Exam 2: Purine & Pyrimidine Metabolism

De novo synthesis

New nucleotide synthesis from smaller precursor molecules rather than recycling an existing base.

Salvage pathway

What pathway recycles preexisting nitrogenous bases or nucleosides to make nucleotides?

Purine = 2 rings; Pyrimidine = 1 ring

How can you distinguish a purine from a pyrimidine by structure?

Purines: adenine and guanine; Pyrimidines: cytosine, thymine, uracil

Which common nitrogenous bases are purines vs pyrimidines?

Adenine and guanine (IMAGE NEEDED — SLIDE 9)

Identify the purine bases from their structures.

Cytosine, thymine, and uracil (IMAGE NEEDED — SLIDE 9)

Identify the pyrimidine bases from their structures.

Nucleoside = sugar + nitrogenous base

What is a nucleoside?

Nucleotide = sugar + nitrogenous base + phosphate

What is a nucleotide?

The presence of phosphate

What structural feature distinguishes a nucleotide from a nucleoside?

Modified/unusual base

A nitrogenous base that has undergone a chemical modification after or during synthesis.

Methylation

Addition of a methyl group to DNA or RNA by methyltransferases; can be removed by demethylases.

Pseudouridylation

Isomerization of uracil in RNA; the lecture identifies it as the most abundant RNA modification.

Reduction

Base modification in which hydrogens are added by reductases.

Glycosylation and acetylation

Which DNA modifications are related modifications but are NOT base modifications according to the slide?

N4-acetylcytosine

Cytosine with an acetyl group added to the nitrogen at position 4.

5-methylcytosine (5mC)

Which modified base is associated with DNA methylation and gene silencing?

N6-methyladenine (m6A)

Which common RNA modification has various effects on RNA biogenesis?

Epigenome

All biochemical modifications of DNA.

Epitranscriptome

All biochemical modifications of RNA.

Age, tissue specificity, disease, environmental exposures

What factors can alter the epigenome and epitranscriptome even though DNA/RNA sequence is mostly fixed?

Nucleic acid formation, energy homeostasis, and cell signaling

What three major roles of purine and pyrimidine nucleotides are emphasized?

Glutamine ×2, glycine, N10-formyl-THF ×2, CO2, and aspartate

Which compounds contribute atoms to the purine ring?

The purine ring is assembled directly on a ribose-phosphate molecule

Explain the basic construction strategy of de novo purine synthesis.

Purine ring atom donors (IMAGE NEEDED — SLIDE 22)

Using the diagram, explain which precursor molecules contribute atoms to the purine ring.

PRPP synthesis → 5-phosphoribosylamine synthesis → IMP synthesis

Which three steps does the professor say to focus on in the long de novo purine pathway?

PRPP

What activated form of ribose-5-phosphate is used in both purine and pyrimidine nucleotide synthesis?

Ribose-5-phosphate → PRPP by PRPP synthetase

What is the first step of de novo purine nucleotide synthesis?

Pi, Mg2+, and ATP

What does PRPP synthetase require?

ADP and GDP

Which molecules inhibit PRPP synthetase?

Pi

Which allosteric activator of PRPP synthetase is specifically listed?

Committed step

A pathway reaction after which the substrate is committed to proceed through that metabolic pathway.

5-phosphoribosylamine

What product is generated in the second committed step of purine synthesis?

GPAT: glutamine phosphoribosylpyrophosphate amidotransferase

Which enzyme catalyzes formation of 5-phosphoribosylamine?

Glutamine donates the amino group; PPi is removed

Explain what chemically happens during the GPAT step.

End-products inhibit GPAT; PRPP concentration increases the reaction rate

How is the GPAT step regulated?

IMP (inosine 5′-monophosphate)

What is the first fully formed purine nucleotide?

Hypoxanthine

What nitrogenous base is found in IMP?

IMP is the branch point for AMP and GMP synthesis

Why is IMP an important product of de novo purine synthesis?

Glutamine, glycine, N10-formyl-THF ×2, CO2, and aspartate

Which precursors are required to generate IMP?

Tetrahydrofolate (THF)

N10-formyltetrahydrofolate is synthesized from what molecule?

Dietary folate

Folate used to make THF must come from what source in humans?

Humans obtain folate from the diet instead of synthesizing it

Explain why PABA analogs such as sulfonamides affect bacteria but not human folate synthesis.

Methotrexate

A folic-acid analog that inhibits THF synthesis and therefore harms rapidly dividing cells.

Purine synthesis and dTMP synthesis

Which two nucleotide-related processes are impaired by methotrexate in this lecture?

Adenylosuccinate synthetase

Which enzyme initiates AMP synthesis from IMP?

Aspartate and GTP

What notable substrates/energy source are used during AMP synthesis from IMP?

AMP

What molecule feedback-inhibits the AMP branch?

IMP dehydrogenase

Which enzyme initiates GMP synthesis from IMP?

Glutamine and ATP

What notable substrates/energy source are used during GMP synthesis?

GMP

What molecule feedback-inhibits the GMP branch?

