#39 Biochemistry Nucleotide Metabolism I Lecture for Kevin Ahern's BB 451/551

Uploaded by oharow on 10.02.2012

Kevin Ahern: Friday.
Anybody here unhappy that it's Friday?
Everybody's happy that it's Friday.
Wild plans for the weekend?
Studying biochemistry?
That's pretty wild.
So we're actually pretty well caught up now
so I feel pretty good about that.
Hopefully you're not exhausted in getting to this point.
One last thing I did not mention about prostaglandins
was just a term that you'll frequently hear
associated with them and that's the term eicosanoid.
The prostaglandins are called eicosanoids
and that relates to the fact that they have twenty carbons.
"Eicosa -" referring to twenty.
So they're eicosanoid compounds and that's really
important when we think about these because
The eicosanoids creating pain
They're the ones to blame when you get inflamed
And ouch, they hurt inside your brain!
Every throb and ache gets magnified
If you hope to win, cyclo-oxygen's
Generation's got to be denied!
The Vioxx has all been recalled
So go get yourself Tylenol.
And if you aaaaache
Blame PGH synthaaaaase!
We must complain that
You make the aches prostaglandins
Prostaglandin - D2, F1, G2
Prostaglandin, it's you
No, no.
That was really bad.
[class laughing]
I know you guys are being very gratuitous in that.
But I thought a little surprise
to wake everybody up on Friday might be good.
Hopefully you're awake.
If you're asleep after that I don't know what to say,
so maybe you're dead.
Well we move now to something that may make you very happy
or very sad, I don't know,
but it's the last of our topics of metabolism.
So we've been going on metabolic pathways
for awhile since late last term
and now we turn our attention to nucleotide metabolism,
and in many respects nucleotide metabolism
is one of the most interesting pathways.
We don't go into it in the detail that we go to
in the other pathways although it may seem like we do
because there's a lot of complexity here.
I'm going to go over some reactions very quickly
and you may rest assured that's how much attention
I think you should pay to some of the reactions
I'll be giving you.
So you're going to see a lot of reactions.
I'm not going to hold you responsible for structures.
I want you getting the big picture here.
And probably one of the most important things
we can get out of nucleotide metabolism
is an appreciation of the value of regulation and
how and why cells are doing that regulation.
The why is actually pretty straightforward.
The why of regulation in nucleotide metabolism
is that cells have to balance
the appropriate number of each nucleotide inside of them.
We know all kinds of examples of cells that don't
balance those things properly and every time
those cells are much more prone to mutation.
Every time.
So if cells don't balance the relative amounts
of nucleotides properly they're much more prone
to having mutation.
That's just given.
So the value of regulation,
and we're going to see some interesting,
they're not overly complicated although
they're a little bit more complex than we've seen
in other things, we'll see interestingly
how different regulatory systems work together
to ensure that cells have the proper balance
of things that they need.
Now nucleotide biosynthesis is also interesting
in another perspective and that other perspective
is there's really two ways of getting there.
Two ways of getting there.
One way of getting there is what's called salvage
and salvage of course happens all the time.
We eat food.
The food is full of fats and protein and nucleic acids.
And so our digestive system just like it
takes apart proteins to individual amino acids
and it breaks down fat into fatty acids
that we use for other purposes,
so too does our digestive system take apart DNA and RNA,
and further, it takes apart the nucleotides.
The nucleotides have three components.
So the nucleotides are the building blocks: ATP, GTP, CTP.
By taking apart those three components
the cell can mix and match and put them back together
having a material that's already partly made.
The things that they mostly mix and match are the bases.
So if I have an ATP and I start chopping off the phosphates
and I cut off the ribose away from the adenosine,
I can use that ribose for something else.
I can us that adenosine to make new ATP if I want.
So that phenomenon is called salvage.
So salvage is basically using some preformed pieces
to make finished nucleotides.
We haven't really talked about salvage
with respect to other pathways
but salvage is a very important pathway
in nucleotide metabolism.
I will talk a little bit about salvage.
