Nucleotide Metabolism Flashcards
Carbon can be in different ____ states. ___ ___ has the most electrons and is the most reduced. ___ ___ is the most oxidized state.
Oxidation
Methyl carbon
Carbon dioxide
___, ____, and _____ are three ‘one carbon’ donors aka ‘methyl donors’ that allow the body to perform reactions that shuffle ___ ___.
Folate, vitamin B12,
S-adenosylmethionine
Single carbons
Deficiencies in either folate or vitamin B12 result in ____ ___ due to impaired ____ synthesis.
Macrocytic anemia
Nucleotide
Carbons are donated to ____ at different oxidation states. Once bound to Tetrahydrofolate, the ____ state of the one carbon can be changed. After donating the one carbon for biosynthesis reactions, the ____ is regenerated.
Tetrahydrofolate
Oxidation
Tetrahydrofolate
The vitamin precursor for the active cofactors is ____. It is abundant in green leafy vegetables, liver, legumes, yeast, and fortified flour. It has a _____ tail that is digested in the gut to _____.
Folate
Poly-glutamate
Mono-glutamate
Folate is reduced to ____ _____ in the intestinal epithelial cells (this is the major form in the blood) and ____ in the liver.
N5-methyl Tetrahydrofolate
Poly-glutamate
Proton coupled folate transporter (PCFT) is encoded on the ______ gene and expressed on enterocytes and hepatocytes
SCL46A1
____ ____ ____: is an inherited mutation in the proton coupled folate transporter (PCFT) and causes functional folate deficiency despite adequate folate in the diet
Hereditary folate malabsorption
Folate is reduced to ____ and reduced again to ____ by dihydrofolate reductase (DHFR)
Dihydrofolate (FH2)
Tetrahydrofolate (FH4)
____ ____ is important for metabolism of dietary folate and for recycling oxidized folate to FH4. It is also an important drug target of ____ for cancer and rheumatoid Arthritis, ____ as an antibacterial, and ____ as an antimalarial.
Dihydrofolate reductase
Methotrexate
Trimethoprim
Pyrimethamine
Once Tetrahydrofolate has been produced, it can take ___ ___ in different ___ states.
Single carbons
Oxidation
Oxidation states of Tetrahydrofolate:
Serine can donate a carbon through ____ _____ forming glycine and ______ FH4.
Serine hydroxymethyltransferase
N5N10-methylene
The amino acid ___ is the most important contributor to the one carbon pool.
Serine
Glycine can also donate carbon to Tetrahydrofolate through ___ ___ ___, forming _____FH4, NADH, NH4+, and CO2
Glycine cleavage enzyme
N5N10-methylene
Serine, glycine, choline, histidine, and formate contribute to the ___ ___ ___.
One carbon pool
Thymidine nucleotides, purine bases, methionine, and S-adenosyl methionine are _____ of the one carbon donations.
Products
One carbon transfer in thymidine nucleotide synthesis:
The biosynthesis of ____ ____ from deoxyuridine monophosphate (dUMP) is a methylation reaction. The carbon donor is ____ ___, the carbon is in the ___ oxidation state. During the reaction, FH4 supplies electrons and oxidizes to ____, which then must be reduced to regenerate FH4.
Deoxythymidine monophosphate (TMP)
N5N10-methyl Tetrahydrofolate (FH4)
Methylene
Dihydrofolate (FH2)
Thymidine nucleotide synthesis:
After N5N10-methylene TH4 donates a carbon to dUMP to for dTMP, it is left as _____. Dihydrofolate reductase (DHFR) must then use ____ oxidation to regenerate ____.
Dihydrofolate
NADPH
Tetrahydrofolate
Thymidine nucleotide synthesis:
___ ____ reduces a methylene carbon to methyl during transfer to dUMP to make dTMP. Once FH2 is reduced by to FH4 via ____, it can then accept another one carbon group from ___ _____.
Thymidylate synthase (TS)
DHFR
Serine hydroxymethyltransferase
____ (_____) is found in the diet in the meat, eggs, and dairy, either free or protein bound
Vitamin B12 (cobalamin)
The ____ at the center of the ring in vitamin B12 can bind either a ____ group or an ____ ____.
