CHEMISTRY OF

NUCLEIC ACIDS
dr. Winarsi
DNA and RNA are nucleic acids (deoxyribonucleic acids
and ribonucleic acids).
Nucleic acid is a polymer of nucleotides.
A nucleotide consisits of:
1. a heterocyclic nucleobase (purine or pyrimidine),
2. a pentose sugar (ribose or deoxyribose),
3. A phosphate or polyphosphate group
(monophosphate, diphosphate, or triphosphate).
Nucleotides are phosphate esters of C5 sugars (ribose or
deoxyribose) linked to a nitrogenous base.

Nucleosides don’t contain the phosphate.

Purine and pyrimidine bases

The various purine and pyrimidine bases which occur in the

nucleotides of nucleic acids are derived by appropiate
substitution on the ring structures of the parent substance, purine
or pyrimidine.
Purines have two fused rings and pyrimidines have a single ring.

The purine bases, adenin and guanin are 2 purines found in all
nucleic acids.
The pyrimidine bases

There are 3 main pyrimidine bases in the nucleic

acids: cytosine, thymine, and uracil.
Cytosine is found in all nucleic acids except the
DNA.
Thymine occurs mainly in DNA.
Uracil is confined to RNA.
Nomenclature of nucleotides and nucleosides

Nucleosides:
- in DNA : deoxyadenosine, deoxyguanosine, deoxycytidine,
deoxythymidine.
- in RNA : adenosine, guanosine, cytidine, uridine.

Nucleotides:
- in DNA: deoxyadenilate (dAMP), deoxyguanylate (dGMP),
deoxycytidylate (dCMP), thymidylate (dTMP).
- in RNA: adenylate (AMP), guanylate (GMP), cytidylate (CMP),
uridilate (UMP).
Primary polymeric structure of nucleic acids.
Linkage of nucleotides.
Nucleotides are linked together by phosphodiester bonds between
the 3’ hydroxyl on the sugar of one nucleotide through a
phosphate molecule to the 5’ hydroxyl on the sugar of another
nucleotide.
The sugar-phosphate linkages form a symmetrical “backbone”,
with the 5’ end of one sugar always linked through a phosphate
molecule to the 3’ end of the adjacent sugar.
It is standard to use the one-letter abbreviation for the bases when
writing the order of nucleic acid polymer. By convention, DNA
sequences are written in the 5’ to 3’ direction.
DNA secondary structure.

Double-helical (B-form)DNA or B-form DNA is the

predominant conformation.

1. Two antiparallel strands form a right-handed helix. B-form

DNA consists of two polymers, or strands, of DNA paired to
each other and coiled around a common axis in a right handed
manner. Each strand has an opposite polarity to the other. That
is, where one sugar-phosphate backbone has a 5’ to 3’
symmetry, the adjacent, paired strand is oriented oppositely in
a 3’ to 5’ direction.
2. Complementary base pairing.
The two DNA strands of the double helix are held together
by complementary base pairing. Specific hydrogen bonds
can only form between complementary bases in a double
helix.
The purine adenine pairs with the pyrimidine thymine
through two hydrogen bonds (AT), and the purine guanine
pairs with the pyrimidine cytosine through three hydrogen
bonds (GC).
Therefore, in double-helical DNA, there are always the
same number of adenine bases as thymine bases, and
always the same number of guaine bases as there are
cytosine bases.
Human mitochondria contain small number of
DNA molecules : mtDNA.
Mitochondrial DNA is maternally inherited.
The structure of RNA

1. RNA differs from DNA.

- The polynucleotide structure of RNA is similar to
DNA except that RNA contains the sugar ribose
rather than deoxyribose and uracil (U) rather than
thymine. (a small amount of thymine is present in
tRNA).
- RNA is generally single stranded .
a. When strands loop back on themselves, the
bases on opposite sides can pair : adenine with
uracil (A to U) and guanine with cytosine (G to C).
 b. RNA molecules have extensive base pairing,
which produces secondary and tertiary
structure that are important for RNA
function.
- Some RNA molecules act as catalyst of
reactions; thus, RNA as well as protein, can
have enzymatic activity.

2. There are three major RNA: mRNA, tRNA, rRNA.

The function of DNA : replication (gene
production) and transcription (gene
expression).

The main function of RNA: gene expression

(translation to produce protein).
SEKIAN