Week 3 - Nucleotide Metabolism Flashcards
What are purine bases?
Adenine (A), Guanine (G)
What are pyrimidine bases?
Cytocine (C), Thymine (T)
What is structure of a nucleotide?
Pic.. Always leaves free hydroxyl group on 3’ end.
What are other bases and nucleosides?
What are nucleotide functions?
DNA RNA
Handles for enzyme cofactors
Energizing Substrates
Second Messagers
Allosteric Activators
Nucleotide ‘Handles’ for enzyme cofactors:
CoASH
NAD+
FAD
Adenosylcobalamin
Nucleotide Energizing Substrates
UDP-glucose
CDP-choline
Nucleotide Second Messangers
cAMP
Nucleotide Allosteric activators
AMP
ADP
ATP
Initial steps for Nucleotide synthesis:
Different for purines and pyridamines.
Both use same substrate which is synthesized from glucose in the pentose phosphate pathway to make Ribose 5-phosphste.
R5P is then phosphorylated to 5 Phosphoribosyl 1-pyrophosphate (PRPP) by PRPP synthase and ATP
From there purines and pyrimadines can be synthesized
What is common substrate for both purines and pyrimidines? Draw the reaction. What is it inhibited by?
PRPP This is key regulatory step for nucleotide synthesis.
Inhibited by GDP and ADP
What is enzyme to turn Ribose - 5-phosphate into PRPP? What energy does it use? What inhibits it?
PRPP synthetase ATP to ADP GDP and ADP
Purine Metabolism vs Pyridamine Metabolism
Puring starts with PRPP, builds it up from there..
Pyrimadine - base is assembled THEN tranferred onto PRPP…
What are the first two steps in purine metablolism from PRPP? Where is the carbon and nitrogen from? Where does the energy come from?
The first committed step in purine synthesis is the transfer of an amine from glutamine by the glutamine phosphoribosyl aminotransferase with the addition of water
The second step is the addition of glycine to make glycinamide ribosyl 5-phosphate (powered by ATP).
In order to form IMP in purine synthesis, where is the carbon and nitrogen from?
Carbon and nitrogen are added from tetrahydrofolate, carbon dioxide, glutamine and aspartate to form inosine monophosphate (IMP).
What is IMP? What is it turned into?
Inosine Monophosphate. It is the first monophosphate formed in purine synthesis. It can be turned into AMP and GMP which can be further turned into ADP, ATP, GDP, GTP (for RNA synthesis) and the dexoy ADP, dATP, dGDP, and dGTP (for DNA synthesis)
Reaction from IMP to AMP.
Similar to the amine transfer in the Urea Cycle…
Aspartate bonds to IMP to make adenylosuccinate, then fumarate is cleaved to to make AMP
GTP provides the energy in the first step - not ATP*
Reaction from IMP to GMP
To form guanosine monophosphate, IMP is first oxidized to xanthine monophosphate. Then an amine group is transferred from glutamine, using ATP hydrolysis to power the reaction
How to get ribos sugars to deoxy ribose sugars?
Adenosine monophosphate and guanosine monophosphate are then phosphorylated to diphosphates.
ADP and GDP can then be phosphorylated again and . . .
hydrolyzed for energy or enzyme regulation incorporated into RNA
Or. . .
The ribose sugar of ADP and GDP can be reduced to make dADP and dGDP.
Draw Reaction of NDP to dNDP. What is the enzyme?
2 carbon on the ribose sugar of ADP and GDP (or UDP or CDP) can be reduced to make dADP and dGDP
Reducing factor is NADPH* Depends on this.
The NADPH and ribose sugar comes from the pentose phosphate pathway
Thioredoxin reductase and ribonucleotide reductase are the enzymes
Takes a lot of energy to make nucleotides. How much energy can come out of their degradation?
Not much compared to what it takes to make them.
Purine salvage: Cells expend a lot of energy to make nucleotides. To conserve this energy, there are different pathways to recycle nucleosides and bases in the cell
What enzyme is defective in SCID?
An inherited deficiency in adenosine deaminase causes severe cobined immunodeficiency. Purine synthesis
AMP deaminase (only muscle issues if deficient) this is different then adenosine deaminase which has system wide effects if defective… Look at Purine Salvage chart.
What enzyme is defective in CID?
An inherited deficiency in purine nucleoside phosphorylase (PNP) causes combined immunodeficiency. Purine synthesis
What enzyme is defective in Lesch-Nylan Syndrome?
An inherited deficiency in hypoxanthine-guanine phosphoribosyltransferase causes. Purine synthesis
What is CID? What are the symptoms and what is defective enzyme?
Deficiency in purine nucleoside phosphorylase (PNP) is a rare cause of combined immunodeficiency.
Symptoms:
Low but not absent T-cells, chronic infections, failure to thrive (FTT), neurlologic symptoms.
What does ADA deficiency cause?
SCID.. Deficiency in adenosine deaminase (ADA) is the second most common cause of autosomal recessive SCID. ADA deficiency leads to accumulation of 2-deoxyadenosine in the blood. This is toxic to lymphocytes.
What are symptoms of ADA deficiency? Treatment?
Symptoms: Lymphocytes < 500 / mm3 (normal 3,000 – 9,000/mm3 for children) Costrochondral junction dysplasia (skeletal abnormalities)
Treatment: Bone marrow transplant, +/- chemotherapy
What does a deficiency in HGPRT cause?
