LEVELS OF STRUCTURE IN NUCLEIC ACIDS

Primary structure of nucleic acids is the order of bases in the

polynucleotide sequence. It makes the primary structure of DNA
and RNA. Each sugar in a sugar phosphate backbone is attached
to a group.

The 3’- OH group of the sugar in one nucleotide forms an ester

bond to the phosphate group on the 5’ carbon of the sugar of the
next nucleotide.

Secondary structure is the set of interaction between

bases, i.e., which parts of strands bound to each other. In
DNA double helix, the two strands of DNA are held
together by hydrogen bonds. The nucleotides on one
strand base pairs with the nucleotide on the other strand.
The secondary structure is responsible for the shape that
the nucleic acid assumes. The bases in the DNA are
classified as Purines and Pyrimidines.

The purines are Adenine and Guanine. Purines consist of a double ring structure, a six
membered and a five membered ring containing nitrogen. The pyrimidines are Cytosine and
Thymine. It has a single ringed structure, a six membered ring containing nitrogen. A purine
base always pairs with a pyrimidine base (Guanosine (G) pairs with Cytosine (C) and Adenine
(A) pairs with Thymine (T) or Uracil (U)). DNA’s secondary structure is predominantly
determined by base-pairing of the two polynucleotide strands wrapped around each other to
form double helix.

Tertiary structure is specifically the

supercoiling of the molecule. It is a higher order
than the secondary structure, in which large-
scale folding in a linear polymer occurs and the
entire chain is folded into a specific 3
dimensional shape.
HOW DO DNA AND RNA DIFFER?

DNA RNA
Deoxyribonucleic acid Ribonucleic acid

mostly located in nucleus particularly in Located outside the nucleus

eukaryotes

Stores genetic information that serves as the Transfer genetic information from one part of
library of a cell the cell to another.

 Important differences between DNA and RNA appear in their secondary and
tertiary structures

THE COVALENT STRUCTURE OF POLYNUCLEOTIDES

Polymers can always be broken down into smaller and smaller units until we are left with
the smallest single unit of the polymer, called a monomer. The monomers of nucleic acids are
nucleotides. An individual nucleotide consists of three parts—a nitrogenous base, a sugar, and
a phosphoric acid residue—all of which are covalently bonded together.

WHAT ARE THE STRUCTURES AND COMPONENTS OF THE NUCLEOTIDES?

The nucleic acid bases (also called nucleobases) are of two types— pyrimidines and
purines. In this case, the word base does not refer to an alkaline compound, such as NaOH;
rather, it refers to a one- or two-ring nitrogenous aromatic compound. Three pyrimidine bases
(single-ring aromatic compounds)—cytosine, thymine, and uracil—commonly occur. Cytosine is
found both in RNA and in DNA. Uracil occurs only in RNA. In DNA, thymine is substituted for
uracil; thymine is also found to a small extent in some forms of RNA. The common purine bases
(double-ring aromatic compounds) are adenine and guanine, both of which are found in RNA
and in DNA In addition to these five commonly occurring bases, there are “unusual” bases, with
slightly different structures, that are found principally, but not exclusively, in transfer RNA. In
many cases, the base is modified by methylation.

The two categories Nitrogenous Bases

Purine Pyrimidine
Contains two ring Only 1 ring

1st ring is 6 membered ring and the other one 6 membered ring
is a 5 membered ring
Adenine/ Guanine Cytosine/ Thymine/ Uracil

Structures of the common nucleobases

KEYS
Pyrimidine- 3 individual H
and 3 double bond
Purines- 4 double bond
NH2/ CH3/ hydroxyl group

 Always start with a 6 membered ring with 2 Nitrogen and has a double bond between
Carbon 5 and 6.
 And for the purines they have a second ring with 2 Nitrogen
 The thymine has an attachment on every single point of the ring
 Wherein the cytosine has attachment in every part except in N.
 Both of the pyrimidine have double bond oxygen and thymine has another double
bonded oxygen at the top and so as guanine.
 And at the top of adenine and cytosine they have a NH2 group and guanine has NH2
and thymine has a CH3 group.
 And all the structure in pyrimidine have 3 individual hydrogens.
 For the purines 2 Hydrogen attach to the 5 membered ring
 A nucleoside is a compound that consists of a base and a sugar covalently linked
together. It differs from a nucleotide by lacking a phosphate group in its structure.

Nitrogenous Bases Nucleoside

Adenine Adenosine
Guanine Guanosine
Cytosine Cytidine
Thymine Thymidine
Uracil Uridine

When the sugar is b-D-ribose, the resulting

compound is a ribonucleoside; when the sugar is b-D-
deoxyribose, the resulting compound is a
deoxyribonucleoside. The glycosidic linkage is from the C-
1' carbon of the sugar to the N-1 nitrogen of pyrimidines or
to the N-9 nitrogen of purines. The ring atoms of the base
and the carbon atoms of the sugar are both numbered,
with the numbers of the sugar atoms primed to prevent
confusion. Note that the sugar is linked to a nitrogen in
both cases (an N-glycosidic bond).

When phosphoric acid is esterified to one of the hydroxyl groups of the sugar portion of a
nucleoside, a nucleotide is formed). A nucleotide is named for the parent nucleoside, with the
suffix -monophosphate added; the position of the phosphate ester is specified by the number of
the carbon atom at the hydroxyl group to which it is esterified—for instance, adenosine 3'-
monophosphate or deoxycytidine 5'-monophosphate.
How do nucleotides combine to give nucleic acids?

The polymerization of nucleotides gives rise to nucleic acids. The linkage between
monomers in nucleic acids involves formation of two ester bonds by phosphoric acid. The
hydroxyl groups to which the phosphoric acid is esterified are those bonded to the 3' and 5'
carbons on adjacent residues. The resulting repeated linkage is a 3', 5'-phosphodiester bond.
The nucleotide residues of nucleic acids are numbered from the 5' end, which normally carries a
phosphate group, to the 3' end, which normally has a free hydroxyl group. The sugar–
phosphate backbone repeats itself down the length of the chain. The most important features of
the structure of nucleic acids are the identities of the bases.

Abbreviated forms of the structure can be written to convey this essential information. In
one system of notation, single letters, such as A, G, C, U, and T, represent the individual bases.
Vertical lines show the positions of the sugar moieties to which the individual bases are
attached, and a diagonal line through the letter P represents a phosphodiester However, an
even more common system of notation uses only the single letters to show the order of the
bases. When it is necessary to indicate the position on the sugar to which the phosphate group
is bonded, the letter p is written to the left of the single-letter code for the base to represent a 5'
nucleotide and to the right to represent a 3' nucleotide. For example, pA signifies 5'-adenosine
monophosphate (5'-AMP), and Ap signifies 3'-AMP.
 A portion of a DNA chain differs from the RNA chain just described only in the fact that
the sugar is 2'-deoxyribose rather than ribose. In abbreviated notation, the deoxyribonucleotide
is specified in the usual manner. Sometimes a letter d is added to indicate a
deoxyribonucleotide residue; for example, dG is substituted for G, and the deoxy analogue of
the ribooligonucleotide in the preceding paragraph would be d(GACAT). However, given that the
sequence must refer to DNA because of the presence of thymine, the sequence GACAT is not
ambiguous and would also be a suitable abbreviation.