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Nucleic acids
Dr Sairindhri Tripathy
For Internal Circulation only
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Definition
Any of a group of complex compounds found in all living cells and viruses, composed of purines, pyrimidines, carbohydrates, and phosphoric acid.
Two forms of nucleic acids :-
• DNA (deoxyribonucleic acid )
• RNA (ribonucleic acid )
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Functions
Functions of DNA:-
• A permanent storage place for genetic information.
• Controls the synthesis of RNA.
• Determines the protein development in new cells.
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Functions of RNA :-
• Messenger RNA (m RNA )
• Ribosomal ( rRNA)
• Transfer (tRNA)
• In post transcription modify the other RNA’s
• Transfer genetic information
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Component of nucleic acids
Nucleic acids are build up by the monomeric units -nucleotides that have a pentose sugar, nitrogen base, and phosphate
nucleoside
PO4
Sugar
Base
Nucleoside +Phosphate = Nucleotide
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Function of nucleotides
• Build blocks or monomeric units
• Structural component of several coenzymes of B-complex vitamins.
e.g. FAD. Coenzyme A
• Serve as intermediates in biosynthesis of carbohydrate, lipid & protins.
e.g. S-adenosylmethionine
• Control several metabolic reaction.
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Structure of Nucleotides
N
N
N
N
H
NH2
N
N
O
CH3
O
H
H
N
N
N
N
O
H
NH2
H
N
N
NH2
CH3
O
H
N
N
O
CH3
O
H
H
adenine (A) thymine (T)
guanine (G) cytosine (C) uracil (U)
Nitrogen-Containing Bases (Purines &pyrimidines)
Structure of purine (A,G) & pyrimidines (C, T, U)
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Sugars
O OHCH2
OHOH
HO HO O OHCH2
OH
ribose deoxyribose
(no O)
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Nucleosides in DNA
Base Sugar NucleosideAdenine (A) Deoxyribos Adenosine
Guanine (G) Deoxyribose Guanosine
Cytosine (C) Deoxyribose Cytidine
Thymine (T) Deoxyribose Thymidine
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Nucleosides in RNA
Base Sugar Nucleoside
Adenine (A) ribose Adenosine
Guanine (G) ribose Guanosine
Cytosine (C) ribose Cytidine
Uracil (U) ribose Uridine
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Nucleoside di and triphosphate
Adenosine 5’ monophosphate Thymidine 5’ monophosphate
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Different form of DNA double helix
• DNA exist in at least 6 different form-A to E and Z
• B-form of DNA double helix described by Watson ad crick.
• B-form has 10 base pairs spanning a distance of 3.4nm.ad width of double helix is 2nm.
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The size of DNA• DNA huge in size.
• B-DNA with a thickness of 0.34nm
• Molecular weight 660.
• The term kilo base paire [kb=1000 base paire] is commonly used in the DNA structure.
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THE WASTON AND CRICK MODEL OF DNA
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• James Watson (American biologist) and Frances Crick (English chemist) proposed Model of DNA to explain its structure in 1953
• DNA is right handed double helix . Consists of two polydeoxyriboncleotide chains
• Two strands are anti parallel
• Diameter of double helix is 2 nm
• Two polynucleotide chains complementary to each
• A – T pair has 2 hydrogen bonds while G – C pair has 3 hydrogen bonds
• Major grooves and minor grooves .
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RNA
The RNAs are synthesized by DNA,and are primarily involved in protein synthesis.
It is the polymer of polynucleotide held together by 3,5-phosphodiester bridge.
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How RNA different from DNA
• Pentose- The suger in RNA is ribose in DNA it is deoxyribose.
• Pyrimidine- RNA contain Uracil while in DNA it is thymine.
• Single strand- RNA is single stranded nucleotides and in DNA it may be folded or double stranded.
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Types of RNA
• Messenger RNA ( mRNA )
• Transfer RNA ( tRNA )
• Ribosomal RNA ( rRNA )
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Messenger RNA ( mRNA )
• It synthesized in nucleus as heterogeneous nuclear RNA and on processing it liberates functional mRNA.
• It has high molecular weight with short half life.
• It carries the information from DNA to the
Ribosome i.e. the site of protein synthesis.
• coding sequence of mRNA determines the amino acid sequence in proteins.(4-5%)
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Transfer RNA ( tRNA )
• tRNA contains 71-80 nucleotides (mostly75)
• 20 species of tRNAs as 20 amino acids present the protein structure.