Most of what I will talk about with respect to salvage
will come later when I talk about mutations in enzymes
that are important in salvage and some of the bizarre phenotypes
that they give in people who possess those mutant enzymes.
The other general mechanism for making
nucleotides is what's called de novo,
and de novo means literally "from anew."
So the de novo pathway we can think of
as starting from scratch.
We start with the very simplest of materials
and we build them into the very same end products
that the salvage pathway does
but we start at a different point.
So if we look at what we start with in a salvage pathway
we start with something called activated ribose
which you'll more commonly call PRPP.
That's got a longer name that I'll show you
but for our purposes you'll probably call it PRPP.
I can take PRPP and I can join to a base
and make a nucleotide.
Bang, one step, I have made a nucleotide.
When I go through the de novo pathway
which we're going to spend a little bit more time on
it's about ten steps starting from scratch
to get to a finished nucleotide.
Now, why do cells do this versus this?
If they've got salvage they'll use it
because salvage saves a lot of energy.
If they don't have enough things to salvage
they will start from scratch.
Now the scratch materials are basic simple things
that are found in every cell: amino acids, ATP,
carbon dioxide and a few other things.
Very simple starting materials
to start making nucleotides from scratch.
That's very cool.
Well let's go through a little bit of nomenclature.
So it's important to understand,
if we're going to walk the walk we have to talk the talk.
I said there are three components to a nucleotide.
A nucleotide contains a base.
That base would be adenosine.
I'm sorry, the base would be either guanine,
adenine, thymine, cytosine, or uracil.
So those are bases.
They're not nucleotides.
They're the things that are in nucleotides
that we think of, "Oh, A goes with T and G goes with C,"
but they're only part of a nucleotide.
If I take a base and I link it to a sugar
I create a nucleoside.
A nucleoside can be a ribonucleoside if I link it to ribose.
It becomes a deoxyribonucleoside
if I link it to deoxyribose.
Adenosine is what results when I connect
an adenine to a ribose.
Deoxyadenosine is what arises when I connect
an adenine to a deoxyribose.
A nucleotide can exist in two forms,
either a ribonucleotide which started out as a ribose,
or a deoxyribonucleotide that contains a deoxyribose.
Well what differentiates a ribonucleoside
from a ribonucleotide?
It's at least one phosphate.
So if I take a ribonucleoside
and I put a phosphate onto it I've got a ribonucleotide.
If I take a deoxyribonucleoside
and I put a phosphate on it I've got a deoxyribonucleotide.
Notice I said at least one phosphate.
It can have two, it can have three.
But that's what's happening in,
or that's what the important nomenclature
is with respect to what we're talking about here.
So a base, a nucleoside, and a nucleotide.
Yes, questions, Connie?
Student: Does that mean that it has, like,
two phosphates is it still considered a nucleotide?
Kevin Ahern: Yes, if it has two phosphates
it's a nucleotide, yes.
If I say nucleotide it basically encompasses both
ribonucleotides and deoxyribonucleotides.
If I say nucleoside it encompasses both of these
obviously as well.
So yeah, ADP is a nucleotide.
Student: So nomenclature-wise would it still be considered
for example adenylate if it was ADP or ACP or...
Kevin Ahern: Yes.
So the question is would this be considered adenylate
if you had that?
See I don't like these nomenclatures
because they really refer to monophosphates
and I prefer to call it AMP or ADP or ATP.
So I'm not going to hold you responsible
for knowing those names right there.
I just think that's a little busy.
And we don't use that nomenclature for an ADP, for example.
Because this refers to adenylic acid for what that's worth.
But we should know what the difference is between a base,
a nucleoside, a nucleotide,
in terms of general components.
The sugars that are found,
you've already seen ribose before.
We talked about carbohydrates last term.
Ribose is a five-carbon sugar, a five-carbon sugar
that looks like this guy over here.
You can ignore the six, that's a six-membered ring
it's not a six-membered sugar, remember?
We have five carbons so in the making of the six
this oxygen is combining with this carbon here.
We're not going to worry about that.
