.
Succinyl-CoA oxidized in the TCA cycle, generate ATP,
but also can use it as a substrate anaplerosis
for the TCA cycle, so it can be used to generate glucose.
And so that's why valine is a glucogenic amino acid.
All right.
Last branched chain amino acid is isoleucine.
So isoleucine is both ketogenic and glucogenic.
So let's see how that happens.
So if we start with isoleucine, first we
undergo transformation.
alpha-ketoglutarate to glutamate,
and you get the branched chain alpha-keto acid.
So that's isoleucine as an alpha-keto acid rather than
an amino acid.
Next step, do the alpha decarboxylation
with branched keto acid dehydrogenase.
That removes that CO2, oxidizes that carbon to the acid,
and we end up with this branched chain acyl-CoA.
Same first steps as we saw before.
Metabolize that as if it's a fatty acid.
So oxidize that carbon-carbon bond.
Add water across the double bond.
OK.
Get this intermediate.
Now oxidize this alcohol to the ketone.
Electrons go to an NAD+, which is reduced to NADH.
Now we can use CoA to take off this end of the molecule here,
which is acetyl-CoA, hence ketogenic.
The remainder of the molecule is this three-carbon acyl-CoA.
We saw this from odd chain fatty acid metabolism.
This is propionyl-CoA.
Remember, to deal with that, we can add CO2.
So that, of course, requires biotin, and ATP.
So remember, we had CO2 to this molecule.
That gives us methyl--
not going to draw it all out for the sake of time,
but that gives us methylmalonyl-CoA.
Methylmalonyl-CoA shown up there,
so it's adding CO2 to this molecule.
And then we can do the vitamin B12 rearrangement
to get succinyl-CoA.
And so that can be turned into glucose.
And so it generates an acetyl-CoA and a succinyl-CoA,
isoleucine is both glucogenic and ketogenic.
And so a little tedious to go through how you break down all
three of those branched chain amino acids,
but it really illustrates that it's just
variations on the same chemistry that we've
seen before with fatty acid metabolism, TCA cycle
reactions, that ultimately generate intermediates that
can be fed into the TCA cycle, oxidized further to CO2,
generate ATP, generate NADH, electron transport chain,
oxidative phosphorylation, supply the cell with energy
to do various kinds of work.
Or can be turned into a ketone if you're a human
and you start with acetyl--
and what you get is acetyl-CoA or acetoacetate.
Or even into glucose if you start
with something like succinyl-CoA that
can be turned back into glucose by the liver,
defining the difference between the glucogenic
and the ketogenic amino acids.
All right.
Now going through branched chain amino acid metabolism
also allows transition into a discussion
of another topic which are the so-called inborn
errors of metabolism.
So what's an inborn error of metabolism?
Well, sometimes individuals are born
that have deficiencies in enzymes
that are necessary to carry out some function of metabolism.
Some aspect of the biochemistry we've been learning about.
Now you can imagine that some of these genetic deficiencies,
if it's somewhere smack in the middle of central carbon
metabolism and you can't generate energy,
it's not going to be compatible with life.
But it turns out that some of them
are quite compatible with life, like deficiency
in branched chain keto acid dehydrogenase.
So BCKDH deficiency is something that children are sometimes
born with, and this deficiency results in a disorder
called maple syrup urine disease.
So it's called maple syrup urine disease
because the unit smells like maple syrup,
but effectively what this is is this is a disorder where
there's a deficiency in the activity of branched
chain keto acid dehydrogenase.
That means the cells can't break down
branched chain amino acids.
They end up generating some otherwise side toxic product.
Some of it ends up in the urine, smells like maple syrup.
But it also can result in damage to the CNS
and problems with thinking, mental retardation, et cetera.
And so it can be quite devastating to have
loss of this enzyme, which prevents you from breaking down
branched chain amino acids, a so-called inborn error
of metabolism.
Now this is a relatively rare disease.
All of these are.
But if you go to medical school, these
are questions because they lend themselves
to questions that often show up on various board-type exams.
And so it's good to know that deficiencies
of some of these enzymes can result in diseases.
So maple syrup urine disease caused by an inability
to break down branched chain amino acids because you're
deficient in the enzyme branched chain amino acid--
or branched keto acid dehydrogenase,
which catalyzes the stuff I showed you up there
in the breakdown of all three branched chain amino acids.
By no means is this the only one.
Often these are associated with amino acid breakdown.
And so two of the other more common--
all of these are very rare, but relatively more common ones
is a disease called alkaptonuria.
So what's alkaptonuria?
Well, that's missing an enzyme--
so enzyme deficiency in tryptophan metabolism.