Mycophenolic acid

Which drug reversibly inhibits IMP dehydrogenase and therefore GMP synthesis?

GTP supports AMP synthesis; ATP supports GMP synthesis

Explain the cross-regulation that helps balance AMP and GMP production.

AMP vs GMP synthesis (IMAGE NEEDED — SLIDE 28)

From the pathway diagram, compare the enzyme, substrate/energy source, and inhibitor of each IMP branch.

Kinase

An enzyme that transfers a phosphate group to a substrate.

Adenylate kinase

Which base-specific kinase acts on AMP?

Guanylate kinase

Which base-specific kinase acts on GMP?

Nucleoside diphosphate kinase

Which nonspecific kinase acts on all nucleoside diphosphates to generate triphosphates?

ATP

What is the phosphate source used by the kinases shown in nucleoside di- and triphosphate synthesis?

Nucleases

Which enzymes initially chop nucleic acids into smaller products during nucleic-acid degradation?

Pancreas

Where does the lecture say dietary nucleic-acid degradation is most active?

Pancreatic nucleases and phosphodiesterases

Which enzymes reduce dietary DNA/RNA to mononucleotides?

Nucleotidase

In the small intestine, what enzyme converts mononucleotides to nucleosides?

Nucleosidases

After uptake into enterocytes, what enzymes cleave nucleosides to deoxy-ribose-1-phosphate and free bases?

Uric acid

What is the final degradation product of dietary purine bases?

Adenosine deaminase

Which enzyme converts adenosine to inosine?

Purine nucleoside phosphorylase

Which enzyme acts on both inosine and guanosine to release their nitrogenous bases?

Xanthine oxidase

Which enzyme converts xanthine to uric acid?

Adenosine → inosine → hypoxanthine → xanthine → uric acid

Trace the major adenosine/purine degradation sequence emphasized in the lecture.

Gout

A disorder characterized by high blood uric acid and deposition of monosodium urate crystals.

Overproduction or underexcretion of uric acid

What are the two general mechanisms that can produce gout?

Allopurinol

Which drug is used to inhibit uric-acid production in gout?

Adenosine deaminase deficiency

Which purine degradation defect causes adenosine accumulation?

Adenosine ↑ → dATP ↑ → RNR inhibition → impaired DNA synthesis → cell death

Explain why ADA deficiency impairs DNA synthesis.

Lymphocytes

Which cells are especially affected by ADA deficiency because the enzyme is highly active in them?

SCID

What severe clinical disease can result from profound ADA deficiency?

Purine salvage pathway

A pathway that conserves energy by recycling purine bases rather than synthesizing the rings de novo.

APRT and HGPRT

Which two enzymes salvage purine bases?

PRPP

What provides the ribose-5-phosphate used by both APRT and HGPRT?

Irreversible

Are APRT/HGPRT salvage reactions reversible or irreversible?

HGPRT

Hypoxanthine + PRPP → IMP and guanine + PRPP → GMP are catalyzed by what enzyme?

APRT

Adenine + PRPP → AMP is catalyzed by what enzyme?

Adenosine

Which purine nucleoside does the lecture specifically say can be salvaged?

Adenosine kinase

Which enzyme converts salvaged adenosine to AMP?

HGPRT deficiency

What lecture-supported enzyme defect causes Lesch-Nyhan syndrome?

Prevalence, inheritance, affected gene, salvaged purines, PRPP changes, and clinical features

What Lesch-Nyhan details does slide 38 tell you to research but does NOT provide answers for?

The ring is synthesized first, then attached to ribose-5-phosphate

Explain the basic construction strategy of de novo pyrimidine synthesis.

Purines are built ON ribose; pyrimidines are built BEFORE attachment to ribose

What is the most important construction difference between de novo purine and pyrimidine synthesis?

Glutamine, CO2, and aspartate

Which compounds contribute atoms to the pyrimidine ring?

Carbamoyl phosphate synthesis

What is the first regulated step of pyrimidine synthesis?

CPS II

Which carbamoyl phosphate synthetase functions in pyrimidine synthesis?

UTP

What inhibits CPS II?

PRPP

What activates CPS II?

CPS I = mitochondria, urea cycle, NH3; CPS II = cytosol, pyrimidine synthesis, glutamine

Compare CPS I and CPS II by location, pathway, and nitrogen source.

N-acetylglutamate

What activator of CPS I is shown in the CPS I vs CPS II table?

CPS III

Which carbamoyl phosphate synthetase is found in fish and invertebrates?

Ornithine transcarbamylase (OTC)

Which urea-cycle enzyme combines ornithine and carbamoyl phosphate to form citrulline?

Increased carbamoyl phosphate becomes available for pyrimidine synthesis

Explain why OTC deficiency can promote pyrimidine synthesis.

Orotate (orotic acid)

Formation of what nitrogenous base represents completion of the pyrimidine ring?

FMN

Which oxidizing agent is highlighted during orotate synthesis?

Vitamin B2

From which vitamin is FMN derived?