Nucleotide Metabolism Flashcards

1
Q

Carbon can be in different ____ states. ___ ___ has the most electrons and is the most reduced. ___ ___ is the most oxidized state.

A

Oxidation
Methyl carbon
Carbon dioxide

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2
Q

___, ____, and _____ are three ‘one carbon’ donors aka ‘methyl donors’ that allow the body to perform reactions that shuffle ___ ___.

A

Folate, vitamin B12,
S-adenosylmethionine
Single carbons

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3
Q

Deficiencies in either folate or vitamin B12 result in ____ ___ due to impaired ____ synthesis.

A

Macrocytic anemia
Nucleotide

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4
Q

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.

A

Tetrahydrofolate
Oxidation
Tetrahydrofolate

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5
Q

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 _____.

A

Folate
Poly-glutamate
Mono-glutamate

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6
Q

Folate is reduced to ____ _____ in the intestinal epithelial cells (this is the major form in the blood) and ____ in the liver.

A

N5-methyl Tetrahydrofolate
Poly-glutamate

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7
Q

Proton coupled folate transporter (PCFT) is encoded on the ______ gene and expressed on enterocytes and hepatocytes

A

SCL46A1

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8
Q

____ ____ ____: is an inherited mutation in the proton coupled folate transporter (PCFT) and causes functional folate deficiency despite adequate folate in the diet

A

Hereditary folate malabsorption

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9
Q

Folate is reduced to ____ and reduced again to ____ by dihydrofolate reductase (DHFR)

A

Dihydrofolate (FH2)
Tetrahydrofolate (FH4)

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10
Q

____ ____ 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.

A

Dihydrofolate reductase
Methotrexate
Trimethoprim
Pyrimethamine

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11
Q

Once Tetrahydrofolate has been produced, it can take ___ ___ in different ___ states.

A

Single carbons
Oxidation

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12
Q

Oxidation states of Tetrahydrofolate:

A
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13
Q

Serine can donate a carbon through ____ _____ forming glycine and ______ FH4.

A

Serine hydroxymethyltransferase
N5N10-methylene

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14
Q

The amino acid ___ is the most important contributor to the one carbon pool.

A

Serine

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15
Q

Glycine can also donate carbon to Tetrahydrofolate through ___ ___ ___, forming _____FH4, NADH, NH4+, and CO2

A

Glycine cleavage enzyme
N5N10-methylene

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16
Q

Serine, glycine, choline, histidine, and formate contribute to the ___ ___ ___.

A

One carbon pool

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17
Q

Thymidine nucleotides, purine bases, methionine, and S-adenosyl methionine are _____ of the one carbon donations.

A

Products

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18
Q

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.

A

Deoxythymidine monophosphate (TMP)
N5N10-methyl Tetrahydrofolate (FH4)
Methylene
Dihydrofolate (FH2)

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19
Q

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 ____.

A

Dihydrofolate
NADPH
Tetrahydrofolate

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20
Q

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 ___ _____.

A

Thymidylate synthase (TS)
DHFR
Serine hydroxymethyltransferase

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21
Q

____ (_____) is found in the diet in the meat, eggs, and dairy, either free or protein bound

A

Vitamin B12 (cobalamin)

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22
Q

The ____ at the center of the ring in vitamin B12 can bind either a ____ group or an ____ ____.

A

Cobalt
Methyl
Adenine nucleotide

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23
Q

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 ____.

A

Cobalamin
Methylcobalamin
Homocysteine
Methionine

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24
Q

Adenosylcobalamin (5’-deoxyadenosylcobalamin) participates in only one reaction: catalyzes the isomerization of a methyl group in converting ____ ___ to ___ ___.

A

Methylmalonyl CoA
Succinyl CoA

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25
Q

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 ____.

A

R-binder
Intrinsic factor
Transcobalamin II
Cubillin

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26
Q

Vitamin B12 deficiency causes ___ ___: megaloblastic anemia plus neurological problems

A

Pernicious anemia

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27
Q

B12 deficiency can be dietary or the result of loss of function of ___ ___, _____, or ____.

