Purine & Pyrimidine

Question 1

Nucleotide structure

Answer 1

Base + Pentose + p

Question 2

Which type of base has 2 rings?

Answer 2

Purines

Question 3

Which are the Purines?

Answer 3

A+G

Question 4

Which are Pyrimidines?

Answer 4

C+U+T

Question 5

Where is the OH attached on Ribose?

Answer 5

2’ C

Question 6

What can be salvaged?

Answer 6

Both Purines and Pyrimidines

Sugar+Base

Question 7

Denovo synthesis takes place mainly where?

Answer 7

Brain and Liver

Question 8

How do we build purines?

Answer 8

Start with R5P and build on the purine base

Question 9

How do we build pyrimidines?

Answer 9

Synthesize with the pyrimidine ring then attach the R5P

Question 10

Purine ring energy cost

Answer 10

6 ATP per nucleotide

Question 11

How many N’s in Purine ring?

Answer 11

4

Question 12

Where does N1 come from on purine?

Answer 12

Aspartate

Question 13

Where does N3 come from on Purine?

Answer 13

Glutamine

Question 14

Where does N9 come from on Purine?

Answer 14

Glutamine

Question 15

Where does N7 come from on Purine?

Answer 15

Glycine

Question 16

Where to the Purine Carbons come from?

Answer 16

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

Question 17

Purine Synthesis requires what substrate?

Answer 17

PRPP

Question 18

What are the constituents of PRPP

Answer 18

R5P, ATP, Pyrophosphate

Question 19

Committed step of Purine Synthesis?

Answer 19

Phosphoribosyl Amidotransferase (PRAT)

Question 20

Purine Synthesis major intermediate

Answer 20

IMP

Question 21

IMP synthesis Pathway?

Answer 21

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

Question 22

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

Answer 22

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

Question 23

Lesch Nyhan Syndrome Cause, Sx, Tx?

Answer 23

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)

Question 24

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

Answer 24

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.

Question 25

SCID cause, Effects,

Answer 25

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)

Question 26

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

Answer 26

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.

Question 27

Causes of Hyperuricemia and Gout

Answer 27

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

Question 28

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

Answer 28

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.

Question 29

Overall salvage pathway

Answer 29

AMP --> IMP --> HX ---> Xanthine Uric Acid ---> Urate

Question 30

Link Between Fructose and gout?

Answer 30

Fructose metabolism = increased Fructose-6P This drains the (P) pool, which lowers ATP available. This results in increased Uric Acid.

Question 31

Pyrimidine synthesis starts with

Answer 31

N base, then you add sugar and phosphate

Question 32

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

Answer 32

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

Question 33

Overall Pyrimidine Synthesis Reaction

Answer 33

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

Question 34

High orotate is indicative of what? | Why?

Answer 34

OTC defect in urea cycle Orotate is a small base and can leak out cell

Question 35

UMP synthase function? What happens when you are deficiency?

Answer 35

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

Question 36

Difference between NDP and NTP synthesis...

Answer 36

NDPs are made base-specific | NTPs are made with broad specificity

Question 37

NDP synthesis (enzyme and reaction)

Answer 37

Adenylate Kinase and Guanylate Kinase (=Nucleoside Monophosphate Kinases) AMP + ATP --> 2ADP

Question 38

NTP synthesis (enzyme and reaction)

Answer 38

Nucleoside Diphosphate Kinase GDP + ATP ---> GTP + ADP **intervonversion**

Question 39

Deoxynucleotide Synthesis first 2 steps (including RLS)

Answer 39

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

Question 40

Weird stuff with dNT synthesis

Answer 40

dCDP --> dCTP -OR- dCMP --> dUMP via DEOXYCYTIDYLATE DEAMINASE dUDP --> dUMP dUMP (from either of the above)-->dTMP via THYMIDYLATE SYNTHASE

Question 41

Effect of deoxyribonucleotides? When are they elevated?

Answer 41

Toxic! Normally only elevated in S-Phase

Question 42

Ribonucleotide Reductase properties (4)

Answer 42

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

Question 43

dTMP synthesis enzyme

Answer 43

Thymidylate synthase, needs N5N10 THF

Question 44

N5N10THF is converted to ___ during dTMP synthesis?

Answer 44

Dihydrofolate Regenerated by (1) Dihydrofolate Reductase (-->THF) (2) Hydroxymethyltransferase (N5N10)

Question 45

Inhibitors of dihydrofolate reductase

Answer 45

Aminopterin and Methotrexate

Question 46

The Thymidylate Synthase inhibitor that also inhibits dTMP synthesis is...

Answer 46

Fluorouracil

Question 47

Fluorouracil function, use, and mechanism

Answer 47

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

Question 48

What is fdUMP? and what does it do?

Answer 48

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

Question 49

Cytosine Arabinoside Mechanism and use

Answer 49

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

Question 50

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

Answer 50

It inhibits Dihydrofolate Reductase (DHF-->THF) Normal cells are rescued by N5-Formyl-THF (LEUCOROVIN, an analog that can be used similarly)

Question 51

Hydroxyurea function and mechanism

Answer 51

Inhibits DNA synthesis (not RNA or protein) Acts on Ribonucleotide reductase

Question 52

Acyclovir and Gancyclovir properties, mechanism, uses

Answer 52

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

Question 53

AZT properties and mechanism

Answer 53

Pyrimidine analog Blocks HIV by inhibiting DNA

Question 54

Fialuridine used for ___

Answer 54

Hep B