And another one is fennel phenylketonuria,
which is an enzyme deficiency in phenylalanine metabolism.
Branched chain amino acids are very common, but tryptophan,
phenylalanine, two of the more rare amino acids,
it turns out these are two of the amino acid breakdown
deficiencies that have less severe phenotypes,
and so they're somewhat--
more people walking around with those conditions.
If any of you have had children or someday
when you have children, what will happen
is that you will notice that when babies are born,
one of the first things that's done with infants
is they have a blood test sent out.
They do a little heel stick, collect some blood,
and send it to the state lab where
they test for various inborn errors of metabolism.
What they're looking for is things like phenylketonuria,
maple syrup urine disease, et cetera.
Why do they want to find these things?
Well, it's because if you have too much of the product,
too much phenylalanine, too much tryptophan, too much branched
chain amino acid, and you can't break them down,
it's not the lack of the ability to break them down
that's necessarily the problem.
The problem is is that the inability to break them down
leads to overwhelming a system building up
of toxic intermediates that damage the brain.
And so by doing these newborn screening panels,
it's greatly enhanced the management of these things,
because often you can control the symptoms
by dietary intervention.
Simply limiting the phenylalanine
or the branched chain amino acid or the tryptophan intake
in the diet is a treatment for these diseases,
and so therefore, if you know about them early,
limiting exposure to those things
limits the exposure to the toxic breakdown products that
can't be metabolized because of the deficiency, and therefore,
limits the effects on the brain.
If you drink diet soda and you look at the side of your diet
soda can, what's written on the side of it is phenylketonurics,
contains phenylalanine.
Why is that written there?
Well, because if you happen to be a phenylketonuric,
you shouldn't drink diet soda.
Why?
Because the artificial sweetener in there contains
phenylalanine, and so this would give you
a big dose of phenylalanine, and if you can't break down
phenylalanine, that's a problem.
So it's a warning to the people in the population who
happen to have phenylketonuria not to drink diet soda.
All right.
Now, I want to say a few other things
about amino acid metabolism, only because these things will
come up for you as you go through other aspects
of biology.
And that is that amino acids are very versatile starting points
to build all kinds of hormones and neurotransmitters
and bioactive molecules.
So I know some people--
some of the MIT students in the class are course 9.
That's the brain and cognitive science.
Classes you take, you'll learn a lot
about different neurotransmitters.
Well, one of the canonical neurotransmitters
is an amino acid itself.
It's the amino acid glutamate.
So obviously that's important for the brain to work.
But what are the other neurotransmitters?
Well, there's things like dopamine,
epinephrine, norepinephrine.
These are all bioactive molecules,
have to come from somewhere.
Well, it turns out all of these ultimately come
from the metabolism of tyrosine, which, of course, can also
come from the metabolism of phenylalanine.
And so don't have time to go into it,
but you can look up the pathways to generate
these various neurotransmitters from tyrosine
if you're interested.
What's the other big neurotransmitter?
Well, it's acetylcholine.
What's acetylcholine?
Well, let's break it down.
Well, it's an acetyl group, so that comes from acetyl-CoA.
And choline-- and what's choline?
Well, choline comes from, ultimately as I showed you--
alluded to before, ethanolamine, and ethanolamine
comes from serine.
We'll come back to this later.
And so serine metabolism, as well acetyl-CoA,
is how you get acetylcholine.
It's also choline the phospholipids and ethanolamine
for the phospholipids.
If you're not into the brain but into other aspects
pathophysiology-- so thyroid hormone,
very common thing that many people
need replacement of, very important to manage physiology
in our body.
Thyroid hormone also comes from thyroxine.
Melanin, the pigment that makes our skin different shades,
melanin, the skin pigment, it is basically
produced from dopamine--
or actually, a dopamine metabolite.
So dopamine precursor.
Which comes from tyrosine as well.
And so if you're interested in any
of these particular molecules, of course,
you can look up in the book and you'll see how they're made,
and I promise, you have the ability to understand it,
it's repurposing some reactions that we've already seen.
There's some unique ones in there
like melanin synthesis is actually parts
of it are non-enzymatic, even.
But this-- I like to mention this because obviously we
don't have time to study and discuss
the entire complexity of the metabolic map,
but really, you understand the basics, the central parts
of it, and it's the same reactions repurposed out
in different directions that allows
this complexity and this diversity of metabolism,
making all of these different biomolecules that
are necessary for the cells to do things, and, of course,
you can go look these up if you're interested in any
of them specifically.
And regardless, you should have some appreciation
of how these things all interconnect
with the other pathways that we've talked about.
All right.
