Purine and Pyrimidine Metabolism Flashcards
What are the sources of the atoms in purine bases?
Variety of sources including several amino acids as well as small molecule sources.
The purine base is made by starting with a ribose sugar and then building the base on the sugar, one step at a time.
What are the key co-factors in the synthesis of purine and pyrimidine bases?
Purines: Tetrahydrofolate
What are the sources of energy involved in the de novo synthesis of purine and pyrimidine bases?
Purines: ATP
What are the differences between the synthesis of purine and pyrimidine nucleotides?
- Whether the base is made on the ribose sugar (purines) or made separately and then added to the sugar (pyrimidines)
- where the atoms come from
- the intermediates that are produced
- how these intermediates are converted to yield the full set of bases.
What are the key regulated steps and feedback loops within the de novo purine synthesis pathway?
The key regulated step of purine de novo synthesis is at the start, when PRPP (contains the ribose sugar) and glutamine are used by glutamine phosphoribosyl pyrophosphate amidotransferase to add the first nitrogen to the PRPP.
The secondary regulated step is conversion of a ribose 5’-phosphate to PRPP.
The pathway involves the addition of several amino acids and CO2 to the growing base as well as tetrahydrofolate and ATP as important elements in the pathway.
The first base that is produced by this pathway is inosine mono-phosphate (IMP). IMP is then used to make the GMP and AMP bases by the action of enzymes that act on the IMP. Failure of one of the enzymes involved in AMP synthesis can lead to a form of autism.
Feedback loops are a critical mechanism of regulation in purine synthesis. Specifically, IMP, GMP, and AMP inhibit enzymes that act early in the pathway.
What enzyme reduces ribose to deoxyribose, and what strategy does it use for catalysis? What are its substrates?
Ribonucleotide reductase
Ribonucleotide reductase operates on diphosphates (NDPs; ADP, GDP, CDP, and UDP).
Regulated by a complex mechanism that ‘senses’ the concentration of dNTPs. The enzyme has a primary regulation site (“on/off” switch) that controls the overall activity of the enzyme, and a substrate specificity site (“dial”). The primary regulation site is active in the presence of ATP, inactive when dATP builds up. The substrate specificity switch is sensitive to the concentrations of individual dNTPs, and as each builds up, the enzyme changes from operating on one NDP, to operating on another. This remarkable bit of enzyme regulation ensures that equal and adequate amounts of each NDP are converted to dNDP (and then to the dNTPs).
Gout
Caused by a buildup of uric acid in the blood.
Uric acid is the result of the purine degradation pathway.
Can be caused by deficiencies or hyperactivities of some enzymes, and several risk factors (age, diet, etc.) are associated with the disease.
Severe Combined immunodeficiency syndrome
Caused by a mutation in the gene encoding adenosine deaminase, an enzyme used in the purine degradation pathway.
This leads to a buildup of dATP, which inhibits ribonucleotide reductase, which prevents enough dNTPs from being made.
Rapidly proliferating cells (such as those in the immune system) are affected.
Lesch-Nyhan syndrome
Caused by a deficiency in one of the primary enzymes in the purine salvage pathway (HGPRT), leading to higher rates of de novo synthesis of purines.
Patients may have gout symptoms, self-mutilating behavior and other severe mental disorders.
Difference between a nucleoside and nucleotide
A nucleoside is a base combined with a pentose sugar.
Nucleotide: If the sugar is phosphorylated
What are the sources of the atoms in pyrimidine bases
The atoms that make up the pyrimidine bases come from both amino acid and small molecule sources
What are the key regulated steps and feedback loops within the de novo pyrimidine synthesis pathway?
The first step in the synthesis of the pyrimidine ring is the primary source of regulation. The enzyme that catalyzes this key step is carbamoyl phosphate synthetase II (different from the one in the urea cycle). It is activated by PRPP and inhibited by UTP.
The first nucleotide produced by this pathway is uracil mono-phosphate (UMP). To make cytosine, the nucleotides must first be converted to a triphosphate form.
Once UMP is converted to UTP, it can be converted to CTP by the action of the CTP synthase enzyme.
Nucleotide degradation
We consume far more nucleotides than we need, so many of these are degraded and excreted by the intestine.
Degradation of purines: Remove the base from the sugar, yielding a free base (adenosine or guanine). The free bases are then further broken down to uric acid, which is what is excreted from the body in urine.
Pyrimidines are broken down by first removing the base ring from the ribose, as in purine degradation. However, unlike purine degradation, the base ring is then opened up (the uric acid from purine degradation is a closed ring). Ultimately, the breaking down of the base ring leads to molecules that can be used in other pathways (Succinyl-CoA, Malonyl-CoA, and Acetyl-CoA). These products are water soluble and so do not cause problems like uric acid can.
Changes in phosphorylation states and conversion of rNDPs to dNDPs
To convert nucleotide monophosphates (NMPs) to the diphosphate (NDP) and triphosphate (NTP) forms, a set of kinases are used and take phosphate from an ATP donor and transfer it to other nucleotides.
How do you make dTTP from dUDP?
Once UDP is converted to dUDP, it can then be dephosphorylated to make dUMP, which is then converted to dTMP by thymidylate synthase. Kinases can then convert dTMP to dTDP and dTTP.
