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biochem > Nucleotide Metabolism Lecture 1-4 - Dr. Venk > Flashcards

Nucleotide Metabolism Lecture 1-4 - Dr. Venk Flashcards

1
Q

For de novo synthesis of purine, name three amino acids that are required

A

glutamine (nitrogen)
aspratate (nitrogen)
glycine (carbon and nitrogen)

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2
Q

Name the cofactor (vitamin derivative) that serves as a carbon donor in purine syntehesis

A

THF

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3
Q

Name the ribose compound on which purines are constructed

A

Ribose-5-phosphate –> 5-phosphoribosyl 1-pyrophosphate (PRPP)

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4
Q

Name the rate limiting enzyme in purine synthesis and it’s positive and negative allosteric effectors

A

Enzyme: phosphoribosylamine Transferase (PRAT)

(+): PRPP
(-): AMP, IMP, GMP

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5
Q

Name a compound other than ATP that is used in the biosynthesis, which is common for fatty acid synthesis, urea cycle, purine and pyrimidine synthesis

A

Bicarbonate!

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6
Q

What is the common branch point precursor for AMP and GMP synthesis?

A

IMP

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7
Q

Name two rate limiting enzymes and their allosteric effectors in purine synthesis (After IMP production)

A

Adenylosuccinate synthase: (+) GTP

IMP dehydrogenase: (+) ATP

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8
Q

Name two salvage pathway enzymes

A

1) hypoxanthine-guanine phosphoribosyl transferase (HGPRT)

2) APRT

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9
Q

Name a cell type that is solely dependent upon salvage pathway enzymes for nucleotide synthesis

A

erythrocytes

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10
Q

Name the immediate precursor of uric acid

A

Xanthine

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11
Q

Name the enzyme that converts xanthine into uric acid

A

Xanthine Oxidase

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12
Q

Explain the reason for excess uric acid production in gout patients.

A

Increased PRPP synthetase activity or decreased HGPRT activity leads to overproduction of purine nucleotides due to the increased availability of PRPP. This leads to an overproduction of uric acid.

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13
Q

Name the nucleotide from which tetrahydrobiopterin is synthesized

A

GTP via cyclohydrolase

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14
Q

Name two drugs that are used for treatment of gout

A

Allopurinol and Alloxanthine (also cholchine)

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15
Q

Explain the reason for gout in Von Gierke’s patients

A

Decreased glucose 6-phosphatase activity leads to excess glusose 6-phosphate, which enters the HMP shunt and creates excess ribose-5-Phosphate. This leads to excess uric acid production.

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16
Q

Name two enzymes that are deficient in combined immunodeficiency

A

Adenosine deaminase (ADA) deficiency leads to defective T-cell and B-cell immunity

Purine nucleoside phosphorylase (PNP) deficiency leads to T-cell dysfunctions.

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17
Q

Carbamoyl phosphate synthase II, which is involved in pyrimidine synthesis is located in the _____ part of the cell.

A

cytosol

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18
Q

Name two amino acids that are required for pyrimidine synthesis

A

Glutamine and aspartate

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19
Q

True or False: Pyrimidine synthesis involves cytosolic as well as mitochondrial compartments

A

True

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20
Q

True or False: In pyrimidine synthesis, the ring structure is first formed and then the nitrogenous base is transferred to PRPP

A

True. Ring first then add PRPP

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21
Q

True or False: In purine synthesis, it is the PRPP molecule on which the purine ring is constructed

A

TRUE. PRPP starts first

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22
Q

OMP is converted to UMP by the enzyme _______.

A

UMP synthase

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23
Q

CTP is directly synthesized from the nucleotide ________.

A

UTP

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24
Q

Name the enzyme that is deficient in hereditary orotic aciduria

A

UMP synthase

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25
Q

Name an amino acid that serves as a carbon source for pyrimidine synthesis

A

Aspartate

26
Q

Ribonucleotide reductase converts NDP into dNDP and uses the coenzyme _________.

A

Thioredoxin

27
Q

For thioredoxin reductase activity, the reducing compound that is required is ________.

A

NADPH

28
Q

Name two enzymes that are required for deoxynucleotide synthesis

A

ribonucleotide reductase and thioredoxin reductase

29
Q

dCMP is converted into dUMP by the ________ enzyme

A

CMP deaminase

30
Q

dTMP is formed from dUMP by _________ which uses the cofactor _____.

A

thymidylate synthase ; N5-N10-Metylene THF

31
Q

The conversion of dihydrofolate to tetrahydrofolate during dTMP synthesis is catalyzed by the enzyme _____.

A

dihydrofolate reductase

32
Q

Name the four nucleotide triphosphates (dNTP) that are required for DNA synthesis

A

dATP, dGTP, dCTP, and dTTP.

33
Q

During the S phase of cell proliferation, name the enzymes that are upregulated in purine metabolism

A

PRPP amindotransferase

IMP dehydrogenase

34
Q

During the S phase of cell proliferation, name the enzymes that are upregulated in pyrimidine metabolism.

