Nucleotide metabolism Flashcards
Purine and pyrimidine ring structures
how are they found in tissues
Purines are double rings with N groups at 1, 7, 9, 3
Pyrimidines are single rings with N groups at 3 and 1
They are found in tissues as:
Free bases
Nucleosides (base+sugar) (via glycosidic linkage)
Nucleotides (Base+ sugar + phosphate) (via ester)
Purines
PUR As Gold with X and HX (I)
* you need to have an O before you can put an amine group so HX serves as the precursor
Purines differ at the 6 and 2 position Hypoxanthine: has an O at pos 6 Xanthine: has Os at positions 2 and 6 Adenine: only has an NH2 at position 6 Guanine: has NH2 group at position 2 and and an O at position 6
HX> X
HX> A
HX> X> G
Pyrimidines
CUT the PY
they differ at position 4 and 5
They all have an O at the 2 position
Again you need an O before you can make an NH2
Uracil has an O at 4
Cytosine has an NH2 at 4
Thymine has an O at 4 but a CH3 at 5
Uracil is the building block for pyrimidines
U-> C
U-> T
Nucleoside vs Nucleotide
Nucleoside: a pentose sugar attached to free base via glycosidic linkage (Can be oxy or deoxy ribose at 2’)
Nucleotide: a phosphate (or 2 or 3) is added to the nucleoside
Ribonucleoside-5’- MONO/ DI/ TRI phosphate (NM/D/TP)
Terminology of nucleosides and nucleotides depending on free base
BASE—-NUCLEOSIDE—NUCLEOTIDE
Adenine—adenosine—adenylic acid or AMP
Guanine—guanisine—guanylic acid or GMP
Hypoxanthine—ionosine—ionisinic acid or IMP
Xanthine—xanthinosine—xanthynic acid or XMP
Uracil—Uridine—Uridylic acid or UMP
Cytosine—Cytidine—Cytidylic Acid or CMP
Thymine—thymidine—Thydylic Acid or TMP
De novo synthesis of purines
linear pathway:
PRPP-> phosphoribosylamine (COMITTED STEP)
Phosphoribosylamine ->->-> IMP (first complete purine ring)
Branch point pathways:
IMP-> adenylosuccinate-> AMP
IMP-> XMP-> GMP
Linear synthesis for Purine de novo pathway
PRPP-> phosphoribosylamine (Comitted step)
Phosphoribosylamine-»»IMP
- base is built on ribose
- energy costly requiring 5 ATP
- Glutamine, glycine, and aspartate provide nitorgens
- Formate, CO2, and glycine provide carbons
Branch point synthesis
IMP-> AMP or GMP
IMP-> adenylylsuccinate-> AMP (needs 1 GTP and Asp)
IMP-> XMP-> GMP (needs ATP and Gln)
PRPP sythetase
PRPP sythetase catalyzes the makeing of PRPP (from ribose) its not comitted to de novo purine synthesis bc its needed elsewhere
ATase
ATase catalyzes PRPP-> phosphoribosylamine
IE THE FIRST COMITTED sTEP in DE NOVE PURINE and THE RATE LIMITING STEP
ATase is allosterically regulated by PRPP and end products of the de novo pathway
when lots of PRPP, ATase active O O
When lots of IMP/GMP/AMP, ATase inactive 00
Synthesis of NDP and NTP
And the relative ratios of NMPs to NDPs to NTPs
NMP to NDP needs a Base specific monophosphate kinase
- adenylate kinase or guanylate kinase
NDP to NTP has broad specificity
- nucleoside diphosphate kinase
adenylate kinase keeps is in equilibrium and keeps the ratios at 100x ATP, 10x ADP, 1x AMP
Regulation of De novo pathway
Feedback Regulation: End products (IMP, A MDT P, G MDT P) will inhibit PRPP synthetase, ATase, and their respective specific branch point pathway catalysts
Cross Regulation:
GTP will increase adenylosuccinate synthetase to make more AMP
ATP will increase IMP dehydrogynase to make more XMP to make more GMP
Degredation and Excretion of purine nucleotides
You need to Dephosphorylate, Deaminate, and Phosphorolysis
AMP has two degradations: Adenosine and IMP
In heart ichemia/anoxia adenosine is a vasodialator to bring O 2 back to heart tissue
In vigorous exersize muscle, IMP facilitates resythesis of ATP
