Nucleotides



 NUCLEOTIDES:

The nucleotides are the buildings blocks ( monomers) of the nucleic acids, the information molecules of the cell. They also take part in energy systems of cells.Nucleic acids are chains of nucleotides. Nucleotides are basic essential components for the existence of the known human life.These nucleic acids can be DNA or RNA .



Percentage:

The nucleotides form about 2% of the cell contents. 

Composition:

Nucleotides are compounds of carbon, hydrogen,  oxygen, nitrogen and phosphorus. A molecules of nucleotide consists of three smaller molecules of different types: 
(i) Phosphoric acid,

(ii)A 5_ carbon or pentose sugar molecule, and 

(iii) A molecule of nitrogenous ( nitrogen __ containing) organic base, all linked together by covalent bonds.

(i) Phosphoric Acid:  Phosphoric acid ( H3PO4) is biologically called phosphate group because it dissociates under physiological conditions, freeing hydrogen ions. A nucleotide may have 1,2 or 3 phosphate groups. The phosphate group gives acidic nature to the nucleotide.




(ii) Sugar Molecule: The sugar molecule in a nucleotide may be ribose ( C5H10O5) or deoxyribose ( C5H10O4) .Both sugar are in furanose or Pentagon state with four carbon and one oxygen atom. The fifth carbon along with H2OH occurs outside the ring. Ribose molecule differs from deoxyribose molecule in having a hydroxyl group (__OH) instead of hydrogen at carbon 2. Thus, deoxyribose sugar has one oxygen atom less than ribose sugar, hence its name.



(iii) Nitrogenous Base Molecule:The organic base of a nucleotide is either a pyrimidine or a purine . The pyrimidines and purines are flat, heterocyclic* compounds nitrogen and carbon in the ring structure. Nitrogen in the rings tends to take up H+ from solution and gives the molecules their basic nature, hence the term nitrogenous base. A pyrimidine molecule is smaller and has 6__ membered ring, with nitrogen at 1' and 3' positions. A purine molecule is larger and has two rings, a 6__ member ring joined to a 5_ member ring at 4' and 5' positions, and carries nitrogen at 7' and 9' positions also besides at 1' and 3' positions. There are three important pyrimidines : thymine ( T), cytosine ( C) and uracil ( U). There are two important purines: adenine ( A) and guanine ( G) . The bases are commonly represented by their initial latters A, G, T, U, C.



    The avoid ambiguity between numbering systems of heterocyclic rings and sugars, positions on pentose are given a prime(').


* Heterocyclic compounds have more than one kind of atoms.

Purines 

1) : Purine molecule is larger than pyrimidine molecule.

2):  Purine is a 9__ membered molecule.

3): Its molecule consists of 2 rings joined at 4' and 5' positions. 

4): It has nitrogen atom at 1', 3', 7', and 9' positions. 

5): There are 2 important purines : adenine ( A) and guanine ( G).

Pyrimidines:

1): Pyrimidines molecule is smaller than purine molecule. 

2): Pyrimidine is a 6__ membered molecules. 

3): Its molecule is a single ring.

4): It has nitrogen atom at 1' and 3' positions. 

5): There are 3 important Pyrimidines: thymine (T), cytosine ( C), and uracil ( U).

Linking of Nucteotide Components: 

The  nitrogenous base molecule is joined to the sugar molecule by a glycosidic bond. The latter generally develops between the first carbon of the sugar and the nitrogen at position 1 in case of pyrimidine base and at position 9 in case of purine base. The compound formed in the above manner is called a nucleoside. For instance, the combinations adenine __ ribose and adenine__ deoxyribose are nucleosides. For instance, the combinations adenine __ ribose and adenine__ deoxyribose are nucleosides. A nucleoside with ribose sugar is known as ribonucleoside, or simply deoxyriboside. The various nucleosides are adenosine ( adenine + ribose), deoxyadeno__ sine ( adenine + deoxyribose), guanosine ( guanine + ribose), deoxyguanosine ( guanine + deoxyribose), cytidine ( cytosine + ribose), deoxycytidine ( cytosine + deoxyribose), deoxythymidine ( thymine+ deoxyribose), and uradine ( uracil + ribose).


      The nucleoside combine with a phosphate group at 5' position by an ester bond to form a nucleotide, or nucleoside monophosphate.


For example, the combination adenine_ ribose __ phosphate and adeninedeoxy__ ribose _ phosphate are nucleotides. A nucleotide having ribose sugar is called ribonucleotide, or simple robotide, and a nucleotide containing deoxyribose sugar is termed deoxyribo_nucleotide,or simpley deoxyribostide. Both glycosidic and ester bonds are formed by condensation reactions, involving elimination of water.



      There are two series of nucleotides: one with ribose sugar and the other with deoxyribose sugar. Each series has four nucleotides.Uracil forms a nucleotide of ribose series only ; thymine of deoxyribose series only, adenine, cytosine and guanine of both the series. The nucleotides are named after the nitrogenous base present in them.


