Nucleotide Metabolism

List some products for which amino acids are precursors

immune system signals, hormones, membrane lipid constituents, electron carriers, and nucleotide bases

base attached to a sugar

nucleoside

base+sugar+phosphoryl groups

nucleotide

DNA Base

adenine (A), guanine (G), uracil (U), cytosine (C)

DNA ribonucleoside

ribonucleoside

DNA ribonucleotide (5’-monophosphate)

adenylate (AMP), guanylate (GMP), uridylate (UMP), cytidylate (CMP)

RNA Base

adenine (A), guanine (G), thymine (T), cytosine (C)

RNA deoxyribonucleoside

deoxyadenosine, deoxyguanosine, thymidine, deoxycytidine

RNA deoxyribonucleotide (5’-monophosphate)

deoxyadenylate (dAMP), deoxyguanylate (dGMP), thymidylate (TMP), deoxycytidylate (dCMP)

Identify the amino acids that provide the atoms that make up the purine rings.

glycine(GLY,G), glutamine(GLN,Q), and aspartate (ASP,D)

Identify the amino acids that provide the atoms that make up the pyrimidine rings.

aspartate(ASP,D) and glutamine (GLN,Q)

Identify the sugar on which purines are synthesized in the de novo pathway

ribose molecule

Explain the conversion of PRPP to 5-phosphoribosyl-1-amine, including the enzyme.

PRPP —(glutamine phosphoribosyl amidotransferase)→ 5-phosphoribosyl-1-amine

5-phosphoribosyl-1-amine is formed from

PRPP and glutamine

Identify the product of 5-phosphoribosyl-1-amine after nine steps (you do not need to know the 9 steps)

5-phosphoribosyl-1-amine → inosinate

Outline the pathways leading to the formation of AMP

inosinate → adenylsuccinate → adenylate (AMP)

Outline the pathways leading to the formation of GMP

inosinate → xanthylate → guanylate (GMP)

adenine phosphoribosyltransferase (APRT) acts on _____ to form _____

adenine; AMP

______ acts on adenine to form AMP

adenine phosphoribosyltransferase (APRT)

hypoxanthine guanine phosphorbosyltransferase (HGPRT) acts on _______ to form ______

hypoxanthine or guanine; IMP or GMP

______ acts on hypoxanthine or guanine to form IMP or GMP

hypoxanthine guanine phosphorbosyltransferase (HGPRT)

glutamine-PRPP amidotransferase is inhibited by ______ (end products)

IMP, AMP, and GMP

formation of xanthylate from inosinate by IMP dehydrogenase is inhibited by excess ____

GMP

• GMP and AMP concentrations are reciprocally inhibited

  • ____ is needed for AMP synthesis

GTP

• GMP and AMP concentrations are reciprocally inhibited

  • ____ is needed for GMP synthesis

ATP

PRPP is inhibited by ___

ADP and GDP

Explain the three-step process by which pyrimidines are synthesized. Include key intermediates and key enzymes.

1. bicarbonate —(carbamoyl phosphate synthetase II (CPS II)→ carbamoyl phosphate

• intermediates: carboxyphosphate and carbamic acid

  2. carbamoyl phosphate —(aspartate transcarbamoylase (ATCase))→ carbamoylaspartate → dihydroorotate → orotate + PRPP → orotidylate

  • ribose 5-phosphate + ATP —(PRPP synthetase)→ PRPP

  3. orotidylate —(orotidylate decarboxylase)→ uridine monophosphate (UMP or uridylate)

Identify the enzyme responsible for the conversion of UTP to CTP.

• UMP → UDP → UTP → CTP

  • UTP —(cytidylate synthetase)→ CTP

Identify the enzyme responsible for salvaging thymine during DNA degradation

• _________ is the enzyme that salvages thymine by incorporating it into a nucleoside

  • thymine is a product of DNA degradation

thymidine phosphorylase

Identify the enzyme responsible for generating thymine nucleotides

• _________ is the enzyme responsible generating thymine nucleotides

  • converts thymidine, a nucleoside, into a nucleotide

thymidine kinase

• Explain the production of deoxyribonucleotides from ribonucleotides.

  • The production of deoxyribonucleotides (dNDPs) from ribonucleotides (rNDPs) involves the direct reduction of the 2'C-OH bond in the ribose sugar of rNDPs to a 2'-H bond, forming deoxyribose. This reaction is catalyzed by the enzyme ______.

  • The process requires two hydrogen atoms, which are ultimately supplied by NADPH and transferred via two redox pathways that involve the proteins thioredoxin and glutaredoxin.

ribonucleotide reductase

In the thioredoxin pathway, NADPH donates electrons to the FAD (flavin adenine dinucleotide) of _______. This enzyme then reduces oxidized thioredoxin by transferring the electrons to its disulfide bond. Reduced thioredoxin can then reduce ribonucleotide reductase.

thioredoxin reductase

_____ can also facilitate the reduction of ribonucleotide reductase by accepting electrons from NADPH via glutathione and transferring them to the enzyme.

Glutaredoxin

_______ is a key enzyme in the production of dTMP (deoxythymidine monophosphate), one of the four nucleotides required for DNA synthesis.

• catalyzes the methylation of dUMP (deoxyuridine monophosphate) to form dTMP. This reaction requires N5,N10-methylenetetrahydrofolate, which serves as a one-carbon donor and is converted to dihydrofolate in the process.

Thymidylate synthase

______, an anticancer drug, is converted by cancer cells into fluorodeoxyuridylate (F-dUMP), which acts as a suicide inhibitor of thymidylate synthase, thereby blocking DNA synthesis and tumor growth

Fluorouracil

_______ adds a methyl group to dUMP to form thymidylate in a reaction that requires N5,N10-methylenetetrahydrofolate

thymidylate synthase

• Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate to tetrahydrofolate, a reaction that is essential for the continued production of dTMP. This is because the production of dTMP by thymidylate synthase requires N5,N10-methylenetetrahydrofolate, which serves as a one-carbon donor and is converted to dihydrofolate in the process

  • dihydrofolate —(dihydrofolate reductase)→ tetrahydrofolate

• The regeneration of tetrahydrofolate from dihydrofolate by DHFR is therefore crucial to maintain a sufficient pool of tetrahydrofolate for dTMP synthesis. Inhibiting DHFR blocks this regeneration step, ultimately leading to a depletion of tetrahydrofolate and a cessation of dTMP production

• Methotrexate and aminopterin are competitive inhibitors of DHFR and are used as chemotherapeutic agents because they can block DNA synthesis and tumor growth by inhibiting the production of dTMP