Molecular Biology

Dr Nzar A. A. Shwan
MLT department
Lecture 01: Monday, 16th September 2024
4th Year (Semester 7)

Molecular Biology, is the study of the biochemical mechanisms

of inheritance. It is the study of the biochemical nature of the
genetic material and its control of phenotype. It is the study of
the connection between genotype and phenotype.
Identification of DNA as the genetic material
To fulfil its role, the genetic material must meet four criteria.
1. Information: The genetic material must contain the
information necessary to construct an entire organism. In
other words, it must provide the blueprint (design) to
determine the inherited traits of an organism.

2. Transmission: During reproduction, the genetic material

must be passed from parents to offspring.

3. Replication: Because the genetic material is passed from

parents to offspring, and from mother cell to daughter cells
during cell division, it must be copied.

4. Variation: The genetic material must undergo changes to

produce variations that allow organisms to adapt to
modifications in the environment so that evolution can
occur. Within any species, a significant amount of
phenotypic variability occurs. For example, Mendel studied
several characteristics in pea plants that varied among
different plants. This included height (tall versus dwarf)
and seed colour (yellow versus green).

1
 Experiments with Pneumococcus Suggested
That DNA Is the Genetic Material
Frederick Griffith studied a type of bacterium known then as
pneumococci and now classified as Streptococcus pneumoniae.
Certain strains of S. pneumoniae secrete a polysaccharide
capsule (smooth colony morphology), whereas other strains do
not (rough colony appearance).
The different forms of S. pneumoniae also affect their virulence,
or ability to cause disease.
• When smooth strains of S. pneumoniae infect a mouse, the
capsule allows the bacteria to escape attack by the mouse’s
immune system. As a result, the bacteria can grow and
eventually kill the mouse.
• In contrast, the non-encapsulated (rough) bacteria are
destroyed by the animal’s immune system.
In 1928, Griffith conducted experiments that involved the
injection of live and/or heat-killed bacteria into mice. He then
observed whether or not the bacteria caused a lethal infection.
Griffith was working with two strains of S. pneumoniae, a type S
(S for smooth) and a type R (R for rough) (Figure 1).

Figure 1. Griffith’s experiments on genetic transformation in pneumococcus.

2
 At this point, let’s look at what Griffith’s observations mean in
genetic terms:
 The transformed bacteria acquired the information to
make a capsule.

 Among different strains, variation exists in the ability to

create a capsule and to cause mortality in mice.

 The genetic material that is necessary to create a capsule

must be replicated so that it can be transmitted from
mother to daughter cells during cell division.

 These observations are consistent with the idea that the

formation of a capsule is governed by the bacteria’s
genetic material, meeting the four criteria described
previously.

 Griffith’s experiments showed that some genetic material

from the dead bacteria had been transferred to the living
bacteria and provided them with a new trait.

Based on Griffith’s observations, Oswald Avery, Colin

MacLeod, and Maclyn McCarty asked the question, what
substance is being transferred from the dead type S bacteria to
the live type R?
At the time of these experiments in the 1940s, researchers
already knew that DNA, RNA, proteins, and carbohydrates are
major constituents (components) of living cells. To answer this
question, Avery and colleagues did their experiments as it its
shown in Figure 2.
 As One can argue that a small amount of contaminating
material in the DNA extract might actually be the
genetic material.

3
 Figure 2. Experimental protocol used by Avery, MacLeod, and McCarty to identify the
transforming principle.

DNA STRUCTURE: THE DOUBLE HELIX

One of the most exciting breakthroughs in the history of
biology occurred in 1953 when James Watson and Francis Crick (
Figure 1) deduced the correct structure of DNA. Watson and
Crick’s double-helix structure was based on two major kinds of

4
evidence:

1. When Erwin Chargaff and colleagues analysed the

composition of DNA from many different organisms, they
found that:
a. The concentration of T = A and the concentration of C
= G (Table 1).

5
 b. The total concentration of pyrimidines (T + C) was
always equal to the total concentration of purines (A +
G; see Table 1). These are known as Chargaff’s rule.

Table 1. Chargaff’s data

2. Rosalind Franklin and Maurice Wilkins used X-rays

crystallography to capture images of DNA, they found:
a. First, it was consistent with a helical structure.

b. The diameter of the helical structure was too wide to

be only a single stranded helix.
c. The diffraction pattern indicated that the helix
contains about 10 base pairs (bp) per complete turn.

6
The Molecular Structure of the DNA
Double Helix Has Several Key Features
• In a DNA double helix, two DNA strands
(polynucleotides) are twisted together around a common
axis to form a structure that resembles a spiral staircase.

• This double-stranded structure is stabilized by base pairs

(bp)—pairs of bases in opposite strands that are hydrogen
bonded to each other.

