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Blake_Biochemistry Test II > Blake_Biochem_20-21_Nucleotides > Flashcards

Blake_Biochem_20-21_Nucleotides Flashcards

1
Q

Nucleotides

A

Phosphate esters of nucleosides

Containe a base, a sugar, and a phosphate

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2
Q

Heirarchy of Nucleic acids

A
  • Nucleic acids (polynucleotides)
    • Covalently-Bonded Nucleotides
    • H-Bond bind complementary Nucleic Acids
  • Nucleotides (base - sugar - phosphate)
    • Nucleosides
    • Phosphoric Acid
  • Nucleosides
    • Bases (purines and pyrimidines)
    • Sugars (ribose and deoxyribose
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3
Q

Nucleosides

A

a base (purine or pyrimidine) with a sugar (ribose or deoxyribose) with NO phosphate

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4
Q

List the Purine bases

A

Adenine*

Guanine*

Hypoxanthine

Xanthine

*involved in genetic code

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5
Q

List the pyrimidine bases

A

Cytosine

Uracil

Thymine

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6
Q

Nucleoside of Hypoxanthine

A

Inosine

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7
Q

How are nucleosides abreviated?

A

Prefix+sine

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8
Q

How are nucleotides abbreviated?

A

Nucleoside monoposphate

eg Inosine -> IMP

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9
Q

how are ribose nucleotides converted to deoxynucleotides?

A

ribonucleotide reductase

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10
Q

what else is required for reduction of ribose by rionucleotide reductase?

A

NADPH

(ATP stimulates)

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11
Q

what inhibits ribonucleotide reductase?

A

dATP

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12
Q

How are sugars (ribose or deoxyribose) attached to bases?

A

N-glycosidic bond

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13
Q

what kinds of bonds attach the first phosphate to the ribose-sugar in a nucleotide?

A

Phosphoric acid ester bonds

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14
Q

what kind of bonds link the 2nd and 3rd phosphates to a nucleotide?

A

Phosphoric acid anhydride bonds

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15
Q

Hydrolysis Energies:

ATP⇒ADP+Pi

ATP⇒AMP+PPi

PPi⇒Pi+Pi

A
  • ATP⇒ADP+Pi (Delta G= -7.3 kcal/mol)
  • ATP⇒ AMP+PPi (DeltaG= -10.9 kcal/mol)
  • PPi ⇒Pi+Pi (DeltaG= -4.0kcal/mol)
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16
Q

How many base pairs per turn of the double helix?

How long is the spacing of one nucleotide pair?

A

10

3.4Å

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17
Q

What is the rate limiting nucleotide in DNA synthesis?

Why?

A

Thymine

The fact that TTP is almost never synthesized and only dTTP is generated, unlike the other 3. The other 3 are synthesized at a higher concentration because they can be incorporated into RNA and readily available to be reduced to dNTPs for DNA when needed. So, the concentration of dTTP have to reach a level equal to the other dNTPs before DNA synthesis can begin.

18
Q

How is DNA/RNA digested?

A
  • ribonucleases (RNA); deoxyribonucleases (DNA) separate chains of double helix to leave short oligomers
  • Phosphodiesterase seperates nucleic acids to form Nucleotides (NMP or dNMP)
  • Nucleotidase cleaves phosphate groups to form Nucleosides
  • Nucleosidase cuts N-glycosidic bonds to cleave base and ribose-sugars
19
Q

ADA

A

Adenosine Deaminase

Plays an important role in adenosine homeostasis and modulates signaling by extracellular adensosine and so contributes indirectly to signaling

20
Q

Overproduction of ADA

A

Causes hemolytic anemia (rare). Increased degradatioin of adenosine depletes adenine nucleotide pool and triggers premature destruction of RBCs

21
Q

Underproduction of ADA

A

associated with the second most comon form of severe combined immunodeficiency (SCID)

22
Q

Xanthine Oxidase

A
  • Catalyzes the oxidation of hypoxanthine to xanthine AND xanthine to Uric acid
  • Has 2 Flavin adenine dinucleotides (FADs), 2 Mo atoms, and 8 Fe atoms per moledule of enzyme
  • Drug target for Allopurinol in the treatment of Gout
23
Q