A

Intrinsic factor, transcobalamin II, cubillin

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28
Q

Many causes of pernicious anemia are caused by ____ destruction of ____ ___.

A

Autoimmune
Parietal cells

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29
Q

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.

A

Carboxylic acid
Succinyl CoA

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30
Q

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 ____ ___.

A

Methylcobalamin
Homocysteine
Methionine

N5-methyl TH4

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31
Q

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 _____.

A

S-adenosylmethionine (SAM)
Carbon
N5-methyltetrahydrofolate

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32
Q

S-adenosylmethionine (SAM)

A
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33
Q

S-adenosylmethionine as a donor for bio synthetic regulatory enzymes:

A
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34
Q

Congenital Intrinsic factor deficiency can cause ____ ___. It is an inherited mutation in the gene encoding intrinsic factor.

A

Pernicious anemia

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35
Q

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.

A

Methyl
Cobalamin
Folate

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36
Q

Nucleotide metabolism allows the body to synthesize nucleotides as needed and to break down excess nucleotides into ___ ___. Nucleotide metabolism provides little ___.

A

Excretable products
Energy

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37
Q

Nucleotides have many functions:

A

Nucleic acids, energy, second messenger cAMP, Allosteric regulators, ‘handles’ for cofactors such as NADH, CoSH, etc.

38
Q

Key parts to a nucleotide: ____ is linked through a nitrogen to a ____ ___ which is linked to a ____.

A

Base
Ribose sugar
Phosphate

39
Q

Nucleotide picture:

A
40
Q

Purines: ___ and ___
Pyrimidines: ___ and ___

A

Adenine and Guanine
Cytosine and thymine

41
Q

Base and nucleoside pairs:

A
42
Q

The ribose sugar component of nucleotides is derived from _____ _____ (PRPP).

A

5-phosphoribosyl 1-pyrophosphate

43
Q

Purines are constructed by adding atoms from ______, glutamine, glycine, Aspartate, and carbon dioxide sequentially to ____ ____.

A

Formyltetrahydrofolate
5-phosphoribosyl 1-pyrophosphate

44
Q

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.

A

Aspartate
Glutamine

5-phosphoribosyl 1-pyrophosphate (PRPP)

45
Q

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.

A

Ribose
Pyrophosphate
PRPP synthetase
Purine diphosphonucleosides (GDP and ADP)

46
Q

Purine synthesis:
The first committed step is the transfer of an ____ from glutamine by the ____ ____ ____. The second step is addition of glycine to make ____ ___ ____.

A

Amine

Glutamine phosphoribosyl amidotransferase

Glycinamide ribosyl 5-phosphate

47
Q

Purine synthesis:
___ and ___ are added from N10-formyltetrahydrofolate, carbon dioxide, glutamine, and Aspartate to form _____ ____.

A

Carbon
Nitrogen
Inosine monophosphate (IMP)

48
Q

Inosine monophosphate then gains an amine from _____ to form ____ ____, or an amine from ____ to form ___ ___.

A

Aspartate
Adenosine monophosphate

Glutamine
Guanosine monophosphate

49
Q

Purine synthesis: review of the urea cycle
_____ is an amine donor in the urea cycle
____ is cleaved off arginosuccinate

A

Aspartate
Fumarate

50
Q

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 ____.

A

IMP
AMP
Aspartate
Fumarate
AMP
GTP

51
Q

Purine metabolism: Anaplerotic
Through the purine nucleotide cycle, ___ from protein breakdown can supply ____ to the TCA cycle as an _____ substrate.

A

Aspartate
Fumarate
Anaplerotic substrate

52
Q

Purine synthesis:
To form guanosine monophosphate, ____ is first oxidized to ___ ____. Then an amine group is transfers from ____, using ATP hydrolysis to power the reaction.

A

IMP
xanthine monophosphate
Glutamine

53
Q

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 ____.

A

Phosphorylated
Phosphorylated
ATP
GTP
dADP
dGDP

54
Q

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.

A

Ribose
Reduced
Thioredoxin
Cysteine

55
Q

Purine metabolism:

A
56
Q

Ribonucleotide reductase (RR) uses ___ ____ as substrates.

