Biosynthesis and Degradation of Nucleotides: Juan David Marin Chiguachi

Departamento de Estudios educativos
Semillero Maestros y contextos

Universidad de Caldas
Biosynthesis and Degradation of Nucleotides
Juan David Marin Chiguachi

University of Caldas
Chemistry and Biology degree`s
The APA format is used for this presentation

1 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 1/18
Contents in Brief
1. Structural composition of nucleobases, nucleosides, and nucleotides.

2. Nucleotides participate in many biochemical reactions and functions
3. Origin of the ring atoms of purines
4. De novo synthesis
5. Biosynthesis of AMP and GMP from IMP
6. Nucleoside Monophosphates Are Converted to Nucleoside
Triphosphates
7. Degradation of Purines and Pyrimidines Produces Uric Acid and
Urea
8. Curious Fact: Gout-Gouty Arthritis
9. Summary


Nucleobases, Nucleosides, and Nucleotides.

For the nucleobases ‘R’ is simply a proton. For the nucleosides ‘R’ is a sugar moiety
which can be ribose or deoxyribose (carrying a proton instead of a hydroxyl group at
the 2’ carbon of the ribose).
Figure 1. Strucutural composition of nucleobases, nucleosides, and nucleotides

Zhang X, Chen Y, Lin X, Hong X, Zhu Y, Li W, He W, An F, Guo H. (2013). Adenine phosphoribosyl transferase 1 is a
key enzyme catalyzing cytokinin conversion from nucleobases to nucleotides in Arabidopsis. Mol Plant 6: 1661–1672.

Nucleobases, Nucleosides, and Nucleotides.

Figure 2. Strucutural differences of nucleobases, nucleosides, and nucleotides

Figure 3. A Schematic Model of the Interconversions among Cytokinin (CK) Nucleotides, Nucleosides, and Nucleobases.
Zhang X, Chen Y, Lin X, Hong X, Zhu Y, Li W, He W, An F, Guo H (2013) Adenine phosphoribosyl transferase 1 is a key
enzyme catalyzing cytokinin conversion from nucleobases to nucleotides in Arabidopsis. Mol Plant 6: 1661–1672.

Nucleotides participate in many biochemical reactions and functions
• ATP and GTP as energy sources

• Coenzymes (NAD, FAD, CoA) are nucleotide derivates
• They are precursors of DNA and RNA
• Some, such as cAMP and cGMP, are also cellular second messengers
A B Figure 5. Estructure of ATP

Figure 4. Estructure of A. NAD +
B NADH
Nelson L. David & Cox M. Michael. (2017). Lehninger principles of biochemistry. New York: W. H. Freeman. Seventh edition
Modified image of ”ATP: Trifosfato de adenosina” from OpenStax College, Biology
Modified image of ”Energía en sistemas vivos ” from OpenStax College, Biology
Origin of the ring atoms of purines

Figure 6. Origin of the ring atoms of purines This information was

obtained from isotopic experiments with 14C- or 15N-labeled precursors. Formate is
supplied in the form of N10- formyltetrahydrofolate.

De novo synthesis Departamento de Estudios educativos
Nelson L. David & Cox

Figure 4. Metal-complex with Zn2+ M. Michael. (2017).
Lehninger principles of
biochemistry. New
York: W. H. Freeman.
Figure 7. De novo synthesis. Construction of IMP Seventh edition

Figure 8. De novo and salvage biosynthesis of pyrimidine nucleotides in humans
Ayse Okesli, Chaitan Khosla, Michael C Bassik. (2017). Human pyrimidine nucleotide biosynthesis as a target for antiviral
chemotherapy. Current Opinion in Biotechnology. 48: 127-134
Biosynthesis of AMP and GMP from IMP