We will worry about this.
This guy is the form in which is we find ribose
in ribonucleotides.
The only difference between ribose and deoxyribose
is at carbon number two.
Carbon number two is where deoxyribose
is lacking in oxygen.
So we'll take a look at that.
Deoxyribose is right here.
And it's lacking an oxygen.
There's actually a hydrogen it's not showing there
which is kind of misleading but this guy's lacking
an oxygen there.
Now it turns out that lack of that oxygen
has some fairly significant effects on the chemistry
of ribonucleotides versus deoxyribonucleotides.
Of course RNA contains ribonucleotides,
DNA contains deoxyribonucleotides
because that's where the D comes from.
The significant difference,
there are two that come to my mind.
One is if we put an OH on this guy, making it a ribose,
it makes this guy actually chemically less stable than DNA.
Chemically less stable.
What does that mean?
It means that if I take RNA and I treat it
with sodium hydroxide that extra OH there
will allow this bond to break very readily.
In fact it's one of the ways in the laboratory
in which we break RNA is by treating it with alkali.
So when we think about evolutionary time and people go out
and they isolate DNA from some species
that was in an extinct muskox from 40,000 years ago,
what they're getting is DNA.
RNA is not chemically stable under that long period of time
and under more severe chemical conditions.
So that extra OH makes RNA, a less
chemically stable molecule.
Another thing that that extra OH group does is it changes,
or I shouldn't say changes but it strongly influences
the structure of the nucleic acid in the duplex.
When we talk about DNA,
we talked about about it last term briefly,
we said the most common form of DNA
is what we call the "B" form.
That's what Watson and Crick discovered along,
by stealing the data of Rosalind Franklin.
RNA can also exist in a duplex.
You've got the same bases.
You've got the same arrangements.
You can make double stranded RNA
if you make it complementary,
and there are some viruses in fact use double stranded RNA
as their genetic material.
But they don't have the same arrangement
of those structures.
RNA forms what's called the "A" form.
And DNA can form an A form too
but it really prefers the B form.
So RNA cannot exist in the B form
and the reason it can't is that extra oxygen
actually precludes RNA making it into the B form.
So two things that happen as a result
of that hydroxyl group.
Okay, let's see.
What else do I want to say?
There are the bases.
I'm not going to ask you to memorize the structures
but I think that you should know
the generalities of the structure.
We break the bases into two groups,
pyrimidines and purines.
There are three pyrimidines:
uracil, cytosine, and thymine.
And the common feature that they have structurally
is that they have a single six-membered ring.
They're smaller.
The purines, which include adenine
and guanine look different.
They have a six-membered ring
joined to a five-membered ring.
They're bigger.
Now if you think about it,
when we have the structure of a DNA duplex
or for that matter a RNA duplex, A always pairs with T.
G pairs with C.
That means a purine is always paired with a pyrimidine.
A big goes with a little and as a consequence
the dimensions are virtually identical
whether we have an AT or a GC.
That is the width of the duplex
doesn't change based on whether it's an AT basepair
or a GC basepair.
That's good.
We don't want a lot of fluctuation there.
There are the deoxyribonucleotides.
And again you see the structure here.
I wish they would put an H on there
to indicate there's an H, but suffice it to say
that's what dCTP would look like.
Well let's dive in and say a few words about synthesis
and about how we make these.
So what I'm going to be talking about in the lecture today
will completely be de novo, starting from scratch.
So we're completely starting from scratch.
The pathway that leads to pyrimidines
is completely separate from the pathway
that leads to purines.
And they also have different starting points.
Different starting points.
We will see that in working with pyrimidines
that the bases are made separate from the ribose.
We'll see in the case of the purines
that the bases are built on the ribose.
So in the case of the pyrimidines, ribose over here,
base built over here, then they get joined together.
In the case of purines,
start with ribose and start building a ring on that ribose.
So it's a fundamentally different approach.
Let's talk first about pyrimidines.
This figure illustrates very nicely
the simple materials we need
to make the ring structure of pyrimidines.