GOUT

  • How is gout identified?
  • What are the two types?
  • Why is gout painful?
  • What are preventable causes?
  • What is the standard treatment?
A
  • high levels of uric acid in the blood
  • Primary hyperuricemia (over production of UA); Secondary hyperuricemia (under-extretion of UA)
  • Sodium Urate precipitate; Phagocytic cells release factors that innitiate and acute inflammatory response
  • Diet: purines: beans, meat, seafood, alchohol
  • colchicine (deceases movement of granulocytes to affected area); Allopurinol (inhibits xanthine oxidase)
24
Q

GOUT

  • What is the normal serum U.A. level?
  • Urinaty U.A.?
A
  • adult males: 4-8.6mg/dL
  • adult females: 3-5.9mg/dL
  • <750mg/24hr
25
Q

Pyrimidine Nucleotide Catabolism:

UTP ptwy:

Substrate/Enzyme

A
  • (d)UTP/nucleotidase
  • ⇒Uridine or (DeoxyU)/Uridine phosphorylase
  • ⇒Uracil + ribose 1-P (or 2-deoxyribose 1-P)
  • ⇒ß-alanine
  • ⇒Malonyl CoA (ketogenic)
26
Q

Pyrimidine Nucleotide Catabolism:

Substrates/Enzymes:

A
  • dTTP to Deoxythymidine/nucleotidase
  • Deoxythymidine to Thymine/Uridine phosphorylase
  • ⇒Thymine + 2-deoxyribose 1-P
  • ⇒ß-aminoisobutyrate
  • ⇒Methylmalonyl CoA (glucogenic) +Succinyl CoA (glucogenic)
27
Q

Purine Nucleotide Catabolism:

GMP ptwy

substrate/Enzyme

A
  • GM​P/nucleotidase
  • Guanosine/PNP (purine nucleoside phosphorylase
  • Guanine +Ribose 1-P/Guanine deaminase
  • Xanthine/Xanthine oxidase
  • Uric Acid
28
Q

Pyrimidine Nucleotide Catabolism:

CTP ptwy:

Substrate/Enzyme:

A
  • (d)CTP/nucleotidase
  • ⇒Cytosine (deoxyC)/ aminohyrolase
  • ⇒Uridine or Deoxyuridine/Uridine phosphorylase
  • ⇒Uracil + ribose 1-P (or 2-deoxyribose 1-P)
  • ⇒ß-alanine
  • ⇒Malonyl CoA (ketogenic)
29
Q

Purine Nucleotide Catabolism:

Adenosine Ptwy

Substrate/Enzyme

A
  • AMP/nucleotidase
  • Adenosine/Adenosine Deaminase (ADA)
  • Inosine/Purine Nucleoside Phosphorylase (PNP)
  • Hypozanthine + Ribose 1-P/ Xanthine Oxidase
  • Xanthine/ Xanthine Oxidase
  • Uric Acid
30
Q

Purine Nucleotide Catabolism

IMP ptwy

Enzyme/Substrate

A
  • AMP/ AMP deaminase
  • IMP + Phosphate
  • Inosine/ PNP
  • Hypoxanthine/ Xanthine Oxidase
  • Xanthine/ Xanthine Oxidase
  • Uric Acid
31
Q

Phase I-III: Purine Synthesis:

  • Substrate to Products/Enzyme
    • +/-
    • byproducts or additional substrate
A
  • I. a-D-ribose 5P to PRPP/PRPP synthease
    • +Pi/ - Purine Nucleotides (GMP, AMP, IMP)
    • ATP⇒AMP
  • II: PRPP to PRA/glutamine PRPP Amidotransferase
    • + PRPP/ - Purine Nucleotides (GMP, AMP, IMP)
    • Gln⇒Glu, ⇒PPi
  • III: PRA to IMP/ 9 rxns (tetrahydrofolate: N10-fTHF)
    • - Methotrexate
    • ​CO2, Gly, Gln, Asp, N10-fTHF (additional substrates)
32
Q

Methotrexate

A
  • Antineoplastic agent
  • inhibits DNA replication/synthesis
  • Binds dihydrofolate reductase 100x more tightly
33
Q