Cobalt
Methyl
Adenine nucleotide
N5-methyl TH4 can only donate it’s one carbon to ____ to form ____, which participates in only one reaction: donation of methyl to _____ to make ____.
Cobalamin
Methylcobalamin
Homocysteine
Methionine
Adenosylcobalamin (5’-deoxyadenosylcobalamin) participates in only one reaction: catalyzes the isomerization of a methyl group in converting ____ ___ to ___ ___.
Methylmalonyl CoA
Succinyl CoA
Vitamin B12 absorption and transport:
Vitamin B12 first binds to ____ proteins secreted in the stomach. As this is digested, B12 binds ___ ___ (a protein). This complex is taken up by the intestinal epithelial cells and transported to the blood within ______ protein. Most of it is stored in the liver in complex with ____.
R-binder
Intrinsic factor
Transcobalamin II
Cubillin
Vitamin B12 deficiency causes ___ ___: megaloblastic anemia plus neurological problems
Pernicious anemia
B12 deficiency can be dietary or the result of loss of function of ___ ___, _____, or ____.
Intrinsic factor, transcobalamin II, cubillin
Many causes of pernicious anemia are caused by ____ destruction of ____ ___.
Autoimmune
Parietal cells
Vitamin B12 Reaction 1:
Methylmalonyl CoA mutase rearranges the ___ ___ to form ___ ___, which can then enter the TCA cycle. Adenosyl cobalamin is not consumed in the reaction.
Carboxylic acid
Succinyl CoA
Vitamin B12 Reaction 2:
Methionine synthase catalyzes the transfer of methyl from ____ to ____ to make ____.
Methylcobalamin is regenerated by accepting a methyl from fully reduced ____ ___.
Methylcobalamin
Homocysteine
Methionine
N5-methyl TH4
Cells have a continuous cycle between methionine, S-adenosylmethionine (SAM), S-adenosyl homocysteine (SAH), and homocysteine. ____ is a methyl donor for many bio synthetic and regulatory enzymes, and it must be regenerated with ____ that comes from _____.
S-adenosylmethionine (SAM)
Carbon
N5-methyltetrahydrofolate
S-adenosylmethionine (SAM)
S-adenosylmethionine as a donor for bio synthetic regulatory enzymes:
Congenital Intrinsic factor deficiency can cause ____ ___. It is an inherited mutation in the gene encoding intrinsic factor.
Pernicious anemia
The methyl trap hypothesis:
The only metabolic fate of N5-methyl TH4 is to lose its ____ to ____. In a dietary or functional deficiency of cobalamin, _____ becomes trapped as N5-methyl TH4, unable to participate in other carbon transfers.
Methyl
Cobalamin
Folate
Nucleotide metabolism allows the body to synthesize nucleotides as needed and to break down excess nucleotides into ___ ___. Nucleotide metabolism provides little ___.
Excretable products
Energy
Nucleotides have many functions:
Nucleic acids, energy, second messenger cAMP, Allosteric regulators, ‘handles’ for cofactors such as NADH, CoSH, etc.
Key parts to a nucleotide: ____ is linked through a nitrogen to a ____ ___ which is linked to a ____.
Base
Ribose sugar
Phosphate
Nucleotide picture:
Purines: ___ and ___
Pyrimidines: ___ and ___
Adenine and Guanine
Cytosine and thymine
Base and nucleoside pairs:
The ribose sugar component of nucleotides is derived from _____ _____ (PRPP).
5-phosphoribosyl 1-pyrophosphate
Purines are constructed by adding atoms from ______, glutamine, glycine, Aspartate, and carbon dioxide sequentially to ____ ____.
Formyltetrahydrofolate
5-phosphoribosyl 1-pyrophosphate
Pyrimidines are constructed by building the orotate base from ____, carbon dioxide, and ____. The bad is then transferred to ____ and further modified by cytosine, thymidine, and uracil.
