Nucleotide Metabolism (Week 4--Kurdistani) Flashcards
Nucleotide vs. nucleoside
Nucleotide: base + pentose/ribose sugar + phosphate (ex: AMP, GMP, CMP, UMP, dTMP)
Nucleoside: base + pentose/ribose sugar (ex: adenosine, guanosine, cytidine, uridine, deoxythimidine)
What are the 2 types of pentose sugars?
Ribose (in RNA) has 2’ OH
Deoxyribose (in DNA) has 2’ H
What are the 2 types of bases?
Purines: adenine (A), guanine (G)–have 2 rings
Pyrimidines: cytosine (C), uracil (U), thymine (T)–have 1 ring
Note: T only in DNA and U only in RNA
Where does the base attach to the pentose sugar?
Base attaches to 1’ carbon of pentose sugar, on same side of base as 5’ carbon (which eventually picks up phosphate)
Attachment is by beta-glycosidic linkage (enzyme that cleaves linkage is called phosphorylase)
Cellular roles of nucleotides
1) Monomeric units of nucleic acids
2) Energy metabolism: ATP, activated intermediates (UDP-glucose)
3) Regulation of physiological processes: adenosine and coronary blood flow, cAMP/cGMP as signaling molecules, allosteric regulators
4) Coenzyme components: FAD, NAD+, CoA
How do you synthesize nucleotides (purines and pyrimidines)?
1) De novo biosynthesis: from scratch; from AAs, ribose-5-P, CO2, NH3
2) Salvage pathway: recycling from pre-existing nucleotides (cells die and you can use their old nucleotides)
Note: purines do de novo more; pyrimidines do salvage more
Why do we do de novo synthesis?
Don’t get enough nucleotides in diet
How does de novo synthesis of nucleotides occur?
Occurs in most cells, but liver is major site of de novo synthesis
Purines: the purine rings are built onto ribose-5-phosphate
Pyrimidines: the pyrimidine ring is synthesized then attached onto the ribose-5-phosphate
Phosphoribosylpyrophosphate (PRPP) is intermediate in both purine and pyrimidine synthesis
What is PRPP?
Phosphoribosyl-pyrophosphate (PRPP) is an activated ribose sugar that is used to synthesize nucelotides de novo
Ribose 5-phosphate + ATP –> PRPP + AMP
(PRPP synthetase catalyzes reaction; ribose 5-phosphate comes from pentose phosphate pathway, which is a shunt off of glycolysis)
Takes energy to synthesize PRPP (and thus nucleotides)
Steps in de novo biosynthesis of PURINEs
1) Regulated step: Ribose-5-phosphate + ATP –> PRPP + glutamine (via PRPP synthetase); at this step, control enzyme activity via feedback/feedforward to slow/speed process
2) Committed step: PRPP + glutamine –> 5-phosphoribosyl amine + glutamate +PPi (via amidophosphoribosyl transferase); this is point of no return (and often is regulated by final product)
3) 9 more steps then get IMP (inosine monophosphate)
4) IMP converted to GMP (by ATP) or AMP (by GTP)
5) GMP and AMP are phosphorylated, then phosphorylated again or acted on by ribonucleotide reductase (RNR) to make dGDP and dADP
6) Get GTP, ATP, dGTP, or dATP
What are purines degraded to?
Purines (AMP, GMP) degraded to xanthine then to uric acid which is excreted in urine
If uric acids loses H+, turns into urate, which is insoluble and can cause gout if it accumulates enough
Note: food purines are degraded to uric acid by gut epithelium
Gout
Caused by too much uric acid in the blood (hyperuricemia)
Primary gout: inherited; more in males, overactivity of PRPP synthetase; Lesch-Nyhan syndrome is X-linked recessive (get gout AND neurological symptoms)
Secondary gout: medications, too much cell death (chemo), chronic kidney failure
Clinical characteristics: hyperuricemia, arthritis (usually in big toe), kidney malfunction
Pathology: precipitation of sodium urate crystals in joints or other tissues, or in urinary tract (or kidneys); tophi are large visible crystals in joints/soft tissue
Treatment of gout
NSAIDs, corticosteroids, colchicine, allopurinol, avoid alcohol and foods with purines
Colchicine interferes with function of microtubules so inflammatory cells (neutrophils) can’t get to site where crystals formed so can’t cause inflammation
Allopurinol is similar to hypoxanthine (which is a substrate for xanthine oxidase in the process of degrading purines) so it essentially inhibits xanthine oxidase so that xanthine can no longer be turned to uric acid (“suicide inhibitor” because enzyme converts it to oxipurinol (alloxanthine) which does not dissociate and inhibits the enzyme)
Probenecid inhibits uric acid reabsorption at PCT (tx chronic gout)
Sulfinpyrazone Inhibits uric acid reabsorption (tx chronic gout or gouty arthritis)
Pseudogout
Arthritis caused by deposition of calcium pyrophosphate crystals, in knee or wrist
Caused by excessive Ca2+ in blood (overactive parathyroid gland, hemochromatosis, hypothyroidism); incidence increases with age
Adenosine deaminase (ADA)
Enzyme that degrades d-adenosine –> d-inosine that then goes to hypoxanthine (via purine nucleoside phosphorylase) then uric acid
This is how dAMP is degraded; note that AMP is degraded to uric acid differently–using AMP deaminase for AMP –> IMP –> inosine –> hypoxanthine –> uric acid
Severe Combined Immunodeficiency Disorder (SCID)
Severe defects in level and activity of B and T cells causes recurrent infections and failure to thrive
Caused by deficiency in adenosine deaminase (ADA) that causes elevated levels of ATP and thus dATP
dATP is highly toxic because inhibits RNR, so inhibits synthesis of other deoxynucleotides and DNA so cells can’t divide/signal. Lymphoid cells most susceptible to ADA deficiency
Treatment: bone marrow transplant or gene therapy
What hapens when you have deficiency in purine nucleoside phosphorylase (PNP)?
