NUCLEOTIDES NUCLEOTIDES CHEMISTRYCHEMISTRY

DR AMENA RAHIMDR AMENA RAHIM

BIOCHEMISTRYBIOCHEMISTRY

“The whole art of teaching is only the art of awakening the natural curiosity of young minds for the purpose of satisfying it afterwards”

NUCLEOPROTEINSNUCLEOPROTEINS

One of the conjugated proteins, One of the conjugated proteins, characterized by the presence of a characterized by the presence of a prosthetic group ( nucleic acid),prosthetic group ( nucleic acid),

Attached to a simple protein- Histone or Attached to a simple protein- Histone or Protamine.Protamine.

Biomedical ImportanceBiomedical Importance

Building blocks of nucleic acidsBuilding blocks of nucleic acids

Energy currencyEnergy currency

Carriers of activated intermediatesCarriers of activated intermediates

Allosteric regulators of metabolismAllosteric regulators of metabolism

Control oxidative phosphorylationControl oxidative phosphorylation

Second messengersSecond messengers

Synthetic analogues used in Synthetic analogues used in chemotherapychemotherapy

NUCLEIC ACIDSNUCLEIC ACIDS

Genetic material of all known organismsGenetic material of all known organisms

DNA: deoxyribonucleic acidDNA: deoxyribonucleic acid

RNA: ribonucleic acid (e.g., some viruses)RNA: ribonucleic acid (e.g., some viruses)

Consist of chemically linked sequences of Consist of chemically linked sequences of nucleotidesnucleotides

Nitrogenous Nitrogenous basebase

Pentose- 5-carbon Pentose- 5-carbon sugarsugar (ribose or deoxyribose) (ribose or deoxyribose)

Phosphate groupPhosphate group

The sequence of bases provides the genetic The sequence of bases provides the genetic

informationinformation

There are two classes of nitrogen bases There are two classes of nitrogen bases called called purinespurines (double-ringed structures) (double-ringed structures) and and pyrimidinespyrimidines (single-ringed (single-ringed structures). The four bases in DNA's structures). The four bases in DNA's alphabet are: alphabet are: adenine (A)adenine (A) - a purine - a purine cytosine(C)cytosine(C) - a pyrimidine - a pyrimidine guanine (G)guanine (G) - a purine - a purine thymine (T)thymine (T) - a pyrimidine - a pyrimidine

BASESBASES

Two types of bases:Two types of bases:

1. Purines1. Purines are fused five- and six-membered are fused five- and six-membered ringsrings

AdenineAdenine AA DNADNA RNARNA

GuanineGuanine GG DNADNA RNARNA

2. Pyrimidines2. Pyrimidines are six-membered rings are six-membered rings

CytosineCytosine CC DNADNA RNARNA

ThymineThymine TT DNADNA

UracilUracil UU RNARNA

Nitrogenous BasesNitrogenous Bases

Planar, aromatic, and heterocyclicPlanar, aromatic, and heterocyclic

Derived from Derived from purinepurine or or pyrimidinepyrimidine

Numbering of bases is “unprimed”Numbering of bases is “unprimed”

Nucleic Acid BasesNucleic Acid Bases

Purines Pyrimidines

SUGARSSUGARS

There are two different kinds of sugars There are two different kinds of sugars in a nucleotide, deoxyribose and ribose. in a nucleotide, deoxyribose and ribose.

If the polynucleotide chain forms DNA If the polynucleotide chain forms DNA then the sugars in its nucleotides are then the sugars in its nucleotides are deoxyribose while nucleotides deoxyribose while nucleotides containing ribose as its sugar form RNA.containing ribose as its sugar form RNA.