We've seen that a thousand times already.
These guys come together in red
and contribute those two atoms right there.
Aspartic acid.
You've seen aspartic acid.
There's the other guys there.
This makes a pyrimidine ring.
We join it with PRPP which is our source of ribose.
We make a nucleotide,
we add some more phosphates to it and we get down here.
So I'm going to take you through these steps
but this is a general view of what's happening.
Very simple starting materials
making some fairly complicated structures.
Let's look at some of these simple,
these very first reactions.
I'm only going to give you the names of a couple of enzymes.
There are, you're going to see,
about ten reactions in making the pyrimidines
and about ten reactions in making the purines,
and going through either structures or enzymes
for all those is really not very useful I think
in terms of learning material.
So where I talk about an enzyme you're responsible for it
but I'm not going to talk about most of the enzymes.
And I'm not going to hold you responsible for structures
except as I said in a general way
where you know the pyrimidines have the smaller ring
and the purines have the larger ring.
So that means a lot of this you can relax on.
Here's bicarbonate.
We phosphorylate it and make carboxyphosphate
and we add an amine to it and we make carbamic acid.
[phone rings]
My phone just rang.
Okay, bye.
[class laughing]
I pick it up and the thing's ringing on the other end.
And the help desk, "Can I help you?"
I answered because you know they do have these emergencies
so you have to make sure...
probably just a prank call.
So one of the things about what you see on the screen
is that this intermediate in particular is very unstable.
So we've talked about some strategies
for dealing with unstable intermediates.
If you recall we talked about perfect enzymes.
Perfect enzymes were perfect because
they wanted to work so fast they eliminated
or reduced significantly the time it took
for an unstable intermediate to be present.
We saw in the case of nucleoside monophosphate kinase
that they had a lid that came down and closed
and kept that unstable intermediate
from having access to water.
I'm going to show you an enzyme here
that uses a third strategy
for protecting an unstable intermediate.
It's this enzyme here that I will mention the name of.
It's carbamoyl phosphate synthetase
and it's catalyzing those reactions that you just saw.
Both of those reactions.
What it does is this enzyme uses a tunnel.
The intermediates actually move through the inside
of the enzyme in the process of those catalytic reactions,
and as a result the intermediates
never get access to water.
So the tunnel provides yet another way of keeping water
away from, in this case, carbamic acid
and making problems that the unstable intermediate
will fall apart.
Well that's kind of a cool mechanism.
We look at our product here, carbamoyl phosphate,
and we are ready to start assembling a ring
or pretty close to it.
And in doing this we bring in an aspartic acid.
We see the aspartic acid coming in here
and we make carbamoyl aspartate.
You guys have actually seen this before.
You probably don't remember it
but when we talked about ATCase,
aspartate transcarbamoylase,
it catalyzed this reaction right here.
And you recall ATCase was really interesting
because we used it as a prime example
of an enzyme under allosteric control.
If you recall, ATCase had some interesting things
that affected it allosterically.
Two that were of relevance to us
were CTP and ATP.
ATP we said turned the enzyme on,
and CTP turned the enzyme off.
Well that turns out to be really relevant to our purposes
because CTP is the end product
of this pyrimidine synthesis pathway.
It's the end product.
So the end product is feeding back,
turning off the enzyme by feedback inhibition saying,
"Hey, we've got plenty of CTP.
"We don't need any more."
I probably said a little bit about this
when I talked about it last term.
ATP on the other hand is an indicator of energy
and, importantly, it's an indicator
of the level of purines.
If ATP's in greater concentration than CTP
this enzyme is going to be more likely to be activated
because ATP wins the race.
And that's good because when we have more purines
we want to balance and make more pyrimidines.
This is our first example of a balancing reaction
that's very important for nucleotide biosynthesis.
This enzyme, ATCase, plays a very critical role
in balancing the relative amounts
of pyrimidines versus purines.
A very important role.
Which way does it tip?
Well, we see.
If we have too many pyrimidines the enzyme gets turned off.
If we have too many purines, the enzyme gets turned on.