Get increased levels of GTP and dGTP, which also inhibit RNR (like ATP and dATP) and cause toxicity to immune system
Get less severe form of immunodeficiency
Purine salvage pathways to synthesize nucleotides
Adenine and Guanine use different enzymes for the purine salvage pathway:
1) Adenine + PRPP –> AMP + PPi (via adenine phosphoribosyl transferase (APRT))
2) Guanine (or hypoxanthine) + PRPP –> GMP (or IMP) + PPi (via hypoxanthine (guanine) phosphoribosyl transferase (HGPRT))
What exactly is “salvaged” in the purine salvage pathways?
The base–adenine or guanine (so the rings with the nitrogen in them!)
(note that this is different from pyrimidine salvage, which uses nucleosides!)
Lesch-Nyhan Syndrome
Defective HGPRT causes increased uric acid (orange crystals in diaper!)
X-linked so primarily in males
Get neurological defects (dystonia, choreoathetosis, ballismus), behavior problems (aggressive, compulsive self-mutilation)
Mechanism of hyperuricemia: decreased salvage leads to (1) more purine degradation and (2) buildup of PRPP which stimulates committed step in de novo purine synthesis so get more uric acid generation
Treatment: allopurinol to reduce uric acid production, hydration to prevent urate crystal deposition (esp in kidney)
Pyrimidine de novo biosynthesis
Pyrimidine ring synthesized first then attached to ribose (unlike purine, which is built ON ribose)
However, note that it’s not exactly the final pyrimidine ring that is synthesized–it still has a CO2 on there that shouldn’t be, and this ring is called orotate
Orotate attached to PRPP to form UMP
From UMP –> UTP –> CTP
Last pyrimidine we need to synthesize is thymidine: dUTP –>dUMP –> dTMP
6 steps to synthesize UMP
1) NH3 (from AA glutamine) + HCO3- + 2 ATP –> carbamoyl phosphate
2) Carbamoyl phosphate + aspartate –> carbamoyl aspartate
3) Carbamoyl aspartate –> dihydroorotate
4) Dihydroorotate –> orotate
5) Orotate + PRPP –> orotidine monophosphate (OMP)
6) Orotidine monophosphate –> uridine monophosphate (UMP)
In the pyrimidine ring that is formed de novo, where do the N’s and C’s come from?
N1, C4,5,6 come from aspartate
C2, N3 come from carbamoyl phosphate (and furthermore, N3 usually comes from glutamine)
Enzymes that catalyze the 6 steps of de novo synthesis of UMP
CAD catalyzes steps 1, 2, 3: multifunctional polypeptide (CPSII, ATCase, DHOase)
UMPS catalyzes steps 5, 6: multifunctional polypeptide (OPRT, ODC)
Reactions 1, 5, 6 are regulated
Where do the 6 steps of pyrimidine de novo biosynthesis occur, and what is the significance of this?
All steps occur in cytoplasm, except step 4 which is in the mitochondria
Step 4 is dihydroorotate –> orotate (via dihydroorotate dehydrogenase, enzyme that is in the intermembrane space of the mitochondria)
Significance is that this links synthesis of nucleotides to availability of energy! If limited O2 (decreased ATP), decrease activity of DHODH and get decreased synthesis of nucleotides, which is good because don’t want to be making nucleotides when you don’t have enough energy)
What does UMPS do, and how does it interact with the chemotherapeutic 5FU?
