Nucleotide biosynthesis

Dr\ Gamal Alhazmi

Pyrimidine nucleotide biosynthesis
through a de novo pathway
Nucleotides are also produced through a de novo pathway
synthesizing new bases.
Pyrimidine nucleotide synthesis starts with the
.synthesis of carbamoyl phosphate from carbonate
ATP provides the energy needed for the reaction and
.the -NH 2 group is from glutamine
–
.
As shown in Figure 6.20, orotate is synthesized as a
precursor of pyridine nucleotides before binding to
PRPP by the action of phosphoribosyltransferase as in
. the salvage pathway described previously
Mononucleotides are phosphorylated in two steps to
trinucleotide by nucleotide kinases, consuming ATP,
. before being used in RNA synthesis
The first enzyme of pyridine nucleotide biosynthesis,
aspartate transcarbamoylase, is regulated through
feedback inhibition by cytidine trinucleotide, the final
.product
De novo synthesis of purine nucleotides
Purine nucleotides are synthesized in a more complicated
.pathway than pyrimidine nucleotides
Glutamine donates -NH 2 to PRPP before
inosine 5’-monophosphate (IMP) is synthesized with the
addition of carbons and nitrogens in the forms of glycine,
methenyl tetrahydrofolate, glutamine, aspartate and
.formyl tetrahydrofolate (Figure 6.21)
IMP is converted to adenosine 5’-monophosphate (AMP) and
.guanosine 50-monophosphate (GMP)
The first enzyme of this pathway, PRPP
amidotransferase, is regulated through feedback
inhibition by the final products AMP and GMP. These
are phosphorylated to dinucleotides in reactions
catalyzed by nucleotide kinases that consume ATP.
GDP is further phosphorylated to GTP in a similar
reaction, and ADP to ATP in the normal ATP
synthesis mechanisms either by substrate-level
. phosphorylation or by the membrane-bound ATPase
Transcription
Transcription is the process of RNA synthesis from the DNA
.template
Major RNA types include mRNA, rRNA and tRNA with specific
functions in expression of the genetic information. They are all
synthesized in a similar way before being modified to their own
.specific forms through post-transcriptional processing
RNA synthesis
RNA is synthesized through transcription, a process as complex
as replication. RNA polymerase (DNA-dependent RNA
polymerase) catalyzes the formation of phosphodiester bonds
between ribonucleotides consuming GTP, CTP, ATP or UTP
.depending on the base pairing within DNA
The synthesis proceeds in the 5’–3’ direction as in
.Replication
Certain regions in DNA have a strong affinity for RNA
polymerase and are referred to as promoters. RNA
polymerase recognizes and binds the promoter region of
.DNA to start RNA synthesis
RNA polymerase consists of five subunits in the ratio of α2ββ’
in bacteria. The σ-factor of the enzyme recognizes the
.promoter region of DNA, and the enzyme complex binds to it
At this point, the σ-factor is separated from the complex and
the core enzyme α2 ββ’ moves along the DNA synthesizing
.RNA according to a base-pairing mechanism
Multiple σ-factors are known in bacteria which recognize
different promoter regions. Proteins known as activators and
repressors control the activity of some promoters
.)Section 12.1(
Transcription is terminated either by an intrinsic input
mechanism involving a specific DNA region known as
atermination site or by an extrinsic input mechanism exerted by
. a protein ρ-factor
 Translation
Translation is the process in which the genetic information
passed on to mRNA is used to make proteins. As the genetic
information carried by DNA is passed to RNA during
transcription, the information in mRNA is translated into
protein through an amino acid sequence encoded by the
sequence of bases in the mRNA
Amino acids are activated before being polymerized .)Table 6.7(
.into peptide
Amino acid activation
:Amino acids are activated to aminoacyl-tRNA consuming ATP

enzyme : aminoacyl tRNA synthetase

The aminoacyl-tRNA synthetase catalyzing this reaction
recognizes not only amino acids but also tRNA. More than one
tRNA is needed for each amino acid since most of the amino
acids are coded by multiple codons, except methionine and
tryptophan (Table 6.7), and a tRNA is needed for each codon
base pairing with its specific anticodon
Synthesis of peptide: initiation, elongation
and termination
The coding region in mRNA starts with AUG. Peptide synthesis
starts with methionine in eukaryotes and with
.N-formylmethionine in bacteria
.AUG (TAC on DNA) is referred to as the initiation codon
Though peptide synthesis is a continuous process, translation
can be described for convenience as initiation, elongation and
termination steps