Nucleotide Metabolism: Introduction and De novo Purine Metabolism

by Kevin Ahern, PhD

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    00:00 Virtually every school kid today learns that ATP, GTP, CTP, and UTP are the nucleotide building blocks used to make RNA and the deoxyribonucleotide versions of those are the building blocks used to make DNA. What they don’t know and what you probably haven’t learned is how those nucleotides themselves are made, and that will be the subject of these lectures. I started to talk about the structure of the nucleotides as we can see here and introduced some nomenclatures so that we’re all on the same page. All nucleotides contain 3 distinct components. The first of those is in the center of the structure on the left and that’s the pentose. A pentose is a 5-carbon sugar. On the right side attached to the pentose is seen in blue is a base. That base corresponds to either a pair of purines or the pyrimidines. The purines being adenine and guanine, the pyrimidines being cytosine, uracil, or thymine. The third component of a nucleotide is at least 1 phosphate shown in red on the left. Those phosphates can be single, double, or triple as you see on the screen here. Now the bases are distinguished by their size basically. The purines, of course, having a 2-ring system, adenine and guanine, and the pyrimidines having a single ring, a simpler structure, cytosine, uracil, and thymine. Now, nucleotides as they say, are the building blocks of the nucleic acid’s DNA and RNA. Cells make their nucleotides by 2 distinct pathways. One pathway is called the de novo pathway, meaning that those nucleotides are made completely from scratch from very, very simple compounds. The other pathway strategy is to use salvage synthesis, and as the name would suggest, that means that those nucleotides are made by using pieces of other nucleotides that have been broken down. Now, purines are made in the distinct pathway as well, distinguised from the pathway that’s used to make pyrimidines. So we’ll talk about them separately. The deoxyribonucleotides that are used to make DNA are made from ribonucleoside diphosphates. So, in order to make DNTPs, we first need to make the ribonucleotide versions of those. Last, thymidine nucleotides are made from uridine nucleotides as we will see.

    02:26 So, in order to make thymine to put into DNA, we first got to make the uridine equivalent. Now, as I said, nucleotides are made from very simple components: amino acids, 1 carbon donors, and carbon dioxide. Now, we can see that in the illustration in the figure here. If we look at the sources of the atoms used to make purines, we see that they’re not very complicated. We see in green a set of atoms that come from the amino acid glycine. In purple, we see the ones that come from glutamine. We also see a single carbon from carbon dioxide, a nitrogen from aspartic acid, and 2 other carbons that come from folate derivatives, and those were described in another lecture in this series. When we look at the pyrimidines, it’s even simpler. Only 3 components are necessary to make the ring of the pyrimidine: carbon dioxide, glutamine, and aspartic acid.

    03:24 And those 3 components were also used to make purines. So, we think that making nucleotides, it takes very simple precursors, it’s not a difficult process to understand. The synthesis of the nucleotides is very tightly regulated. This is a very important concept to understand because the cell needs to have the proper ratio of purines to pyrimidines and if each of the individual nucleotides compared to each other. Now, the reason for that is that if the cell gets those out of balance in any way, it makes it much more likely that that cell will suffer mutation. Mutations in cells are usually bad and cells go to extraordinary links to avoid having that happen as much as they can. Now, purine synthesis is different from pyrimidine synthesis in that the purine synthesis begins with the ring being assembled on the ribose sugar. Pyrimidine synthesis, on the other hand, synthesizes the ring first and then attaches it to the sugar later. As we study and learn nucleotide metabolism, we can look at it in a couple of ways. We can look at it from a perspective of looking out on to the process from a bigger picture, such as what I show on the screen here, or we can zoom in and focus on individual reactions. Now, for the most part when I talk about nucleotide metabolism, I like to use the zoomed out version because while the individual reactions are important, the important message isn’t exactly how each process happens but rather how the overall process happens and how that balance that I’ve described is maintained in assembling the purine and pyrimidine nucleotides. Now looking at this in a big picture scenario, we see that the starting molecule is a molecule called ribose 5 phosphate. That’s the source of the ribose pentose sugar that appears in there. You can see on the left that it takes several steps and will briefly go through those to go from the ribose biphosphate to make an intermediate known as IMP, inosine monophosphate. IMP is a branchpoint. You can see that branch working down from IMP. One side going to the left making ultimately the very bottom ATP and the other branch going to the right making GTP. These are the 2 purine nucleotides that we make. Now, the important thing than we get to that point of IMP is that that’s one of the places where the balancing occurs to make the proper amounts of each one. We’ll also see prior to that point that there is a balance that starts in the very beginning that may be a little difficult to understand but after we see the bigger picture I think it will make sense. So, the first thing that’s done to ribose biphosphate is to get a pyrophosphate attached to its carbon number 1 and we see that happen in this process and if I look on the right side on the bottom, we see that there’s 2 phosphates that’ve been added. Those 2 phosphates come from ATP and the product of that reaction is AMP. The enzyme catalyzing that process is known as PRPP synthetase.