So now I want to turn to amino acid synthesis
and say a few words about how amino acids are built.
So of course, we've covered some of these already,
and as a very general statement, many of them
are made by transamination.
So first you build the alpha-keto acid,
and then you transaminate that alpha-keto acid from glutamate
to generate the amino acid.
Now of course, the pathways that you use to make amino acids
are not the same as the pathways that you
use to break down amino acids.
So again, if you paid attention for the entire course,
it should be clear for both thermodynamic energetic reasons
that you can't have the same pathways to build and break
stuff down because all pathways delta G has to be less than 0.
So we saw this with glucose and fatty acids.
We can repurpose-- some steps can be the same,
but the ones that allow the energetic driving have
to be different because you have to couple one direction
to energy consumption and the other one
could be spontaneous if it releases energy,
and you have to have pathways that
can work in either direction.
But, in general, if you can build an alpha-keto acid
like oxaloacetic acid or alpha-ketoglutarate
or pyruvate, well, obviously we can
transaminate all of these things to get the amino acid.
So alpha-ketoglutarate to glutamate
can also be from glutamate dehydrogenase.
That's how you can get new nitrogen into the system.
And that way we can generate aspartame
glutamate and alanine, and aspertate into asparagine,
asparagine by adding the ammonia to it.
That would be a very similar reaction
to glutamate into glutamine.
That's glutamate synthase, asparagine synthase.
Same mechanism describe glutamate synthase last time
to make glutamine.
And of course, proline, as I showed you earlier,
is cyclized, and in this case, oxidized--
or sorry, cyclized then reduced glutamate.
And then-- so that's six of the amino acids.
We covered arginine earlier, that seven.
And so 13 other amino acids.
Here's another figure from a book just showing
the starting material to make all of the various amino acids.
Obviously we know how to make oxaloacetate,
phosphoenolpyruvate, erythrose 4-phosphate, pyruvate,
ribose 5-phosphate, 3-phosphoglycerate,
and alpha-ketoglutarate.
And so generation of those by the pathways
we've already talked about then allows those molecules
to be shunted into pathways to generate
all of the various amino acids.
Now I want to reiterate, humans, we
can't make all 20 amino acids.
Animals can't do that.
Many organisms, of course, can.
We lost the ability to make nine of our amino acids,
and in fact, if you count the two conditional ones, really
11 of amino acids, even though we can turn phenylalanine
into tyrosine, we still need a source of phenylalanine
to do so.
And so each of these nine or 11, depending on how you count it,
essential amino acids must be eaten in the diet.
So there are obviously pathways to do them,
we just don't have the enzymes in humans to do it.
And then the other ones we do retain.
You can obviously look up the pathway
that's used by whatever organism to make
your favorite amino acid.
Today what I want to discuss is how we will make--
today I want to discuss how we will make serine and glycine,
because it turns out, serine and s metabolism
play a key role in other pathways,
including nucleotide synthesis which we
will cover in the next lecture.
Serine glycine metabolism also is a way
to make one carbon units that are more reduced than CO2.
And these will be critical for one-carbon transfer reactions
that you'll encounter throughout other aspects of biology.
So, serine and glycine, very important amino acids.
And so just to be clear about this,
so it turns out serine-glycine metabolism,
important for nucleotides among carbon units,
we'll see that a lot.
But serine and glycine also used to make phospholipid head
groups.
Nucleotides, one-carbon units we're going to talk about.
I want you to appreciate, you also
need serine to make phospholipid head groups.
So what do I mean by that?
Well, of course, there's phosphatidylserine.
Obviously that's serine is the head group, and so serine--
the amino acid is required for that.
But also used to generate ethanolamine.
So what is ethanolamine?
Well again, just to remind you of this,
so here is the amino acid serine.
So, to generate ethanolamine, it's
decarbonization of serine to do that.
So loss of this CO2.
This is a reaction I don't have time to go into,
you can look it up.
It is another repurposing of pyridoxal phosphate.
And that generates this molecule,
which is ethanolamine.
That ends up head group on phosphatidylethanolamine.
And if I want to turn it into choline,
either for acetylcholine as a neurotransmitter
or for phosphatidylcholine as a head group,
it's basically adding 3 methyl groups
onto this nitrogen of ethanolamine.
And so those three methyl groups,
that's a carbon that's more reduced than CO2.
That's a so-called one carbon unit.
It turns out, as you'll see, those also come from serine.
Last thing is serine is necessary to make
head groups for a class of lipids called sphingolipids.
There's a-- sphingosine is another amino alcohol that
is generated from serine and ends up being the head
group for sphingolipids.