Multifunctional, but adds orotate to PRPP then converts that to UMP
UMPS is also what targets and activates 5FU (chemotherapeutic drug): give cells 5FU, and UMPS places 5FU onto PRPP (as if 5FU was a base like orotate) to make active form of 5FU drug which is like a nucleotide
Note: cancer cells can be resistant to 5FU if they don’t have UMPS since UMPS is needed to get active form of 5FU
How does 5FU target cancer cells?
Since cancer cells upregulate the pyrimidine synthesis pathway compared to normal cells (which still do have some of this pathway), 5FU acts mostly to inhibit UMP synthesis in cancer cells
What is the link between the urea cycle and pyrimidine synthesis and what is the significance of that?
Carbamoyl phosphate is the product of step 1 of pyrimidine synthesis and is necessary for urea cycle to proceed (ornithine –> citrulline)
Significance is that if problem with urea cycle, will get backup of carbamoyl phosphate in the mitochondria –> carbamoyl phosphate will leak out into cytoplasm and cause increase in pyrimidine biosynthesis pathway –> causes more uracil production, and get uracil in blood
Regulation of pyrimidine synthesis (what activates/inhibits pathway)?
Inhibition occurs by end products UTP and CTP on initial step, and UMP inhibits its own formation
Activation by ATP and PRPP on first step
Hereditary Oroticaciduria
Can’t make UMP because deficiency of OPRT (orotate-phosphoribosyl transferase; step 5) and/or ODC (orotidine monophosphate decarboxylase; step 6) (both part of UMPS)
Causes accumulation of orotic acid (orotate), which is excreted in urine, also causes anemia, retarded growth, immunodeficiency
Treatment: include uridine (nucleoside) in diet to increase UMP levels, which allows you to make pyrimidines again AND gives negative feedback on system so don’t get buildup of orotic acid
Very rare, only 17 cases worldwide
We give uridine (nucleoside) to increase UMP in people with hereditary oroticaciduria, not uracil (base). Why wouldn’t giving uracil help?
Remember, we use nucleosides for salvage pathway of pyrimidines, NOT bases!
If we gave uracil, we’d have to attach it to PRPP, and that’s the step that is defective!
What happens when you degrade pyrimidines?
Pyrimidine rings fully degraded to soluble structures!
(unlike purines that make uric acid)
Pyrimidine salvage
Salvage pathway dominates over de novo synthesis for pyrimidines
Food pyrimidines are absorbed as their nucleosides –> pyrimidine nucleoside + PRPP (via pyrimidine phosphoribosyl transferase) –> UMP??
Note: since pyrimidines are recycled at the level of the nucleotide you shouldn’t have to react with PRPP…looks like Uridine has to react with PRPP (wikipedia) but Cytidine and deoxyThymidine probably don’t and are just used as they are…
Purines vs. pyrimidines (de novo synthesis, salvage, degradation)
Purines: de novo synthesized onto PRPP; first nucleotide made is IMP; salvaged through base; degraded to uric acid
Pyrimidines: de novo synthesize rings first then add to PRPP; first nucleotide made is UMP; salvaged through nucleoside; degraded to AA, CO2, NH3
Ribonucleotide reductase (RNR)
Fe-containing multifunctional enzyme with redox-active thiol groups that can transfer electrons during reduction reactions
RNR reduces NDP (ribonucleotide) –> dNDP (deoxyribonucleotide)
After catalyzing reaction, RNR needs to be re-oxidized by thioredoxin (note ultimate source of electrons is NADPH)
Note that at this stage, have 2 phosphates attached (XX DI phosphate)
Also, dATP inhibits RNR just because of feedback inhibition
How are dNTPs produced?
Phosphorylation of dNDPs (duh…di to tri-phosphate) catalyzed by nucleoside diphosphate kinase
What is thymine?
Thymine is a pyrimidine that is only in DNA, and is different from uracil just by 1 methyl group (thymine = 5-methyluracil)
How do we make dTMP?
dUMP + THF –> dTMP + dihydrofolate (DHF) (via thymidylate synthase)
Why do we use dUMP and not dUTP to make dTTP for DNA synthesis?
Because DNA polymerase isn’t good at distinguishing between dUTP and dTTP but we don’t want dUTP incorporated into DNA!
Don’t want lots of dUTP around!
How do we regenerate THF from DHF (after THF has helped to make dTMP from dUMP)?
DHF + NADPH + H+ –> THF + NADP+ (via dihydrofolate reductase)
The enzyme dihydrofolate reductase is very important because this whole cycle is required for DNA synthesis to occur!
What drugs inhibit dihydrofolate reductase and what is the significance of this?
Chemotherapeutic drugs and antibiotics target and inhibit dihydrofolate reductase so you can’t regenerate THF from DHF
This means you can’t continue doing DNA synthesis (because don’t have thymidine nucleotide)!
These drugs can be used to kill ectopic pregnancy embryo
What compounds are “carriers” of methyl groups, and what is actually the source of the methyl group?
