NBME - 6/11 - Purine and Pyrimidine Nucleotide Metabolism I/II

Question 1

Where does purine and pyrimidine synthesis occur?

Answer 1

In the liver and the brain in some cases

Question 2

What happens to nucleotides produced in the liver?

Answer 2

Nucleotides produced in the liver leave the liver as nucleosides which travel to other tissues to be tuned back to nucleotides to be further metabolized.

Question 3

Discuss where the base of our purine structure comes from and what affects this first step.

Answer 3

It’s important to note that purine bases are generated on the ribose moiety directly.

PRPP, which provides our ribose moiety, reacts initially with glutamine to form phosphoribosylamine, beginning our building process by providing the N9 of our purine ring.

We now are stable enough to start stacking a bunch more on. This pathway will continue to form our precursors AMP and GMP, so it is important to note that those products inhibit this step as a feedback mechanism.

Question 4

So now we’ve got our base structure ready to go, phosphoribosylamine. The next thing to occur is things just start stacking on this guy. There are 6 things that get added. List them off.

Answer 4

1. Glycine molecule
2. C8 added by formyl FH4
3. N3 added by glutamine
4. C6 by CO2
5. N1 by aspartate
6. C2 by formyl FH4 (he’s back with seconds)

Now we have IMP!

The way I remember this is that Glycine in its entirety gets added, followed by 8 Crazy Farmers (C8 by F-FH4) and 3 Naughty gangsters (N3 by Glutamine). When they come together, they breath so much that 6 CO2s are made (C6 by CO2), and the only way for them all to survive all the gas is to eat aNyone (N1) Asparagus (Aspartate) that they can get their hands on. Luckily they all have 2 cans per farmer (C2 by F-FH4) to survive, but they are so high off the CO2 that they hallucinate seeing imps (end product is IMP)

Question 5

Alright so we just added a bunch of things to phosphoribosylamine to make IMP. What happens next?

Answer 5

IMP is cleaved in the liver. Its free base, or nucleoside, travels to various tissues where it is converted to the nucleotide.

Question 6

Wait, why do we care about IMP if its just gonna be shuttled all over the place, what do we do with it in all these places

Answer 6

IMP is the precursor of both AMP and GMP. Each product, by feedback inhibition, can regulate its own synthesis. AMP and GMP can be phosphorylated to the triphosphate level.

Question 7

Ok wait a minute I thought the main point of this purine stuff was to make DNA, when did we start making ATP and stuff…how do I make DNA from this process?

Answer 7

This occurs at the diphosphate level. Turn the AMP from the IMP to an ADP (say that 5 times fast). Ribonucleotide reductase (which requires thioredoxin) turns this ribose moiety to a deoxyribose one. Thus we make dADP (from ADP) or dGDP (if we had used GMP to GDP instead of AMP to ADP). These guys get put into DNA.

Question 8

Discuss the breakdown of Adenine.

Answer 8

This is complex, and we don’t need to know much more than what diseases are linked to it.

Adenine, one of our mature purine products, can just go backwards back to AMP with APRT enzyme. AMP can go down one of two paths now:

1. Back to IMP via AMP deaminase
2. To Adenosine.

Question 9

Who cares about degrading Adenine down to AMP, which becomes Adenosine or IMP? What’s the point?

Answer 9

The point of breaking these guys down is to recylce them. We can trace IMP and Adenosine in really funny ways:

Adenosine via Adenosine Deaminase turns to Inosine. Inosine can turn to Hypoxanthine via purine nucleoside phosphorylase, and then to IMP via HGPRT.

IMP can become GMP (remember, it was able to go AMP or GMP before depending on which purine base we wanted) and then turn to Guanine.

Question 10

Adenosine deaminase deficiency

Answer 10

Leads to SCID (Severe Immunodeficiency Disease). Deoxyadenosine derivatives build up in immune cell precursors without new DNA able to be formed.

Thymus is virtually absent with no T Cell or B Cells

Question 11

Partial Immune Deficiency

Answer 11

Partial immune deficiency from loss of activity of purine nucleoside phosphorylase (recall this is the guy that turns Inosine to Hypoxanthine in the degradation process).

Only T Cell function is lost, normal B Cell function.

Question 12

Lesch-Nyhan Syndrome and how it presents

Answer 12

Secondary to defective HGPRT so purine bases cannot be salvaged (i.e., reconverted to nucleotides). Purines are converted instead to uric acid, which accumulate in the blood and can lead to gout. Leads to self mutilation and mental retardation. X - Linked

Question 13

What is the basic sequence for purine degradation?