Especially if you're interested in the immune system
of the brain, these end up being important molecules.
And so you can look up how they're
related to serine, but just appreciate that for now
that they--
another important downstream thing that's
generated from serine metabolism.
Also illustrating how amino acids
can be very important to generate
lots of other biomolecules.
OK.
So, how do we make serine?
Well, if we go over here, you'll see
that serine is downstream of 3-phosphoglycerate
from glycolysis.
So what's 3-phosphoglycerate?
OK, here's 3-phosphoglycerate from glycolysis, or the product
of rubisco if you like.
So photosynthesis.
So there's 3-phosphoglycerate.
So if I oxidize this alcohol to ketone,
electrons have to go somewhere.
NAD+ reduced to NADH, I get this intermediate.
It's phosphohydroxypyruvate So pyruvate with a phospho on it,
hydroxypyruvate.
This molecule can undergo a transamination reaction.
So pick up nitrogen from glutamate,
make the alpha-keto acid.
Take this alpha-keto acid and generate phosphoserine.
The amino acid that's phosphorylated, phosphoserine.
And then all I need to do is dephosphorylate it,
and I end up with the amino acid serine.
Cool.
All right.
To make glycine from serine--
so remember, glycine is one basically the amino acid
with no side chain on it.
So I need to remove this carbon and the alcohol.
So I'll just redraw serine this way.
So that's redrawing serine.
Need to lose that group to get glycine.
This is helped along by pyridoxal phosphate.
So a reminder, this is pyridoxal phosphate.
OK.
So this is exactly what we drew, is the first steps
in transamination.
Except if instead of basically going like this,
I do this to break this carbon-carbon bond,
what do I get?
Well, I release a one-carbon unit.
In this case, it's the one-carbon unit
as formaldehyde.
The one-carbon aldehyde, formaldehyde.
And generate this intermediate.
And it's just exactly what we showed before for resolving
the transamination.
And I am left with glycine, as well as I regenerated pyridoxal
phosphate for the next catalytic cycle of the enzyme.
And so illustrates the flexibility
of pyridoxal phosphate.
In this case, helping convert serine into glycine
and a one-carbon unit shown here as formaldehyde.
Now the enzyme that carries out this reaction
is an enzyme called SHMT, which stands
for serine hydroxymethyltransferase.
Serine hydroxymethyltransferase.
And it actually doesn't release the formaldehyde directly.
Instead, it transfers that formaldehyde
to an important one-carbon donor for many one-carbon reactions
that is called folate species or folic acid.
So remember, if we transferred CO2 in a carboxylation
reaction, we use a cofactor biotin.
Biotin's useful to transfer CO2.
But if we're going to do something like transfer
the methyl groups shown up there for choline synthesis, that's
transferring carbon that's more reduced than CO2,
and you don't use biotin for that.
Instead, you use a cofactor called
folate that's derived from the vitamin folic acid.
So folic acid, very important vitamin.
It's the primary thing that's included in prenatal vitamins.
Why is that?
Because deficiency in folic acid was shown a while back
to cause neural tube defects--
so developmental defects where the neural tube does not close.
This leads to things like spina bifida.
One of the real successes of public health intervention
was the recognition of this and fortifying various cereals
with folic acid.
And doing so has greatly reduced the incidence
of these birth defects involving folate deficiency.
Folate deficiency's also a common cause of anemia.
And so folic acid is a vitamin that lots of people
take for that reason.
And in fact, folic acid, also very important in the history
of cancer treatment.
And if you want to learn more about that,
take 745, which is offered in the fall.
All right.
So, folic acid is a complex molecule
that is converted in cells to a molecule called THF, which
stands for tetrahydrofolate.
So I'll draw out folic acid for you and tetrahydrofolate.
OK.
So, this here is folic acid.
The folic acid molecule is tetrahydrofolate.
It has a peptide bond here to a glutamate molecule,
and it's actually a polyglutamate tail that
is there to trap it in cells.
It's this central part of the molecule here
that actually carries the one-carbon unit.
And so the way that the nitrogens are numbered,
this is nitrogen-5.
This is nitrogen-10.
That will be important in a minute.
But it's really this sort of central part here
of the molecule that I will draw over and over again
as the one-carbon unit-carrying species.
To show how this works, it's easier
if I start off by showing how it can pick up a more
oxidized one-carbon unit.
So the one-carbon carboxylic acid is this, that's formate.
And so if I phosphorylate formic acid,
this formic acid can then be picked up by the--
so here's that carrying part of the one-carbon--
the box part of tetrahydrofolate.
And so this can pick up formic acid like this.
OK.