• Structure -- clover leaf
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• Accepter arm
•Anticodon arm
•D arm
•T C arm
•The variable arm
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Ribosomal RNA ( rRNA )
• Protein synthesis takes place.
• It is the catalytic component of the ribosomes.
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RNAs and their functionsTypes of RNA Abbreviation Function
Messenger RNA mRNA Trancfer of genetic information from genes to ribosomes to synthesis proteins
Transfer RNA tRNA Transfer amino acid to mRNA for protein synthesis
Ribosomal RNA rRNA Provide structural framework for ribosomes.
Small nuclear RNA snRNA Involved in mRNA processing
Small cytoplasmic RNA scRNA Involved in selection of protein for export
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Important features of DNA replication
• DNA replication is Semiconservative.
(First experiment evidence was provided by Mathew Meselson and
Franklin Stahl in 1958.)
• Replication begins at the origin and usually proceeds bidirectionally.
• DNA synthesis proceeds in 5’ to 3’ direction.
• DNA synthesis is semidiscontinous.
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• Replication fork:
• Single stranded DNA binding (SSB) proteins:
• Lagging strand:
• Leading strand:
• Okazaki pieces:
• RNA primer:
• Enzymes: Helicase polymerase
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DNA replication:
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Process:
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Life cycle:
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Transcription: overview
• In prokaryotes transcription and translation are coupled.
• In eukaryotes transcription and translation are separated. Transcription occurs in the nucleus, and translation occurs in the cytoplasm on ribosomes.
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Stages of Transcription
• Chain Initiation
• Chain Elongation
• Chain Termination
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TRANSLATION
genetic code : composed of 4 nucleotide bases.
Produce 64 different combination of codon.
Termination codons - UAA,UAG and UGA.
Initiating codon – AUG (Met) , GUG (Val).
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Protein Synthesis It occurs in three stages-
1. Requirement of the components
Amino acids Ribosome m RNA t RNA Energy sources
2. Activation of amino acids – Aminoacyl-tRNA synthetase Corresponding t-RNA
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3. Protein synthesis proper
Initiation :
Elongation :
Termination :
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Nucleic Acid Bases
Purines Pyrimidines Derived from purine or pyrimidine
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Sugars
D-Ribose and 2’-Deoxyribose
*Lacks a 2’-OH group
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Nucleosides
• Result from linking one of the sugars with a purine or pyrimidine base through an N-glycosidic linkage
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Nucleosides
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Nucleotides
• Result from linking one or more phosphates with a nucleoside onto the 5’ end of the molecule through esterification
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Nucleotides
• RNA (ribonucleic acid) is a polymer of ribonucleotides
• DNA (deoxyribonucleic acid) is a polymer of deoxyribonucleotides
• Both deoxy- and ribonucleotides contain Adenine, Guanine and Cytosine– Ribonucleotides contain Uracil
– Deoxyribonucleotides contain Thymine
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Nucleotides
• Monomers for nucleic acid polymers
• Nucleoside Triphosphates are important energy carriers (ATP, GTP)
• Important components of coenzymes– FAD, NAD+ and Coenzyme A
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Naming Conventions
• Nucleosides:– Purine nucleosides end in “-sine”
• Adenosine, Guanosine
– Pyrimidine nucleosides end in “-dine”• Thymidine, Cytidine, Uridine
• Nucleotides:– Start with the nucleoside name from above and