Answer 13

Phosphate and ribose are removed first, then the nitrogenous base is oxidized

Question 14

Degradation of guanine makes

Answer 14

Xanthine

Question 15

Degradation of adenine makes Hypoxanthine as we discussed. What can we do with Hypoxanthine besides just making IMP with HGPRT?

Answer 15

We can oxidize it to xanthine with xanthine oxidase, which requires molybdenum. Instead of a recycling route like with HGPRT, this is how we get rid of this stuff.

Use xanthine oxidase again (we really aren’t to original here) to make uric acid, which gets excreted by the kidneys since its not very water soluble.

Question 16

Why is allopurinol so good against gout?

Answer 16

Gout is just uric acid crystals inflamming joints. Allopurinol is a base that forms a nucleotide that inhibits xanthine oxidase and prevents hypoxanthine and xanthine from being converted to uric acid.

Question 17

First step of pyrimidine synthesis is the same as purine synthesis right? With the glutamines and stuff?

Answer 17

Almost. It happens in the cytosol, not the mitochondria.

Glutamine reacts with CO2 and 2ATP to form carbamoyl phosphate. This is catalyzed by carbamoyl phosphate synthesis II

(Take a step back, what does this remind you of? That’s right, Urea cycle. The first step of the urea cycle was to turn CO2 and NH4 to carbomyl phosphate using synthesis I. This time, to make a pyrimidine, we are taking CO2 and the nitrogen from glutamine, using synthesis II)

It’s also important to note with this first step that as usual, the later products inhibit this, never forget Le Chatlier’s Principle. UTP, a later product, inhibits this enzyme.

Question 18

What do we do next to this big stick of a molecule (Carbomyl phosphate) in this next step of pyrimidine synthesis?

Answer 18

Turn it into the ring (only one for pyrimidine!)

If you want to grow up, you gotta eat your asparagus. Asparate gets added to the carbamoyl phosphate and helps it to close to make the ring,

But this ring is still a teenager. It want’s to grow up to be just like Ori, so it takes a couple deep breaths full of oxygen, (oxidizes) to become orotate.

Question 19

Wait, we made a ring and oxidized it. Now what? Are we close?

Answer 19

Ori (Orotate) is oxidized now, so it can react with PRPP, producing Ori-5P (orotidine 5’phosphate).

Ori, now that she has PRePPed with her 5 Pound weights (Ori-5P) can now work out, cut out the CARBs (decarboxylate) and get swole.

We now have, after decarboxylation of Ori 5-P, a Uridine monophosphate (UMP) (Ori is pUMPed up)

Question 20

Alright so now we’ve got this phosphate molecule that seems closer to our final goal. What happens with this monophosphate?

Answer 20

We turn UMP to UTP, which can now obtain an amino group from glutamine to form CTP.

(Now that we are pUMPed up, we can Change to CTP)

Question 21

How do we make deoxyribose from CTP?

Answer 21

As with the purines, you have to use the right form. Use CDP, reduce it to deoxyribose to make dCDP via ribonucleotide reductase

Remember how we were pUMPed up before? Then we Changed to CTP/CDP? Well with a little R and R (rest and relaxation, ribonucleotide reductase), we got d-umb, cause all we did was eat and sleep, so now we’re dCDP)

Question 22

How do we convert dCDP to our final products?

Answer 22

dCDP can turn to dCTP, a final product for pyrimidines (we can always add phosphates, di turns to tri) We now have one of two final products for pyrimidines.

dCDP can also go down to dCMP (mono, from di), and by releasing ammonia (since it can’t release any more phosphates), turn to dUMP (we dUMPed ammonia).

dUMP can turn to dTMP via methylene-FH4.

Phosphorylating (adding phosphates) causes creations of dTDP and then dTTP, the other final product.

Question 23

What products do we make from pyrimidine degradation?

Answer 23

Carbons go to CO2 and the nitrogens make urea. You don’t really need to know much more than this for examination purposes.

Question 24

Hereditary orotic aciduria

Answer 24

Orotic acid is excreted into the urine because the ezymes that convert it to UMP are defective. Pyrimidines can’t be made so we get growth retardation. Oral administration of uridine bypasses the metabolic block and provides the body with a source for pyrimidines.