SugarsSugars

Pentoses (5-C sugars)Pentoses (5-C sugars)

Numbering of sugars is “primed”Numbering of sugars is “primed”

SugarsSugars

D-Ribose and 2’-DeoxyriboseD-Ribose and 2’-Deoxyribose

*Lacks a 2’-OH group

Each nucleotide consists of a sugar Each nucleotide consists of a sugar ((deoxyribosedeoxyribose) bound on one side to a ) bound on one side to a phosphate groupphosphate group and bound on the other and bound on the other side to a side to a nitrogenous basenitrogenous base..

NucleosidesNucleosides

Result from linking one of the sugars with Result from linking one of the sugars with a purine or pyrimidine base through an a purine or pyrimidine base through an N-N-glycosidic linkageglycosidic linkage

– PurinesPurines bond to the C1’ carbon of the sugar at bond to the C1’ carbon of the sugar at their their N9 atomsN9 atoms

– PyrimidinesPyrimidines bond to the C1’ carbon of the bond to the C1’ carbon of the sugar at their sugar at their N1 atomsN1 atoms

NucleosidesNucleosides

Phosphate GroupsPhosphate Groups

Mono-, di- or triphosphatesMono-, di- or triphosphates

Phosphates can be bonded to either C3 or Phosphates can be bonded to either C3 or C5 atoms of the sugarC5 atoms of the sugar

NucleotidesNucleotides

Result from linking one or more phosphates Result from linking one or more phosphates with a nucleoside onto the 5’ end of the with a nucleoside onto the 5’ end of the molecule through esterificationmolecule through esterification

Naming ConventionsNaming Conventions

Nucleosides:Nucleosides:– Purine nucleosides end in “-sine” Purine nucleosides end in “-sine”

Adenosine, GuanosineAdenosine, Guanosine

– Pyrimidine nucleosides end in “-dine”Pyrimidine nucleosides end in “-dine”Thymidine, Cytidine, UridineThymidine, Cytidine, Uridine

Nucleotides:Nucleotides:– Start with the nucleoside name from above Start with the nucleoside name from above

and add “mono-”, “di-”, or “triphosphate”and add “mono-”, “di-”, or “triphosphate”Adenosine Monophosphate, Cytidine Triphosphate, Adenosine Monophosphate, Cytidine Triphosphate, Deoxythymidine DiphosphateDeoxythymidine Diphosphate

NucleotidesNucleotides

RNA (ribonucleic acid) is a polymer of RNA (ribonucleic acid) is a polymer of ribonucleotidesribonucleotides

DNA (deoxyribonucleic acid) is a polymer DNA (deoxyribonucleic acid) is a polymer of deoxyribonucleotidesof deoxyribonucleotides

Both deoxy- and ribonucleotides contain Both deoxy- and ribonucleotides contain Adenine, Guanine and CytosineAdenine, Guanine and Cytosine– Ribonucleotides contain UracilRibonucleotides contain Uracil– Deoxyribonucleotides contain ThymineDeoxyribonucleotides contain Thymine

NucleotidesNucleotides

Monomers for nucleic acid polymersMonomers for nucleic acid polymers

Nucleoside Triphosphates are important Nucleoside Triphosphates are important energy carriers (ATP, GTP)energy carriers (ATP, GTP)

Important components of coenzymesImportant components of coenzymes– FAD, NADFAD, NAD++ and Coenzyme A and Coenzyme A

There are two main cellular functions for There are two main cellular functions for purines and pyrimidines:purines and pyrimidines:

1. the purines adenine and guanine and 1. the purines adenine and guanine and the pyrimidines cytosine, thymine and the pyrimidines cytosine, thymine and uracil are all utilized for the production of uracil are all utilized for the production of DNA and RNA. DNA and RNA.

These nitrogenous bases are synthesized These nitrogenous bases are synthesized linked to a phosphorylated ribose sugar linked to a phosphorylated ribose sugar residue, and these nucleoside residue, and these nucleoside monophosphates are incorporated into monophosphates are incorporated into growing strands of new DNA or RNA growing strands of new DNA or RNA during replication or transcription. during replication or transcription.

