Purine and Pyrimidine Metabolism Flashcards Preview

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Flashcards in Purine and Pyrimidine Metabolism Deck (39):
1

Maybe know the structures of the amino acids

Actually yeah know them
Guanine and Adenine are purines. Adenine has an amine on carbon 6. Guanine has a ketone on carbon 6 (and an amine on carbon 2). The other ring is five carbons (three more).
Cytosine, Uracil, and Thymine are pyrimidines. Uracil has two ketones in the carbon 2 and 4 places. Cytosine has a ketone at carbon 2 and an amine at carbon 4. Thymine is basically uracil (ketone at carbons 2 and 4) with a methyl group at carbon 5.

2

Difference between deoxyribose and ribose

ribose has OH group at 2' carbon

3

Starting material for purines

ribose-5-phosphate (build on the purine base)

Glycine, 2 Glutamine amides, and an aspartate amino combined with bicarbonate, and two C1-H4folate. Requires 6 ATP and 5-phosphoribosyl-1-pyrophosphate (PRPP)

4

Starting material for pyrimidine

synthesize pyrimidine ring and then attache the ribose-5-phosphate

5

Rate-limiting step of purine synthesis

Glutamine:phosphoribosyl amidotransferase (or amido phosphoribosyl transferase)
Converts PRPP (5-phosphoribosyl-1-pyrophosphate), water, and glutamine into Glutamate, pyrophosphate, and 4-phosphoribosyl 1-amine

6

What is required for de novo synthesis of a purine?

Glutamine and PRPP become 5'-phosphoribosylamine
ATP and Glycine
Formyl-THF
ATP and Glutamine
ATP
CO2
ATP and Aspartate
Formyl-THF
(So 4 ATP, 2 Formyl-THF, Glycine, Glutamine, Aspartate, and CO2 forms IMP)
Then GTP and Aspartate is used to make AMP
and ATP and Glutamine is used to make GMP

7

What regulates purine nucleotide synthesis?

PRPP synthetase is inhibited by ADP and GDP
Glutamine phosphoribosyl amido transferase is inhibited by GMP and AMP
IMP dehydrogenase is inhibited by GMP
Adenylosuccinate synthetase is inhibited by AMP

8

True or false: De novo synthesis requires less ATP than the salvage pathway.

False

9

Describe the salvage pathway for purine synthesis

There are two pathways
There is a hypoxanthine-guanine phosphoribosyl transferase pathway (HGPRTase)
(It uses hypoxanthine or guanine and PRPP (5-phosphoribosyl-1-pyrophosphate)
(Makes GMP or IMP and pyrophosphate)

The other pathway uses adenine phosphoribosyltransferase (APRTase), which uses adenine and PRPP to make AMP and pyrophosphate

10

Defective protein in Lesch-Nyhan disease?

HGPRT (Hypoxanthine-guanine phosphoribosyl transferase) (Complete lack of protein)

11

Deficiency of adenosine deaminase can cause?

SCID (Severe combined immunodeficiency)
(No B or T cells)
Causes accumulation of dATP in lymphocytes, which inhibits ribonucleotide reductase

12

Deficiency of purine nucleoside causes?

Lack of T cells
(No degradation of inosines and guanosines to free bases)
(Nucleosides accumulate)

13

What would you see an increase of in those with Lesch-Nyhan disease?

Xanthine and Uric acid (the end product of hypoxanthine and guanine)

14

Regulation of Purine salvage pathway

HGRPTase inhibited by IMP and GMP. APRTase inhibited by AMP
(AMP and GMP also inhibits de novo synthesis pathway. The use of PRPP also reduces de novo synthesis pathway.)

15

What disease is related to lack of HGPRTase?

Lesch-Nyhan disease

16

Description of entirety of Lesch-Nyhan disease

Complete lack of HGPRT
X-linked (males affected)
No salvage pathway, increased uric acid, greater de novo purine synthesis
Severe neurological disease and urate nephrolithiasis (kidney damage)
Hyperuricemia

Left untreated, death in first decade. Treated with allopurinol (competitive inhibitor of xanthine oxidase) (allopurinol prevents nephropathy but does not affect neurological or behavior symptoms)

17

What does allopurinol do?

Inhibits xanthine oxidase, results in buildup up hypoxanthine and xanthine

18

In de novo pyrimidine synthesis, the carbons and nitrogens come from?

The carbons ( and one nitrogen) come from aspartate and the other nitrogen comes from glutamine amide. One other carbon comes from bicarbonate ion.

19

Pyrimidine synthesis process

nitrogenous base assembled, then sugar and phosphate added. Nitrogenous base comes from aspartate, glutamine, and bicarbonate ion

carbamoyl phosphate synthetase takes glutamine, carbon dioxide, and two ATP to create 2 ADP, glutamate, phosphate, and carbamoyl phosphate. That is converted to N-carbamoyl aspartate, then hihydroorotate, orotate, and then OMP (Orotidine 5'-mono-phosphate). Orotidine 5'-mono-phosphate decarboxylase converts it to UMP, which is converted to UTP and then CTP.

