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Nucleotide Biosynthesis - 2017
Nucleotide Biosynthesis - 2017
Marcos Alcocer
School of Biosciences
University of Nottingham
Main learning objectives Marcos Alcocer
Functions
Nomenclature
Energy
Purines de novo synthesis
Purines salvage synthesis
Pyrimidines de novo synthesis
Biosynthetic regulation
Degradation -
Clinical applications
de novo:
Aspartate
Glycine
CO2
Aspartate
Methenyl Glutamine
tetrahydrofolate
Methenyl Aspartate
Tetrahydrofolate
Glutamine
Overview
AMP
GMP
Overview
Dementia
Can be caused by problems in the synthesis of the neurotransmitter
Serotonin. This can be due to:
• Tryptophan is precursor of nicotinate and serotonin
• Endocrine tumour that consumes large amount of tryptophan
• lack of tryptophan in the diet (pellagra)
OH
ATP PPi Gln Glu
Marcos Alcocer
Overview
Marcos Alcocer
Uric acid crystals can deposit in tiny fluid-filled sacs (bursae) around the joints. These urate crystals
can incite inflammation in the bursae leading to pain and swelling around the joints, a condition called
bursitis. In rare instances, gout leads to a more chronic type of joint inflammation which mimics
rheumatoid arthritis. In chronic (tophaceous) gout, nodular masses of uric acid crystals (tophi) deposit
in different soft tissue areas of the body. Even though they are most commonly found as hard nodules
around the fingers, at the tips of the elbows, and around the big toe, tophi nodules can appear
anywhere in the body. They have been reported in unexpected areas such as in the ears, vocal cords, or
(rarely) around the spinal cord!
Overview
Lesch-Nyhan syndrome
Overproduction Urate
Overview
Anticancer drugs
• Rapid dividing cells require abundant supply of thymidylate for DNA synthesis
• Inhibitors of TMP synthesis such as Fluorouracil, aminopterin and
methotrexate are largely employed. Trimethoprim has high affinity for
bacteria and protozoa.
Overview
“Long life” X
Malignant cells
HGPRT- or
TK- Cell A
+ HAT X
(Hypoxanthine
Thymidine
Aminopterin)
Cell Death !!!
Nucleotide Biosynthesis Marcos Alcocer
http://highered.mheducation.com/sites/0072507470/student_view0/chapter25/animation__how_the_nad__works.html
Nucleotide Biosynthesis Marcos Alcocer
Guanine
Purines
Adenine
Cytosine
Pyrimidines
Uracyl
Thymine
Nomenclature Marcos Alcocer
Adenine
Guanine
Cytosine
Uracil
Thymine
Nomenclature Marcos Alcocer
Nucleoside=
Adenosine
Guanosine
Uridine
Cytidine
The 5’ hydroxy=
Esterification
Nucleotides=
Nitrogenous base + sugar + phosphate ester:
Marcos Alcocer
ENERGY !!!!
http://www.sumanasinc.com/webcontent/a
nimations/content/electrontransport.html
Why energy??? Marcos Alcocer
Chemical energy –
For synthesis of complex biological molecules.
“to make more of themselves”.
Transport –
Cells often live in dilute environments. They need to expend
energy to transport that nutrient into the cell.
Mechanical Energy –
Cells may be able to change their physical location. All cells need to
move structures (DNA replication, wound repair etc…) within them.
https://www.youtube.com/watch?v=wJyUtbn0O5Y
Marcos Alcocer
Marcos Alcocer
Nucleotide Biosynthesis Marcos Alcocer
http://lecturer.ukdw.ac.id/dhira/Metabolism/nucleotidesyn.html
Synthesis of Purines (1950, Buchanan et al.) Marcos Alcocer
- Glycine +
de novo - Aspartate +
- Glutamine +
- Tetrahydrofolate +
- CO2 +
- PRPP = Nucleotide
All nucleotides contain a ribose sugar and phosphate that form the
backbone of DNA and RNA. These are synthesized from ribose 5-
phosphate, a central metabolite of the pentose phosphate pathway. In
this single step reaction, two of the phosphates of ATP are transferred
to ribose 5-phosphate to form 5-phospho-a-D-ribosyl 1-pyrophosphate
(PRPP). This intermediate is required for the biosynthesis of purines,
pyrimidines, NAD, histidine and tryptophan. It plays a critical role in
anabolism.
