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Introduction to Nucleic Acid:
Chemistry of Nucleotides
Dr. Ifat Ara Begum
Associate Professor
Department of Biochemistry
Dhaka Medical College
What is Nucleic Acid?
 Nucleic acids, the biopolymers essential for all known forms
of life, may be defined as-
“High molecular weight polyanionic molecules built up by
monomeric units- nucleotides which are linked together by 3'-
5' phosphodiester bond and consist of:
- Pentose sugar
- Nitrogen base
&
- Phosphate group”
 Synonym: Polynucleotides
 Nucleic acids were named for their initial discovery within
the nucleus and for the presence of phosphate group
(related to phosphoric acid) in their structure.
Components of nucleic acids are similar to those of its monomer-
nucleotide
 If the sugar is ribose, the polymer is RNA (ribonucleic acid)
 If the sugar is deoxyribose, the polymer
is DNA (deoxyribonucleic acid).
DNA:
 Polymer of deoxyribonucleotide
/ d-ribonucleotide
 d-ribonucleotide
=
deoxy ribose sugar + phosphate
+ nitrogen base
RNA:
 Polymer of
ribonucleotide
 Ribonucleotide
=
Ribose sugar +
phosphate + nitrogen
base
If phosphate is removed from the structure of nucleotide, the
remaining structure is called “Nucleoside”
Nucleotides
 Nucleotides are organic molecules consisting of
nucleoside and phosphate
In other words,
Phosphorylated nucleosides are known as nucleotides.
 They serve as monomeric units (building block) of DNA
and RNA
 They occur in mono /di / tri phosphate form
Nucleosides
 Derivative of purine / pyrimidine base and
composed of ribose/d-ribose sugar attached
with the nitrogen base
If ribose sugar : Ribonucleoside
If d-ribose sugar: deoxy ribonucleoside (d-
ribonucleoside)
Structure of a nucleotide
1. Pentose sugar
2. Nitrogen base
3. Phosphate
Ribonucleotide
Deoxyribonucleotide
 Phosphate remains attached with 5th carbon of pentose sugar
 Nitrogen base remains attached with 1st carbon of pentose sugar
1. Ribose / Deoxy Ribose Sugar
Ribose is a pentose sugar with
aldehyde function.
Deoxyribose {d-ribose} is the ribose
sugar with oxygen atom removed from
its 2nd carbon atom
To avoid confusion between the numerals of various atoms of nitrogen base & ribose
sugar,, the carbons of ribose sugar is designated by numerals with a prime
Example: 1’, 2’, 3’,4’,5’
2. Phosphate
 Total number of phosphate in a nucleotide may be 1 or
2 or 3
 Nucleotides of mono phosphate variety (AMP, GMP etc)
can be converted to their corresponding diphosphate
variety (ADP, GDP etc) & triphosphate variety (ATP, GTP
etc) by subsequent phosphorylation
3. Nitrogen Base
 A nitrogen containing ring structure which is attached to 1′
carbon of pentose sugar by N-glycosidic bond to form
nucleoside.
 Two types:
1. Purine base.
2. Pyrimidine base.
Nucleoside
 Purine bases are derivatives of
purine nucleus
 Purine nucleus is an aromatic
heterocyclic 09 atom ring
composed of 04 nitrogen & 05
carbons
 Pyrimidine bases are derivatives of
pyrimidine nucleus
 Pyrimidine nucleus is an aromatic
heterocyclic 06 atom ring composed
of 02 nitrogen & 04 carbons
Raw materials for synthesis of
purine nucleus
Raw materials for synthesis of
pyrimidine nucleus
 Purine bases found in nucleic acids:
1. Adenine (6-amino-purine).
2. Guanine (2-amino-6-oxy-purine).
 Other purine bases:
1. Hypoxanthine.
2. Xanthine.
3. Uric acid.
Hypoxanthine and xanthine are not incorporated into the nucleic acid but important in
purine nucleotide metabolism.
 Pyrimidine bases found in nucleic acids:
1. Cytosine (2-oxy-4-amino-pyrimidine)
2. Uracil (2, 4-di-oxy-pyrimidine)
3. Thymine (2, 4-di-oxy-5-methyl-
pyrimidine)
 Other pyrimidine bases:
1. Orotic acid.
Purines Pyrimidines
Composed of two ring structures. Composed of one ring structure.
