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Metabolic Pathways > Lecture 6 (3B) - Purines Biosynthesis > Flashcards

Lecture 6 (3B) - Purines Biosynthesis Flashcards

1
Q

Nucleotides act as precursors of

A

nucleotides

DNA or RNA

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2
Q

Nucleotides and energy

A

critical components of metabolism - ATP

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3
Q

Nucleotides form structural parts of

A

coenzymes - CoA

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4
Q

Nucleotides as regulators and signal molecules

A

cAMP

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5
Q

Nucleotides and associated defects

A

inheritable diseases

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6
Q

Nucleotides - targets for

A

anti-microbials and anti-cancer agents

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7
Q

Nucleotide roles

A
  • precursors of nucleic acids - DNA or RNA
  • crtical components of energy metabolism - ATP
  • structural parts of coenzymes - CoA
  • regultors and signal molecules - cAMP
  • associated defects → inheritable diseases
  • targets for anti-microbials and anti-cancer agents
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8
Q

Purines

A

Adenine

Guanine

2 rings

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9
Q

Biosynthesis of purines

A

2 methods

  • de novo - forms inosine monophosphate
  • salvage pathway - reclaimed from hydrolytic degradation of nucleic acids and nucleotides
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10
Q

de novo synthesis

first there are

A

primer reactions

  • necessary before actual process
  • add (ortho) phosphate - activates bond then nucleophilic attack
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11
Q

de novo synthesis

Primer 1

activation of

A

α-D-ribose-5-phosphate

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12
Q

de novo synthesis

Primer 1

adds diphosphate to

A

C1 of ribose ring

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13
Q

de novo synthesis

Primer 1

requires

A

ATP

ATP → AMP + diphosphate (to C1)

  • retains α-configuration on ribose
  • forms 5-phosphoribosyl-α-pyrophosphate (PRPP)
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14
Q

de novo synthesis

Primer 1

forms

A

5-phosphoribosyl-α-pyrophosphate

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15
Q

de novo synthesis

Primer 1

PRPP

A

important precursor

  • pyrimidines
  • histidine
  • tryptophan

enzyme: ribose-pyrophosphokinase

(key enzyme)

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16
Q

de novo synthesis

Primer 1

key enzyme

A

ribose-pyrophosphokinase

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17
Q

de novo synthesis

the process

A

created from successive steps of activation followed by displacement by ammonia or a nucleophile

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18
Q

de novo synthesis

Primer 2

A

N9 atom

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19
Q

de novo synthesis

Primer 2

adds N9 to

A

C1 of ribose ring

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20
Q

de novo synthesis

Primer 2

requires

A

glutamine and water

  • N9 from glutamine amide side chain
    • glutamine → glutamate
  • inverts to β-configration on ribose
  • forms 5-phosphoribosyl-1-amine
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21
Q

de novo synthesis

Primer 2

glutamine → glutamate

A
  • N9 from glutamine amide side chain
  • inverts to β configuration on ribose
  • forms 5-phosphoribozyl-1-amine
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22
Q

de novo synthesis

Primer 2

important…

A

flux generating step

  • allows increase of purine production
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23
Q