A

UMP synthase, CTP synthase, and CAD

35
Q

Name the respective vitamins that are required for the synthesis of FAD+, NAD+, and CoA

A

FAD+ : Vitamin B2 (riboflavin)
NAD+ : Vitamin B3 (niacin/nicatinamide)
CoA : Vitamin B5 (pantothenate)

36
Q

Name the amino acid that is required for CoA synthesis

A

Cysteine

37
Q

In CoA, the “Business end” of the molecule has the following group: __________

A

thiol

38
Q

Name two anti leukemic drugs.

A

6MP, FU, and AraC

39
Q

Describe the mechanism of action of 6-MP.

A

6-MP is transferred to PRPP to produce 6MP-ribonucleotide monophosphate, which is a negative effector of PRPP amidotransferase and adenylatosuccinate synthase. This results in the arrest of the de novo synthesis of DNA.

Can be prolonged by coadministering allopurinol.

40
Q

Describe the mechanism of action of 5-FU

A

Converted to FdUMP, an analog of dUMP. It is an inhibitor of thymidylate synthase, stopping dTMP synthesis.

41
Q

Describe the mechanism of action of AraC

A

With an arabinose carbohydrate moiety instead of the 2’-deoxy ribose of dNTP, DNA polymerizaiton terminates prematurely.

42
Q

Name a compound that inhibits tumor cell growth.

A

Hydroxyurea

43
Q

Describe the mechanism of action of TAD

A

inhibits IMP dehydrogenase b/c it decreases GTP availability

44
Q

Describe the mode of action of AZT.

A

A pyrimidine analog that is converted into AZT-triphosphate and gets incorporated into DNA, but cannot polymerize further since no phosphodiester bonds can form.

Affects viral RNA dependent DNA polymerase b/c they are 100x more sensitive to AZT.

45
Q

Describe the mode of action of Acyclovir.

A

Acyclovir is converted into its active form by viral thymidine kinase, which is converted into acycloguanosine triphosphate and incorporated into viral DNA. This results in the termination of polymerization b/c there is no deoxyribose available for polymerization.

46
Q

Name two glutamine antagonists

A

DON and Azaserine

47
Q

Describe the mode of action of MTX

A

MTX inhibits dihydrofolate reductase activity, preventing the conversion of dihydrofolate into tetrahydrofolatte. This reduces TMP production.

48
Q

Name the two types of drug resistance and the mechanisms of resistance

A

Specific Drug Resistance and Multi drug resistance

Specific Drug Resistance:

a) MTX resistance
b) Amplification of DHFR (dihydrofolate reductase)
c) DHFR isoform resistance to MTX

Multi-drug resistance
a) synthesis of MDR1 (glycoprotein) or MRP

49
Q

The nucleotide analog that is used in DNA sequencing is _________.

A

didoxy analogs (ddNTP)

50
Q

The DNA polymerase used in PCR reaction is obtained from the organism

A

Thermus aquaticus

51
Q

Name the components that are required for gene cloning

A

1) DNA template
2) Primers
3) normal dNTPS
4) DNA polymerase @ 37 degrees

52
Q

Name the steps of gene cloning.

A

1) Denaturation (melting) @ 95 degrees C
2) Annealing (Cooling) @ 44-55 degrees C
3) Synthesis @ 75 degrees C

53
Q

What is the role of restriction enzymes in molecular cloning?

A

To cut the DNA into vectors with similar endings so that they may be annealed back in any order/fashion

54
Q

Describe the process involved in molecular cloning.

A

1) Use restriction enzymes to create vectors of interest and cut open the cloning vector
2) Ligate the DNA of interest into plasmid
3) Transform bacteria by CaCl2 or heat shock method

55
Q

Name a few restriction enzymes.

A

EcoR1, Bgal1, HACIII

56
Q

Name a few recombinant screening techniques

A
  • antibiotic sensitivity toward ampicillin or kanamycin

- marker genes like beta-lactamase or beta-galactosidase (blue/white color selection method)

57
Q

FAD+ is formed from…

a) nicotinamide adenine dinucleotide and adenosine triphosphate (ATP)
b) beta alanine and beta-aminoisobutyrate
c) adenosine triphosphate (ATP) and flavin mononucleotide (FMN).
d) fiboflavin and deoxyguanosine triphosphate (dGTP)
e) riboflavin and ADP-ribose.

A

c) adenosine triphosphate (ATP) and flavin mononucleotide (FMN). (riboflavin)

58
Q

NAD+ is formed from…

a) nicotinamide adenine dinucleotide and adenosine triphosphate (ATP)
b) beta alanine and beta-aminoisobutyrate
c) adenosine triphosphate (ATP) and flavin mononucleotide (FMN).
d) fiboflavin and deoxyguanosine triphosphate (dGTP)
e) riboflavin and ADP-ribose.

A

a) nicotinamide adenine dinucleotide (niacin) and adenosine triphosphate (ATP)

59
Q

Coenzyme A is synthesized in part from

a) ATP and niacin
b) ATP and cysteine
c) CTP (cytidine triphosphate)
d) ATP and aspartate
e) GTP (guanosine triphosphate)

A

b) ATP and cysteine

pantothenate, 4 ATP, and Cysteine]

60
Q

PCR (polymerase chain reaction) might be used to amplify DNA for direct use in

a) a yeast expression system
b) a eukaryotic expression system
c) a bacterial expression system
d) a microarray experiment
e) sequencing

A

e) sequencing

biochem (10 decks)

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