(Hes Got Purine Recycling Trouble)
Causes lesch-Nyhan Syndrome - is a rare X linked (only in men) syndrome is due to inherited deficiency in hypoxanthine-guanine phosphoribosyltransferase
It is characterized by self mutilation - chewing of fingers and lips.
Elevated uric acid in urine, mental retardation, dystonia, recurrent vomiting are also common with LND.
Patients with LND often die in their 30s from renal failure. Renal failure can be prevented with drugs aimed at reducing uric acid (allopurinol), but this does not affect self mutilation or other neuroligical symptoms
Symptoms of Lesch-Nyhan Syndrome? What is the deficient enzyme?
Lesch – Nyhan Disease (LND) is a rare X linked syndrome is due to inherited deficiency in hypoxanthine-guanine phosphoribosyltransferase
LND is characterized by self injury, often biting of the fingers and lips.
Elevated uric acid in urine, mental retardation, dystonia, recurrent vomiting are also common with LND.
Patients with LND often die in their 30s from renal failure. Renal failure can be prevented with drugs aimed at reducing uric acid (allopurinol), but this does not affect self mutilation or other neuroligical symptoms.
Lesch-Nyhan hypothesized reason for self mutilation?
Animal models suggest a disturbance in dopamine signaling as a cause of self mutilation in Lesch-Nyhan…
What is Gout caused by in regards to purine metabolism?
GMP and AMP are degraded to xanthine, which is oxidized to uric acid by xanthine oxidase.
Purine degradation can lead to hyperuricemia, which is usually subclinical. However, uric acid is not very soluble, and purine degradation can lead to precipitation of uric acid in the distal joints. This condition is gout.
Gout effects distal extremeties.. (it is related to temp, places in body that gets cold). If ppl eat a lot of organ meats which contain a lot of nucleotides, the body has to degrade them creating uric acid..
What is allopurinol?
A competitive inhibitor of Xanthine oxidase. Medication to treat gout.
What is CPS II? What are first steps in pyrimadine sythesis?
First steps are to combine glutamine with CO2 and ATP to create UMP
Cytosolic* carbamoyl phosphate synthase (CPS II) (unlike mitochondral CPS I) uses glutamine as an amine donor to form carbamoyl phosphate.
CPS II is allosterically inhibited by UTP and activated by PRPP.
Carbamoyl phosphate bonds with aspartate to make carbamoyl aspartate, which is then cyclized to orotate.
Orotate combines with PRPP to make a nucleotide, which is then decarboxylated to form uridine monophosphate (UMP).
Where is carbomyl phophate synthesized?
What is the enzyme and its inhibitors?
What happens in OTC deficiency?
In mitochondrial from CPS I in the urea cycle (activated by arginine throug NAG)
In cytoplasm from CPS II (inhibitors are UTP and activated by PRPP)
… If have OTC deficiency.. carbomyl builds up in mitochondria where it leaks out into pyrimidine synthesis…this leads to too much carbomyl phosphate in cytoplasm and it can add with aspartate to carbamoyl aspartate to then create orotic acid!
Draw the steps to create UTP, dUDP and eventually CTP for RNA synthesis and dTTP for DNA synthesis…
The DNA nucleotides are harder to make..
UDP can be reduced, 2’ hydroxyl can be removed by enzyme to makde dUDP or it can be reduced to UTP for RNA synth.. etc..
Key enzyme is ribonucleotide reductase (RR)
*Remembre reductase occurs at diphophate level…
What are products of pyridamine degredation?
Blocks the step between dUMP to dTMP and 5, 10 methylene FH4 to FH2
What are pruducts of pyrimadine degredation?
*No major pathologies associated with it.
Pyrimidine degradation:
Cytosine uracil CO2, NH4+, and b-alanine
Thymine CO2, NH4+, and b-aminoisobutyrate
Clinical Case… two month old male presented with..
2 Mo male. Fever, sore throat, and diarrhea. amoxicilin did not work. Lymophocytes low albumin low elevated liver enzymes white count up protein up, glucose down Why culture neg? might have had wrong media.. ADA defficiency
Case 2. 7 year old girl
7 y/o female. Concurrent URI, LRI. Perhaps FTT, various growth abnormalities Hb low Leukocyte low neutrophil and lymphsite low Ig (immunoglobin) so B cells appear normal HIV neg If suspect immi issues.. look at bloodd.. Partial deficiency in making T cells. Liver damage Uric acid is down PNP (purine neucleotide phophorylase) this is defective.. ADA is good. Diagnose would be CID caused by PNP deficiency.. Most important factor.. Age of pt was 7.. not 2mo like previous case.. Damage had been occuring for years vs only a short period.
What are the enzymes involved with converting IMP to GMP?
IMP to GMP - IMP dehydrogenase and GMP synthase
What is thioredoxin?
Protein redox cofactor that, like glutathione, can exist in reduced or oxidized states depending on cysteine side chain sulfur atoms
Purine Salvage Chart.. Draw it
Purine salvage: Cells expend a lot of energy to make nucleotides. To conserve this energy, there are different pathways to recycle nucleosides and bases in the cell.
Highlights:
Only adenosine can be directly phosphorylated to AMP by adenosine kinase.
The other purine nucleosides must have their ribose sugars removed, then added back from PRPP, to make monophosphate nucleotides
What is the enzyme that needs to be inhibited in order to inhibit gout?
Xanthine oxidase.. treated with allopurinol