Aspartate
Glutamine
5-phosphoribosyl 1-pyrophosphate (PRPP)
PRPP is an activated ____ sugar created by transfer of _____ to ribose 5-phosphate by ___ ____, which is allosterically inhibited by ___ ____ (___ and ___). This is a key regulatory step in nucleotide synthesis.
Ribose
Pyrophosphate
PRPP synthetase
Purine diphosphonucleosides (GDP and ADP)
Purine synthesis:
The first committed step is the transfer of an ____ from glutamine by the ____ ____ ____. The second step is addition of glycine to make ____ ___ ____.
Amine
Glutamine phosphoribosyl amidotransferase
Glycinamide ribosyl 5-phosphate
Purine synthesis:
___ and ___ are added from N10-formyltetrahydrofolate, carbon dioxide, glutamine, and Aspartate to form _____ ____.
Carbon
Nitrogen
Inosine monophosphate (IMP)
Inosine monophosphate then gains an amine from _____ to form ____ ____, or an amine from ____ to form ___ ___.
Aspartate
Adenosine monophosphate
Glutamine
Guanosine monophosphate
Purine synthesis: review of the urea cycle
_____ is an amine donor in the urea cycle
____ is cleaved off arginosuccinate
Aspartate
Fumarate
Purine synthesis:
The conversion of ____ to ____ as an amine transfer simile to that in the urea cycle. ____ binds to IMP to make adenylosuccinate, then ____ is cleaved off to make ____. The energy to make adenylosuccinate comes from ____.
IMP
AMP
Aspartate
Fumarate
AMP
GTP
Purine metabolism: Anaplerotic
Through the purine nucleotide cycle, ___ from protein breakdown can supply ____ to the TCA cycle as an _____ substrate.
Aspartate
Fumarate
Anaplerotic substrate
Purine synthesis:
To form guanosine monophosphate, ____ is first oxidized to ___ ____. Then an amine group is transfers from ____, using ATP hydrolysis to power the reaction.
IMP
xanthine monophosphate
Glutamine
Purine synthesis:
Adenosine monophosphate and guanosine monophosphate are then ____ to diphosphates. ADP and GDP are then ____ again to make ___ and ___. OR the ribose sugar of ADP and GDP can be reduced to make ____ and ____.
Phosphorylated
Phosphorylated
ATP
GTP
dADP
dGDP
Purine metabolism: ribonucleotide reductase:
The #2 carbon on the ___ sugar of ADP and GDP (or UDP or CDP) can be ____ to dADP and dGDP.
_____ is a protein redox cofactor that, like glutathione, can exist in reduce or oxidized states depending on ____ side chain sulfur atoms.
Ribose
Reduced
Thioredoxin
Cysteine
Purine metabolism:
Ribonucleotide reductase (RR) uses ___ ____ as substrates.
Nucleoside diphosphates
Purine salvage:
Because nucleoside synthesis requires a lot of energy, the body recycles them as much as possible. The goal of purine salvage pathway is to generate ____ and ____ from nucleotide degradation products.
AMP
GMP
Purine salvage:
To convert free bases to nucleotides, ______ (APRT and HGPRT) add ribose from _____ ____ (PRPP).
Phosphoribosyltransferases
5-phosphoribosyl 1-pyrophosphate
Purine salvage:
To convert nucleosides to nucleotides, ____ ____ ____ removes ribose, leaving the free base.
Purine nucleoside phosphorylates
Purine salvage:
Adenosine can be converted adenosine monophosphate (AMP) directly through phosphorylation by ___ ___.
Adenosine kinase
____ ____: 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.
Purine salvage
Purine salvage highlights:
Purine catabolism:
GMP and AMP are degraded to _____, which is oxidized to uric acid by ____ ___, which uses a _____ atom in its catalytic site.
Xanthine
Xanthine oxidase
Molybdenum
Purine degradation can lead to ____ which is usually subclinical. However, ___ ___ is not very soluble, and purine degradation can lead to precipitation of ___ ___ in the distal joints causing ____.
Hyperuricemia
Uric acid
Uric acid
Gout
Pyrimidines:
In contrast to purines, which are assembled on a ribose sugar, Pyrimidine bases are first assembled then ____ to a ribose sugar.
