Nucleotide Metabolism

Question 1

nucleoSIDE

Answer 1

ribose ring + nitrogenous base at 1’

Question 2

nucleoTIDE

Answer 2

nucleoside + phosphate esterified at 5’

Question 3

deoxyribonucledotides

Answer 3

have H instead of OH at 2’ of ribose ring

Question 4

pyrimidine

Answer 4

one ring w/ 2 nitrogens

cut of py

Question 5

purine

Answer 5

two ring structure each w/ 2 N’s

pur as gold

Question 6

roles of nucleotides

Answer 6

1. energy metabolism (ATP, GTP)
2. nucleic acids (NTPs and dNTPs)
3. coenzymes (NAD, FAD, coA)
4. activated intermediates (UDP-glucose, GDP-mannose, SAM)
5. allosteric modulators (AMP, ATP, cAMP, cGMP)
6. physiological modulators (ADP, adenosine)

Question 7

salvage pathways

what it do

Answer 7

allow generation of nucleotides from free bases and nucleosides from diet

since de novo synthesis energetically expensive

Question 8

de novo synthesis

purines-basic

Answer 8

ring strucutre assembled on a base (PRPP)

Question 9

de novo synthesis

purine pathway

Answer 9

1. assemble PRPP, start w/ ribose-5-phosphate from PPP, w/ PRPP synthetase
2. committed step, convert to PRA using glutamine
3. make IMP w/ carbons and nitrogens from amino acids, carbon and oxygen from HCO3-, carbon from N10formyl THF, ATP hydrolysis
4. convert IMP to AMP or GMP
5. convert to ATP and GTP w/ NMPs aka adenylate kinase or guanylate kinase

GTP and ATP are readily interconverted

Question 10

regulation of purine synthesis

Answer 10

1. PRPP synthetase, feedback inhibition by ADP and GDP
2. commited step (amidophosphoribosyltransferase) aka PRA by allosteric effectors
   -inhibitors: AMP and GMP bc end prodcuts
   -activators: PRPP

ADP and GDP are the purine nucleotides

Question 11

purine degradation

GMP

Answer 11

@ liver
1. GMP to guanosine via 5’nucleotidase removing P
2. convert to free base (guanine) via purine nucleoside phosphorylase removing ribose

GMP>guanosine>guanine

Question 12

purine degradation

AMP

Answer 12

route 1:
1. AMP to adenosine via 5’-nucleotidase remove P
2. convert to inosine via adenosine deaminase
3. convert to free base hypoxanthine via pruine nucleoside phosphorylase removing ribose

route 2:
1. AMP to IMP via AMP deaminase
2. IMP to inosine via 5’-nucleotidase dephosphorylating
3. convert to hypoxanthine via purine nucleoside phosphorylase

adenosine deaminase = lymphocytes
AMP deaminase = muscle

Question 13

purine degradation

final steps

Answer 13

1. hypoxanthine and guanine converted to xanthine
2. xanthine oxidase converts it to uric acid
3. excreted via kidneys

Question 14

hyperuricemia

Answer 14

excess uric acid in blood
from reduced excretion (renal insufficiency, metabolic acidosis)
OR
inc production (inc nucleotide turnover aka sickle cell, G6DP deficiency, chemo, or purine rich diet)

alcohol does both

treat w/ allopurinol

Question 15

gout

Answer 15

crystals of sodium urate deposit in joints of extremities (esp first toe)

bc uric acid is relatively insoluble and close to limit of solubility normally

treat with allopurinol

Question 16

kidney stones

Answer 16

high concentrations of uric acid in urine lead to deposition of stones in kidney aka urolithiasis

10-25% ppl with gout also have stones

Question 17

allopurinol

Answer 17

effective treatment for hyperuricemia
metabolizes to oxypurinol that competitively inhibits xanthine oxidase
=more hypoxanthine and xanthine that are more soluble than uric acid so excreted easier

