Nucleotide metabolism

Question 1

Purine and pyrimidine ring structures

how are they found in tissues

Answer 1

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)

Question 2

Purines

Answer 2

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

Question 3

Pyrimidines

Answer 3

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

Question 4

Nucleoside vs Nucleotide

Answer 4

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)

Question 5

Terminology of nucleosides and nucleotides depending on free base

Answer 5

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

Question 6

De novo synthesis of purines

Answer 6

linear pathway:
PRPP-> phosphoribosylamine (COMITTED STEP)
Phosphoribosylamine ->->-> IMP (first complete purine ring)

Branch point pathways:
IMP-> adenylosuccinate-> AMP
IMP-> XMP-> GMP

Question 7

Linear synthesis for Purine de novo pathway

Answer 7

PRPP-> phosphoribosylamine (Comitted step)
Phosphoribosylamine-»»IMP

1. base is built on ribose
2. energy costly requiring 5 ATP
3. Glutamine, glycine, and aspartate provide nitorgens
4. Formate, CO2, and glycine provide carbons

Question 8

Branch point synthesis

Answer 8

IMP-> AMP or GMP

IMP-> adenylylsuccinate-> AMP (needs 1 GTP and Asp)
IMP-> XMP-> GMP (needs ATP and Gln)

Question 9

PRPP sythetase

Answer 9

PRPP sythetase catalyzes the makeing of PRPP (from ribose) its not comitted to de novo purine synthesis bc its needed elsewhere

Question 10

ATase

Answer 10

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

Question 11

Synthesis of NDP and NTP

And the relative ratios of NMPs to NDPs to NTPs

Answer 11

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

Question 12

Regulation of De novo pathway

Answer 12

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

Question 13

Degredation and Excretion of purine nucleotides

Answer 13

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

Question 14

Xanthine Dehydrogenase/oxidase

Answer 14

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

Question 15

Hyperuricemia

Answer 15

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

Question 16

Treatment of gout

Answer 16

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)

Question 17

Xanthinuria

Answer 17

Similar to patients takin allopurinol you don’t make XDH

Xanthine also causes crystals that cause inflammation as well

Question 18

Immunodeficiency diseases

Answer 18

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

Question 19

Purine salvage pathway

Answer 19

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

Question 20

Lesch-Nyhan Syndrome

Answer 20

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`

Question 21

Pyrimidine de novo pathway

Answer 21

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)

Question 22

Carbamoyl phosphate synthetase activity of CAD

Answer 22

Carbamyl phosphate synthetase (CPS2) uses Gln

Rate limiting Step in de novo Pyrimidine

CAD has regulation via allosteric effectors and protein phosphrylation

Question 23

UMP-> UDP and UTP

Answer 23

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

Question 24

Cynthesis of CTP

Answer 24

UTP -> CTP (Using CTP synthetase) using Gln

Question 25

Degredation and excretion of pyrimidine nucleotides

Answer 25

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

Question 26

The pyrimidine salvage pathway

Answer 26

Occurs primarily at the nucleoside level

denovo uses 5 ATP but only uses 1 atp for salvage

Question 27

Ribonucleotide Reductase

Answer 27

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

Question 28

Synthesis of thymidine nucleotides

Answer 28

TMP is synthesized by thymidylate synthase using dUMP as the substrate

dUMP-> dTMP