2. The second function of pyrimidines and 2. The second function of pyrimidines and purines is short-term energy storage. purines is short-term energy storage.

3. Guanine triphosphate and guanine 3. Guanine triphosphate and guanine diphosphate are utilized by certain diphosphate are utilized by certain enzymes and receptors as an on/off enzymes and receptors as an on/off switch.switch.

4. while cytosine triphosphate and uridine 4. while cytosine triphosphate and uridine triphosphate are both used in the triphosphate are both used in the production of biomoleculesproduction of biomolecules

Adenosine DerivativesAdenosine Derivatives

The most common adenosine derivative is The most common adenosine derivative is the cyclic form, 3'-5'-cyclic adenosine the cyclic form, 3'-5'-cyclic adenosine monophosphatemonophosphate, , cAMP.cAMP.

This compound is a very powerful second This compound is a very powerful second messenger involved in passing signal messenger involved in passing signal transduction events from the cell surface transduction events from the cell surface to internal proteins.to internal proteins.

Regulate glycogen breakdown, lipids Regulate glycogen breakdown, lipids breakdown, stop cholesterol synthesisbreakdown, stop cholesterol synthesis

Regulate transcription and translation. Regulate transcription and translation.

Regulate permeability of cell membraneRegulate permeability of cell membrane

Regulate insulin secretionRegulate insulin secretion

Catecholamines biosynthesisCatecholamines biosynthesis

cAMP is rapidly degraded by cAMP is rapidly degraded by phosphodiesterases.phosphodiesterases.

Phosphodiesterases when activated will Phosphodiesterases when activated will promote the degradation of cAMP.promote the degradation of cAMP.

Phosphodiesterases when inhibited will Phosphodiesterases when inhibited will prevent the degradation of cAMPprevent the degradation of cAMP

Inhibitors are methylxanthines- caffeine, Inhibitors are methylxanthines- caffeine, theophylline, theobromine.theophylline, theobromine.

The most common form of energy in all The most common form of energy in all cells is adenosine triphosphate, or cells is adenosine triphosphate, or ATPATP..

Release of the third phosphate to produce Release of the third phosphate to produce adenosine diphosphate, or adenosine diphosphate, or ADPADP, is an , is an extremely favorable reaction and can drive extremely favorable reaction and can drive reactions requiring energy input.reactions requiring energy input.

S-adenosylmethionine (SAM)S-adenosylmethionine (SAM) is a form is a form of activated methionine which serves as a of activated methionine which serves as a methyl donor in methylation reactionsmethyl donor in methylation reactions

Active sulphate- Active sulphate- Adenosine -3- POAdenosine -3- PO44 5 5

Phosphosulphate.Phosphosulphate.

It incorporates sulfate groups.It incorporates sulfate groups.

Guanosine DerivativesGuanosine Derivatives

GTP- GTP- Protein synthesis, Purine Synthesis, Protein synthesis, Purine Synthesis, ATP formation, gluconeogenesis.ATP formation, gluconeogenesis.

A cyclic form of GMP A cyclic form of GMP (cGMP) (cGMP) is found in is found in cells involved as a second messenger cells involved as a second messenger molecule. In many cases its' role is to molecule. In many cases its' role is to antagonizeantagonize the effects of c-AMP. the effects of c-AMP.

(cGMP) (cGMP) is formed from GTP by guanylyl is formed from GTP by guanylyl cyclase, regulated by effectors.cyclase, regulated by effectors.

The most important cGMP coupled signal The most important cGMP coupled signal transduction cascade is that of: transduction cascade is that of:

1. Photoreception. 1. Photoreception.

2. for Atrial Natriuretic Peptide & 2. for Atrial Natriuretic Peptide &

3. Nitric oxide.3. Nitric oxide.

All these are potent vasodilators and cause All these are potent vasodilators and cause smooth muscle relaxation.smooth muscle relaxation.