• A hydrogen bond is a weak bond in which two negatively

charged atoms share a hydrogen atom.
• Counting the bases, if you move past 10 bp, you have
gone 360° around the backbone.

7
• The linear distance of a complete turn is 3.4 nm; each
base pair traverses 0.34 nm.

• An adenine base in one strand hydrogen bonds with a

thymine base in the opposite strand, or a guanine base
hydrogen bonds with a cytosine.
• Three hydrogen bonds occur between G and C but only
two between A and T. This means that the hydrogen
bonding between G and C is stronger and require more

8
 energy to break.

• The AT/GC rule implies that we can predict the sequence

in one DNA strand if the sequence in the opposite strand
is known.

• For example, let’s consider a DNA strand with the

sequence of 5ʹ–ATGGCGGATTT–3ʹ.

• The opposite strand would have to be 3ʹ–

TACCGCCTAAA–5ʹ.

• In genetic terms, we would say that these two sequences

are complementary to each other or that the two
sequences exhibit complementarity.

• The numbers 5ʹ and 3ʹ designate the direction of the DNA

backbone.

• The direction of DNA strands is illustrated in the below

Figure. When going from the top of this figure to the
bottom, one strand is running in the 5ʹ to 3ʹ direction, and
the other strand is 3ʹ to 5ʹ. This opposite orientation of

9
 the two DNA strands is referred to as an antiparallel
arrangement.

• The units of length of nucleic acids in which genome sizes

are typically expressed are as follows:
o kilobase (kb) 103 nucleotide subunits
o Megabase (Mb) 106 nucleotide subunits
o Gigabase (Gb) 109 nucleotide subunits

Nucleic acid structure and function

Nucleotides are the building blocks of nucleic acids
• The nucleotide is the repeating structural unit of DNA
and RNA.
• A nucleotide has three components: (1) a phosphate
group, (2) a five-carbon sugar (or pentose), and (3) cyclic
nitrogen-containing compound called a base.

• There are two types of sugar: deoxyribose which is found

in DNA and ribose which is found RNA.

• The nitrogenous bases are subdivided into two categories:

the purines and the pyrimidines.
• The purine bases, adenine (A) and guanine (G), contain a
double-ring structure

10
• The pyrimidine bases, thymine (T), cytosine (C), and
uracil (U), contain a single-ring structure.

• The sugar in DNA is always deoxyribose.

• In RNA, the sugar is ribose. Also, the base thymine is not
found in RNA. Rather, uracil is found in RNA instead of
thymine.
• Adenine, guanine, and cytosine occur in both DNA and
RNA.
• The bases and sugars have a standard numbering
system. The nitrogen and carbon
atoms found in the ring structure of
the bases are given numbers 1
through 9 for the purines and 1
through 6 for the pyrimidines (see the
figure above).

• In comparison, the five carbons found

in the sugars are designated with
primes, such as 1ʹ, to distinguish them
from the numbers found in the bases.

• In the sugar ring, carbon atoms are

numbered in a clockwise direction,

11
 beginning with a carbon atom adjacent to the ring oxygen
atom. The fifth carbon is outside the ring structure.
• The repeating unit of nucleotides found in DNA is:
Phosphate group + Deoxyribose + Nitrogen base.

• The repeating unit of nucleotides found in RNA is

Phosphate group + Ribose + Nitrogen base.

• In a single nucleotide, the base is always attached to the

1ʹ carbon atom, and one or more phosphate groups are
attached at the 5ʹ position.
• The –OH group attached to the 3ʹ carbon is important in
allowing nucleotides to form covalent linkages with each
other.
The terminology used to describe nucleic acid units is based on
three structural features: the type of base, the type of sugar,
and the number of phosphate groups.

12
  When a base is attached to only a sugar, we call this pair
a nucleoside.
 If adenine is attached to ribose, this nucleoside is called
adenosine. Nucleosides containing guanine, thymine,
cytosine, or uracil are called guanosine, thymidine,
cytidine, and uridine, respectively.

 When a phosphate group is also attached to the sugar,

the nucleoside becomes a nucleotide.
 If a nucleotide contains adenine, ribose, and one
phosphate, it is adenosine monophosphate,
abbreviated AMP.
 So GMP is guanosine monophosphate, CMP is
cytidine monophosphate, UMP is Uridine
monophosphate
When only the bases are attached to deoxyribose sugar, they
are called deoxyadenosine, deoxyguanosine, deoxythymidine, and
deoxycytidine.
When the bases are attached to deoxyribose sugar and one
phosphate group, they are: dAMP, dGMP, dTMP, and dCMP (See
the figure below)

13
What about the following?
dATP
dGTP
dTTP
dCTP

14