Nucleotide synthesis and metabolism

Question 1

gyrase

Answer 1

prokaryotic enzyme (type II topoisomerase) that introduces breaks in dsDNA that cause negative supercoiling; uses ATP; is a target of antibiotics (cipro) that block the resealing of the dsDNA.

Question 2

CpG islands

Answer 2

regions of the genome that contain a large number of CpG dinucleotide repeats. CpG islands usually extend for 300–3000 base pairs and are located within and close to sites of about 40% of mammalian gene promoters.

Question 3

methylation of CpG islands

Answer 3

turns the DNA off - leads to chromatin compaction and gene silencing

Question 4

acetylation

Answer 4

generally results in open conformation with gene transcription turned ON

Question 5

Salvage pathway

Answer 5

pathway of nucleotide synthesis that provides us with 97% of our nucleotides. Enzyme HGPRT catalyzes the degradation of guanine/adenine/hypoxanthine into GMP, AMP, IMP.

Question 6

HGPRT

Answer 6

enzyme responsible for salvage pathway from purine back to GMP/AMP/IMP. Uses PRPP as a substrate.
Has higher affinity for PRPP than glutamine PRPP amidotransferase, thus, the salvage pathway is used more often than the de novo pathway.

Question 7

PRPP

Answer 7

substrate for purine synthesis from both salvage and de novo pathways; stimulates the de novo pathway

Question 8

de novo pathway - purines

Answer 8

pathway of purine synthesis in which PRPP uses as substrate, with glutamine PRPP amidotransferase as rate limiting enzyme. Requires folate.
*Not used as much as the salvage pathway due to enzyme’s lower affinity for PRPP.

*Stimulated by PRPP, inhibited by AMP, GMP, IMP.

Question 9

uric acid

Answer 9

major degradation product of nucleic acids. Insoluble, so may precipitate into yellow, needle-like crystals with negative birefringement which accumulate in the joints and kidneys causing gout and nephrolithiasis.

Question 10

allopurinol

Answer 10

treatment for gout, Lesch-Nyhan syndrome, and tumor lysis syndrome. Inhibits the synthesis of uric acid by inhibiting xanthine oxidase.

Question 11

glutamine PRPP amidotransferase

Answer 11

rate limiting enzyme of purine de novo synthesis; stimulated by PRPP and inhibited by AMP, GMP, IMP.
Has a lower affinity for PRPP than HGPRT does, thus the salvage pathway normally wins out.

Question 12

de novo pyrimidine synthesis

Answer 12

occurs in cytosol and mitochondria; starts with glutamine and HCO3 instead of PRPP. CAD complex enzymes in the cytosol, then dihydroorotate dehydrogenase in the mitochondria, then UMP Synthase (2 enzyme complex) degrades orotic acid into UMP.

Question 13

xanthase oxidase

Answer 13

enzyme that catalyzes the conversion of xanthine into uric acid; inhibited by allopurinol

Question 14

which reactions require folate?

Answer 14

De novo synthesis of purines, and dTMP synthesis

Question 15

ribonucleoside diphosphate reductase

Answer 15

enzyme that catalyzes the synthesis of deoxyribonucleotides from nucleotides. (NDP to dNDP.)

inhibited by hydroxyurea and dATP

Question 16

hydroxyurea

Answer 16

used as a cancer drug, inhibits ribonucleoside diphosphate reductase thus inhibiting deoxyribonucleotide synthesis

Question 17

Lesch-Nyhan syndrome

Answer 17

loss of HGPRT causes increased PRPP levels which increases uric acid to 20x the normal amount. X-linked disorder.

Symptoms: hyperuricidemia, gout, nephrolithiasis, severe mental retardation, severe self-mutilating behavior.

Treatment: allpurinol will help with gout symptoms but no treatment is available for the mental deficits

Question 18

SCID

Answer 18

severe combined immunodeficiency can be caused by loss of ADA enzyme which normally converts deoxyadenosine to deoxyinosine. Results in an inability to synthesize any deoxynucleotides (because increased dATP inhibits ribonucleoside diphosphate reductase which results in lower levels of all other dNTPs)

Question 19

Tumor lysis syndrome

Answer 19

usually due to cytoxic cancer drugs, seen often in blood cancers. Increase in free nucleotides in the body results in large amount of purines being converted to uric acid, overwhelming the salvage pathway and stimulating the de novo pathway as well — together this means a huge increase in uric acid levels and can result in death.

Question 20

gout

Answer 20

can be caused by any increase in uric acid levels, including decreased excretion by the kidneys as seen in pts with CKD and gout

Question 21

megaloblastic anemia

Answer 21

Can be caused by:

1. Folate deficiency - blocks de novo synthesis pathway, decreasing nucleotide synthesis.
2. Hereditary orotic aciduria - defect in UMP synthase causes inability to convert orotic acid into UMP = build up of orotic acid and decreased pyrimidine synthesis = severe megaloblastic anemia and reduced growth. (treat with dietary uridine)

Question 22

UMP synthase

Answer 22

2 enzyme complex that converts orotate to UMP in the de novo pyrimidine pathway; if defective = hereditary orotic aciduria and megaloblastic anemia

Question 23

CAD complex

Answer 23

enzymes that convert glutamine + HCO3 to dihydroorotate in the cytosol portion of de novo pyrimidine synthesis

Question 24

6-mercaptopurine

Answer 24

immunosuppressant drug used for leukemia; converted to thio-IMP in the body. Allopurinol increases the efficacy.

Question 25

5-Fluorouracil

Answer 25

highly mutagenic cancer drug that is converted to 5F-UTP, 5F-dUTP, 5F-dUMP in the body which inhibits nucleotide synthesis

Question 26

Methotrexate

Answer 26

anticancer and immunosuppressant drug; a folate analog that competitively blocks DHF=>THF, which prevents purine and pyrimidine synthesis. Causes megaloblastic anemia.

Question 27

Hereditary orotic aciduria

Answer 27

defect in UMP synthase causes inability to convert orotic acid into UMP = build up of orotic acid and decreased pyrimidine synthesis = severe megaloblastic anemia and reduced growth. (treat with dietary uridine to bypass UMP synthase)