Structure of a polynucleotide chain.

Before starting with the structure of polynucleotide chain, you must have to get the knowledge on :

1. Nucleotides.
2. Base pairs.
3. DNA vs RNA.
4. Pentose Sugar.
5. And, the phosphate group.

Linkages term means bonds between atoms, compound or chains.
A Polynucleotide chain shows following types of linkages or bond in its compound :

(i) N-glycosidic linkage : 

= In biochemistry, a glycosidic bond or linkage is like an covalent bond that joins a sugar molecule to another group, which may or may not be another sugar.

= N-base is linked to the pentose sugar through a N-glycosidic linkage to form a nucleoside. 

= Pure nucleosides have 1'-9 glycosidic linkage (carbon 1' of sugar and 9 position of A/G).

= Pyrimidine nucleosides have 1'-1 linkage i.e., sugar carbon 1' and 1 position of T/C.

A Nucleoside and the N-Glycosidic Linkage

(ii) Phosphoester linkage : 

=  A type of covalent bond that links two C-atoms through a phosphate group.

= When a phosphate group (PO₄^2-) is linked to 5'-OH of a nucleoside  through phosphoester linkage a             corresponding nucleotide is formed.

= Two nucleotides are linked through 3'-5' phosphodiester linkage to form a dinucleotide.

Nucleotide

Dinucleotide going to be formed

A polymer thus formed has a free phosphate moiety at 5'-OH, which is referred as 5'-end of polynucleotide chain.

 x x x x x x x x x x x x x x x x x x x x x x Under Construction x x x x x x x x x x x x x x x x x x x x x x

Phosphate in Nucleic acids

1. From the figure, it is observable that there are two atoms in a phosphate group i.e, P-Phosphorus and O-oxygen. 
2. So,a phosphate group an ion like compound in which phosphorus atom is bounded to four oxygen atoms. 
3. The phosphate group is added to the sugar as phosphoric acid.
4. Along with sugars and bases, it makes up nucleic acids, like DNA and RNA. 
5. As part of energy carriers, like ATP, it provides energy for moving our muscles.

Pentose Sugar

Complete hydrolysis of Nucleic acids yields :

1. Pentose Sugar.
2. Nucleotide (or a base pair).
3. And Phosphoric acid.

I already had written about them, check the links marked above.

Pentose Sugar : 

These sugars are the compound having a 5-C ring structure.

* In DNA molecule, the sugar moiety is B-D-2-Deoxyribose.

* In RNA molecule, the sugar moiety is B-D-Ribose. 

{ NOTE : Here B-Beta which is an annomeric form, while D means

                the location of a functional group (F gp.) i.e., -OH right

                and above the last C-atom and the number is the change

                in the F gp. at the 2nd C-atom. }

* Well the importance of Pentose sugar in a nucleotide is, that it provides

   site for the Base and the Phosphate group as shown below.

       Base                          Base                           Base

          |                                 |                                  |

----Sugar---Phosphate--(-Sugar---Phosphate-)_n--Sugar---
Well I designed it my own LOL !!!

So, Sugar+Phosphate is a kind of backbone to the nucleic acids or the polynucleotide chain.

Polynucleotide chain or DNA

          

Base Pairs

It is a pair of complementary bases in a nucleic acid molecule, having a purine in one strand linked to a pyrimidine in the other by hydrogen bonds. Cytosine pairs with guanine, and adenine with thymine (DNA) or uracil (RNA).

Well, base pairs are the pairs of bonded nucleotides
through the H-bonds.

I have already posted on : Nucleotides

DNA vs RNA

Basis of Difference	DNA	RNA
Location	Present in nucleus.	Present in nucleus and cytoplasm.
Sugar	Deoxyribose	Ribose
Bases	A T G C	A U G C
Functions	Contains the genetic instructions used in the development and functioning of all known living organisms .	involved in protein synthesis and sometimes in the transmission of genetic information.
Strands	Double- stranded molecule	Single-stranded molecule
Unique Feature	The helix geometry of DNA is of B-Form. DNA is completely protected by the body i.e. the body destroys enzymes that cleave DNA. DNA can be damaged by exposure to Ultraviolet rays .	The helix geometry of RNA is of A-Form. RNA strands are continually made, broken down and reused. RNA is more resistant to damage by Ultra-violet rays.
Complementary base pairing	A-T(Adenine-Thymine), GC(Guanine-Cytosine)	A-U(Adenine-Uracil), GC(Guanine-Cytosine)

DNA - Other Features : 

1. DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules. 
2. These two long strands entwine like vines, in the shape of a double helix. 
3. This arrangement of DNA strands is called antiparallel. 
4. The asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′ (three prime) ends. 

DNA Double Helix

RNA - Other Feature : 

RNA usually exists in two ways -
(i) Single Stranded
(ii) Hairpin loop - Double Stranded.

Nucleotides

A nucleotide is a basic unit of DNA, which looks like the image given
aside. From the picture, it is clear that a nucleotide is made up of :
    1. A nitrogenous base.
    2. A pentose sugar.
    3. And, a phosphate group.

OK, time to derive them,

NITROGENOUS BASE :

A nitrogen containing compound. They are important as they make up the building blocks of nucleic acids. The term is especially used due to presence of organic ring in them. Well, there are two types of N-bases:

(i) Purines : 

• Heterocyclic aromatic organic compound, consists of a pyrimidine ring fused to an imidazole ring. 
• IUPAC Name = 9H-purine. 
• Chemical formula = C₅H₄N₄. 



Purine

• Well there are 9 notable purines occuring naturally, but there are only two purines associated with the nucleic acids. They are Adenine and Guanine. 

*Adenine and Guanine characteristics :

1.  Both are purine derivative. They have variety of roles in biochemistry like cellular  respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the  cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide  (FAD). 
2.  Have functions in protein synthesis and as a chemical component of DNA and RNA. 
3.  The shape of adenine is complementary to either thymine in DNA or uracil in RNA. 
4.  The shape of guanine is complementary to cytosine.

I will represents them throughout the posts as (A) and (G).

(ii) Pyrimidines :

• Aromatic heterocyclic organic compound same as pyridine. 
• Six-membered single ring with two nitrogen atoms at 1 and 3 (positions). IUPAC Name = Pyrimidine. 
• Chemical formula = C₄H₄N₂. 
• There are only found as derivatives (also k/a Diazines), like nucleotides, thiamine (vitaminB₁) and alloxan. And in nucleotides as Cytosine, Thymine and Uracil. 

Pyrimidine

*Cytosine, Thymine and Uracil Characteristics :

1. In nucleotide, these bases form hydrogen bonds with their complementary purines. Thus, in DNA, the purines adenine (A) and guanine (G) pair up with the pyrimidines thymine (T) and cytosine (C), respectively.
2. In RNA, the complement of adenine (A) is uracil (U) instead of thymine (T), so the pairs that form are adenine:uracil and guanine:cytosine.
3. Very rarely, thymine can appear in RNA, or uracil in DNA, but when the other three major pyrimidine bases are represented, some minor pyrimidine bases can also occur in nucleic acids. 
4. These minor pyrimidines are usually methylated versions of major ones and are postulated to have regulatory functions.

Still have doubts, then contact me below.