Number-1 atom(nitrogen)in 11-O’clock
position.
Number-1 atom (nitrogen) in 6-O’clock
position.
No variation in DNA and RNA. Variation occurs in DNA and RNA.
(Uracil present in RNA stead of thiamine).
Larger heterocycle has the shorter name. Smaller heterocycle has the longer name.
The atoms are numbered counter-
clockwise direction.
The atoms are numbered clockwise
direction.
Nomenclature of different
nucleosides & nucleotides
Functions of nucleotides
28
Functions of Nucleotides
 Monomer of nucleic acid &
thus conveys genetic
information
 Participate in energy
metabolism
&
serve as energy store : ATP,
GTP etc
 Regulatory function as physiological mediator:
 Acts as intracellular 2nd messenger: cAMP,
cGMP
 Helps in signal transduction : G-Protein (made
of GTP)
 Causes platelet aggregation : ADP
 Regulation of coronary blood flow: Adenosine
 Acts as:
 Coenzymes: e.g. NAD, FMN, FAD etc
 Allosteric effector to regulate enzyme activity: e.g. ATP, AMP,
ADP etc
 Carrier of active intermediates in synthetic processes : e.g.
UDP glucose for glycogen synthesis
 Methyl donor
Nucleotide Biosynthesis
De-novo synthesis Salvage pathway
Synthesis of nucleotides from basic
metabolites.
It is required in growing cells / rapidly
proliferating cells
It recycles preformed bases and
nucleosides.
It provides an adequate supply of
nucleotides in non-dividing or slowly
dividing cells
Very expensive energy wise, only done
when absolutely necessary
Much less energy consuming process
A) De-Novo synthesis of
Ribonucleotides
a) Purine Ribonucleotides de-novo synthesis
 Site: Purine synthesis occurs in all tissues. The major site of
purine synthesis is in the liver and, to a limited extent, in the
brain.
 Substrates:
 Aspartic acid (Asp), Glutamine (Gln), Glycine (Gly)
 CO2
 Formyl tetrahydrofolate (F-FH4) & methenyl
tetrahydrofolate (M-FH4)
 Products: GMP; AMP
 Ribose-5-phosphate (as provided by the pentose-
phosphate pathway) is converted into PRPP
(Phosphoribosyl pyrophosphate) by PRPP synthetase, in a
step requiring one ATP.
 In the committed step in the process, an α-amino group is
then added to PRPP from glutamine to form 5-
phosphoribosylamine. This reaction is catalyzed by
glutamine PRPP amidotransferase
 A series of nine reactions results in the formation of IMP
(Inosine 5′-monophosphate).
 IMP can then be transformed either to GMP by IMP
dehydrogenase , or to AMP by adenylosuccinate synthetase .
 Feedback inhibition controls both the overall rate of purine
biosynthesis and the balance between AMP and GMP
production
b) Pyrimidine Ribonucleotides
 The pyrimidine ring is synthesized first
 Then ribose phosphate is added from PRPP (phospho ribosyl
pyrophosphate) to form a pyrimidine nucleotide
Difference in de-novo
synthesis of purine &
pyrimidine
B) De-Novo synthesis of deoxy-
Ribonucleotides
 Ribonucleotides are converted to deoxyribonucleotides
 This conversion is done by direct reduction of ribose sugar by
ribonucleotide reductase ,
which involves removal of oxygen from 2nd carbon of ribose
 This reduction of ribonucleotides to d-ribonucleotides occurs only in
diphosphate form.
C) Salvage Pathway for
nucleotides
 A salvage pathway is a pathway in
which nucleotides (purine & pyrimidine) are
synthesized from intermediates in the degradative
pathway for nucleotides / nucleic acids.
 Use:
To recover bases and nucleosides that are formed
during degradation of RNA and DNA. The salvaged
bases and nucleosides can then be converted back into
nucleotides.