A

Nucleoside diphosphates

57
Q

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.

A

AMP
GMP

58
Q

Purine salvage:
To convert free bases to nucleotides, ______ (APRT and HGPRT) add ribose from _____ ____ (PRPP).

A

Phosphoribosyltransferases
5-phosphoribosyl 1-pyrophosphate

59
Q

Purine salvage:
To convert nucleosides to nucleotides, ____ ____ ____ removes ribose, leaving the free base.

A

Purine nucleoside phosphorylates

60
Q

Purine salvage:
Adenosine can be converted adenosine monophosphate (AMP) directly through phosphorylation by ___ ___.

A

Adenosine kinase

61
Q

____ ____: 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.

A

Purine salvage

62
Q

Purine salvage highlights:

A
63
Q

Purine catabolism:
GMP and AMP are degraded to _____, which is oxidized to uric acid by ____ ___, which uses a _____ atom in its catalytic site.

A

Xanthine
Xanthine oxidase
Molybdenum

64
Q

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 ____.

A

Hyperuricemia
Uric acid
Uric acid
Gout

65
Q

Pyrimidines:
In contrast to purines, which are assembled on a ribose sugar, Pyrimidine bases are first assembled then ____ to a ribose sugar.

A

Transferred

66
Q

Pyrimidine synthesis:
_____ ____ ____ ____ (CPS II) used glutamine as an amine donor to form carbamoyl phosphate. CPS II is allosterically inhibited by ____ and activated by ____.

A

Cytosolic carbamoyl phosphate
UTP
PRPP

67
Q

Pyrimidine synthesis:
Carbamoyl phosphate bonds with ____ to make carbamoyl Aspartate, which is then cyclized to ____.

A

Aspartate
Orotate

68
Q

Orotate combines with ____ to make a nucleotide, which is then decarboxylated to form ____ ____.

A

PRPP
Uridine monophosphate (UMP)

69
Q

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.

A

Carbamoyl phosphate
Orotic acid

70
Q

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.

A

Ribonucleotide reductase (RR)
Thymidine synthase
Dephosphorylated
Phosphorylated
DNA

71
Q

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.

A

dTTP
anti-metabolites
5-fluorouracil

72
Q

Pyrimidine catabolism:
Unlike purine degradation, accumulation of Pyrimidine metabolites are not associated with ____.

A

Pathology

73
Q

Pyrimidine catabolism:
Cytosine is degraded to ____
Thymine is degraded to _____

A

Beta-alanine
Beta-aminoisobutyrate

74
Q

Disorders of nucleotide metabolism:

A
75
Q

____ ____ ____ 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:

A

PRPP synthetase superactivity
Purine
Uric acid

Uric acid crystalluria, urinary stones, and gout arthritis

Neurodevelopmental disorders

76
Q

In PRPP synthetase superactivity disorder, the ___ ___ of the enzyme is lost.

A

Allosteric inhibition

77
Q

Review:

A
78
Q

Review case:

A
79
Q

Review case:

A
80
Q

Case review:

A
81
Q

Adenosine deaminase deficiency severe combined immunodeficiency:

A
82
Q

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:

A

SCID
adenosine
2-deoxyadenosine

Low lymphocyte count, costrochondal junction dysplasia

Bone marrow transplant , chemotherapy

83
Q

Review case:

A
84
Q

Review case:

A
85
Q

Review case:

A
86
Q

Review case:

A
87
Q

____ ____ ____ deficiency is a rare cause if combined immunodeficiency. Symptoms include low but not absent T cells, chronic infections, failure to thrive, neurologic symptoms.

A

Purine nucleoside phosphorylase (PNP)

88
Q

______ 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.

A

Lesh-Nyhan

Hypoxanthine-guanine phopsphoribosyltransferase

Uric acid
Renal
Allopurinol

89
Q

Animal models suggest a disturbance in ___ ___ as a cause of self mitigation in Lesch-Nyhan.

A

Dopamine signaling

90
Q

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.

A

Allopurinol
Xanthine oxidase
Allopurinol