Chemistry of Nucleosides, Nucleotides & Nucleic acid

Chemistry of Nucleosides, Nucleotides

& Nucleic acid

Dr.Almoeiz Yousif MS.c.,Ph.D.,MEE

Nucleosides

•Nucleosides composed only of base and sugar.

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N. Base Sugar

Nucleotides

• nucleotides define as a monomer of Nucleic acids ( DNA & RNA).

• Nucleotides are intracellular molecules having the following structure:

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N.Base Sugar Phosphate

Nitrogenous Bases

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The nitrogenous bases are either purine or pyrimidine

Pyrimidine bases

•A pyrimidine bases -containing, a single six

membered ring.

•Numbering is clockwise

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Pyrimidine bases

•There are three pyrimidines commonly found in

nucleic acids: Fr

iday

, Ap

ril 2

4, 2

02

0

7

Uracil

Thymine Cytosine

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Uracil Thymine Cytosine

Pyrimidine bases

•The pyrimidines in DNA are cytosine (C) and thymine (T).

•The pyrimidines in RNA are cytosine ( C) and uracil (U).

•Cytosine can be found in DNA and RNA.

•Thymine is found only in DNA, while uracils are found only in RNA.

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Purines

• Purines consist of linked five - membered and six- membered rings.

•Numbering is anticlockwise

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Purines

•There are two purines commonly found in

Nucleic acids.

•Each can be found in nucleic acid.

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Purines

• Other purine bases produce during metabolism, present in free state in cells:

1. Hypoxanthine.

2. Xanthine.

3. Uric acid. (end product of Adenine & Guanine catabolism)

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Sugars

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• The sugars enter in the nucleotides are Pentose sugars (5-Carbon sugars)

Sugars

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• DNA and RNA have different sugars.

• RNA nucleotides or Ribonucleotides , contain ribose sugar

which have a hydroxyl group in both the 2, and 3 – position of

the sugar ring.

Sugars

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• DNA nucleotides or deoxyribonucleotides have 2-

deoxyribose sugars.

•These sugars have only a single hydroxyl group in the 3

position of the sugar ring.

Phosphate Groups

• A nucleotide contain a single phosphate group, which is a strong acid that gives nucleic acids their acidity.

• Phosphates can be attached through the oxygen of the hydroxyl group of either C3 or C5 atoms of the sugar.

• It is more commonly attached to C5.

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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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Nucleotides • Nucleotides are phosphorylated nucleosides

• Result from linking one or more phosphates with a nucleoside onto OH group 5’ end of the sugar.

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Nucleosides and nucleotides

Naming Conventions

•Nucleosides:

•Purine nucleosides end in “-sine”

•Adenosine, Guanosine.

•Pyrimidine nucleosides end in “-dine”

• Thymidine, Cytidine, Uridine

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Naming Conventions

•Nucleotides:

• Start with the nucleoside name from above and add “mono-”, “di-”, or “triphosphate”

•Adenosine Monophosphate, Cytidine Triphosphate, Deoxythymidine Diphosphate

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Purine Base Nucleoside Nucleotide

Adenine (A) Adenosine Adenosine mono phosphate

(AMP, ADP,ATP)

Guanine (G) Guanosine Guanosine Mono P.

(GMP)

Xanthine Xanthosine Xanthosine Mono

Phosphate

Hypoxanthine Inosine Inosine Mono Phospate

Pyrimidine Base Nucleoside Nucleotide

Cytosine (C) Cytidine CMP

Uracil (U) Uridine UMP

Thiamine (T) Thymidine TMP

Functions of Nucleotides

1. They enter in the structure of nucleic acid, ( DNA , RNA).

2. Nucleoside Triphosphates are major biologic transducer of free energy (ATP,

GTP).

3. Important components of coenzymes

FAD, NAD+ and Coenzyme A.

