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Biochem Exam 3 > Purine & Pyrimidine > Flashcards

Purine & Pyrimidine Flashcards

1
Q

Nucleotide structure

A

Base + Pentose + p

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2
Q

Which type of base has 2 rings?

A

Purines

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3
Q

Which are the Purines?

A

A+G

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4
Q

Which are Pyrimidines?

A

C+U+T

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5
Q

Where is the OH attached on Ribose?

A

2’ C

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6
Q

What can be salvaged?

A

Both Purines and Pyrimidines

Sugar+Base

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7
Q

Denovo synthesis takes place mainly where?

A

Brain and Liver

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8
Q

How do we build purines?

A

Start with R5P and build on the purine base

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9
Q

How do we build pyrimidines?

A

Synthesize with the pyrimidine ring then attach the R5P

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10
Q

Purine ring energy cost

A

6 ATP per nucleotide

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11
Q

How many N’s in Purine ring?

A

4

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12
Q

Where does N1 come from on purine?

A

Aspartate

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13
Q

Where does N3 come from on Purine?

A

Glutamine

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14
Q

Where does N9 come from on Purine?

A

Glutamine

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15
Q

Where does N7 come from on Purine?

A

Glycine

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16
Q

Where to the Purine Carbons come from?

A

C2 and C8 from THF
C6 from Bicarb
C4 and C5 from Glycine

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17
Q

Purine Synthesis requires what substrate?

A

PRPP

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18
Q

What are the constituents of PRPP

A

R5P, ATP, Pyrophosphate

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19
Q

Committed step of Purine Synthesis?

A

Phosphoribosyl Amidotransferase (PRAT)

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20
Q

Purine Synthesis major intermediate

A

IMP

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21
Q

IMP synthesis Pathway?

A

(Glutamine+PRPP), Glycine, Formyl THF, Glutamine, CO2, Aspartate, Formyl THF

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22
Q

4 Regulated Reactions of Purine Synthesis (and what regulates them)

A
  1. PRPP Synthase (-ADP/GDP)
  2. PRAT (A & G Mono, Di, Triphosphates)
  3. IMP DH (-GMP)
  4. Adenylosuccinate Synthetase (-AMP)
23
Q

Lesch Nyhan Syndrome Cause, Sx, Tx?

A

HGPRTase deficiency = No salvage pathway
Everything shunted to URIC ACID (via increased de novo synthesis)
Sx = Severe Neuro and Nephrolithiasis
Tx = Allopurinol (helps Nephro Sx but not CNS)

24
Q

Purine Nucleoside Phosphorylase (PNP) … What does it do, and what happens when you don’t have it?

A

Normally takes inosine-> Hypoxanthine, Adenosine -> Adenine, and Guanosine -> Guanine. Basically converts nucleosides to free bases + Ribose-1P.

Nucleosides accumulate = Elevated dGTP = NO T-CELL function.

25
Q

SCID cause, Effects,

A

Adenosine Deaminase deficiency.

Buildup of dATP. This is toxic to T cells, B cells, and NK cells.
Also inhibits SAM hydroxylase = reduced methylation rxns and accumulation of S-Adenosylhomocysteine (SAH)

26
Q

Describe regulation in the Purine Salvage Pathway (3 ways is regulated or regulates stuff)

A

IMP/GMP inhibits HGPRTase
AMP inhibits APRTase

These also feed back to the de novo synthesis path enzymes (IMPDH and Adenylosucc. Synthetase)

PRPP is used in salvage, so it isn’t available as a substrate for de novo.

27
Q

Causes of Hyperuricemia and Gout

A

High PRPP Synthetase activity (R5P –> PRPP)
HGPRTase deficiency
VonGierkes

28
Q

How the hell does VonGierke’s result in hyperuricemia and gout anyway?

A

No Glucose 6 Phosphatase = Buildup of G6P, which gets shunted into the Pentose Phosphate Pathway. This results in increased R5P, which is a precursor to PRPP, resulting in increased denovo synthesis of purines and synthesis of uric acid.

29
Q

Overall salvage pathway

A

AMP –> IMP –> HX —> Xanthine Uric Acid —> Urate

30
Q

Link Between Fructose and gout?

A

Fructose metabolism = increased Fructose-6P

This drains the (P) pool, which lowers ATP available.

