Nucleic Acid (Organic Chemistry) : By: Septiana Saputri (1800023180)

NUCLEIC ACID
(Organic Chemistry)
By:
Septiana Saputri (1800023180)
UNIVERSITAS AHMAD DAHLAN

FACULTY OF PHARMACY
2019
I. DEFINITION
Nucleic acid is a giant molecule that has a special function, namely, storing genetic
information and transmitting it to its descendants. The arrangement of nucleic acids
determines whether the creature becomes animal, plant, or human. Similarly, the arrangement
in cells, whether the cell becomes a muscle cell or blood cell. Some important functions of
nucleic acids are storing, transmitting, and translating genetic information; intermediary
metabolism and energy information reactions; energy-carrying coenzyme; transfer coenzyme
of acetic acid, sugar, amino compounds and other biomolecules; reduction coenzyme
oxidation reaction.
There are two types of nucleic acids in cells, DNA (deoxyribonucleic acid) or
deoxyribonucleic acid and RNA (ribonucleic acid) or ribonucleic acid. Both DNA and RNA
are anions and are generally protein bound and alkaline. For example DNA in the cell nucleus
is bound to histones. Compound compound between protein and nucleic acid is called
nucleoprotein. Nucleic acid molecules are polymers like protein but their constituent units are
nucleotides. One example of a free nucleic acid nucleutide is ATP which functions as an
energy carrier
II. STRUCTURE
Nucleotides are joined together through the phosphate group of one nucleotide
connecting in an ester linkage to the OH group on the third carbon atom of the sugar unit of
a second nucleotide. This unit joins to a third nucleotide, and the process is repeated to
produce a long nucleic acid chain (Figure 1). The backbone of the chain consists of
alternating phosphate and sugar units (2-deoxyribose in DNA and ribose in RNA). The
purine and pyrimidine bases branch off this backbone.
Each phosphate group has one acidic hydrogen atom that is ionized at physiological
pH. This is why these compounds are known as nucleic acids.
Figure 1. Structure of a Segment of DNA. A similar segment of RNA would have OH
groups on each C2′, and uracil would replace thymine.
Like proteins, nucleic acids have a primary structure that is defined as the sequence of
their nucleotides. Unlike proteins, which have 20 different kinds of amino acids, there are
only 4 different kinds of nucleotides in nucleic acids. For amino acid sequences in proteins,
the convention is to write the amino acids in order starting with the N-terminal amino acid.
In writing nucleotide sequences for nucleic acids, the convention is to write the nucleotides
(usually using the one-letter abbreviations for the bases, shown in Figure 2.) starting with
the nucleotide having a free phosphate group, which is known as the 5′ end, and indicate the
nucleotides in order. For DNA, a lowercase d is often written in front of the sequence to
indicate that the monomers are deoxyribonucleotides. The final nucleotide has a free OH
group on the 3′ carbon atom and is called the 3′ end. The sequence of nucleotides in the
DNA segment shown in Figure 1 would be written 5′-dG-dT-dA-dC-3′, which is often
further abbreviated to dGTAC or just GTAC.
The three-dimensional structure of DNA was the subject of an intensive research
effort in the late 1940s to early 1950s. Initial work revealed that the polymer had a regular
repeating structure. In 1950, Erwin Chargaff of Columbia University showed that the molar
amount of adenine (A) in DNA was always equal to that of thymine (T). Similarly, he
showed that the molar amount of guanine (G) was the same as that of cytosine (C). Chargaff
drew no conclusions from his work, but others soon did.
At Cambridge University in 1953, James D. Watson and Francis Crick announced that
they had a model for the secondary structure of DNA. Using the information from
Chargaff’s experiments (as well as other experiments) and data from the X ray studies of
Rosalind Franklin (which involved sophisticated chemistry, physics, and mathematics),
Watson and Crick worked with models that were not unlike a child’s construction set and
finally concluded that DNA is composed of two nucleic acid chains running antiparallel to
one another—that is, side-by-side with the 5′ end of one chain next to the 3′ end of the
other. Moreover, as their model showed, the two chains are twisted to form a double helix—
a structure that can be compared to a spiral staircase, with the phosphate and sugar groups
(the backbone of the nucleic acid polymer) representing the outside edges of the staircase.
The purine and pyrimidine bases face the inside of the helix, with guanine always opposite
cytosine and adenine always opposite thymine. These specific base pairs, referred to
as complementary bases, are the steps, or treads, in our staircase analogy (Figure 2).
Figure 2. DNA Double Helix. (a) This represents a computer-generated model of the
DNA double helix. (b) This represents a schematic representation of the double helix,
showing the complementary bases.
The structure proposed by Watson and Crick provided clues to the mechanisms by
which cells are able to divide into two identical, functioning daughter cells; how genetic
data are passed to new generations; and even how proteins are built to required
specifications. All these abilities depend on the pairing of complementary bases.
Figure 2. shows the two sets of base pairs and illustrates two things. First, a
pyrimidine is paired with a purine in each case, so that the long dimensions of both pairs are
identical (1.08 nm).
Figure 3. Complementary Base Pairing. Complementary bases engage in hydrogen
bonding with one another: (a) thymine and adenine; (b) cytosine and guanine.
If two pyrimidines were paired or two purines were paired, the two pyrimidines would
take up less space than a purine and a pyrimidine, and the two purines would take up more
space, as illustrated in Figure 3. If these pairings were ever to occur, the structure of DNA
would be like a staircase made with stairs of different widths. For the two strands of the
double helix to fit neatly, a pyrimidine must always be paired with a purine. The second
thing you should notice in Figure 3. is that the correct pairing enables formation of three
instances of hydrogen bonding between guanine and cytosine and two between adenine and
thymine. The additive contribution of this hydrogen bonding imparts great stability to the
DNA double helix.
Figure 4. Difference in Widths of Possible Base Pairs
III. CLASSIFICATION
If the pentose sugar is ribose, the nucleotide is more specifically referred to as
a ribonucleotide, and the resulting nucleic acid is ribonucleic acid (RNA). If the sugar is 2-
deoxyribose, the nucleotide is a deoxyribonucleotide, and the nucleic acid is DNA.
The nitrogenous bases found in nucleotides are classified as pyrimidines or purines.

