CHAPTER V.

Introduction to Nucleic Acid

A. Nucleic Acids
1. Structure
Two kinds of nucleic acids are found in cells: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Each has its own
role in the transmission of hereditary information. As we just saw, DNA is present in the chromosomes of the nuclei of eukaryotic cells.
RNA is not found in the chromosomes, but rather is located elsewhere in the nucleus and even outside the nucleus, in the cytoplasm.
Both DNA and RNA are polymers. Just as proteins consist of chains of amino acids, and polysaccharides consist of chains of
monosaccharides, so nucleic acids are also chains. The building blocks (monomers) of nucleic acid chains are nucleotides. Nucleotides
themselves, however, are composed of three simpler units: a base, a monosaccharide, and a phosphate.
a. Bases
The bases found in DNA and RNA aare basic because they are heterocyclic aromatic amines. Two of these bases—
adenine (A) and guanine (G)—are purines; the other three—cytosine (C), thymine (T), and uracil (U)—are pyrimidines. The
two purines (A and G) and one of the pyrimidines (C) are found in both.

B. Sugars
The sugar component of RNA is D-ribose. In DNA, it is 2-deoxy-D-ribose (hence the name deoxyribonucleic acid).
**The full name of 𝛽 -D-ribose is 𝛽-D-ribofuranose and that of b-2-deoxy-D-ribose is b-2-deoxy-D-
ribofuranose.

The combination of sugar and base is known as a nucleoside. The purine bases are linked to C-1 of the monosaccharide
through N-9 (the nitrogen at position 9 of the five-membered ring) by a 𝛽-N-glycosidic bond:
**Nucleoside- A compound composed of ribose or deoxyribose and a base.
CHAPTER V. Introduction to Nucleic Acid

The nucleoside made of guanine and ribose is called guanosine. Table 25.1 gives the names of the other nucleosides.
The pyrimidine bases are linked to C-1 of the monosaccharide through their N-1 by a 𝛽-N-glycosidic bond.

C. Phosphate
The third component of nucleic acids is phosphoric acid. When this
group forms a phosphate ester bond with a nucleoside, the result is a
compound known as a nucleotide. For example, adenosine
combines with phosphate to form the nucleotide adenosine 5’-
monophosphate (AMP):
The ‘ sign in adenosine 5’-monophosphate is used to distinguish
which molecules the phosphate is bound to. Numbers without
primes refer to positions on the purine or pyrimidine base. Numbers
on the sugar are denoted with primes.
Most notably, adenosine 5’- triphosphate (ATP) serves as a common
currency into which the energy gained from food is converted and
stored. In ATP, two more phosphate groups are joined to AMP in
phosphate anhydride bonds. In adenosine 5 diphosphate (ADP), only one phosphate group is bonded to the AMP. All other
multiphosphorylated forms. For example, guanosine exists as GMP, GDP, and GTP.
In summary:
A nucleoside= Base + Sugar
A nucleotide= Base + Sugar + Phosphate
A nucleic acid= A chain of nucleotides
CHAPTER V. Introduction to Nucleic Acid
Structure of DNA and RNA
A. Primary Structure
Nucleic acids are polymers of nucleotides, as shown schematically in
Fig ure 25.2. Their primary structure is the sequence of nucleotides. Note
that it can be divided into two parts: (1) the backbone of the molecule
and (2) the bases that are the side-chain groups. The backbone in
DNA consists of alternating deoxyribose and phosphate groups. Each
phosphate group is linked to the 3’ carbon of one deoxyribose unit and
simultaneously to the 5’ carbon of the next deoxyribose unit (Figure
25.3). Similarly, each monosaccharide unit forms a phosphate ester at
the 3 position and another at the 5’ position. The primary structure of RNA
is the same except that each sugar is ribose (so an OH group appears in
the 2 position) rather than deoxyribose and U is present instead of T.
Thus, the backbone of the DNA and RNA chains has two ends: a 3 -OH
end and a 5 -OH end. These two ends have roles similar to those of the
C-terminal and N-terminal ends in proteins. The backbone provides
structural stability for the DNA and RNA molecules. As noted earlier, the
bases that are linked, one to each sugar unit, are the side chains. They
carry all of the information necessary for protein syn thesis. Analysis of
the base composition of DNA molecules from many different species was
done by Erwin Chargaff (1905–2002), who showed that in DNA taken
from many different species, the quantity of adenine (in moles) is always
approximately equal to the quantity of thymine, and the quantity of
guanine is always approximately equal to the quantity of cytosine,
although the adenine/guanine ratio varies widely from species to species
(see Table 25.2). This important information helped to establish the
secondary structure of DNA, as we will soon see.
CHAPTER V. Introduction to Nucleic Acid
The form of the DNA double helix shown in Figure 25.4 is called B-DNA. It is the most common and most stabile form. Other forms
become possible where the helix is wound more tightly or more loosely, or is wound in the opposite direction. With B-DNA, a distinguishing
feature is the presence of a major groove and a minor groove, which arise because the two strands are not equally spaced around the
helix. Interactions of proteins and drugs with the major and minor grooves of DNA serve as an active area of research.