de novo Synthesis of Purines Marcos Alcocer
http://lecturer.ukdw.ac.id/dhira/Metabolism/nucleotidesyn.html
de novo Synthesis of Purines–AMP from IMP Marcos Alcocer
R ATP ADP R O
| || || NH3
C=O C - O – P – O-
| | |
R’ R’ O-
R O
R | ||
|| 2HN - C - O – P – O-
C – NH2 | |
| R’ O-
R’
Pi
Aspartate
Methenyl
tetrahydrofolate
Methenyl
Tetrahydrofolate
Glutamine
de novo Synthesis of Purines Marcos Alcocer
PU = GA
AMP
GMP
Synthesis of Purines (1950, Buchanan et al.) Marcos Alcocer
- Glycine +
de novo - Aspartate +
- Glutamine +
= Nucleotide
- Tetrahydrofolate +
- CO2 +
- PRPP
(-)
(-)
Adenylo-
Ribose Phosphoribosyl succinate
AMP
PRPP IMP
5-phosphate amine
Xanthylate GMP
(-) (-)
(-)
Where do purines come from? Marcos Alcocer
de novo biosynthesis
Salvage reactions
“Purine nucleotides can be synthesized from the preformed
bases by a salvage reaction which is simpler and much less
energy costly”
Purine PPi
Purine
Nucleotide Biosynthesis Marcos Alcocer
-------------------------------------
Nucleotide Biosynthesis Marcos Alcocer
-------------------------------------
• Biosynthesis of De novo: Components, intermediaries…
Where do they come from?
pyrimidines: Regulation
Biosynthesis Marcos Alcocer
http://lecturer.ukdw.ac.id/dhira/Metabolism/nucleotidesyn.html
de novo Synthesis of Pyrimidines Marcos Alcocer
http://lecturer.ukdw.ac.id/dhira/Metabolism/nucleotidesyn.html
de novo Synthesis of Pyrimidines Marcos Alcocer
http://lecturer.ukdw.ac.id/dhira/Metabolism/nucleotidesyn.html
de novo Synthesis of Pyrimidines Marcos Alcocer
• Later PRPP is combined with the six membered ring to form orotidine 5'-
phosphate. Removal of CO2 results in the formation of Uridine
monophosphate (UMP).
de novo Synthesis of Pyrimidines Marcos Alcocer
http://lecturer.ukdw.ac.id/dhira/Metabolism/nucleotidesyn.html
Where do pyrimidines come from? Marcos Alcocer
Glutamine
+ Bicarbonate
Aspartate
How are Pyrimidine biosynthesis regulated? Marcos Alcocer
dTMP from dUMP Marcos Alcocer
Several well-defined blocking steps Marcos Alcocer
Nucleotide Biosynthesis Marcos Alcocer
-------------------------------------
• Biosynthesis of De novo: Components, intermediaries…
Where do they come from?
pyrimidines: Regulation
• Degradation: Pyrimidines: DNA/RNA to TCA cycle
Purines: Urea
Synthesis of NAD, FAD, CoA etc…
Where do pyrimidines go ?
Degradation of pyrimidines Marcos Alcocer
Thymine
Dihydrothymine
N-Carbamoylisobutyrate
Aminoisobutyrate
TCA cycle
Where do pyrimidines go?
Marcos Alcocer
Synthesis of nucleotides
Synthesis of deoxynucleotides
Pyrimidines
Synthesis of nucleotides
Synthesis of deoxynucleotides
Purines
Synthesis of FAD
Synthesis of CoA
Synthesis of NAD
Synthesis of NADP
H+ H2O
NADPH NADP+
H
Deoxy
Glutathione
Thioredoxin
NADPH
ADP dADP
OH
ATP PPi Gln Glu
Synthesis of nucleotides
Synthesis of deoxynucleotides
Purines
Synthesis of FAD
Synthesis of CoA
Synthesis of NAD
Synthesis of NADP
Allopurinol
Allantoinase
(Teleost fish)
Uricase
(Mammals
Non primates) Allantoicase
(Amphibians
Fish)
Urease
(Marine invertebrates)
Ribose – 5 Phosphate
PRPP
Phosphoribosyl amine
IMP
Adenylo Xanthylate
succinate
dTTP
AMP GMP
Nucleotide Biosynthesis Marcos Alcocer
-------------------------------------
• Biosynthesis of De novo: Components, intermediaries…
Where do they come from?
pyrimidines: Regulation
• Degradation: Pyrimidines: DNA/RNA to TCA cycle
Purines: Urea
Synthesis of NAD, FAD, CoA etc…
• Clinical applications: Pellagra, Gout, anti-Cancer drugs, Leisch Nyhan syndrome, MAb…
Clinical applications Marcos Alcocer
Dementia
Can be caused by problems in the synthesis of the neurotransmitter
Serotonin. This can be due to:
• Tryptophan is precursor of nicotinate and serotonin
• Endocrine tumour that consumes large amount of tryptophan
• lack of tryptophan in the diet (pellagra)
OH
ATP PPi Gln Glu
L-kynurenine to 3-hydroxykynurenine
http://dehydrogenase.co.uk/NAD/
ACE2 links amino acid malnutrition to microbial ecology
and intestinal inflammation
•Tatsuo Hashimoto, et al. Nature 487, 477–481 (26 July 2012)
Marcos Alcocer
Marcos Alcocer
Marcos Alcocer
Pellagra, a loathsome skin disease, it was called mal de la rosa and often
mistaken for leprosy. In the United States, pellagra has often been called the
disease of the four D's -- dermatitis, diarrhea, dementia, and death.