4. Acts as a second messenger, (c-AMP, c GMP).

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Functions of Nucleotides

5. UDP- glucoronic acid is donor for conjugation reactions

that form urinary glucornide conjugates for biluribin or

drugs as aspirin

6. Cytosine derivatives CTP, is involved in synthesis

ceramide.

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Nucleic acid Chemistry

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What Are Nucleic Acids?

• Nucleic acids are polynucleotides: linear polymers of nucleotides

linked 3 to 5 by phosphodiester bridges .

• They are formed as 5-nucleoside monophosphates

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• Polymers of ribonucleotides are named ribonucleic acid, or RNA.

• Deoxyribonucleotide polymers are called deoxyribonucleic

• acid, or DNA.

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Phosphodiester Bond

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Base pairs

• In Nucleic acids, there is base pairing

• It’s a Complementarity (T=A, C=G)

• Purines always base-pair with pyrimidines

• Cytosine hydrogen bonds with guanine

• Thymine hydrogen bonds with adenine or uracil

• Due to distancing and proximity of unshared pairs and

hydrogens

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GC base pair

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N

N

N

NH

O

N HR

H

Guanine

NN

O

N

H

H

R

-- -- --

-- -- --

-- -- --

cytosine

3 H- bonds

AT base Pair

N

N

N

N

N H

H

R

adenine

NNH

O

O

R

-- -- --

-- -- -- --

thymine

2 H-bonds

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Base Pairs

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Pyrimidines

NH2

O

N

N NH

N

Guanine

N

N

Adenine

N

N

NH2

N O

NH2

N O

NH2

N

Cytosine

Purines

Uracil (RNA)

CH3

N O N

O

NH

N O N

O

NH

Thymine (DNA)

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- +

+

+

-

-

Base Pairing Guanine And Cytosine

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+

- Thymine

-

+ Adenine

Base Pairing Adenine And Thymine

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Base Pairing Adenine And Cytosine

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-

+

-

Base Pairing Guanine And Thymine

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+

+

-

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H

P

O

HO

O

O

CH2

H OH

P

O

O

HO

O

O

CH2

H

P

O

OH

HO

O

O

CH2

NH2

N

N

N

N

O

O

NH2 N

NH

N

N

N O

NH2

N

D

N

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O H

P

O

HO

O

O

CH2

HO

H

H

P HO

O

O

CH2

O

O

H

H2O

H OH

P

O

HO

O

O

CH2

H2O

5’Phosphate group

3’Hydroxyl group

5’Phosphate group

3’Hydroxyl group

Because of specific base paring, any single stranded sequence of DNA or RNA can be used as a template for production of the complimentary strand

DNA structure

• B-DNA is most common

• Antiparallel

• bases inside • Hydrophobic

• Perpendicular to helix

• stands complementary • Very important for information transfer

• Each strand a template for the other.

• right handed

• major and minor groove

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Forms of DNA

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Denaturation and Renaturation

• Heating double stranded DNA can overcome the hydrogen bonds

holding it together and cause the strands to separate resulting in

denaturation of the DNA

• When cooled relatively weak hydrogen bonds between bases can

reform and the DNA renatures

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Double stranded DNA

TACTCGACATGCTAGCAC ATGAGCTGTACGATCGTG

Double stranded DNA TACTCGACATGCTAGCAC

ATGAGCTGTACGATCGTG

Denatured DNA

Single stranded DNA

RNA

• codes for protein

• no consistent secondary structure

• single stranded

• Ribose instead of deoxyribose

• Thymine (T) replaced by Uracil

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. Three Types of RNA

•mRNA

• carries genetic information to the ribosomes

• rRNA

• , along with protein, makes up the ribosomes

• tRNA

• transfers amino acids to the ribosomes where proteins are synthesized

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DNA versus RNA

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DNA RNA

Double-stranded Single-stranded

Holds information Transfers information

A pairs with T A pairs with U (if paired)

C pairs with G C pairs with G (if paired)

Sugar is deoxyribose; lacks OH

at carbon 2

Sugar is ribose; has OH at

carbon 2

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