Transferred
Pyrimidine synthesis:
_____ ____ ____ ____ (CPS II) used glutamine as an amine donor to form carbamoyl phosphate. CPS II is allosterically inhibited by ____ and activated by ____.
Cytosolic carbamoyl phosphate
UTP
PRPP
Pyrimidine synthesis:
Carbamoyl phosphate bonds with ____ to make carbamoyl Aspartate, which is then cyclized to ____.
Aspartate
Orotate
Orotate combines with ____ to make a nucleotide, which is then decarboxylated to form ____ ____.
PRPP
Uridine monophosphate (UMP)
Pyrimidine synthesis: recall from the urea cycle:
____ ____ is a substrate for Pyrimidine synthesis. Elevated urinary ___ ___ is characteristic of urea cycle disorders downstream of CPS-1.
Carbamoyl phosphate
Orotic acid
Pyrimidine synthesis:
___ ___ only acts on the diphosphate form of nucleotides. ___ ___ uses dUMP as a substrate so dUDP has to be _____ before it can be methylated to dTMP. dTMP is then ____ twice to make dTTP, a substrate for ___ synthesis.
Ribonucleotide reductase (RR)
Thymidine synthase
Dephosphorylated
Phosphorylated
DNA
Blocking thymidine synthase deprives DNA polymerase of ____, preventing DNA replication. Cells that proliferate rapidly like cancer, immune cells, and gut epithelial cells are sensitive to ____ like ____ that target nucleotide synthesis.
dTTP
anti-metabolites
5-fluorouracil
Pyrimidine catabolism:
Unlike purine degradation, accumulation of Pyrimidine metabolites are not associated with ____.
Pathology
Pyrimidine catabolism:
Cytosine is degraded to ____
Thymine is degraded to _____
Beta-alanine
Beta-aminoisobutyrate
Disorders of nucleotide metabolism:
____ ____ ____ disorder results in overactivity of the enzyme by preventing inhibition by GDP. It is X-linked and only seen in males. Symptoms are due to increased ____ production and increases ___ ___.
Mild form:
Severe form:
PRPP synthetase superactivity
Purine
Uric acid
Uric acid crystalluria, urinary stones, and gout arthritis
Neurodevelopmental disorders
In PRPP synthetase superactivity disorder, the ___ ___ of the enzyme is lost.
Allosteric inhibition
Review:
Review case:
Review case:
Case review:
Adenosine deaminase deficiency severe combined immunodeficiency:
Deficiency in adenosine deaminase is the second most common cause of autosomal recessive ____. Deficiency leads to accumulation of ___ and ____ in the blood. This is toxic to lymphocytes.
Symptoms:
Treatment:
SCID
adenosine
2-deoxyadenosine
Low lymphocyte count, costrochondal junction dysplasia
Bone marrow transplant , chemotherapy
Review case:
Review case:
Review case:
Review case:
____ ____ ____ deficiency is a rare cause if combined immunodeficiency. Symptoms include low but not absent T cells, chronic infections, failure to thrive, neurologic symptoms.
Purine nucleoside phosphorylase (PNP)
______ syndrome is a X linked syndrome caused by inherited deficiency in ____ ____ ____. Aka purine salvage disorder. Characterized by self injury. Elevated ___ ___ in urine, intellectual disability, dystonia, recurrent vomiting. Often die in 30’s from ___ failure. ____ can reduce uric acid and help prevent renal failure.
Lesh-Nyhan
Hypoxanthine-guanine phopsphoribosyltransferase
Uric acid
Renal
Allopurinol
Animal models suggest a disturbance in ___ ___ as a cause of self mitigation in Lesch-Nyhan.
Dopamine signaling
Purine catabolism disorder: gout:
____ is a structural analog of hypoxanthine. Xanthine oxidase oxides it to oxypurinal, which remains tightly to the active site, permanently inactivating ___ ___. ____ acts as a suicid inhibitor.
Allopurinol
Xanthine oxidase
Allopurinol
