Nucleotide metabolism

khanali9798's version from 2015-12-13 13:04



Question Answer
Purinesadenine, guanine
Pyrimidinescytosine, thymine, uracil
Pyrimidines have how many rings?1 (purine: 2)
nitrogenous base can be added to ribose at C__ positionC1
nucleoside composed ofbase + ribose
nucleotide composed ofbase + ribose, phosphorylated (mono, di, tri)
A names for base, nucleoside, nucleotideadenine, adenosine, adenylate
C names for base, nucleoside, nucleotidecytosine, cytidine, cytidylate
U names for base, nucleoside, nucleotideuracil, uridine, uridylate
T names for base, nucleoside, nucleotidethymine, thymidine, thymidylate
G names for base, nucleoside, nucleotideguanine, guanosine, guanylate



Question Answer
base attached to pentose at C__ positionC1
phosphate attached to pentose at C___ positionC5
can be hydroxyl group or -H at C___ of pentoseC2
if C2 has hydroxyl group attached, molecule is (DNA/RNA)RNA (DNA is DEOXY form)
number atoms in pyrimidine?N attached to pentose "1" - then number clockwise
number atoms in purine?N attached to pentose "9" - then number backwards going up; "top" CH is 6, number going backwards clockwise


Question Answer
adenine structure
guanine structure
cytosine structure
thymine structure
uracil structure
uracil vs. thymine?thymine has methyl group on atom 5 (uracil: hydrogen; can form imide)
adenine vs. guanine?guanine: C=O at atom 6 (where amino group is in adenine), additional amino group on atom 2

Synthesis overview


Question Answer
major difference in synthesis of purines vs. pyrimidines?when ribose added
PRPP1' activated form of ribose
in (purine/pyrimidine) synthesis, start with PRPP and build from therepurine
in (purine/pyrimidine) synthesis, build precursor nitrogenous base first, add to PRPP, modifypyrimidine
ribose 5-phosphate --ribose phosphate pyrophosphokinase + ATP--> _____5-phosphoribosyl-1-pyrophosphate (PRPP)
PRPP intermediate in biosynthesis of which molecules?Trp, His, nucleotides

Purine synthesis


Question Answer
amide N of glutamine donates which atoms of purine ring?9N, 3N
formate donates which atoms of purine ring?8C, 2C
1N of purine ring derived fromaspartate
6C of purine ring derived fromCO2
glycine donates which atoms of purine ring?7N, 4C, 5C
purine ring derived fromAAs, N10-formyl-THF, CO2


Question Answer
order of substrate molecule usage?glutamine, glycine, N10-formyl H4 folate, glutamine, CO2 (HCO3-), aspartate, N10-formyl H4 folate
energy cost?5 ATP
first step (addition of glutamine amino group, elimination of pyrophosphate - committed step) inhibited byGMP, AMP, IMP
what is IMP?intermediate in AMP/GMP synthesis
branch point of synthesis?IMP formation
AMP formation from IMP requires an input of energy in the form ofGTP (lots of GTP, want to favor AMP branch)
GMP from IMP requires an input of energy in the form ofATP (lots of ATP, want to favor GMP branch)
first step of AMP formation after branch point: regulation?AMP inhibits enzyme
first step of GMP formation after branch point: regulation?GMP inhibits enzyme

Pyrimidine synthesis


Question Answer
pyrimidine ring atoms derived from which molecules?aspartate, carbamoyl phosphate
carbamoyl phosphate donates which atoms to ring?2C, 3N
aspartate donates which atoms to ring?1N, 3C, 4C, 5C
carbamoyl phosphate synthesized by?cytoplasmic CPS II
carbamoyl phosphate is from same pool as in urea cycle (Y/N)no - from cytosolic pool; ONLY used for pyrimidine synthesis (formed from CPS II vs. CPS I)


Question Answer
precursor base?orotate
what is added to PRPP?orotate
N donated by carbamoyl phosphate fromGln residue of CPS II (side-chain)
# active sites in CPS II?3
orotidylate converted to which nucleotide?UMP (uridylate)
CTP formed from ____ with input of ATP, glutamineUTP (carbonyl group of UTP converted to amino group)
why is it necessary to form triphosphorylated nucleoside (UTP) instead of just using UMP?enzyme that catalyzes UTP -> CTP reaction can only use UTP as substrate


Question Answer
commitment step of pyrimidine synthesis?addition of carbamoyl phosphate to aspartate
what enzyme catalyzes addition of carbamoyl phosphate to aspartate?aspartate trans-carbamoylase
regulation of aspartate trans-carbamoylase?CTP inhibits: raise apparent K0.5, ATP inhibits CTP (ATP + CTP: essentially normal activity)
logic behind restoration of normal ATCase activity in presence of ATPATP is purine - if have lots of purines, need pyrimidines for pairing; end goal to make DNA, need balance
generally, which nucleotide has higher levels in cell?ATP (also used in energy transfer reactions)