Xanthine Dehydrogenase/oxidase
XDH XO convert hypoxanthine to xanthine and then to uric acid
XO is used in low oxygen conditions and uses molecular Oxygen and makes free radicals
Hyperuricemia
Caused by too much Uric acid production or too little excretion
Uric acid is not very soluble, so it causes cyrstylization in tissues causing inflammation and gout
Primary Gout: Over expression of PRPP synthetase, deficiency in HPRT/HGPRT enzyme, defects in renal urate transport proteins (most common)
Secondary Gout: Drug intake or unusual diet
Treatment of gout
Goal: lower the level of uric acid, you can targed XDH to stop making Urate/Uric acid
Use allopurinol to inhibit XDH
(issue- feedback loops will increase the salvage pathway and make too much end products and that will turn off de novo via ATase)
Xanthinuria
Similar to patients takin allopurinol you don’t make XDH
Xanthine also causes crystals that cause inflammation as well
Immunodeficiency diseases
Catabolic pathway issues
Adenosine deaminase deficiency: associated with SCID (bubble boy, T and B cell dysfunction)
Purine nucleoside phosphorylase PNP-> T cell dysfunction
These lead to an increase in dNTP levels in lymphocytes which inhibit Ribonucleotide reductase (RR) that messes up DNA synthesis and cell division
Purine salvage pathway
because de novo is so energy costly purine rings released in ciculation are recycled by two different mechanisms
Recycling a free base:
Uses PRPP
Adenine+PRPP-> AMP and PPi using APRT
HX, X, G +PRPP -> IMP, XMP, GMP using HPRT
REcycling a nucleoside uses ATP and a kinase
Adenosine + ATP-> AMP and ADP (using adenosine kinase)
Guanosine + ATP -> GMP and GDP (using guanosine kinase)
only 10% of catabolized purine nucleotides are excreted as uric acid 90 is salvaged
Salavage is the normal major pathway of purine nucleotide synthesis
Lesch-Nyhan Syndrome
HPRT is lacking or low
X chromosome linked (mostly guys get it)
They get gout because of the excess uric acid
Low PRPP synthetase and ATase inhibitions, so lots of de novo synthesis
They get neuro ssymptoms because the brain uses a lot more HPRT and the high levels of purines metabolites are toxic to the brain`
Pyrimidine de novo pathway
6 enzymatic reactions mediated by 3 gene products
CAD, DOHDH, and UMP synthase
need to start off with UMP
Use Gln, Asp and CO2 (essentially purine minus the formate and gly)
Carbamoyl phosphate synthetase activity of CAD
Carbamyl phosphate synthetase (CPS2) uses Gln
Rate limiting Step in de novo Pyrimidine
CAD has regulation via allosteric effectors and protein phosphrylation
UMP-> UDP and UTP
You need to make UMP before other pyrimidines,
But to make the other pyrimidines, you need to convert UMP to UDP or UTP
UMP + ATP -> UDP + ADP (using Pyrimidine monophosphate kinase) * specific
UDP +ATP-> UTP + ADP (using the nucleoside kinase) * Broad
Cynthesis of CTP
UTP -> CTP (Using CTP synthetase) using Gln
Degredation and excretion of pyrimidine nucleotides
Same Steps as Purines, Dephosphorylation, Deamination and Phosphorolysis
C is always turned into Uracil
Uracil and Thymine under go further catalysis to make amino acids by the same enzymes
The pyrimidine salvage pathway
Occurs primarily at the nucleoside level
denovo uses 5 ATP but only uses 1 atp for salvage
Ribonucleotide Reductase
To make any ribonucleotide you take an NDP -> dNDP (using RR_ then phosphorylate to make dNTP
activity is allosterically regulated by dNTP, so too much dNTP will stop RR (ADA deficiency
Synthesis of thymidine nucleotides
TMP is synthesized by thymidylate synthase using dUMP as the substrate
dUMP-> dTMP