This results in increased Uric Acid.

31
Q

Pyrimidine synthesis starts with

A

N base, then you add sugar and phosphate

32
Q

Where do N’s come from on Pyrimidine? C’s?

A

Asp gives C4+5 and N1
Bicarb gives C2
Glutamine gives N3

33
Q

Overall Pyrimidine Synthesis Reaction

A

Carbamoyl Phosphate –> N-CP –> Dihidroorotate –> Orotate –> OMP –> UMP

34
Q

High orotate is indicative of what?

Why?

A

OTC defect in urea cycle

Orotate is a small base and can leak out cell

35
Q

UMP synthase function? What happens when you are deficiency?

A 
Dual function enzyme... 
-Orotate phosphoribosyltransferase
-OMP decarboxylase
(takes Orotate --> OMP and OMP--> UMP)
Deficiency = HEREDITARY OROTIC ACIDURIA
36
Q

Difference between NDP and NTP synthesis…

A

NDPs are made base-specific

NTPs are made with broad specificity

37
Q

NDP synthesis (enzyme and reaction)

A

Adenylate Kinase and Guanylate Kinase
(=Nucleoside Monophosphate Kinases)

AMP + ATP –> 2ADP

38
Q

NTP synthesis (enzyme and reaction)

A

Nucleoside Diphosphate Kinase

GDP + ATP —> GTP + ADP
intervonversion

39
Q

Deoxynucleotide Synthesis first 2 steps (including RLS)

A

make the ribonucleotide first, then deoxify!
RLS / 1st step = Ribonucleotide reductase (ex. ADP–>dADP)
2nd Step = Nucleoside-5-diphosphate kinase (ex. dADP –> dATP)

40
Q

Weird stuff with dNT synthesis

A

dCDP –> dCTP
-OR-
dCMP –> dUMP via DEOXYCYTIDYLATE DEAMINASE

dUDP –> dUMP

dUMP (from either of the above)–>dTMP via THYMIDYLATE SYNTHASE

41
Q

Effect of deoxyribonucleotides? When are they elevated?

A

Toxic! Normally only elevated in S-Phase

42
Q

Ribonucleotide Reductase properties (4)

A

RLS for dNT synthesis
Requires THIOREDOXIN
2 sites: Activation and Specificity
ATP activates, dATP feedback inhibits

43
Q

dTMP synthesis enzyme

A

Thymidylate synthase, needs N5N10 THF

44
Q

N5N10THF is converted to ___ during dTMP synthesis?

A

Dihydrofolate

Regenerated by

(1) Dihydrofolate Reductase (–>THF)
(2) Hydroxymethyltransferase (N5N10)

45
Q

Inhibitors of dihydrofolate reductase

A

Aminopterin and Methotrexate

46
Q

The Thymidylate Synthase inhibitor that also inhibits dTMP synthesis is…

A

Fluorouracil

47
Q

Fluorouracil function, use, and mechanism

A

Inhibits thymidylate synthase
Treatment for SOLID tumors
f-UTP is incorporated into RNA which inhibits Ribosome maturation

48
Q

What is fdUMP? and what does it do?

A

Inhibitor of thymidylate synthase (via fluorouracil), keeps dUMP to incorporate into DNA, resulting in strand breakage.

49
Q

Cytosine Arabinoside Mechanism and use

A

5’ Triphosphate that incorporates into DNA and inhibits synthesis
Used for leukemia

50
Q

What does methotrexate inhibit? why doesn’t this work on all cells?

A

It inhibits Dihydrofolate Reductase (DHF–>THF)

Normal cells are rescued by N5-Formyl-THF (LEUCOROVIN, an analog that can be used similarly)

51
Q

Hydroxyurea function and mechanism

A

Inhibits DNA synthesis (not RNA or protein)

Acts on Ribonucleotide reductase

52
Q

Acyclovir and Gancyclovir properties, mechanism, uses

A

Purine analog that inhibits viral Thymidine Kinase (mammals can’t use it)

In virus it is activated to monophosphate

Acyclovir for HSV, Gan for CMV retinitis

53
Q

AZT properties and mechanism

A

Pyrimidine analog

Blocks HIV by inhibiting DNA

54
Q

Fialuridine used for ___

A

Hep B

Biochem Exam 3 (10 decks)

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