Marcos Alcocer
http://www.visibleproductions.com/index.php?page=asset_detail&asset_id=vpl_0696_001
Gout
Uric acid crystals can deposit in tiny fluid-filled sacs (bursae) around the joints. These urate crystals
can incite inflammation in the bursae leading to pain and swelling around the joints, a condition called
bursitis. In rare instances, gout leads to a more chronic type of joint inflammation which mimics
rheumatoid arthritis. In chronic (tophaceous) gout, nodular masses of uric acid crystals (tophi) deposit
in different soft tissue areas of the body. Even though they are most commonly found as hard nodules
around the fingers, at the tips of the elbows, and around the big toe, tophi nodules can appear
anywhere in the body. They have been reported in unexpected areas such as in the ears, vocal cords, or
(rarely) around the spinal cord!
Clinical applications Marcos Alcocer
Antioxidant
Is this the reason for our long life span compared to lower primates?
Clinical applications Marcos Alcocer
Lesch-Nyhan syndrome
Overproduction Urate
Clinical applications Marcos Alcocer
Anticancer drugs
• Rapid dividing cells require abundant supply of thymidylate for DNA synthesis
• Inhibitors of TMP synthesis such as Fluorouracil, aminopterin and
methotrexate are largely employed. Trimethoprim has high affinity for
bacteria and protozoa.
Clinical applications Marcos Alcocer
“Long life”
Malignant cells
Cell A
X =
“Short life” (2-3 days)
Ab producing cells “Long life”
Ab producing cells
Cell B
Clinical applications Marcos Alcocer
“Long life”
Malignant cells
Cell A
Cell B
Clinical applications Marcos Alcocer
“Long life”
Malignant cells
Cell A
+ HAT
(Hypoxanthine
Thymidine
Aminopterin)
Salvage pathway
Clinical applications Marcos Alcocer
“Long life”
Malignant cells
Cell A
+
“Long life” X
Malignant cells
HGPRT- or
TK- Cell A
+ HAT X
(Hypoxanthine
Thymidine
Aminopterin)
Cell Death !!!
Marcos Alcocer
Step 1
Select for myeloma mutants “Poison” salvage pathway
Step 2
Fuse My- cell x spleen cells PEG, electro....
Step 3
Block “de novo” force salvage
X “Long life”
Malignant cells
Cell A
X =
X
“Short life” (2-3 days)
Ab producing cells “Long life” HGPRG+ or TK+
Ab producing cells
Cell B
Marcos Alcocer
César Milstein (October 8, 1927 – March 24, 2002), an Argentine scientist, was born in Bahia Blanca,
Argentina. He graduated from the University of Buenos Aires and obtained a PhD under Professor Stoppani
(Professor of Biochemistry) in the Medical School on kinetic studies with the enzyme aldehyde
dehydrogenase. In 1958, funded by the British Council, he joined the Biochemistry Department at the
University of Cambridge to work for a PhD under Malcolm Dixon on the mechanism of metal activation of the
enzyme phosphoglucomutase. During this work he collaborated with Frederick Sanger whose group he joined
with a short-term Medical Research Council appointment.
The major part of Milstein's research career was devoted to studying the structure of antibodies and the
mechanism by which antibody diversity is generated. It was as part of this quest that in 1975 he, together
with Georges Köhler (a postdoctoral fellow in his laboratory), developed the hybridoma technique for the
production of monoclonal antibodies - a discovery recognised by the award of the
1984 Nobel Prize for Physiology or Medicine. This discovery led to an enormous expansion in the exploitation
of antibodies in science and medicine.
Milstein himself made many major contributions to improvements and developments in monoclonal antibody
technology - especially focussing on the use of monoclonal antibodies to provide markers that allow
distinction between different cell types. He also foresaw the potential wealth of ligand-binding reagents
that could result from applying recombinant DNA technology to monoclonal antibodies and inspired the
development of the field of antibody engineering.
Nucleotide Biosynthesis Marcos Alcocer
-------------------------------------
• Biosynthesis of De novo: Components, intermediaries…
Where do they come from?
pyrimidines: Regulation
• Degradation: Pyrimidines: DNA/RNA to TCA cycle
Purines: Urea
Synthesis of NAD, FAD, CoA etc…
• Clinical applications: Pellagra, Gout, anti-Cancer drugs, Leisch Nyhan syndrome, MAb…