20

Stuff to know about carbamoyl phosphate synthetase

CPSII is cytoplasmic. It uses nitrogen from glutamine. It is activated by PRPP (5-phosphoribosyl-1-pyrophosphate). It is inhibited by UTP

(CPSI is in mitochondria and uses ammonia as a an amino acid source)

21

Hereditary orotic aciduria

results from deficiency in orotate phosphoribosyl transferase or OMP decarboxylase. Treated with uridine (nucleoside, because de novo synthesis not possible).

22

What makes NDPs?

nucleoside monophosphate kinases (adenylate kinase or guanylate kinase

23

What protein makes NTPs?

nucleoside diphosphate kinase

24

True or false: Ribonucleotides are precursors of deoxyribonucleotides.

True

25

Steps of deoxyribonucleotide synthesis

1. Ribonucleotide reductase (rate-limiting)
2. Nucleoside 5'-diphosphate kinase
3. Deoxycytidylate deaminase
4. Thymidylate synthase
5. DNA polymerase

26

True or false: Thymine exists only in deoxy form.

True

27

True or false: Deoxyribonucleotides are toxic to nonproliferating cells.

True

28

Things to know about ribonucleotide reductase

Requires thioredoxin, reduces all four NDPs to dNDPs

Two allosteric sites, one controls activity, one controls specificity

ATP activates enzyme, dATP inhibits enzyme

Substrate specificity regulation is complex. Effector site binding affects preferred substrate in an effort to balance production of all four dNDPs

29

dTMP synthesis

from dUMP, FH4 is the single carbon donor and a reducing agent

Thymidylate synthase converts dUMP to dTMP using FH4 (N5,N10-tetrahydrofolate)

Inhibited by fluoracil

30

Dihydrofolate Reductase

target for anti-cancer drugs. Converts dihydrofolate to tetrahydrofolate. Aminopterin and methotrexate (amethopterin) inhibit dihydrofolate reductase.

31

Pyrimidine degradation

Uracil is degraded to beta-alanine. (converted to dihydrouracil and beta-ureidopropionate first)
Thymine is degraded to beta-aminoisobutyrate (converted to dihydrothymine and beta-ureidoisobutyrate first)

32

Beta-aminoisobutyrate

excreted in urine, exclusively from thymine, measure to estimate DNA turnover, increases in cancer patients receiving chemotherapy or radiation due to cell death and DNA degradation

33

5-fluoracil

Chemotherapeutic agent. Treats solid tumors.
Active species: 5-fluoridine 5'triphosphate FUTP (incorporated into RNA, inhibits maturation of 48S precursor rRNA into 28S and 18S rRNA)
FdUMP (potent inhibitor of thymidylate synthase (inhibits dUMP to dTMP synthesis), dUMP is incorporated into DNA and attempts to remove and repair causes DNA breaks)

34

Cytosine Arabinoside

Antileukemic, 5' triphosphate incorporates into DNA, inhibits synthesis of growing DNA strand

35

Antifolates

Inhibit tetrahydrofolate formation

methotrexate treats human cancers, inhibits dihydrofolate reductase. Toxic unless supplemented with thymidine and hypoxanthine

In leukemia treatment, normal cells are rescued from the toxic effects of high-dose methotrexate by N5-formyl-FH4 (leucovorin), increasing clinical efficacy of methotrexate treatment

36

hydroxyurea

specific inhibition of DNA synthesis without inhibiting RNA or protein synthesis
Acts on ribonucleotide reductase
Limited clinical use due to rapid rate of clearance and the high drug concentrations required for effective inhibition

37

Purine analogs as anti-viral agents

acyclovir:
acycloguanosine (purine analog)
activated to the monophosphate by a viral kinase (HSV-thymidine kinase) (mamalian thymidine kinase can't use as a substrate)
The triphosphate form is a substrate for the HSV-specific DNA polymerase (Causes DNA chain termination of viral gene products)

Ganciclovir (purine analog)
same mechanism as acyclovir, used to treat cytomegalovirus infections in HIV patients

38

Pyrimidine analogs as anti-virals

AZT: Azido-d'-deoxythymidine (pyrimidine analog)
phosphorylated by cellular kinases
Blocks HIV replication by inhibiting HIV-DNA polymerase (an RNA-dependent polymerase)
The HIV polymerase is >100x more sensitive than host

DDI (2',3'-dideoxyinosine) - another pyrimidine analog with chain termination mechanism

39

Fialuridine

FIAU 1-(2-deoxy-2-fluoro-arabinosyl)-5-iodouracil was developed as an anti-viral against hepatitis B virus
5/15 patients died of liver failure in clinical trial
Incorporated into mitochondrial DNA via DNA polymerase gamma, prevents mitochondrial division
Lactic acidosis due to increased anaerobic glycolysis
No side effects detected in animal studies
Led to analysis of clinical trials rules