Nucleotide Biochemistry Stryer Chapter 25

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Nucleotide BiochemistryStryer Chapter 25

• Deoxyribonucleic acid (DNA) contains the
  information prescribing the amino acid sequence
  of proteins
• The central dogma DNA makes RNA makes protein
• DNA and RNA are polymers of nucleotide subunits
• Nucleotide derivatives are activated
  intermediates in many biosyntheses (UDP-glucose
  is required for formation of glycogen)
• ATP is a universal currency of energy, many
  proteins are regulated by ATP binding or ATP
  hydrolysis
• Adenine nucleotides are components of three major
  coenzymes NAD, FAD, and Coenzyme A
• Nucleotides also serve as metabolic regulators
  (cyclic AMP is a ubiquitous mediator in cellular
  signal transduction cascades)

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All nucleotides have a common structure
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There are five principal bases in nucleic acids
Inosine is carbonylated adenosine
A, G, T, C are present in DNA A, G, U, C are
present in RNA
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Pyrimidine is synthesized from carbamoyl
phosphate and aspartate
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STEP 1 Carbamoyl phosphate synthesis in the
cytosol
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STEP 2 Aspartate transcarbamoylase catalyzes
formation of carbamoylaspartate
committed step
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Aspartate transcarbamoylase is allosterically
inhibited by the end product of its pathway
..and activated by ATP
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STEP 3 Pyrimidine ring formation
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STEP 3 Ring closure
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STEP 4 PRPP addition
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Where does the sugar come from?
Supplies ribose for nucleotide metabolism (to
make nucleotides, NOT to produce energy)
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STEP 4 PRPP addition
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STEP 5 Uridylate (UMP) formation and
conversion to UTP
UMP
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STEP 5 UTP formation
UMP kinase
UMP ATP UDP ADP
Nucleoside diphosphate kinase
UDP ATP UTP ADP
XDP YTP XTP YDP
Nucleoside mono-, di and triphosphates are
interconvertable
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STEP 6 UTP conversion into CTP
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STEP 6 Amination of UTP results in CTP
ATP is required to phosphorylate the O-4 atom to
make it reactive
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Pyrimidine and purine bases can be recycled by
salvage reactions that utilize PRPP
Salvage Pathway Activated ribose (PRPP) base
Nucleotides
De Novo Pathway Activated ribose (PRPP) amino
acids ATP CO2 .
Nucleotides
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Purine is synthesized from amino acids,
tetrahydrofolate and CO2
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The committed step in de novo purine synthesis is
the activation of PRPP to phospho- ribosylamine
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C-STEP PRPP activation
Phosphoribosyl- amine Glutamate
PRPP Glutamine
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STEP 1 Addition of glycine
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STEP 2 Formylation by N10-formyltetra- hydrofolat
e
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STEP 3 Transfer of nitrogen from glutamine (befor
e ring closure)
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4
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STEP 4 Dehydration and ring closure
-H2O
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STEPS 5-8 Carboxylation Aspartate
addition Formylation Dehydration and ring
closure
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STEP 9 Conversion of IMP to ATP and GTP
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AMP, GMP and IMP are feedback inhibitors of
purine nucleotide biosynthesis
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UMP
dUMP
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Conversion of ribo-to-deoxyribonucleotides

• 1) Ribonucleotide reductase catalyzes the
• synthesis of deoxyribonucleotides
• Inhibited by hydroxyurea,
  which is used as anti-cancer drug
• 2) Thymidylate synthase catalyzes the
• methylation of dUTP

UMP
dUMP
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Anti-cancer drugs specifically block dTMP
production
Folic acid
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Thymidylate Synthase Suicide
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Defects in the purine salvage pathway cause human
diseases
Salvage Pathway Activated ribose (PRPP) base
Blocked by HGPRT deficiency (Gout,
Lesch-Nyhan)
Nucleotides
PRPP
De Novo Pathway Activated ribose (PRPP) amino
acids ATP CO2 .
Nucleotides
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Purines are degraded to urate
Salvage pathway
GMP IMP

ADA

Catalyzed by Hypoxanthine-guanine phosphoribosyl
transferase (HGPRT)
ADA adenosine deaminase, lack of ADA causes SCID
(severe combined immunodeficiency or bubble boy
disease)
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Accumulation of urate in Gout disease
affects joints (mostly big toes) and kidneys in
1 of population
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What you need to know..
Nomenclature Base structures, nucleotide
structures Committed steps in purine and
pyrimidine syntheses and their regulation AA
utilized in both pathways When is PRPP added? De
novo synthesis and salvage pathways Feedback
inhibition of purine syhthesis What are the
precursors of deoxyribonucleotides/why do you
need ribonucleotide reductase? Importance of
folic acid in your diet Anti-cancer drugs and
which enzymes they inhibit Salvage pathway
defects (Gout disease)