    The various nucleotides are adenylic acid or adenosine monophosphate ( AMP), deoxyadenylic acid or deoxyadenosine monophosphate ( dAMP) 
guanylic acid or guanosine monophosphate ( GMP) , deoxyguanylic acid or deoxyguanosine monophosphate ( dGMP), cytidylic acid or cytidine monophosphate ( CMP), deoxycytidine monophosphate ( dCMP) , deoxythymidylic acid or deoxythymidine monophosphate ( dTMP), and uridylic acid or uridine monophosphate ( UMP).

The free occurring nucleotides many have up to three phosphate groups.

Functions:

The nucleotides serve four major functions __

1): Formation of Necleic Acids: The nucleotides form nucleic acids by polymerization. The ribonucleotides form ribonucleic acid ( RNA). The deoxyribonucleotides form deoxyribonucleic acid ( DNA). 

 2): Formation of Energy Carriers: The nucleotides, by combination with one or two additional phosphate groups, form energy carriers such as ATP and ADP.

3): Formation of Coenzymes: The nucleotides, by combination with other molecules, form coenzymes such as NAD, NADP, FMN, FAD, CoA.

 4): Regulatory Chemicals:  Some nucleotides, such as cyclic AMP ( adenosine 3, 5__ monophosphate), act as regulatory chemicals in diverse cellular functions.

5): They are building block of nucleic acids, ribonucleotides for RNAs while deoxyribonucleotides produce DNA.

6): Cyclic AMP ( cAMP) is the mediator of homone action by acting as a second messenger. 

7): Cyclic GMP ( cGMP) is functional in Ca² or Calmodulin mediated chemical reaction. 

8):Higher nucleotides behave as energy carriers. ATP is known as energy currency  of the cell.

9): Nucleotides produced by nicotinamide and riboflavin function as coenzymes ( NAD+, NADP+, FMN and FAD) of dehydrogenases or oxidases.

10): CoA from pantothenic acid functions as Acyl group carrier.

11): UDP and ADP are involved in synthesis of polysaccharides while CDP and CTP are required  in phospholipid synthesis. 

 ● Energy Carriers ( Higher Nucleotides):

Composition :Energy carriers consist of nucleotides having one or two additional phosphate groups linked up at their phosphate end, forming diphosphates and triphosphates. Linkage of additional phosphate groups occurs at the cost of a large amount of energy because this linkage occurs against a force of repulsion between similarly charged radicals P and P. This energy is provided by oxidation of food, mainly glucose,  and by photosynthesis.  Separation of the additional phosphate groups from the nucleotides by enzymatic hydrolysis releases correspondingly large amount of energy.The bonds joining the additional phosphate groups to the nucleotides are called high energy, or energy rich, bonds, as they carry a great deal of energy.  They are indicated by the ~.The nucleotide called adenine_ ribose __ phosphate, or adenosine monophosphate, or AMP forms the following two energy carriers___ 

1): Adenine __ ribose __ phosphate ~ phosphate or adenosine diphosphate or ADP.

2): Adenine__ ribose __ phosphate ~ phosphate ~ phosphate or adenosine triphosphate or ATP .



  ATP was discovered by Karl Lohmann in 1929 from muscle cell. Its role in a cell was found by Fritz Lipmann in 1941. It is formed in every living cell. ATP is mobile and transports the chemical energy to the energy __ consuming processes anywhere within the cell. However, the ATP molecules do not move from one cell into another cell
 ATP acts as a storehouse of as well as  source of energy in a cell. The ADP + Pi + Energy➡️ATP reaction can take place in a cyclic manner, involving building up and breakdown processes. 



    The nucleotides having more than one phosphate group are called higher nucleotides. Other purines and Pyrimidines also form energy carrier __ 

   1): Guanosine diphosphate and triphosphate ( GDP, GTP),

  2): Cytidine diphosphate and triphosphate ( CDP , CTP).

  3): Thymidine diphosphate and triphosphate ( TDP, TTP).

  4): Uridine diphosphate and triphosphate ( UDP, UTP) respectively .


  Function: The energy of energy carriers,  when set free, is utilized for driving energy  __ dependent reactions in the cells, and is called biologically useful energy.

                       ATPase Enzyme 
ATP + water _______________ADP+Pi + Energy 

     
                            Enzyme 
    ADP + Water ________ AMP + Pi + Energy 


      The third phosphate bond can release about 7.3¹ Kcal of free energy per mole on hydrolysis . This is far more than the energy released by hydrolysis of most other covalent bonds. The second energy __ rich phosphate bond also releases 7.3¹ Kcal of free energy per mole. ATP is the most common energy carrier in the cells, and is often called the universal energy carrier or energy currency of the cell.