Well this figure has been drawn to show you
how we are very close to making a ring structure,
and there's the ring structure
that you see getting close there.
It simply involves loss of a water molecule
catalyzed by a proton, and when we do that the ring closes.
We make something called dihydroorotate.
No, I don't care if you know that name.
Partly because when we get to orotate,
orotate is originally named from orotic acid
and I can't make that, say that without sounding funny.
"Orotic acid."
"What are you talking about man?"
[scattered laughter]
"You dissing me?"
Alright, so...
I don't know what that means.
[class laughing]
Alright, so we've made the ring structure.
This is very close to being a pyrimidine.
In fact when we add a PRPP to it
we actually call it a pyrimidine.
Here is PRPP.
Ribose 5-phosphate which we get from,
by the way we get ribose 5-phosphate from
the pentose phosphate pathway.
We don't really talk much about it in this class
but the pentose phosphate pathway is the source
of ribose 5-phosphate needed to make nucleotides.
Ribose 5-phosphate becomes PRPP by action of this enzyme,
PRPP synthetase.
And yes I think you should know the name of that enzyme.
What's this enzyme doing?
It's taking phosphates off of ATP,
and notice it's taking two of the phosphates,
and putting those two phosphates over here.
Notice it's putting them on in the alpha configuration.
And we're going to see that that bond gets flipped
when the nucleotide itself is made.
PRPP is a starting material to link
that ring we just made to.
So now we're going to take this ring
and we're going to link the two together.
There's the orotate that we made.
There's the PRPP.
We put the two together and we get an even bigger
mouthful name that I can't say very well either
and I won't, alright?
We're almost at a pyrimidine we can recognize.
And by the way we will call this something.
Instead of calling it orotidylate I like to call it OMP.
OMP is easy to say.
Notice that we went from an alpha configuration to a beta.
This enzyme flipped that in the process
and we're almost at our first pyrimidine nucleotide.
That first pyrimidine nucleotide is UMP.
And we're not going to call it uridylate,
we're going to call it UMP.
What does that involve?
That involves loss of a carboxyl.
That carboxyl right there turns out to be interesting.
And you've actually seen this reaction before,
and it's an enzyme I'm not gonna hold you resposible for,
but I'll tell you what it is
and remind you of where you saw it before.
You saw it before, the enzyme is called OMP decarboxylase.
"I don't remember that at all."
Well when I first talked about enzymes
I used this enzyme as an example of an enzyme
that speeds up a reaction incredibly.
The halflife of this reaction is something
on the order of tens of millions of years.
With the reaction, with the enzyme,
this reaction proceeds in seconds.
So this is a pretty interesting enzyme
in terms of how much it speeds up a reaction
and it's simply decarboxylating this guy right here
to leave us with UMP.
So the first pyrimidine that we recognize as a pyrimidine
based on our previous experiences is UMP.
We've just made UMP.
Well UMP we can't use to make DNA or RNA
because that one phosphate.
We have to have triphosphates to use an RNA polymerase
to make RNA or a DNA polymerase to make DNA,
we have to get to the triphosphate level
and we're only at the monophosphate level.
Well now we come up with another enzyme
that you've seen before, and another enzyme that you've
seen before is nucleoside monophosphate kinase.
This is the one that has the lid
to keep the unstable molecule from floating away.
What does it do?
It takes a monophosphate, and it can be any monophosphate,
adds energy from ATP, and look what it makes.
It makes UDP.
So it's transferring a phosphate from ATP onto UMP
to make UDP and ADP.
Now I'm exaggerating a little bit in that
I said it takes any nucleotide.
It doesn't strictly do that,
but there are nucleoside monophosphates
for each nucleotide.
So there's a UMP kinase, there's a CMP kinase,
there's an AMP kinase, et cetera.
And they all do the same thing.
An AMP kinase would take AMP plus ATP
and make ADP plus ADP.
Transferring a phosphate from one to the other.
So a nucleoside monophosphate kinase
will take a phosphate off of ATP
and put it onto a monophosphate.