 Salvage pathway is important in some organs because
some tissues cannot undergo de novo synthesis
Points Salvage pathway for synthesis of purine nucleotides
What happens? Recyclation of free purine bases
Where happens? Primarily in extrahepatic tissues (RBC, Brain)
Salvaged bases Adenine, Hypoxanthine, Guanine
Products IMP, GMP
Enzymes responsible for
recycling
Adenine Phospho Ribosyl Transferase (APRT) &
Hypoxanthine Guanine Phospho Ribosyl Transferase (HGPRT / HPRT)
Effectiveness of the pathway 90% of daily purine nucleotide biosynthesis occurs
Why this pathway occurs? Salvage pathway needs less energy than de-novo biosynthesis
Most purine bases are recycled rather than degraded
HGPRT :
Catalyzes the salvage synthesis
of IMP and GMP from the purine
bases hypoxanthine and guanine
Its defect results in the
accumulation of its substrates,
hypoxanthine and guanine, which
are converted into uric acid by
means of xanthine oxidase
HGPRT deficiency - Lesch–nyhan
syndrome
as a co-substrate
APRT :
 Catalyzes the salvage
synthesis of adenosine
monophosphate (AMP)
from adenine utilizing
PRPP as a co-substrate.
 Elevated APRT activity
may contribute to purine
overproduction.
Points B) Salvage pathway for synthesis of pyrimidine
nucleotides
What happens? Recyclation of free pyrimidine bases
Where happens? Primarily in extrahepatic tissues
Salvaged bases Uracil , Thymine
Products UMP, dTMP
Enzymes responsible for
recycling
Uridine phosphorylase
Uridine kinase
Thymidine phosphorylase
Thymidine kinase
Catabolism of Nucleotides
A) Catabolism of purine nucleotide
.
 Abnormalities with purine
catabolism leads to :
Hyperuricemia & gout
Xanthinuria
Xanthine lithiasis
&
 These conditions can be
treated by drugs inhibiting
enzyme- xanthine oxidase :
Allopurinol & Febuxostat
.
B) Catabolism of pyrimidine nucleotide
.
 End Product CO2, NH3, acetyl CoA,
succinyl CoA
 Highly water soluble, easily
disposable & of no clinical
significance
.
Introduction to nucleic acid, chemistry of nucleotiides , july 2020
Introduction to nucleic acid, chemistry of nucleotiides , july 2020

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Introduction to nucleic acid, chemistry of nucleotiides , july 2020

  • 1. Introduction to Nucleic Acid: Chemistry of Nucleotides Dr. Ifat Ara Begum Associate Professor Department of Biochemistry Dhaka Medical College
  • 2. What is Nucleic Acid?  Nucleic acids, the biopolymers essential for all known forms of life, may be defined as- “High molecular weight polyanionic molecules built up by monomeric units- nucleotides which are linked together by 3'- 5' phosphodiester bond and consist of: - Pentose sugar - Nitrogen base & - Phosphate group”
  • 3.  Synonym: Polynucleotides  Nucleic acids were named for their initial discovery within the nucleus and for the presence of phosphate group (related to phosphoric acid) in their structure.
  • 4. Components of nucleic acids are similar to those of its monomer- nucleotide
  • 5.  If the sugar is ribose, the polymer is RNA (ribonucleic acid)  If the sugar is deoxyribose, the polymer is DNA (deoxyribonucleic acid).
  • 6.
  • 7. DNA:  Polymer of deoxyribonucleotide / d-ribonucleotide  d-ribonucleotide = deoxy ribose sugar + phosphate + nitrogen base RNA:  Polymer of ribonucleotide  Ribonucleotide = Ribose sugar + phosphate + nitrogen base If phosphate is removed from the structure of nucleotide, the remaining structure is called “Nucleoside”
  • 9.  Nucleotides are organic molecules consisting of nucleoside and phosphate In other words, Phosphorylated nucleosides are known as nucleotides.  They serve as monomeric units (building block) of DNA and RNA  They occur in mono /di / tri phosphate form
  • 10.
  • 11.