de novo synthesis

Primer 2

enzyme

A

glutamine phosphoribosyl amidotransferase

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24
Q

The first COMMITTED step in purine biosynthesis

A

Primer 1

formation of 5-phosphoribosyl-1-amine

by glutamine phosphoribosyl amidotransferase

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25
After priming, 9 further steps to
create the purine ring * all require activation (phosphate addition) and nucleophilic attack (often by ammonia) to displace the addition * add on to activate, take off to make energetically favorable
26
de novo synthesis numbered steps
1. C4, C5, N7 atoms 2. C8 atom 3. N3 atom 4. ring closure 5. C6 atom 6. N1 atom 7. fumarate removed (energetically favorable) 8. C2 atom (onto N1 to close the molecule) 9. second ring closure
27
de novo synthesis 1. C4, C5, and N7 atoms
* only step where more than 1 purine ring atom is added * adds glycine to N9 * requires ATP: ATP → ADP + Pi * intermediate: phsphate added to carboxyl of glycine to activate it * activation with PO4 addition * glycine of carboxyl group forms peptide bond with N9 * forms **glycinamide ribonucleotide**
28
de novo synthesis 1. C4, C5, and N7 forms
glycinamide ribonucleotide
29
de novo synthesis 1. C4, C5, and N7 atoms requires
ATP
30
de novo synthesis 2. C8 atom
* adds formyl group to N7 * requires N10-formyl-THF * gives fromy group (C8 on N7 atom) * forms **formylglycinamide ribonucleotide** * activation → nucleophilic attack
31
de novo synthesis 2. C8 atom requires
N10-formyl-THF | (gives formyl group - C8 on N7 atom)
32
de novo synthesis 2. C8 atom forms
formylglycinamide ribonucleotide
33
de novo synthesis 3. N3 atom
* replaces O on C5 * requies glutamine, ATP, and water * N3 from side chain again (glutamine side chain to make glutamate) * added as ammonia (highly reactive + channel so won't react elsewhere, channeled from 1 site to the other) * ATP → ADP + Pi * inermediate adds phosphate * forms **formylglycinamidine ribonucleotide**​
34
de novo synthesis 3. N3 atom requires
glutamine, ATP, and water
35
de novo synthesis 3. N3 atom forms
formylglycinamidine ribonculeotide
36
de novo synthesis after step 3
have all necessary components of 5 membered ring ofpurine, now need ring closure
37
de novo synthesis 4. ring closure and rearrangement
* requires activation but no addition of anything * nucleopholic attack on self to make ring * N3 down off ring = ring must be made around * requires ATP * ATP → ADP + Pi * forms **5-aminoimidazole ribonucleotide**​​
38
de novo synthesis 4. ring closure requires
ATP ATP → ADP + Pi
39
de novo synthesis 4. ring closure forms
5-aminoimidazole ribonucleotide
40
de novo synthesis 5. C6 atom
* adds CO2 to C5 * requires * HCO3- (bicarbonate) * ATP (ATP → ADP + Pi) * added to other side (on C5 atom) * added as bicarbonate, utilization of biotin * 2 steps - attacks on N3 atom 1. displace CO2 onto N3 2. CO2 moved to C5 * forms **carboxyaminoimidazole ribonucleotide**
41
de novo synthesis 5. C6 atom requires
* HCO3- (bicarbonate) * ATP (ATP → ADP + Pi)
42
de novo synthesis 5. C6 atom 2 steps
attacks N3 atom 1. displace CO2 onto N3 2. CO2 moved to C5
43
de novo synthesis 5. C6 atom forms
carboxyaminoimidazole ribonucleotide
44
de novo synthesis 6. N1 atom
* adds aspartate to C6 * aspartate gives N1 - like urea cycle * requires aspartate and ATP (ATP → ADP + Pi) * similar to step 3 * activation → nucleophilic attack * forms** 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide**
45
de novo synthesis 6. N1 atom requires
* aspartate * gives N1 - like urea cycle * ATP * ATP → ADP + Pi
46
de novo synthesis 6. N1 atom forms
5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide
47
de novo synthesis 7. fumarate removed