Alright, so we've gotten to the diphosphate level.
Triphosphate level is catalyzed
by the formation of the triphosphate is catalyzed
by a different enzyme that's actually very simple.
It's called nucleoside diphosphate kinase.
You're welcome to call that NDPK.
Now the reason this is simple is that this enzyme works,
one enzyme works on all of the diphosphates.
It works on all of the diphosphates.
Moreover, it can use any of the triphosphates
as a donor of the phosphate.
That's what the "X "and the "Y" there refer to.
So for example, if I had UDP plus GTP
I would end up with UTP plus-and that's a typo there-
that should be GDP.
That should be a "D" right there.
Sorry about that.
That's my error.
That should be a "D."
So it's just swapping a phosphate from one three
onto a two and that leaves behind a two.
Now this works, this enzyme is interesting
because it works on all the diphosphates
whether it's a ribonucleoside or a deoxyribonucleoside.
This could be, for example,
dGDP plus ATP gives me dGTP plus ADP.
So any of the diphosphates to triphosphates
are catalyzed by this enzyme
nucleoside diphosphate kinase or NDPK.
That's a great simplifying thing in this scheme.
One enzyme takes all the diphosphates to triphosphates.
Yes sir?
Student: Is there an extra [inaudible] phosphate that comes in,
because they're both triphosphates...?
Kevin Ahern: Well that's why I say it's my error.
That should be a diphosphate there.
I'll change that.
Now this enzyme actually turns out to be a balancer also.
Let's imagine I've got an awful lot of GTP
but not so much of CTP.
Well I can swap with this enzyme back and forth
and balance out my relative amounts of triphosphates.
So NDPK helps to balance the relative amounts
of triphosphates.
I'll repeat that because that's an important point.
NDPK helps to balance the relative amounts
of triphosphates.
So we've now gotten to the point where
if this has been a "U" all the way through
we now have UTP right here.
UTP is good for making RNA.
Bang, we're ready!
Well how about CTP?
Because we need for CTP for RNA also.
CTP turns out to be made directly from UTP.
It's the only nucleotide that's made directly
from a different nucleotide as a triphosphate.
So it's made directly from UTP and it looks like this.
Here's UTP.
This is an amination.
We're putting on an amine group in place of an oxygen.
So here's an oxygen in UTP swapping it for an amine in CTP.
This enzyme is called CTP synthetase.
CTP synthetase.
This enzyme is inhibited by CTP.
Well this enzyme now helps to balance
the relative amounts of UTP and CTP.
We don't want to have too much of either one of those.
We get too much CTP this enzyme is inhibited,
we get too much UTP this enzyme is favored.
So balance, again, is very very important.
In fact we'll see there's balancing mechanisms
for every step in these processes ultimately.
Well I haven't said anything about TTP.
We haven't talked about DNA.
It turns out TTP is made by an odd mechanism
that I will talk about separately on the DNA,
when I talk about deoxyribonucleotides.
dTTP is made from UMP but it's a more involved mechanism
than we'll go into here today.
We will talk about it later.
And right now we're only talking about
ribonucleotides anyway.
So keep that in mind.
Everything we're talking about here
all are ribonucleotides that we're making.
Good place to stop and ask for questions.
Everybody's ready for the weekend, aren't they?
Oh, if you guys will stick with me
we'll sing a song at the end of the period.
How's that?
Two in one day.
Or you can get up and leave at that point if you wish, also.
[class laughing]
One of the things that you see on the review
was most people really liked the songs
but there are a few people who say, "No more songs."
"Okay if you want to you can leave.
"That's okay, I'm sorry."
[class laughing]
That's pyrimidines.
Let's talk about purines.
So keep in mind we've just described
how to make the ribonucleotides CTP and UTP.
We haven't talked about deoxyribonucleotides yet.
They have other considerations,
but ribonucleotides we've talked about.
Well let's go through de novo synthesis for a purine.
Here's the same scheme we saw before.
There's a little bit more complexity here.
And purines themselves are a bit more complex.
