02 Molecular biology

For many years most Nucleotides are the building blocks of nucleic acids
scientists all over the As you learned earlier in this chapter, nucleic acids are one of the major carbon-based
world believed it was
protein, not DNA, that groups. There are three major examples of nucleic acids in nature. They are adenosine
contained our genetic triphosphate (ATP), deoxyribonucleic acid (DNA), and ribonucleic acid (RNA). ATP
information. Research functions as an energy storage compound. Other nucleic acids function as coenzymes.
conducted in the first In this section we will focus on DNA and RNA. DNA and RNA are involved with the
few decades of the 20th
century demonstrated that
genetic aspects of the cell.
DNA contains our genetic Both DNA and RNA are polymers of nucleotides. Individual nucleotides are referred
blueprint.
to as monomers and always consist of three major parts: one phosphate group, one
5-carbon monosaccharide, and a single nitrogenous base. Chemical bonds occur at
specific locations in order to produce a functional unit. Look at Figure 2.29.
O OH
phosphate ribose sugar or
group HO P deoxyribose sugar
O
1 of 4
Figure 2.29 The first diagram C5
represents the structure of O
a nucleotide showing bond C4 C1 nitrogenous base
locations. The second diagram
represents the structure of a C3 C2
general nucleotide using the
P
symbols suggested by the IB.
Base
Pentose

It is important to note that in the diagram circles are used to represent phosphates,
pentagons are used to represent 5-carbon sugars (also called pentoses), and rectangles
are used to represent nitrogenous bases. All IB drawings involving nucleotides should
use these symbols.
All the bonds within the nucleotide involve the sharing of electrons, and are therefore
referred to as covalent bonds. The phosphate group is the same in DNA and RNA.
However, there are five possible nitrogenous bases, which are shown in Table 2.9.

Table 2.9 The five nitrogenous bases

RNA nitrogenous bases DNA nitrogenous bases

Adenine (A) Adenine (A)

Uracil (U) Thymine (T)

Cytosine (C) Cytosine (C)

5′
HOCH2
5′
HOCH2 The base uracil only occurs in RNA, not DNA, and the base
O OH O OH thymine only occurs in DNA, not RNA. When drawing
nucleotides, it is common practice to put the capitalized first
C4′ C1′ C4′ C1′
H H H H letter of the base inside the rectangle.
H3′ H H3′ H
C C2′ C C2′ The sugar differs in the nucleotides of DNA and RNA. DNA
nucleotides contain the pentose known as deoxyribose and
OH H OH OH
RNA nucleotides contain ribose. In Figure 2.30, you can see
Deoxyribose Ribose that they are very similar molecules.
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Monomers into polymers
CHALLENGE
Monomers (single nucleotides) in both DNA and RNA may bond together to produce
long chains or polymers. An example of such a chain is shown in Figure 2.31.
YOURSELF
8 Use the symbols mentioned
on page 86 to represent all
In Figure 2.31 each adjoining nucleotide has been drawn in P the possible nucleotides of
a different colour to emphasize the nucleotide structure. DNA. Once you have done
A that for DNA, do the same
Notice that the chain has an alternating pentose–phosphate
for RNA.
backbone, with the nitrogenous bases extending outward.
The importance of the order of these nitrogenous bases P Figure 2.31 Five nucleotides
will be discussed later in conjunction with the genetic code. G bonded to form a very small
The nucleotides attach to one another to form a chain as section of a strand of DNA or
a result of condensation reactions forming connecting RNA.
covalent bonds. P
C CHALLENGE
YOURSELF
Single strand or double strand
P 9 Examine the first diagram
RNA is composed of a single chain or strand of nucleotides, in Figure 2.29 representing
A
while DNA consists of two separate chains or strands of the general structure of a
nucleotides connected to one another by weak hydrogen nucleotide. Notice that the
carbons of the pentose are
bonds. The strands of both DNA and RNA may involve P numbered. These numbers
very large numbers of nucleotides. For the two strands of T are always placed in this
DNA, imagine a double-stranded DNA molecule as a ladder way for both ribose and
(see Figure 2.32). The two sides of the ladder are made up deoxyribose. Now look at
of the phosphate and deoxyribose sugars. The rungs of the Figure 2.31, in which five
nucleotides are connected
ladder (what you step on) are made up of the nitrogenous together. Answer the
bases. Because the ladder has two sides, there are two following.
bases making up each rung. The two bases making up (a) In the polymer, which
one rung are said to be complementary to each other. The numbered carbons are
always attached to the
complementary base pairs are adenine (A)–thymine (T) and phosphate group?
cytosine (C)–guanine (G). (b) In a monomer, what
number carbon is
always attached to the
phosphate group?
2 hydrogen bonds 3′ (c) Which carbon is
P always attached to the
5′
1′ 1′ nitrogenous base?
A T
5′
P
Figure 2.32 A small section
3′ 3′
P of a double-stranded
5′
1′ 1′ DNA molecule showing
G C
hydrogen bonds between
5′
P complementary nitrogenous
3′ bases. The two single strands
P 3′
5′ that make up the double-
1′ 1′ stranded molecule run in
T A
5′ opposite directions to each
P other. The term that describes
3′ this is ‘antiparallel’. Thus we
P 3′
5′ say that the two strands of the
1′
C G 5′ double helix are antiparallel
1′
P and complementary to each
3′ 3 hydrogen bonds other.

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 02 Molecular biology

Even though the first We can now use all of this information to construct a simple, yet accurate, drawing
accurate model of DNA of DNA.
was produced by James
Watson (American) and
Francis Crick (British)
in 1953, many other
scientists from around the
world contributed pieces
of information that were
instrumental in developing
the final model. Erwin
Chargaff (Austrian) had
determined that the
numbers of adenine and
thymine bases were equal,
as were the numbers of
cytosine and guanine
bases. Rosalind Franklin
(British) and Maurice
Wilkins (born in New
Zealand) had calculated
the distance between the
various molecules in DNA
by X-ray crystallography.

Figure 2.33 This artwork

In Figure 2.32, it is essential to note that one strand of DNA has the 5-carbon, often
referred to as the 5-prime (5v) carbon, unattached and on top. At the bottom of that
Even though some same strand notice that the 3- or 3-prime (3v) carbon is unattached. If you look at the
information was
opposite strand of deoxyribose and phosphates, you will notice it is the opposite:
exchanged, the
development of the first the 3v carbon is at the top and the 5v carbon is at the bottom. These two strands
accurate model of DNA are therefore said to be antiparallel to one another. Electrical charges related to the
was highly competitive. molecules of the two strands cause a characteristic twisting action of the DNA ladder
Several groups in different
to produce the double helix shape that Watson and Crick described in the model they
parts of the world were
trying to make sense of proposed in the early 1950s.
shared knowledge to
produce an appropriate
NATURE OF SCIENCE
model. Some scientists did
not share their research or Francis Crick and James Watson used models to arrive at the structure of DNA. They used data
findings. How is this ‘anti- from many different sources to construct this model successfully. They did not have the ability
scientific’? Discuss what to observe the molecule directly, which made the model necessary. The model they produced
can be done to increase was an actual physical model, using wires and symbols representing atoms. Today, many
the sharing of personal models are produced using computer-based mathematical models. Regardless of how a model
knowledge in scientific is produced, it is always subject to modification as more experiments are conducted and more
research. data are collected.

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