* energetically favorable * only step where nothing is added or ring closure * only step where something's removed * eliminates fumarate * forms **5-aminoimidazole-4-carboxamide ribonucleotide**
48
de novo synthesis 7. fumarate removed requires
NOTHING eliminates fumarate
49
de novo synthesis 7. fumarate removed forms
5-aminoimidazole-4-carboxamide ribonucleotide
50
de novo synthesis 8. C2 atom (onto N1 to close the molecule)
* C2 atom onto N1 to close the molecule * adds formyl group to N1 * requires N10-formyl-THF * phosphate activation + nucleophilic attack displaces it * forms **5-formiminoimidazole-4-carboxamide ribonucleotide**​​
51
de novo synthesis C8. C2 atom (onto N1 to close the molecule) requires
N10-formyl-THF
52
de novo synthesis 8. C2 atom (onto N1 to close the molecule) forms
5-formiminoimidazole-4-carboxamide ribonucleotide
53
de novo synthesis 9. second ring closure
* condensation reaction * forms **INOSINE MONOPHOSPHATE** * IMP = precursor to purines used in body * AMP, GMP * IMP is branch point * one branch forms AMP * other branch forms GMP
54
Biosynthesis of AMP
1A. Addition of aspartate * aspartate added to C6 atom * requires energy * requires aspartate and GTP * GTP → GDP + Pi * forms **adenylosuccinate**​​ 2A. Fumarate removed * identical to step 7 (of purine synthesis) * eliminates fumarate * forms **adenosine monophosphate (AMP)**
55
Biosynthesis of AMP 1A. addition of aspartate
* aspartate added to C6 atom * requires aspartate and GTP * forms **adenylosuccinate**​​
56
Biosynthesis of AMP 1A. addition of aspartate requires
aspartate and GTP
57
Biosynthesis of AMP 1A. addition of aspartate forms
adenylosuccinate
58
Biosynthesis of AMP 2A. fumarate removed
* identical to step 7 * eliminates fumarate * forms **adenosine monophosphate (AMP)**
59
Biosynthesis of AMP 2A. forms
adenosine monophosphate (AMP)
60
Why use GTP? | (step 1A in biosynthesis of AMP)
* would destroy ATP to make monophosphate (AMP) which wouldn't make sense * illogical to use energy from ATP * more sense to use GTP to make AMP
61
Biosynthesis of GMP
1B. oxygen onto C2 atom * oxygen replaces a hydrogen * requires NAD+ and water NAD+ + H2O → NADH + H+ (redox) * forms **xanthosine monophosphate (XMP)** 2B. oxygen replaced on C2 atom * amides replace oxygen * requires glutamine, ATP, and water * N from glutamine side chain ATP + H2O → AMP + PPi * forms **guanosine monophosphate (GMP)**
62
Biosynthesis of GMP 1B. oxygen onto C2 atom
* oxygen replaces a hydrogen * requires NAD+ and water NAD+ + H2O → NADH + H+ * forms **xanthosine monophosphate (XMP)**
63
Biosynthesis of GMP 1B. oxygen onto C2 atom requires
NAD+ and water NAD+ + H2O → NADH + H+ (redox)
64
Biosynthesis of GMP 1B. oxygen onto C2 atom forms
xanthosine monophosphate (XMP)
65
Biosynthesis of GMP 2B. oxygen replaced on C2 atom
* amides replace oxygen * requires glutamne, ATP, and water * N from glutamine side chain ATP + H2O → AMP + PPi * forms **guanosine monophosphate (GMP)**
66
Biosynthesis of GMP 2B. oxygen replaced on C2 atom requires
glutamine, ATP, water (N from glutamine side chain) ATP + H2O → AMP + PPi
67
Biosynthesis of GMP 2B. oxygen replaced on C2 atom forms
guanosine monophosphate (GMP)
68
Salvage pathways
breakdwon of nucleic acids for reuse
69
Salvage pathways nucleic acid breakdown
* adenine * guanine * hypoxanthine * all salvaged for reuse adenine + PRPP ⇔ AMP + PPi
70
Salvage pathways Guanine and Hypoxanthine
to GMP and IMP | (same enzyme as deficiency in HGPRT)
71
Salvage pathways Deficiency in HGPRT
* couldn't salvage nucleotides from diet * broken down but not utilized * excessive uric acid * mental retardation * self-mutilation

Metabolic Pathways (11 decks)

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