add “mono-”, “di-”, or “triphosphate”• Adenosine Monophosphate, Cytidine Triphosphate,
Deoxythymidine Diphosphate
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Nucleotide Metabolism• PURINE RIBONUCLEOTIDES: formed de novo
– i.e., purines are not initially synthesized as free bases
– First purine derivative formed is Inosine Mono-phosphate (IMP)
• The purine base is hypoxanthine
• AMP and GMP are formed from IMP
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Purine Nucleotides
• Get broken down into Uric Acid (a purine)
N1: Aspartate AmineC2, C8: FormateN3, N9: GlutamineC4, C5, N7: GlycineC6: Bicarbonate Ion
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Purine nucleotide Synthesis-overview
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Purine Nucleotide Synthesis
OH
H
H
CH2
OH OH
H HO
α
O2-O3P
α-D-Ribose-5-Phosphate (R5P)
O
H
H
CH2
OH OH
H HO α
O2-O3P
5-Phosphoribosyl-α-pyrophosphate (PRPP)
P
O
O
O P
O
O
O
ATP
AMP
RibosePhosphatePyrophosphokinase
H
NH2
H
CH2
OH OH
H HO
β
O2-O3P
β-5-Phosphoribosylamine (PRA)
AmidophosphoribosylTransferase
Glutamine + H2O
Glutamate + PPi
H
NH
H
CH2
OH OH
H HO
O2-O3P
CO
H2C NH2
Glycinamide Ribotide (GAR)
GAR Synthetase
Glycine + ATP
ADP+ Pi
H2C
CNH
O
CH
HN
O
Ribose-5-Phosphate
Formylglycinamide ribotide (FGAR)
H2C
CNH
O
CH
HN
HN
Ribose-5-Phosphate
Formylglycinamidine ribotide (FGAM)
THFN10-Formyl-THF
GAR Transformylase
ATP +Glutamine +H2O
ADP +Glutamate + Pi
FGAM Synthetase
HC
CN
CH
N
H2N
Ribose-5-Phosphate
4
5
5-Aminoimidazole Ribotide (AIR)
ATP
ADP + Pi
AIR Synthetase
C
CN
CH
N
H2N
OOC
Ribose-5-Phosphate
4
5
Carboxyamidoimidazole Ribotide (CAIR)
ATP+HCO3
ADP + PiAIR Car boxylase
Aspartate+ ATP
ADP+ Pi
SAICAR Synthetase
AdenylosuccinateLyase
Fumarate
C
CN
CH
N
NH
Ribose-5-Phosphate
4
5
5-Formaminoimidazole-4-carboxamideribotide (FAICAR)
CH2N
O
CH
O
C
CN
CH
N
H2N
Ribose-5-Phosphate
4
5
5-Aminoimidazole-4-carboxamideribotide (AICAR)
CH2N
O
C
CN
CH
N
H2N
CNH
O
HC
COO
CH2
COO
Ribose-5-Phosphate
4
5
5-Aminoimidazole-4-(N-succinylocarboxamide)ribotide (SAICAR)
THF
AICAR Transformylase
N10-Formyl-
THF
Inosine Monophosphate (IMP)
HN
HCN
C
CC
N
CH
N
O
4
5
HH
CH2
OH OH
H HOO2-O3P
IMPCyclohydrolase
H2O
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IMP Conversion to AMP
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IMP Conversion to GMP
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Purine Catabolism and Salvage
Xazanthine oxydase
Guanase
Phosphorylase
Nucleotidase
Deaminase
Phosphorylas,Oxidase
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What Happened to the toe? Why is it swollen?
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Uric Acid Excretion
• Humans – excreted into urine as insoluble crystals
• Birds, terrestrial reptiles, some insects – excrete insoluble crystals in paste form – Excess amino N converted to uric acid
• (conserves water)
• Others – further modification :
Uric Acid Allantoin Allantoic Acid Urea Ammonia
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Gout
• Impaired excretion or overproduction of uric acid• Uric acid crystals precipitate into joints (Gouty Arthritis),
kidneys, ureters (stones)• Lead impairs uric acid excretion – lead poisoning from
pewter drinking goblets– Fall of Roman Empire?
• Xanthine oxidase inhibitors inhibit production of uric acid, and treat gout
• Allopurinol treatment – hypoxanthine analog that binds to Xanthine Oxidase to decrease uric acid production
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2 ATP + HCO3- + Glutamine + H2O
CO
O PO3-2
NH2
Carbamoyl Phosphate
NH2
CNH
CH
CH2
C
COOO
HO
O
Carbamoyl Aspartate
HN
CNH
CH
CH2
C
COOO
O
Dihydroorotate
HN
CNH
C
CHC
COOO
O
Orotate
HN
CN
C
CHC
COOO
O
HH
CH2
OH OH
H HO
O2-O3P
β
Orotidine-5'-monophosphate(OMP)
HN
CN
CH
CHC
O
O
HH
CH2
OH OH
H HO
O2-O3P
β
Uridine Monophosphate(UMP)
2 ADP +Glutamate + Pi
CarbamoylPhosphateSynthetase II
AspartateTranscarbamoylase(ATCase)
Aspartate
Pi
H2O
Dihydroorotase
Quinone
ReducedQuinone
DihydroorotateDehydrogenase
PRPP PPi
Orotate PhosphoribosylTransferase
CO2
OMP Decarboxylase
Pyrimidine Synthesis