Question Answer
ATP + AMP <---_____---> 2 ADPadenylate kinase
ATP + NMP <---_____---> ADP + NDPnucleoside monophosphate kinases
ATP + NDP <---_____---> ADP + NTPnucleoside diphosphate kinase
phosphate donator?ATP

Formation of deoxynucleotides


Question Answer
enzyme that converts nucleotides to deoxy forms?ribonucleotide reductase
NDP ---> dNDP in ____ reactionreduction
ribonucleotide reductase requires (mono/di/tri)phosphorylated substratedi
ribonucleptide reductase required cofactorNADPH
flow of electrons from NADPH -> dNDP?two possible pathways: (a) NADPH -> 2GSH -> glutaredoxin -> ribonucleotide reductase -> dNDP; (b) NADPH -> FADH2 -> thioredoxin -> ribonucleotide reductase -> dNDP
possible electron donators to ribonucleotide reductaseglutaredoxin, thioredoxin
group oxidized in glutaredoxin and thioredoxin?two thiol (-SH) groups from cysteine residues --> disulfide bond


Question Answer
ribonucleotide reductase subunitsregulatory dimer (R1), catalytic (R2)
why is catalytic activity of ribonucleotide reductase interesting?involves free radical chem
____ of ribonucleotide reductase reduces the substratesulfhydryl pair (-SH)
free radical component?tyrosyl (Ar-O.)
how is free radical component stabilized?proximal Fe3+-O-Fe3+
regulation of ribonucleotide reductasereg to select for specific substrate (substrate-specificity sites), reg to modulate activity (primary regulatory site)
substrate regulation of ribonucleotide reductasedTTP: higher preference for dGTP formation; dGTP: higher pref for dATP formation; overall, lots of purines = activate for pyrimidine
ATP regulation of ribonucleotide reductaseindicator of energy charge; lots of ATP, activate enzyme
dATP regulation of ribonucleotide reductaseinhibit enzyme (feedback inhibition)


Question Answer
in first step of reaction mechanism, tyrosyl donates electron to ____3' C of pentose (formation of 3'-ribonucleotide)
in second step of rxn mxn, 2' is _____ by thiol group of cysteine residueprotonated; formation of great leaving group (+OH2)
in third step of rxn mxn, water is eliminated, forming ____radical-stabilized carbocation (radical on 3C)
in fourth step of rxn mxn, ____ is oxidized, and electrons are transferred to the ____ carbondithiol (disulfide linkage formed); 2C (where carbocation was)
final step of rxn mxnreversal of step one - tyrosyl regenerated (free radical)

dTMP formation


Question Answer
dTMP synthesized from?dUMP
dUMP --____---> dTMPthymidylate synthase
must convert dUTP to ____ for thymidylate synthase actiondUMP
thymidylate synthase carries out (reaction type)one-carbon transfer
thymidylate synthase cofactorPLP (serine --> glycine; CH2 added to THF in methylene form, then to 4N of dUMP with proton from THF)
source of methyl group added to dUMP?methylene from serine --> THF; proton from THF
fate of THF molecule after carbon transfer to dUMP?dihydrofolate form bad, must be reduced back to THF (gets proton from NADPH)


Question Answer
clinical importance of thymidylate synthase?target for chemotherapeutic agents (disrupt synthesis of DNA, no effect on RNA)
fluorouracil--> uracil, inhibits thymidylate synthase
methotrexateinhibits dihydrogolate reductase (can't regenerate THF) - same action as aminopterin, trimethoprim
glutamine analogspotent chemotherapeutics, inhibit glutamine amidotransferases (azaserine, acivicin) - can't synthesize DNA, RNA precursors (adenine, guanine, cytosine)

Nucleotide degradation


Question Answer
nucleotide --> nucleoside general strategy?removal of 5'-phosphate
nucleoside --> free base general strategy?removal of ribose
fate of degraded purinesuric acid --> excreted
AMP degradation--> adenosine --> inosine --> hypoxanthine --> xanthine --> uric acid
GMP degradation--> guanosine --> guanine --> xanthine --> uric acid
overproduction of uric acid causesgout


Question Answer
fate of degraded pyrimidines--> urea (from N); --> Succ-CoA (TCA) (from carbons); ! not primary source of energy, just way to deal with excess nucleotides
CMP degradation--> cytidine --> uridine --> uracil
UMP degradation--> uridine --> uracil
dTMP degradationthymidine --> thymine


Question Answer
recycle free bases?via salvage pathways (combine directly with PRPP vs. de novo synthesis)
AMP regenerationadenine + PRPP via APRT
IMP regenerationhypoxanthine + PRPP via HGPRT
GMP regenerationguanine + PRPP via HGPRT