              ATP + H2 O 🔁 ADP + Pi + kcal/ mol

               ADP+ H2O🔁 AMP + Pi +7.3 kcal/mol


Note : Free energy of 7.3 kcal/mol is released under standard laboratory conditions in a test tube. Under typical conditions inside cells, hydrolysis of ATP to ADP may release about 13 kcal/mol. Biology by Campbell, Reece and Mitchell, 5th ed., 1999, P.90 and 102.

●Coenzymes:

Action: The chemical reactions in a cell often involve removal of a group of atoms from one compound and its addition to another. This process requires the services of a specific enzyme and a specific coenzyme. The coenzyme temporarily joins to, or accepts, the separated group of atoms and hands it over to another acceptor compound.

Definition :  A coenzyme may be defined as an organic carrier molecule which cooperates with a particular enzyme in promoting a chemical reaction in a cell.


 
Composition:  Coenzymes are generally formed from the nucleotides by replacing the nitrogenous base group with some vitamin.


Examples:  Some important coenzymes are nicotinamide adenine dinucleotide or NAD, nicotinamide adenine dinucleotide phosphate or NADP, flavin mononucleotide or FMN , flavin adenine dinucleotide or FAD, and coenzyme A. All contain vitamin B. The  coenzymes containing nicotinamide and riboflavin may occur free or joined to specific proteins


(i) NAD:  It is composed of 2 nucleotides, one containing the base adenine and the other the base nicotinamide. The latter is a derivative of a B vitamin called nicotinic acid or niacin.

Adenin                          Nicotinamide
  |                                         |                                  Ribose___ Phosphate____ Phosphate__Ribose 

 ( ii) NADP:  It is formed from NAD by the addition of another phosphate to adenine.

 Adenin                                         Nicotinamide
  |                                                              |                                   Phosphoribose__Phosphate____Phosphate__Ribose

(iii) FMN: It consists of flavin, sugar ribotol and phosphate. Flavin is a derivative of a B vitamin called riboflavin. 
  
            Flavin
             |
            Ribotol ____ phosphate 


 
 (iv) FAD:  It consists of flavin ribotol phosphate joined to adenine ribotol phosphate. 


Adenin                                Flavin
  |                                         |                                  Ribotol___ Phosphate____ Phosphate__Ribotol

 (v) Coenzyme A  (CoA): Its molecule has three components: a phosphate derivative of adenosine diphosphate, a vitamin B celled pantothenic acid, and a chain of hydrogen __ bearing atoms of nitrogen ,carbon and sulphur .

 Function  Coenzymes help in chemical reactions in the cell.

Nucleoside ( Notrogen Base+ Pentose Sugat) 

The nitrogen base combines with the sugar molecule at its  carbon atom 1'in a ß_ N glycosidic  linkage ( C_ N_ C) by one of its nitrogen  atoms ( usually  1 in Pyrimidines and 9 in purines) . Depending upon the type of pentose sugar, nucleosides are differentiated into ribonucleosides and deoxyribonucleosides.

☆ Uracil produces nucleoside with only ribose sugars. 

☆ Thymine similarly forms nucleoside with only deoxyribose sugar.

☆ Other nitrogen bases produce nucleosides with both ribose and deoxyribose sugars.

☆ The various nucleosides are _ Adenosine ( adenine + ribose ), Deoxyadenosine ( adenine + deoxyribose), Guanosine ( guanine + ribose), Deoxyguanosine ( guanine + deoxyribose), Uridine (cytosine + ribose), Deoxythymidine ( thymine+ deoxyribose), Cytidine ( cytosin + ribose), Deoxycytidine ( cytosine + deoxyribose).

  Nucleotides are phosphoric acid esters of nucleosides and therefore also called nucleoside phosphates. Phosphate attaches to the sugar molecule at its 5' carbon atom but rarely may link to 3' carbon atom or to 2' carbon atom also . The bond between the phosphate and hydroxyl group of sugar is an ester bond. As there is one such  ester bond on either side, it is called phosphodiester bond. The  number of Phosphoric or phosphate residues may be upto there in free occurring nucleotides. Nucleotides may be ribonucleotides ( = ribotides) or deoxyribo_ nucleotides ( = deoxyribotides) depending on the pentose sugar present. The various nucleotides are adenylic acid ( adenosine monophosphate or AMP), deoxyadenylic acid ( dAMP), guanylic acid ( guanosine monophosphate or GMP), deoxyguanylic acid ( dGMP), uridylic acid ( uridine monophosphate or UMP), deoxythymidylic acid ( deoxythymidine monophosphate or dTMP), cytidylic acid ( cytisine monophosphate or CMP) and deoxycytidylic acid ( dCMP).
                                       

Differences between Nucleosides and Nucleotides



 Nucleosides

1) : These are formed by the union of 2 molecules: a nitrogen containing organic base and a pentose sugar.

2): These are slightly basic.

3): These are components of nucleotides. 


 Nucleotides 


1): These are formed by the union of 3 molecules: a nitrogen containing organic base, a pentose sugar and a phosphate.

2): These are acidic in nature.

3) : These are components of nucleic acids, energy carriers and coenzymes. 






















































 

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