Figure 9. Biosynthesis of AMP and GMP from IMP

Nucleoside Monophosphates Are Converted to Nucleoside Triphosphates

Nucleotides to be used in biosynthesis are generally

Converted to nucleoside triphosphates. The conversion
pathways are common to all cells.
Phosphorylation of AMP to ADP is promoted by
adenylate kinase, in the reaction (Nelson & Cox,
2017).
Figure 10. 3D ribbon/surface model of

adenylate kinase in complex with
bis(adenosine)teraphosphate (ADP-ADP).
PDB 2C95. The active center is colored
yellow, the ATP binding site green.
1. Nelson L. David & Cox M. Michael. (2017). Lehninger principles of biochemistry. New York: W. H. Freeman. Seventh edition
2. Bunkoczi, G., Filippakopoulos, P., Jansson, A., Longman, E., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M.,
Knapp, S. (2007). Structure of adenylate kinase 1 in complex with P1,P4-di(adenosine) tetraphosphate. To be published. Taked
from PDB.
Degradation of Purines and Pyrimidines Produces Uric Acid and Urea Universidad de Caldas
Figure 11. Catabolismof purine nucleotides. Note that primates excrete much more nitrogen as urea via the
urea cycle than as uric acid from purine degradation.

Curious Fact. Gout-Gouty Arthritis Universidad de Caldas
A. Qaseem, R.P. Harris, M.A. Forciea. (2017). Management of acute and recurrent gout: a clinical practice guideline from the
american college of physicians Ann Intern Med, 166 (1) , pp. 58-68
Curious Fact: Gout-Gouty Arthritis Universidad de Caldas
In some patients, the

frequency and duration of
acute attacks increase
over time and lead to
chronic gout, which may
be associated with
deposits of uric acid
crystals known as tophi Figure 12. Pharmacologic agents and their mechanism of action for the treatment of gout.
(Qaseem, 2017)
A. Qaseem, R.P. Harris, M.A. Forciea. (2017). Management of acute and recurrent gout: a clinical practice guideline from the
american college of physicians Ann Intern Med, 166 (1) , pp. 58-68
Curious Fact. Gout-Gouty Arthritis Universidad de Caldas
Hypoxanthine is the normal

substrate of xanthine oxidase. A
slight alteration in the structure
of Hypoxanthine (shaded light
red) yields the medically effective
enzyme inhibitor allopurinol
(Nelson & Cox, 2017).
Figure 13. Allopurinol, an inhibitor of xanthine oxidase

Summary


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Departamento de Estudios educativos

Semillero Maestros y contextos

Biosynthesis and Degradation of Nucleotides

Juan David Marin Chiguachi

Chemistry and Biology degree`s

The APA format is used for this presentation

1. Structural composition of nucleobases, nucleosides, and nucleotides.

2 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 2/18

3 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 3/18

Nucleobases, Nucleosides, and Nucleotides.

Figure 1. Strucutural composition of nucleobases, nucleosides, and nucleotides

4 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 4/18

Nucleobases, Nucleosides, and Nucleotides.

Figure 2. Strucutural differences of nucleobases, nucleosides, and nucleotides

5 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 5/18

6 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 6/18

• ATP and GTP as energy sources

A B Figure 5. Estructure of ATP

Origin of the ring atoms of purines

Figure 6. Origin of the ring atoms of purines This information was

8 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 8/18

Nelson L. David & Cox

10 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 10/18

Figure 8. De novo and salvage biosynthesis of pyrimidine nucleotides in humans

Biosynthesis of AMP and GMP from IMP

Figure 9. Biosynthesis of AMP and GMP from IMP

12 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 12/18

Nucleoside Monophosphates Are Converted to Nucleoside Triphosphates

Nucleotides to be used in biosynthesis are generally

Figure 10. 3D ribbon/surface model of

14 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 14/18

Curious Fact. Gout-Gouty Arthritis Universidad de Caldas

Curious Fact: Gout-Gouty Arthritis Universidad de Caldas

In some patients, the

Curious Fact. Gout-Gouty Arthritis Universidad de Caldas

Hypoxanthine is the normal

Figure 13. Allopurinol, an inhibitor of xanthine oxidase

17 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 17/18

(Nelson & Cox, 2017).

(Nelson & Cox, 2017).

(Nelson & Cox, 2017).

(Nelson & Cox, 2017).

18 Doctorado en “Sostenibilidad y Regeneración Urbana” 99/2011 18/18

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