    06:29 PRPP synthetase is important in helping the cell to decide whether to start this process or not.

    06:36 So it’s a regulatory enzyme and we’ll see how that regulation occurs in just a bit. In the next reaction, we start to synthesize that purine ring above the ribose. So we see that the diphosphate on the right side has been changed and that change has replaced it with an amine group as you can see here to make phosphoribosylamine. How did that amine get there? Well that amine got there as a result of the transamination reaction. When I talked about amino acid metabolism in another of these lectures, you may remember that transamination was an important way to get amines on to a compound via sort of an exchange and a common way to do that exchange was to use glutamate or glutamine amino acids. We can see here that glutamine, the GLN, is the source of the amine and glutamine having lost its amine makes glutamate, that’s the GLU, and we’re left then with a phosphoribosylamine. The enzyme catalyzing that reaction is known as PRPP amidotransferase, and that too is a very important enzyme in helping the cell to control which nucleotides is being made and again we’ll see that in just a bit. Now, building a purine ring involves a total of about 7 or 8 steps. It’s a fairly complicated set of reactions and my point of bringing up these reactions and showing them to you isn’t to get you to memorize the individual steps that are there but rather to let you see the process by which that ring begins to assemble.

    08:13 The product of the last reaction was phosphoribosylamine and we see glycine being added to that. Where we had an amine before, we now see that a glycine has been attached to it and we see that ring on the right side starting to take shape. There is the ribose sugar, there is the phosphate, and there is the base that’s starting to be made. The next step of the process adds more to that glycine that was there, and we see it growing, and we see it growing, and now we’ve seen that we started to form or we have completely formed 1 of the 2 rings. The second ring grows and grows and grows and grows. Now, we have almost finished the second ring. You can see on the lower left that the first ring that was made is the bottom and the second ring has almost closed above it. The next step closes that ring.

    About the Lecture

    The lecture Nucleotide Metabolism: Introduction and De novo Purine Metabolism by Kevin Ahern, PhD is from the course Purine and Pyrimidine Metabolism. It contains the following chapters:

    • Nucleotide Metabolism - Introduction
    • De novo Purine Metabolism
    • Building a Purine Ring

    Included Quiz Questions

    1. They are made by de novo and salvage pathways.
    2. They are made in separate, non-overlapping pathways for each nucleotide.
    3. They can have any of three purines or two pyrimidines.
    4. Structurally, pyrimidines have two rings, and purines have one.
    5. They are the building blocks of DNA and RNA.
    1. All of the answers are true.
    2. PRPP synthetase catalyzes the process that converts ATP to AMP.
    3. It begins with ribose-5-phosphate.
    4. It includes the intermediate known as IMP.
    5. It consumes ATP.
    1. Gluteraldehyde
    2. Glycine and glutamine
    3. CO2
    4. Aspartate
    5. N10-formyl-THF
    1. N10-formyl-THF — source of N atoms in purine synthesis
    2. Ribose-5-phosphate — starting point
    3. Inosine monophosphate — branch point between ATP and GTP synthesis
    4. PRPP synthetase — regulatory enzyme for purine synthesis
    5. PRPP amidotransferase — helpful in synthesis of phosphoribosylamine

    Author of lecture Nucleotide Metabolism: Introduction and De novo Purine Metabolism

     Kevin Ahern, PhD

    Kevin Ahern, PhD

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    Clear & understandable
    By Lauren B. on 05. September 2018 for Nucleotide Metabolism: Introduction and De novo Purine Metabolism

    Thanks for focusing on the "big picture!" The lecturer at my school bogged us down with the details, so it was hard to take in what the most important steps were