Phase IV Purine Synthesis:

GMP ptwy

  • Substrate to Products/Enzyme
    • +/-
    • Byproducts or additional substrates
A
  • IMP to XMP (xanthosine phosphate)/ IMP dehyrogenase
      • GMP
    • NAD+ ⇒ NADH
  • XMP to GMP/ GMP synthase
    • Gln ⇒Glu, ATP⇒AMP +PPi
  • GMP to GDP/ 2 paths
    1. ​GDP to dGDP/ribonucleotide reductase
      • dGDP to dGTP
    2. GDP to GTP
34
Q

Phase IV Purine Synthesis:

AMP ptwy

  • Substrate to Products/Enzyme
    • +/-
    • Byproducts or additional substrates
A
  • IMP to adenlylosuccinate MP/ adenylosuccinate synthease
    • -AMP
    • Asp ⇒, GTP⇒GDP
  • Adenylosuccinate MP to AMP
    • ​⇒Fumarate (used in TCA)
  • AMP to ADP/2 paths
    1. ADP to dADP/ribonucleotide reductase
      • ​dADP to dATP
    2. ​ADP to ATP
35
Q

Phase I Pyrimidine Synthesis:

4 steps

  • Substrate to Products/Enzyme
    • +/-
    • Byproducts or additional substrates
A
  • Gln to Carbamoylphosphate/Carbaboyl Phosphate Synthease II
    • +PRPP/-UTP
    • ⇒Glu, 2ATP⇒2ADP, HCO3-(in), Pi (out)
  • Carbanoylphosphate to Carbamoyl Aspartate/ Aspartate transcarbomylase
    • Asp(in), Pi (out)
  • Carbamoyl Aspartate to Dihydroorotate/ dihydroorotase
    • ​H2O (out)
  • Dyhydroorotate to Orotate/ dyhydroorotate dehydrogenase
36
Q

Phase II Pyrimidine Synthesis:

2 steps

  • Substrate to Products/Enzyme
    • +/-
    • Byproducts or additional substrates
A
  • Orotate to OMP/ UMP synthase
    • PRPP (in), PPi (out)
  • OMP to UMP/ UMP synthase
    • H2O (in), HCO3- (out)
37
Q

Phase III Pyrimidine Synthesis:

dTTP

5steps

  • Substrate to Products/Enzyme
    • +/-
    • Byproducts or additional substrates
A
  • UMP to UDP/ Phosphorylase
    • Pi (in)
  • UDP to dUDP/ ribonucleotide reductase
    • H2O (out)
  • dUDP to dUMP/ UTP kinase
  • dUDP to dUTP to dUMP/ dUTPase
  • dUMP to dTMP/Thymidylate synthase
    • N5,N10-mTHF⇒Dihydrofolate
  • dTMP to dTDP to dTTP
38
Q

Phase III Pyrimidine Synthesis

dCTP

5steps

  • Substrate to Products/Enzyme
A
  • UMP to UDP/ ? phosphorylase
  • UDP to UTP/ ? phosphorylase
  • UTP to CTP/ CTP synthase
  • CTP to CDP/ ? kinase
  • CDP to dCDP/ ribonucleotidase reductase
  • dCDP to dCTP/ ? phosphorylase
39
Q

Purine Nucleotide Salvage Pathway

A
  • Adenine to AMP/ Adenine Phosphoribosyl Transferase (APRT)
    • PRPP to PPi
  • Guanine (or Hypoxanthine) to GMP (or IMP)/ Hypoxanthine-guanine phophorybosyl-transferase (HGPRT)
    • PRPP to PPi
40
Q

Pyrimidine Nucleotide Salvage Pathway

A
  • Uracil
    • Uracil to Uridine/ Uridine phosphorylase
      • Ribose 1-P to Pi
    • ​Uridine to UMP/ Kinase
    • UMP to UDP to UTP/ Phoshphorylase
  • Thymine
    • Thymine to Deoxythymidine/ thymidine phosphorylase
      • 2-deoxyribose 1-P to Pi
    • Deoxythymidine to dTMP/ thymidine kinase
    • dTMP to dTDP to dTTP/ Phosphorylase

Blake_Biochemistry Test II (11 decks)

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