Uracil DerivativesUracil Derivatives

UDP- glucose-UDP- glucose--- glucose donor in -- glucose donor in glycogen synthesis.glycogen synthesis.

UDP-sugar derivativesUDP-sugar derivatives participate in participate in sugar epimerization e.g.------ sugar epimerization e.g.------ interconversion of glucose-1- PO4 to interconversion of glucose-1- PO4 to galactose 1-PO4 (UDP-glucose & UDP- galactose 1-PO4 (UDP-glucose & UDP- galactose) (glycoproteins, galactose) (glycoproteins, glycolipids,GAGS).glycolipids,GAGS).

UDP-galactose, UDPglucoronate, UDP-UDP-galactose, UDPglucoronate, UDP-N-acetylgalactosamine N-acetylgalactosamine act as sugar act as sugar donors for biosynthesis of glycoproteins & donors for biosynthesis of glycoproteins & proteoglycansproteoglycans

UDP glucoronate UDP glucoronate ---- glucuronic acid ---- glucuronic acid donor.donor.

Cytidine DerivativesCytidine Derivatives

CMP-N acetylneuraminic acid CMP-N acetylneuraminic acid required required for the biosynthesis of for the biosynthesis of glycoproteins.glycoproteins.

CDP-cholineCDP-choline- required for the - required for the biosynthesis of biosynthesis of sphingomyelin.sphingomyelin.

CTPCTP- required for the biosynthesis of - required for the biosynthesis of phosphoglycerides.phosphoglycerides.

CoenzymesCoenzymes

Many coenzymes are nucleotide Many coenzymes are nucleotide derivatives e.g. derivatives e.g. NAD, NADP, FAD, NAD, NADP, FAD, coenzyme- A.coenzyme- A.

Unusual BasesUnusual Bases

Present in nucleic acids of bacteria and Present in nucleic acids of bacteria and virusesviruses

Also found in DNA and tRNA of both Also found in DNA and tRNA of both prokaryotes and eukaryotes.prokaryotes and eukaryotes.

1-methyl adenosine is a modified adenosine 1-methyl adenosine is a modified adenosine base found on tRNA:base found on tRNA:

N2,N2-dimethylguanosine is a modified N2,N2-dimethylguanosine is a modified guanosineguanosine

Dihydro uridine is a modified UridineDihydro uridine is a modified Uridine

Pseudo uridine is a modified UridinePseudo uridine is a modified Uridine

Methylcytosine is a modified cytosineMethylcytosine is a modified cytosine

Hydroxymethylcytosine is a modified Hydroxymethylcytosine is a modified cytosinecytosine

Free nucleotides are:Free nucleotides are:

1.1. XanthineXanthine

2.2. HypoxanthineHypoxanthine

3.3. Uric acidUric acid

Methylated bases present in plants- they Methylated bases present in plants- they are xanthine derivatives:are xanthine derivatives:

1.1. Caffeine of coffeeCaffeine of coffee

2.2. Theobromine of teaTheobromine of tea

3.3. Theophyline of cocoaTheophyline of cocoa

Synthetic Analogues of Synthetic Analogues of NucleotidesNucleotides

These are also called antimetabolites- --These are also called antimetabolites- --therapeutic applicationtherapeutic application

Prepared by altering the ring or sugar Prepared by altering the ring or sugar moiety.moiety.

Used in chemotherapy.Used in chemotherapy.

Example: removal of the hydroxyl group Example: removal of the hydroxyl group from 3’ carbon of the deoxyribose ring as from 3’ carbon of the deoxyribose ring as in 2’ 3’ dideoxy inosine.in 2’ 3’ dideoxy inosine.

Conversion of deoxyribose to another Conversion of deoxyribose to another sugar as in arabinose (antiviral, sugar as in arabinose (antiviral, anticancer)anticancer)

5-fluorouracil5-fluorouracil

6- mercaptopurine6- mercaptopurine

Cytarabine etc.Cytarabine etc.