Pyrimidine Nucleotide Synthesis

Question 1

What is the precursor for denovo synthesis of pyrimidines?

Answer 1

PRPP

Question 2

How does pyrimidine synthesis differ from purine synthesis?

Answer 2

Pyrimidine base is synthesized prior to attachment to ribose sugar

Question 3

Where do the nitrogens in pyrimidine synthesis come from?

Answer 3

Glutamine and aspartate

Question 4

Into what molecule is the amine from glutamine incorporated?

Answer 4

Carbamoyl phosphate

Question 5

How is orotate formed?

Answer 5

Carbamoyl phosphate is covalently linked to aspartate, then the molecule cyclizes

Question 6

What is produced when orotate reacts with PRPP?

Answer 6

OMP (pyrimidine nucleotide)

Question 7

What enzyme generates carbamoyl phosphate? What are the reactants?

Answer 7

ATP, HCO3-, and glutamine are reacted by carbamoyl phosphate synthetase II to form carbamoyl phosphate

Question 8

What enzyme links carbamoyl phosphate to aspartate?

Answer 8

Aspartate transcarbamoylase

Question 9

What enzyme catalyzes pyrimidine ring closure?

Answer 9

Dihydroorotase

Question 10

What do carbamoyl phosphate synthetase II, aspartate transcarbamoylase, and dihydroorotase have in common?

Answer 10

All encoded by the same polypeptide

Question 11

How is OMP converted to UMP?

Answer 11

Decarboxylation

Question 12

How is CTP synthesized?

Answer 12

UMP + ATP -> UDP + ADP
UDP + ATP -> UTP + ADP

CTP is generated from UTP by accepting amide nitrogen from glutamine

Question 13

How does CTP regulate pyrimidine synthesis?

Answer 13

Negative feedback

CTP allosterically inhibits aspartate transcarbamoylase

Remember…what does this enzyme do?

Question 14

How does the pyrimidine salvage pathway differ from de novo?

Answer 14

No common precursor with denovo

Use different sugars based on what you want to synthesize

ribose-1-phosphate (for C or U)

deoxyribose-1-phosphate (for T)

pyrimidine base reacts to form nucleoside

kinase phosphorylates nucleoside to make nucleotide

Question 15

How are deoxyribonucleotides synthesized?

Answer 15

Reduce ribonucleotides to deoxyribonucleotides using ribonucleotide reductase

Question 16

What are the substrates and products for ribonucleotide reductase?

Answer 16

NDPs (e.g. CDP) and products are dNDPs (e.g. dCDP)

Question 17

Where do the electrons used to reduce NDPs come from?

Answer 17

NADPH

Question 18

How is deoxyribonucleotide production regulated?

Answer 18

dATP binds ribonucleotide reducatse to inhibit

other dNTPs bind to ribonucleotide reductase to alter substrate specificity–mechanism to balance nucleotide production

Question 19

What is oxidized when ribonucleotides are reduced?

Answer 19

Thioredoxin

Question 20

How is thioredoxin reduced? What is oxidized during this process?

Answer 20

Thioredoxin reductase

NADPH is oxidized

Question 21

How are dNTPs produced?

Answer 21

Phosphorylation of dNDPs

Question 22

How is uracil prevented from being incorporated into DNA?

Answer 22

dUDP is dephosphorylated to form dUMP

dUMP is methylated to form dTMP, which is phosphorylated to form dTDP and dTTP

Question 23

What enzyme generates dTTP from dUMP? Where does the carbon that is added come from?

Answer 23

Thymidylate synthase

THF

Question 24

What is 5-fluorouracil? How does it work?

Answer 24

Structure similar to uracil–can be converted into a nucleotide

Inhibits thymidylate synthase (what does this do?)

Anti-cancer drug–prevents DNA synthesis

Question 25

What is methotrexate? How does it work?

Answer 25

Another anti-cancer drug

Inhibits DHFR–this prevents formation of folate–which prevents DNA synthesis

Question 26

What is gemcitabine? How does it work?

Answer 26

Pyrimidine ring analogue–can be converted into nucleotide diphosphate mimic

Suicide inhibitor of ribonucleotide reductase–makes enzyme nonfunctional

Another anti-cancer drug–prevents DNA synthesis

Question 27

Methotrexate reduces the production of which nucleotides? Why?

Answer 27

AMP, GMP, and dTMP

Inhibits DHFR, which prevents 1-carbon transfers