And no I don't expect that you're going to memorize
where each atom comes out of there
because I'm not expecting you to memorize the structures.
But I think it's useful to look at this and think about,
again, the simplicity or the simple molecules
that go into this.
There's an amine coming from aspartic acid.
There's a carbon coming from carbon dioxide.
There's this yellow section.
That's just glycine.
That's a mouthful of a name.
That's fulvic acid.
It's a vitamin and we'll talk about that in a bit.
There is ribose down there.
And last there's an amine coming from glutamine.
So with the exception of this mouthful of a name,
very simple precursors that are coming together
to make this.
That makes a purine ring.
Creates another new nucleotide
we haven't heard of before called IMP.
And IMP as you will see is a branch between the synthesis
of the adenine nucleotides and the guanine nucleotides.
This figure is very misleading.
You do not go from ATP to dATP.
Very misleading.
So you can ignore the very bottom part of that figure.
Now here's some of that complexity I told you about.
If you were taking a major's class in biochemistry
which I know you're all thanking yourself right now
that you're not, you probably would learn
most of these guys on here.
We're not going to do that.
We're only going to talk about a couple of interesting
enzymes on here and look mainly at the end products,
the end product here being IMP.
Well let's start here.
For reasons that aren't clear to me
your book shows this as the starting material and it's not.
And the last edition of the book did the same thing.
The starting material is actually ribose 5-phosphate.
Ribose 5-phosphate.
And if we take ribose 5-phosphate
and we put an amine onto it we create phosphoribosylamine.
That's what this guy is here.
So this is actually the second molecule.
I don't know why your book does this.
Why do I mention that?
Well I mention that because the enzyme that makes this
molecule is a very important regulatory enzyme.
The enzyme that makes phosphoribosylamine
has a mouthful of a name.
It's called PRPP amidotransferase.
And I said it's started with ribose 5-phosphate.
It's not, it's started with PRPP.
PRPP amidotransferase.
PRPP amidotransferase catalyzes the formation
of phosphoribosylamine.
PRPP amidotransferase is important
because it's a regulatory enzyme and its regulation
is really interesting.
You may not fully appreciate it until
I go all the way through the pathway
but I'll tell you what it is.
The enzyme is partly or fully inhibited
by its end products of the pathway.
What does that mean?
Well the end products of the pathway for making purines,
at least from this perspective, is AMP and GMP.
Yes we have to put phosphates on but for this pathway
AMP and GMP are the end products.
The enzyme is fully inhibited
when both AMP and GMP bind to it.
So PRPP amidotransferase is fully inhibited
when both AMP and GMP bind to the enzyme.
It turns the enzyme off just like that.
If only one of them bind, let's say only AMP binds,
the enzyme is a little bit active.
If only GMP binds the enzyme is a little bit active.
Now that you're not going to appreciate until
we get near the end of the pathway
but let's say first of all that the binding of AMP and GMP
will occur under conditions when we've got a lot of AMP
and GMP, right?
This is turning off purine biosynthesis.
It's helping to control how many purines we make.
Now what we're going to see is this enzyme plays a role
in balancing purines as well.
But for our purposes right now the main thing that we know
is that it controls if we make purines or not
and thereby controls the level of purines
that we're going to have.
Well let's see, what do we want to see here?
let's start right here.
THF with a carbon on it going to a THF here.
Don't worry about the structures.
A couple days ago I talked about SAM,
Does anybody remember what SAM does?
Student: It donates methyl groups.
Kevin Ahern: It donates methyl groups.
It's a source of single carbons in a metabolic process.
We use it to make phosphatidylcholine, right?
And I said at the time that there are other molecules
that donate single carbons to reactions
and this is one of them.
The folates function to donate single carbons.
They're not donating methyl groups
but they're donating single carbons to reactions.
This carbon right here in blue has been donated.
There it is right there.
This carbon in blue has been donated by this THF right here.
Now I show you that not because
it's a little piece of esoteric trivia,
but it turns out that folate metabolism
has some very important implications both for making
antibiotics against bacteria and for treating cancer.