So that gives us this molecule, which
is called N10-formyltetrahydrofolate,
THF.
I can create a ring out of this molecule.
This.
OK.
And if I remove water from this ring, we draw it like this.
OK.
This is called N5,N10-methenyl THF.
And if I reduce that molecule, it's NADPH.
So hydride ion.
OK.
Then I end up with this molecule,
which is N5,N10-methylene THF.
And if I further reduce this molecule,
then I end up with this molecule,
which is N5-methyl THF.
Appears incredibly complex what's going on here,
but I went through this, because what I want you to realize
is that each of these species are simply
tetrahydrofolate carrying a one-carbon unit
in a different oxidation state.
So this N10 formyl THF is carrying formic acid,
the one-carbon acid.
I can reduce it to N5,N10-methylene THF.
That's carrying the one-carbon aldehyde, formaldehyde.
Or I could reduce it further.
This is carrying the one-carbon methyl group as N5-methyl THF.
And it turns out that this allows a lot of flexibility
in carrying out one-carbon reactions.
Here is a same thing written from a textbook.
The direction-- the order is shown a little bit differently,
the molecules are rotated.
And it includes a couple other species
that are added in for histodine metabolism.
But if you look at this, you'll see
it's exactly what I just drawn where
you get these key species.
Where N5-methyl THF is effectively
carrying a methyl group.
So a one-carbon methyl donor.
N5,N10-methylene THF is carrying the formaldehyde.
And N10-formyl THF is carrying the formate group
to donate as a one-carbon unit.
This will be the donor, ultimately, for things
like choline synthesis.
Formaldehyde-- and N5,N10-methylene and formyl THF
will be important in nucleic acid synthesis and we'll see
that next time.
And so now if we go back to our SHMT reaction,
I can show you how these things really work.
And so here's a THF molecule.
And so here is the intermediate in serine-glycine conversion
found to pyridoxal phosphate, et cetera.
And that will release glycine and eventually PLP.
So glycine and PLP can be generated from that.
And what ends up here on the folate is--
which is N5,N10-methylene THF.
And if I take this and I oxidize it,
I can take the aldehyde to the acid.
So oxidation.
NAD+ is reduced to NADH.
Now I get an N10-formyl THF.
And if instead I reduce it, so electrons from NADPH go
to NADP+.
So NADPH gets oxidized, electrons go there.
And then I get an N5-methyl THF.
This gives me a donor of methyl groups.
This gives me a donor of formyl groups.
All right.
Very last thing I want to talk about today
is we'll talk a lot about how we use the more oxidized species
next time to generate nucleotides,
but I want to say a few words about how these methyl
groups are used to be involved in methylation
reactions, things like choline synthesis shown up
there, but also not just choline synthesis.
Also can be used for reactions involved in, say, epigenetics.
And so for those of you who will never
think about biochemistry again after taking
this class but we'll take--
think about genetics, you'll certainly
know the gene expression is controlled
by methylation of DNA and histones and things like that.
Those methyl groups have to come from somewhere,
and they come ultimately from these methylation reactions,
the serine there.
Now I don't have time to go through all
of one-carbon metabolism.
This is very complex.
But it turns out the one-carbon donor
for most methylation reactions isn't N5-methyl THF,
even though that's where the methyl group comes from.
It's actually this molecule.
So this here is the amino acid methionine.
And if I put it here onto an adenine, what I end up with
is this molecule called S-adenosylmethionine or SAM.
This methyl group on SAM is very labile.
And so it is the universal methyl donor
to be used in methylation reactions,
choline synthesis, epigenetic methylation of DNA or histones,
whatever.
And if you transfer that methyl group off,
you're left with this non-proteinogenic amino acid
that's called homocysteine.
And that homocysteine is here onto an adenine
to make S-adenosylhomocysteine, which is abbreviated as SAH.
SAH picks up-- needs to regenerate SAM.
Methyl group has to come from somewhere.
This comes from N5-methyl THF.
Of course, generates THF.
And then THF can pick up another methyl group, ultimately
from serine-to-glycine conversion and reduction
with NADH to make N5-methyl THF.
I show here on the slide, here's just
a picture of one-carbon metabolism
that I took from a review article.
And so here's SAM metabolism.
Lots and lots of complicated reactions
that are linked to cystine metabolism and polyamine
metabolism.
Obviously don't have time to get into this,
but I want you to appreciate that this happens, where
SAM and SAH come from, how they're involved
in one-carbon metabolism, because this will come up
again in your future endeavors if you do something
with biology.
All right.
Final topic next time is nucleic acid metabolism,
and then we will have covered all
of the basics of metabolism.
Thanks.