  • 13.  Derivative of purine / pyrimidine base and composed of ribose/d-ribose sugar attached with the nitrogen base If ribose sugar : Ribonucleoside If d-ribose sugar: deoxy ribonucleoside (d- ribonucleoside)
  • 14. Structure of a nucleotide
  • 15. 1. Pentose sugar 2. Nitrogen base 3. Phosphate Ribonucleotide Deoxyribonucleotide  Phosphate remains attached with 5th carbon of pentose sugar  Nitrogen base remains attached with 1st carbon of pentose sugar
  • 16. 1. Ribose / Deoxy Ribose Sugar Ribose is a pentose sugar with aldehyde function. Deoxyribose {d-ribose} is the ribose sugar with oxygen atom removed from its 2nd carbon atom To avoid confusion between the numerals of various atoms of nitrogen base & ribose sugar,, the carbons of ribose sugar is designated by numerals with a prime Example: 1’, 2’, 3’,4’,5’
  • 17. 2. Phosphate  Total number of phosphate in a nucleotide may be 1 or 2 or 3  Nucleotides of mono phosphate variety (AMP, GMP etc) can be converted to their corresponding diphosphate variety (ADP, GDP etc) & triphosphate variety (ATP, GTP etc) by subsequent phosphorylation
  • 18.
  • 19. 3. Nitrogen Base  A nitrogen containing ring structure which is attached to 1′ carbon of pentose sugar by N-glycosidic bond to form nucleoside.  Two types: 1. Purine base. 2. Pyrimidine base. Nucleoside
  • 20.  Purine bases are derivatives of purine nucleus  Purine nucleus is an aromatic heterocyclic 09 atom ring composed of 04 nitrogen & 05 carbons  Pyrimidine bases are derivatives of pyrimidine nucleus  Pyrimidine nucleus is an aromatic heterocyclic 06 atom ring composed of 02 nitrogen & 04 carbons
  • 21. Raw materials for synthesis of purine nucleus Raw materials for synthesis of pyrimidine nucleus
  • 22.  Purine bases found in nucleic acids: 1. Adenine (6-amino-purine). 2. Guanine (2-amino-6-oxy-purine).  Other purine bases: 1. Hypoxanthine. 2. Xanthine. 3. Uric acid. Hypoxanthine and xanthine are not incorporated into the nucleic acid but important in purine nucleotide metabolism.
  • 23.  Pyrimidine bases found in nucleic acids: 1. Cytosine (2-oxy-4-amino-pyrimidine) 2. Uracil (2, 4-di-oxy-pyrimidine) 3. Thymine (2, 4-di-oxy-5-methyl- pyrimidine)  Other pyrimidine bases: 1. Orotic acid.
  • 24. Purines Pyrimidines Composed of two ring structures. Composed of one ring structure. Number-1 atom(nitrogen)in 11-O’clock position. Number-1 atom (nitrogen) in 6-O’clock position. No variation in DNA and RNA. Variation occurs in DNA and RNA. (Uracil present in RNA stead of thiamine). Larger heterocycle has the shorter name. Smaller heterocycle has the longer name. The atoms are numbered counter- clockwise direction. The atoms are numbered clockwise direction.
  • 26.
  • 28. 28 Functions of Nucleotides  Monomer of nucleic acid & thus conveys genetic information  Participate in energy metabolism & serve as energy store : ATP, GTP etc  Regulatory function as physiological mediator:  Acts as intracellular 2nd messenger: cAMP, cGMP  Helps in signal transduction : G-Protein (made of GTP)  Causes platelet aggregation : ADP  Regulation of coronary blood flow: Adenosine  Acts as:  Coenzymes: e.g. NAD, FMN, FAD etc  Allosteric effector to regulate enzyme activity: e.g. ATP, AMP, ADP etc  Carrier of active intermediates in synthetic processes : e.g. UDP glucose for glycogen synthesis  Methyl donor
  • 30.
  • 31. De-novo synthesis Salvage pathway Synthesis of nucleotides from basic metabolites. It is required in growing cells / rapidly proliferating cells It recycles preformed bases and nucleosides. It provides an adequate supply of nucleotides in non-dividing or slowly dividing cells Very expensive energy wise, only done when absolutely necessary Much less energy consuming process
  • 32.
  • 33. A) De-Novo synthesis of Ribonucleotides
  • 34.
  • 35. a) Purine Ribonucleotides de-novo synthesis  Site: Purine synthesis occurs in all tissues. The major site of purine synthesis is in the liver and, to a limited extent, in the brain.  Substrates:  Aspartic acid (Asp), Glutamine (Gln), Glycine (Gly)  CO2  Formyl tetrahydrofolate (F-FH4) & methenyl tetrahydrofolate (M-FH4)  Products: GMP; AMP
  • 36.