Now I'm not going to tell you that right now.
We'll have to come back to that
probably the lecture next time,
but both of those are important considerations
in folate metabolism.
Folates are necessary to make purine nucleotides.
We have to have these folates
to make these purine nucleotides.
It turns out that folates are used in a couple places.
There's one right there, there's another one over here.
And no you don't need to know where they are
and no you don't need to know these names
or these structures.
I'd like to point out some interesting things that happen
along the way, though.
Look at this guy over here.
There is a mouthful of a name for you.
And look what gets split off in the process.
Our friend fumarate.
I told you that metabolic pathways are integrated.
I gave you examples about how CDP was necessary
for making glycerophospholipids
and I said it was a barometer of energy for cells.
And I said GTP was used for making protein
and ATP-all of these nucleotides play roles
in metabolic pathways and now we see that
the synthesis of these nucleotides
contribute to metabolic pathways as well.
We can't think of nucleotide metabolism as being separate
from metabolic processes that occur in the cell.
They're totally dependent on them
and they totally contribute to them as well.
That's really important because again,
cells have to make decisions.
Do I have the resources necessary to replicate?
By taking simple measures of certain molecules in cells,
cells know if they have the resources
they need to replicate.
That's very cool.
Well the upshot of this whole process is that
we get down to make this nucleotide called inosinate
which you're more than welcome to call IMP.
IMP is a purine nucleotide.
And by the way I didn't put out, I should point out,
all of these guys already have ribose in them.
See, we started with a ribose over here.
So before when we made pyrimidines we made the ring
and then we put it together with PRPP and we did it.
We're starting over here with PRPP
and building that ring on the PRPP.
That's what all these reactions are doing.
Notice there's the ribose right here.
So we've got the ribose.
We've got the phosphate.
Because it started out as a PRPP
it's a phosphoribose that's there.
We've got a nucleotide at this point.
We've got a purine nucleotide.
And I will remind you later you will see IMP again.
IMP turns out to be very important in some transfer RNAs.
IMP is an important nucleotide for some transfer RNAs.
Well to go from IMP to AMP and GMP is interesting
and important and I'm going to go through it briefly
and I'll start next time with it also but here's IMP.
We see it's a branch point in going upwards to AMP
or going downwards to GMP.
Both can be made from IMP.
Let's look at what happens going up.
If we start with IMP and we go over to AMP,
GTP energy is necessary.
If we start with IMP and we go over to GMP we discover that
ATP energy is necessary.
If I have plenty of GTP I'm going to go this way.
If I have plenty of ATP I'm going to go this way.
Further, AMP right here will feedback inhibit this enzyme.
I'm not giving you the name
but it will feedback inhibit this enzyme.
AMP will feedback inhibit its own synthesis.
GMP will inhibit its own synthesis by feedback inhibition.
Yeah I heard that sigh.
These are providing balance for us.
Energy from GTP making AMP, energy from ATP making GMP,
each one inhibiting its own synthesis.
Now I know this lecture is a bit of a nightmare
so I thought we would do a song at the end about nightmares.
It's to the tune of an old Beatles song.
It's an obscure Beatles song called Norwegian Wood.
So please join me if you know it and sing it loud because
I don't sing very well.
[singing Student Nightmares]
Lyrics: I answered three "B"
But then I thought it might be "C"
Or was the false true?
I can't undo.
It makes me blue.
It asked me to sing all the enzymes that regulate fat
As I wrote them down I discovered I didn't know Jack
I ought to give thanks,
Scoring some points, filling in blanks
I squirmed in my seat
Feeling the heat, shuffling my feet
Professor then told me there wasn't a chance I would pass
So I started crying and fell through a big pane of glass
I suffered no harm
'Cause I awoke, to my alarm
Oh nothing compares
To deadly scares, student nightmares
Happy weekend.
[class murmur]
Kevin Ahern: Hey Emily how are you doing?
Did you know the song or not?
Student: No...
Kevin Ahern: I'm too old, i'm too old.
Student: I like Beatles, but i don't know that one.