Pyrimidines are heterocyclic amines with two nitrogen atoms in a six-member ring and
include uracil, thymine, and cytosine. Purines are heterocyclic amines consisting of a
pyrimidine ring fused to a five-member ring with two nitrogen atoms. Adenine and guanine
are the major purines found in nucleic acids (Figure 5).
Figure 5. The Nitrogenous Bases Found in DNA and RNA
The formation of a bond between C1′ of the pentose sugar and N1 of the pyrimidine
base or N9 of the purine base joins the pentose sugar to the nitrogenous base. In the formation
of this bond, a molecule of water is removed. Table 5. summarizes the similarities and
differences in the composition of nucleotides in DNA and RNA. The numbering convention
is that primed numbers designate the atoms of the pentose ring, and unprimed numbers
designate the atoms of the purine or pyrimidine ring.
Composition DNA RNA
purine bases adenine and guanine adenine and guanine
pyrimidine bases cytosine and thymine cytosine and uracil
pentose sugar 2-deoxyribose ribose
inorganic acid phosphoric acid (H3PO4) H3PO4
IV. REACTION
Nucleotide molecules will form nucleic acids by forming phosphodiester bonds where
the 5'-phosphate group in the nucleotide unit will bind to the 3'-hydroxyl group in other
nucleotide units. Covalent bonds in nucleic acids consist of phosphate groups and pentose
sugars which are linear with heterocyclic nitrogen bases as interval branches. All
phosphodiester bonds can form long chains that are linear with specific polarity at 5-end and
3-end. The nucleotide end that has a 5 'position is called 5-end while the other end which has
a 3 position' is called 3-end. Based on the convention, the single chain of nucleic acids is
always represented by 5-end on the left and 3 '-end on the right so that the direction is 5' -> 3
'.
Figure 6. Phosphodiester bonds in the DNA and RNA chains

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NUCLEIC ACID

UNIVERSITAS AHMAD DAHLAN

Figure 4. Difference in Widths of Possible Base Pairs

The nitrogenous bases found in nucleotides are classified as pyrimidines or purines.

Figure 5. The Nitrogenous Bases Found in DNA and RNA

purine bases adenine and guanine adenine and guanine

pyrimidine bases cytosine and thymine cytosine and uracil

pentose sugar 2-deoxyribose ribose

inorganic acid phosphoric acid (H3PO4) H3PO4

Figure 6. Phosphodiester bonds in the DNA and RNA chains

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