6th Unit / Ch 22 Nucleotide Metabolism Flashcards
Nucleotide Structure and Function 22 1.1
Which nitrogenous base shown is used (as a component of a nucleotide) in DNA
but not RNA synthesis? In addition to a purine or pyrimidine base, what are the
other two components of a nucleotide?
T (as dTTP) is used in DNA synthesis, whereas U (as UTP) is used in RNA synthesis. Structurally, T is methylated U. In addition to a purine or pyrimidine
nitrogenous base, a nucleotide contains a pentose monosaccharide (ribose in RNA and 2-deoxyribose in DNA) plus one to three phosphate groups.
[Note: Compared to a nucleotide, a nucleoside lacks phosphate groups. The terms “nucleoside phosphate” and “nucleotide” are used interchangeably.]
Nucleotide Structure and Function 22 1.2
Why are nucleotides and nucleosides referred to as N-glycosides?
Nucleotides and nucleosides are referred to as N-glycosides because a N in the base is linked to C-1’ of the sugar.
[ Note: The number of a C atom in the
sugar includes a prime sign (‘) to distinguish it from the atoms in the base.]
Nucleotide Structure and Function 22 1.3
What is the role of nucleotide sugars in the body? What group of disorders
results from defects in nucleotide sugar-dependent protein N-glycosylation?
Nucleotide sugars are activated monosaccharide donors in the synthesis of polysaccharides, glycoproteins, proteoglycans, and glycolipids. For example,
UDP-glucose is used in glycogen synthesis, GDP-mannose in glycoprotein synthesis, and CMP-NANA in ganglioside (glycolipid) synthesis.
Congenital disorders of glycosylation (CDG) result from defective production, transport, and processing of nucleotide sugars required for protein N-glycosylation.
Purine Nucleotide De Novo Synthesis 22 2.1
The origins of the atoms in a purine base during nucleotide de novo synthesis
are shown. What is the order of addition of these atoms?
The order of the addition of atoms in purine base synthesis is (1) the amide N from Gln,
(2) the N + C atoms from Gly,
(3) a C from N 10 -formyl-THF,
(4) the amide N from another Gln,
(5) the C from CO 2,
(6) the N of Asp, and
(7) a C from another N 10 -formyl-THF.
Purine Nucleotide De Novo Synthesis 22 2.2
What enzyme catalyzes the committed step of purine nucleotide de novo synthesis. How is it regulated?
What is the fate of IMP, the first purine
nucleotide made?
The committed step of purine nucleotide de novo synthesis is catalyzed by glutamine:PRPP amidotransferase (shown). The enzyme is activated by PRPP
and inhibited by AMP and GMP. IMP, the first purine nucleotide made, is converted to AMP and GMP in separate two-step, energy-requiring processes.
Purine Nucleotide De Novo Synthesis 22 2.3
Why does methotrexate cause a decrease in DNA synthesis?
Why do sulfonamides decrease DNA synthesis in bacterial but not human cells?
Methotrexate inhibits DHFR, which catalyzes the reduction of DHF to the THF required (as N10 -formyl-THF ) for purine synthesis. Sulfonamides inhibit folate (and consequently THF) synthesis in bacteria. With each drug, ↓ purines cause ↓ DNA synthesis. Humans, however, cannot synthesize folate and are
unaffected by sulfonamides.
Purine Nucleotide Degradation 22 3.1
What highly oxidized purine (indicated by a red question mark) is the end product of purine nucleotide degradation?
How is it excreted from the body? What enzyme catalyzes its production from xanthine? Where is this
enzyme found primarily?
UA, a highly oxidized purine, is the end product of purine nucleotide degradation and is excreted (as urate)
primarily in urine and also in feces. Xanthine Oxidize catalyzes the oxidation of xanthine to UA. The enzyme is found in the
intestine (for degradation of dietary purines) and the liver (for degradation of endogenously synthesized purines).
Purine Nucleotide Degradation 22 3.2
AMP can be deaminated to IMP by AMP deaminase and then converted to inosine by a 5 ‘- nucleotidase. By what
other path is AMP converted to inosine? What pathology results from an enzymatic deficiency in this conversion?
AMP can be converted by a 5’-nucleotidase to adenosine, which is deaminated to inosine by ADA. ADA deficiency results in a type of severe combined immunodeficiency disease (SCIDS).
[Note: Less than 15% of SCIDS is caused by ADA deficiency with the majority caused by an X-linked deficiency in the common y chain of several cytokine receptors.]
SCIDS results in a decrease in the number and/or function of T, B, and NK cells. A less severe immunodeficiency that affects only T cells is caused by PNP deficiency.
Purine Nucleotide Degradation 22 3.3
Why might administration of recombinant uricase be a rational approach to gout treatment?
Humans do not express uricase, the enzyme that degrades UA (low solubility in aqueous solutions) to allantoin
(high solubility). Because gout is initiated by hyperuricemia, conversion of urate to allantoin by administration
of recombinant uricase reduces blood urate levels and, therefore, the risk for gout.
Purine Salvage and Hyperuricemia 22 4.1
Why do mutations that increase the activity of PRPP synthetase (shown) result in hyperuricemia?