THF and SAM are carriers of methyl groups, but serine is the original source of the methyl group
FdUMP
5-fluorodeoxyuridylate
When 5FU is given as a drug, remember UMPS adds a ribose sugar onto it to make it like a nucleotide, and FdUMP is the “nucleotide” it is converted to
FdUMP is a suicide inhibitor of thymidylate synthase, so prevents thymidine synthesis and thus DNA synthesis
Enzyme thymidylate synthase tries to react with FdUMP, but FdUMP has a F where UMP just has an H, and thymidylate synthase trying to react with that C-F bond inactivates the thymidylate synthase
5FU is called a DNA synthesis inhibitor but why is this technically not true?
Because 5FU inhibits nucleotide synthesis, specifically it inhibits thymidine synthesis.
However, that in turn inhibits DNA synthesis since you need thymidine to synthesize DNA
Antifolates
DHF analogs that competitively bind to and inhibit DHF reductase (can’t re-form THF)
Ex: aminopterin, methotrexate (amethopterin)
Trimethoprim
Antibiotic
Antifolate that binds better to bacterial DHF reductase (can’t re-form THF) so is used as antibiotic
Folate and folic acid
Folate is natural form
Folic acid is synthetic form
Does 1 carbon transfers
Metabolic roles: synthesis of thymidine (using methylene-THF) and purines (which we didn’t talk about), synthesis of methyl donor S-adenosylmethionine (SAM), conversion of homocysteine to methionine (N5-methyl-THF)
Can humans synthesize folic acid?
No, only bacteria can so we have to eat folate in our diet to get it
How do sulfa drugs work?
Since bacteria use para-amino benzoid acid (PABA) as a precursor for folic acid synthesis, we can give sulfonamide, an analog of PABA to inhibit folic acid synthesis in bacteria
Inhibiting folic acid synthesis in bacteria eventually causes bacteria to not be able to make thymidine, so get DNA synthesis inhibition in bacteria
What are vitamin B12 and folic acid important for?
Need vitamin B12 and folic acid in the reaction where you take methyl group from THF, transfer it to methionine to make SAM and turn homocysteine –> methionine
Homocysteine –> methionine (this rxn is very important because need SAM and THF to do make purines and dTMP (DNA synthesis!!!))
Deficiency in vitamin B12 and folic acid
Caused by inadequate intake or for B12 also could be due to poor absorption due to lack of intrinsic factor
Low folic acid can cause neural tube defects
Low vitamin B12 can cause megaloblastic anemia, pernicious anemia, paresthesias, peripheral neuropathy, irritability, dementia, depression, psychosis
Anti-metabolites
Inhibit nucleotide synthesis or inhibit DNA synthesis directly
Used as cancer drugs
Antifolates (deplete cells of thymidine), 5FU, 6-MP, araC, 5-azacytidine, AZT, acyclovir, other pyrimidine or purine analogs
Like 5FU, are activated in specific cell type (cells growing rapidly)
6-mercaptopurine (6-MP)
Is an antimetabolite (purine analog) that inhibits amido-phosphoribosyl-transferase (enzyme that catalyzes committed step in purine de novo synthesis, NOT APRT!)
Converted to nucleotide analog by HGPRT in salvage pathway: 6-MP + PRPP –> 6-MP-ribose-phosphate + PPi
Used for childhood leukemia
Note: relies on salvage pathway to be activated but inhibits de novo pathway
Other derivatives exist with similar effects: Imuran (Azathioprine) used as immunosuppressant
Cytosine arabinose (araC)
Another nucleotide analog (anti-metabolite) that has same base but slightly different ribose sugar
Gets incorporated into DNA but because of slightly different structure, inhibits DNA chain synthesis
5-Azacytidine
Another anti-metabolite (similar to cytidine) thats base has nitrogen group instead of carbon
When you try to make thymidine from cytidine (I thought you made T from U…) by methylating that carbon, realize it’s nitrogen instead so can’t methylate!
Used to treat myelodysplastic syndrome (inhibits DNA synthesis)
Used in basic science to decrease DNA methylation in cultured cells
Azido-3’-deoxythymidine (AZT)
Nucleotide (pyrimidine) analog that was one of the first HIV anti-retroviral drugs
Instead of OH group, has N3 (azide) group
Inhibits viral polymerase, inhibits reverse-transcription
Acyclovir
Acycloguanisine (purine analog) is like guanine but ribose sugar ring is actually open!
Must be phosphorylated by viral thymidine kinase to be activated (our kinases can’t)
Activated acyclovir is a DNA polymerase inhibitor
What happens to that hypoxanthine that builds up if you use a xanthine oxidase inhibitor for treating gout?
Hypoxanthine is more soluble, so is just excreted!