B. Secondary Structure of DNA

In 1953, James Watson and Francis Crick (1916–2004) established the three-
dimensional structure of DNA. Their work is a cornerstone in the
history of biochemistry. The model of DNA developed by Watson and Crick was based on
two important pieces of information obtained by other workers:
(1) the Chargaff rule that (A and T) and (G and C) are present in equimolar quantities
and (2) x-ray diffraction photographs obtained by Rosalind Franklin (1920–1958) and
Maurice Wilkins. By the clever use of these facts, Watson and Crick concluded that DNA
is composed of two strands entwined around each other in a double helix, as shown in
Figure 25.4.
In the DNA double helix, the
two polynucleotide chains run in
opposite directions. Thus, at each end of the double helix, there is one 5 -OH and
one
3 -OH terminus. The sugar–phosphate backbone is on the outside, exposed to the
aqueous environment, and the bases point inward. The bases are hydrophobic, so
they try to avoid contact with water. Through their hydrophobic interactions, they
stabilize the double helix. The bases are paired according to Chargaff’s rule: For each
adenine on one chain, a thymine is aligned opposite it on the other chain; each
guanine on one chain has a cytosine aligned with it on the other chain. The bases so
paired form hydrogen bonds with each other, two for A—T and three for G C, thereby
stabilizing the double helix (Figure 25.5). A-T and G-C are complementary base
pairs. The important thing, as Watson and Crick realized, is that only adenine could fit
with thymine and only guanine could fit with cytosine. Let us consider the other
possibilities. Can two purines (AA, GG, or AG) fit opposite each other? Figure 25.6
shows that they would overlap. How about two pyrimidines (TT, CC, or CT)? As shown
in

Figure 25.6, they would be too far apart. There

must be a pyrimidine opposite a purine. But could
A fit opposite C, or G opposite T? Figure 25.7
shows that the hydrogen bonding would be much
weaker. The entire action of DNA—and of the
heredity mechanism—depends on the fact that,
wherever there is an adenine on one strand of
the helix, there must be a thymine on the other
strand because that is the only base that fits and
forms strong hydrogen bonds with adenine, and
similarly for G and C. The entire heredity
mechanism rests on these aligned hydrogen
bonds (Figure 25.5), as we will see in Section
25.6.

C. Higher-Order Structures of DNA

The DNA molecules in the nuclei are not stretched out, but rather coiled around basic protein molecules called histones. The
acidic DNA and the basic histones attract each other by electrostatic (ionic) forces, combining to form units called nucleosomes. In a
nucleosome, eight histone molecules form a core, around which a 147-base-pair DNA double helix is wound. Nucleosomes are
further condensed into chromatin when a 30-nm wide fiber forms in which nucleosomes are wound in a solenoid fashion, with six
nucleosomes forming a repeating unit (Figure 25.8). Chromatin fibers are organized still further into loops, and loops are arranged into
bands to provide the superstructure of chromosomes. The beauty of establishing the three-dimensional structure of the DNA molecule
was that the knowledge of this structure immediately led to the explanation for the transmission of heredity—how the genes transmit traits
from one generation to another. Before we look at the mechanism of DNA replication, let us summarize the three differences in structure
between DNA and RNA:
1. DNA has four bases: A, G, C, and T. RNA has three of these bases—A, G, and C—but its fourth base is U, not T.
2. In DNA, the sugar is 2-deoxy-D-ribose. In RNA, it is D-ribose.
3. DNA is almost always double-stranded, with the helical structure
CHAPTER V. Introduction to Nucleic Acid

Different Types of RNA

There are six types of RNA:
1. Messenger RNA (mRNA) - mRNA molecules are produced in the process called transcription, and they carry the genetic information
from the DNA in the nucleus directly to the cytoplasm, where most of the protein is synthesized. Messenger RNA consists of a chain of
nucleotides whose sequence is exactly complementary to that of one
of the strands of the DNA. This type of RNA is not long-lived, however. It is synthesized as needed and then degraded, so its concentration
at any given time is rather low. The size of mRNA varies widely, with the average unit containing perhaps 750 nucleotides. Figure 25.9
shows the basic flow of genetic information and the major types of RNA.