Increased PRPP synthetase activity increases production of PRPP ,an activator of the regulated enzyme of purine nucleotide de novo synthesis glutamine:PRPP amidotransferase. Excess purine nucleotides are degraded to UA, resulting in hyperuricemia.
Purine Salvage and Hyperuricemia 22 4.2
What is “purine salvage”? Why is it important? Why do defects in purine base salvage result in hyperuricemia?
Purine salvage primarily refers to the HGPRT-catalyzed conversion of hypoxanthine and guanine (purine bases) to IMP and GMP (purine nucleotides) by the addition of ribose 5-P from PRPP, shown. Salvage allows recycling of the bases, the synthesis of which requires ATP.
[Note: Some salvage of adenine and adenosine to AMP does occur.] Salvage defects increase PRPP availability as a consequence of decreased use and increased production, the latter because there are fewer purine nucleotides from salvage to inhibit PRPP synthetase . ↑ PRPP results in ↑ UA.
Purine Salvage and Hyperuricemia 22 4.3
What disorder is caused by a nearly complete HGPRT deficiency?
Nearly complete defi ciency of X-linked HGPRT causes Lesch-Nyhan syndrome with accompanying hyperuricemia.
[ Note: The most characteristic finding is
behavioral disturbances that include self-mutilation. Motor dysfunction and cognitive defects also are seen. Less severe deficiencies with less severe presentations
are known.]
Pyrimidine Nucleotide Metabolism 22 5.1
What are the sources (A, B, and C shown) of the atoms in a pyrimidine base?
The sources of the atoms in a pyrimidine base are the C of CO2 , the amide N of Gln, and the N+ 3C atoms of Asp.
[ Note: Gln and Asp each provides a N
in purine synthesis.]
Pyrimidine Nucleotide Metabolism 22 5.2
What is the regulated step in de novo pyrimidine synthesis? What is the first pyrimidine base formed, and how is
it converted to the first pyrimidine nucleotide?
The regulated step of pyrimidine synthesis is formation of carbamoyl phosphate (CP) from 2 ATP, CO2, and Gln by cytosolic carbamoyl phosphate synthetase (CPS II), which is activated byPRPPand inhibited byUridine-5’-triphosphate(UTP).Orotate is the first pyrimidine base formed.
[ Note: Deficiency of ornithine transcarbamylase OTC of the Urea Cycle
upregulates orotate synthesis by increasing Carbamoyl phosphate availability.]
A transferase uses PRPP to add ribose 5-P generating orotidine
5’-monophosphate (OMP), the first nucleotide. A decarboxylase
converts OMP to uridine monophosphate (UMP), which is phosphorylated toUridine-5’-triphosphate(UTP)then aminated tocytidine triphosphate (CTP).
[Note: PRPP is used in purine and pyrimidine synthesis and salvage.]
Pyrimidine Nucleotide Metabolism 22 5.3
What is the cause of hereditary orotic aciduria?
Hereditary orotic aciduria is caused by a defect in bifunctional Uridine Monophosphate (UMP) synthase, which catalyzes the transferase and decarboxylase reactions of UMP synthesis. The treatment is administration of uridine, which gets salvaged to UMP.
Pyrimidine Nucleotide Metabolism 22 5.4
How is dTMP (deoxythymidine monophosphate) synthesis inhibited pharmacologically?
dUMP is methylated to dTMP as shown. In this thymidylate synthase – catalyzed reaction, the methyl group is supplied by N5,N10-methylene THF
(not SAM) as THF (tetrahydrofolate) is oxidized to DHF (dehydrfolate).
1. 5-FU (5-Fluorouracil) made into (as 5-FdUMP) inhibits thymidylate synthase.
2. Inhibition of DHFR by methotrexate (cancer fighter) inhibits the reduction of
DHF to THF, thereby decreasing the availability of THF for purine and dTMP synthesis.
Deoxynucleotide Synthesis 22 6.1
What enzyme (shown as a red question mark) catalyzes the
reduction of the pyrimidine (and purine) ribonucleotides to
their 2’-deoxyribonucleotide forms? In what phase of the cell cycle is
the enzyme active?
RNR (Ribonucleoside reductase) catalyzes reduction of the purine and pyrimidine ribonucleoside diphosphates to their
2’-deoxyribonucleoside diphosphate forms using NADPH.
RNR is active in the _S phas_e (DNA synthesis phase) of the eukaryotic cell cycle.
Deoxynucleotide Synthesis 22 6.2
How is the enzyme regulated?
This is accomplished by effectors binding to two different allosteric sites. “Activity” sites bind ATP (activates RNR) or dATP (inhibits).
[Note: The dATP accumulation seen in ADA deficiency inhibits RNR in
lymphocytes.] “Substrate-specificity” sites bind specific (deoxy)nucleoside triphosphate effectors, allowing a specific ribonucleoside diphosphate bound to the active site to be reduced to its deoxy form.
[Note: RNR is oxidized as the substrate is reduced. Oxidation of the coenzyme thioredoxin regenerates functional RNR. Functional thioredoxin is
regenerated by thioredoxin reductase and NADPH.]