Question 18

de novo synthesis

pyrimidines-basic

Answer 18

start as synthesis of free bases then get transferred to ribose

Question 19

synthesis of UMP

first pyrimidine made

Answer 19

1. syn carbamoyl phosphate w/ glutamine + bicarb
2. carbamoyl aspartate by adding aspartate
3. cyclization = dihydroorotate
4. dehydrogenation = orotate
5. syn OMP w/ PRPP
6. decarboxylate = UMP

Question 20

CAD

Answer 20

single multifunctional protein w/ 3 distinct active sites for steps 1/2/3 of pryrimidine syn

Carbamoyl phosphate synthetase II
Aspartate transcarbamoylase
Dihydroorotase

Question 21

UMP synthase

Answer 21

single multifunctional protein for last two steps of pyrimidine syn

orotate phosphoribosyltransferase
OMP decarboxylase

Question 22

orotic aciduria

Answer 22

defect in UMP synthase so orotic acid accumlates in urine

symptoms of megaloblastic anemia and maybe cellular immunity

treat w/ pyrimidine supplement (uridine)

Question 23

synthesis of CMP

Answer 23

1. UMP to UTP w/NMP
2. UTP to CTP w/CTP synthase and glutamine

Question 24

regulation of pryimidine

Answer 24

1. carbamoyl phosphate synthetase II
   -inhibited by UTP
   -activated by PRPP
2. CTP synthase
   -inhibited by CTP
   -activated by UTP

Question 25

deoxyribonucleotide synthesis

Answer 25

triggered by cell division bc require DNA NDP to dNDP via ribonucleotide reductase and thioredoxin oxidation regulated by allosteric effectors -specific NTP or dNTP for reduction of a NDP= positive effector -some dNTPs potent negative effectors aka dTNP | NTP and dNTPs regulate ribonucleotide reductase and dATP key inhibitor

Question 26

hydroxyurea

Answer 26

pharmacological inhibitor of ribonucleotide reductase blocks activity so no dNTP synthesis so no cell division | chemotherapy

Question 27

SCID | severe combined immuodeficiency

Answer 27

mutations in adenosine deaminase (purine degradation) = build up adenine metabolites aka dATP ribonucleotide reductase activity inhibited so all purine/pyrimidine conversion to dNDPs blocked immune response requires cell proliferation so inhibited from lack of dNTPs adenine metabolites toxic for immune system

Question 28

synthesis of dTMPs

Answer 28

must come from dUMP via thymidylate synthase = dTMP -uses N5N10-methylene THF dTMP kinase converts to dTDP

Question 29

cytotoxic therapy

Answer 29

inhibit thymidylate synthase = prevent cell proliferation bc dec dTTP available 5-fluorouracil>FUMP>FUDP>FUTP or FdUDP>FdUMP = irreversible inhibition lack of dTTP = dUTP and FdUTP in DNA instead = strand breakage and death

Question 30

pyrimidine degradation

Answer 30

UMP, CMP, dCMP > beta-alanine (>acteyl CoA) dTMP > beta-aminoisobutyrate (>succinyl CoA) both betas water soluble so eliminated in urine OR further metabolized | beta-amino unique to thymine degradation so measures DNA turnover

Question 31

salvage pathways | liver

Answer 31

converts nucleotides to nucleosides and free bases > enter blood > tissues via RBCs

Question 32

salvage pathways | diet

Answer 32

1. nucleic acids DNA/RNa in food digested by pancreatic nucleases = free nucleotide 2. convert to nucleosides via phosphatases and taken up by intestinal epithelial cells nucleosides and free basees precursors for nucleotide synthesis

Question 33

salvage of purines

Answer 33

requires 1. HGPRTase for hyposxanthine and guanine 2. APRTase for adenine plus PRPP = IMP (hypox) or GMP (guanine and adenine) product inhibition | only adenosine only nucleoside directly phos to nucleotide AMP

Question 34

lesch-nyhan syndrome

Answer 34

hyperuricemia, uric acid stones, intellectual diability, self-injurious/destructive biting of fingers and lips severe or complete deficiency of HGPRTase activity

Question 35

salvage of pyrimidines

Answer 35

pyrimidine phosphoribosyltransferase uracil + PRPP = UMP orotate + PRPP = OMP conversion to nucleotides via uridine-cytidine kinase