Figure 25.9 The fundamental process of information transfer in cells. (1)

information encoded in the nucleotide sequence of DNA is transcribed through
synthesis of an RNA molecule whose sequence is dictated by the DNA sequence.
(2) as the sequence of this RNA is read (as groups of three consecutive
nucleotides) by the protein synthesis machinery, it is translated into the sequence
of amino acids in a protein. This information transfer system is encapsulated in
the dogma: DNA→RNA→protein.
CHAPTER V. Introduction to Nucleic Acid

2. Transfer RNA (tRNA)- Containing from 73 to 93 nucleotides per chain, tRNAs are relatively
small molecules. There is at least one different tRNA molecule for each of the 20 amino acids from
which the body makes its proteins. The three-dimensional tRNA molecules are L shaped, but they
are conventionally represented as a cloverleaf in two dimensions. Transfer RNA molecules contain
not only cytosine, guanine, adenine, and uracil, but also several other modified nucleotides, such
as 1-methylguanosine.

3. Ribosomal RNA (rRNA) -Ribosomes, which are small spherical bodies located in the cells but outside the nuclei, contain rRNA. They
consist of about 35% protein and 65% ribosomal RNA (rRNA). These large molecules have molecular weights up to 1 million. Protein
synthesis takes place on the ribosomes. Dissociation of ribosomes into their components has proved to be a useful way of studying their
structure and properties. A particularly important endeavor has been to determine both the number and the kind of RNA and protein
molecules that make up ribosomes. This approach has helped elucidate the role of ribosomes in protein synthesis. In both prokaryotes
and eukaryotes, a ribosome consists of two subunits, one larger than the other. In turn, the smaller subunit consists of one large RNA
molecule and about 20 different proteins; the larger subunit consists of two RNA molecules in prokaryotes (three in eukaryotes) and
about 35 different proteins in prokaryotes (about 50 in eukaryotes) The subunits are easily dissociated from one another in the
laboratory by lowering the Mg2+ concentration of the medium. Raising the Mg2+ concentration to its original level reverses the process,
and active ribosomes can be reconstituted by this method.

4. Small Nuclear RNA (snRNA) - A recently discovered RNA molecule is snRNA, which is found, as the name implies, in the nucleus
of eukaryotic cells. This type of RNA is small, about 100 to 200 nucleotides long, but it is neither a tRNA molecule nor a small subunit
of rRNA. In the cell, it is complexed with proteins to form small nuclear ribonucleoprotein particles, snRNPs, pronounced “snurps.” Their
function is to help with the processing of the initial mRNA transcribed from DNA into a mature form that is ready for export out of the
nucleus. This process is often referred to as splicing, and it is an active area of research. While studying splicing, scientists realized that
part of the splicing reaction involved catalysis by the RNA portion of a snRNP and not the protein portion. This recognition led to the
discovery of ribozymes, RNA-based enzymes, for which Thomas Cech received the Nobel Prize.

5. Micro RNA (miRNA)- A very recent discovery is another type of small RNA, miRNA. These RNAs are only 22 nucleotides long but
are important in the timing of an organism’s development. They bind to sections of mRNA and prevent their translation.

6. Small Interfering RNA (siRNA)-The process called RNA interference was heralded as the breakthrough of the year in 2002 by science
magazine. Short stretches of RNA (20–30 nucleotides long), called small interfering RNA, have been found to have an enormous control
over gene expression. This process serves as a protective mechanism in many species, with the siRNAs being used to eliminate
expression of an undesirable gene, such as one that causes uncontrolled cell growth or one that came from a virus. siRNAs lead to the
degradation of specific mRNA molecules. Scientists who wish to study gene expression are also using these small RNAs. In what has
become an explosion of new biotechnology, many companies have been created to produce and market designer siRNAs to knock out
hundreds of known genes. This technology also has medical applications, as siRNA has been used to protect mouse liver from hepatitis
and to help clear infected liver cells of the disease.