  • 37.  Ribose-5-phosphate (as provided by the pentose- phosphate pathway) is converted into PRPP (Phosphoribosyl pyrophosphate) by PRPP synthetase, in a step requiring one ATP.  In the committed step in the process, an α-amino group is then added to PRPP from glutamine to form 5- phosphoribosylamine. This reaction is catalyzed by glutamine PRPP amidotransferase
  • 38.  A series of nine reactions results in the formation of IMP (Inosine 5′-monophosphate).  IMP can then be transformed either to GMP by IMP dehydrogenase , or to AMP by adenylosuccinate synthetase .  Feedback inhibition controls both the overall rate of purine biosynthesis and the balance between AMP and GMP production
  • 39. b) Pyrimidine Ribonucleotides  The pyrimidine ring is synthesized first  Then ribose phosphate is added from PRPP (phospho ribosyl pyrophosphate) to form a pyrimidine nucleotide
  • 40.
  • 41.
  • 42.
  • 43.
  • 44.
  • 45. Difference in de-novo synthesis of purine & pyrimidine
  • 46.
  • 47. B) De-Novo synthesis of deoxy- Ribonucleotides
  • 48.  Ribonucleotides are converted to deoxyribonucleotides  This conversion is done by direct reduction of ribose sugar by ribonucleotide reductase , which involves removal of oxygen from 2nd carbon of ribose  This reduction of ribonucleotides to d-ribonucleotides occurs only in diphosphate form.
  • 49.
  • 50. C) Salvage Pathway for nucleotides
  • 51.  A salvage pathway is a pathway in which nucleotides (purine & pyrimidine) are synthesized from intermediates in the degradative pathway for nucleotides / nucleic acids.
  • 52.  Use: To recover bases and nucleosides that are formed during degradation of RNA and DNA. The salvaged bases and nucleosides can then be converted back into nucleotides.  Salvage pathway is important in some organs because some tissues cannot undergo de novo synthesis
  • 53. Points Salvage pathway for synthesis of purine nucleotides What happens? Recyclation of free purine bases Where happens? Primarily in extrahepatic tissues (RBC, Brain) Salvaged bases Adenine, Hypoxanthine, Guanine Products IMP, GMP Enzymes responsible for recycling Adenine Phospho Ribosyl Transferase (APRT) & Hypoxanthine Guanine Phospho Ribosyl Transferase (HGPRT / HPRT) Effectiveness of the pathway 90% of daily purine nucleotide biosynthesis occurs Why this pathway occurs? Salvage pathway needs less energy than de-novo biosynthesis Most purine bases are recycled rather than degraded
  • 54.
  • 55. HGPRT : Catalyzes the salvage synthesis of IMP and GMP from the purine bases hypoxanthine and guanine Its defect results in the accumulation of its substrates, hypoxanthine and guanine, which are converted into uric acid by means of xanthine oxidase HGPRT deficiency - Lesch–nyhan syndrome as a co-substrate APRT :  Catalyzes the salvage synthesis of adenosine monophosphate (AMP) from adenine utilizing PRPP as a co-substrate.  Elevated APRT activity may contribute to purine overproduction.
  • 56. Points B) Salvage pathway for synthesis of pyrimidine nucleotides What happens? Recyclation of free pyrimidine bases Where happens? Primarily in extrahepatic tissues Salvaged bases Uracil , Thymine Products UMP, dTMP Enzymes responsible for recycling Uridine phosphorylase Uridine kinase Thymidine phosphorylase Thymidine kinase
  • 57.
  • 59.
  • 60. A) Catabolism of purine nucleotide .
  • 61.  Abnormalities with purine catabolism leads to : Hyperuricemia & gout Xanthinuria Xanthine lithiasis &  These conditions can be treated by drugs inhibiting enzyme- xanthine oxidase : Allopurinol & Febuxostat .
  • 62. B) Catabolism of pyrimidine nucleotide .
  • 63.  End Product CO2, NH3, acetyl CoA, succinyl CoA  Highly water soluble, easily disposable & of no clinical significance .