Introduction to Molecular Biology

By Mebrie Zemene (DVM, MSc.)

Department of Veterinary Biomedical Sciences,
College of Veterinary Medicine and Animal Sciences,
University of Gondar, Ethiopia

November 2022
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 Objectives of the lesson

Define what molecular biology mean?

Give highlight on the historical background of

molecular biology.

Explain Genetic materials and genes.

 Brainstorming question

What is molecular biology?

Tell something about gene.

What is genetic material? What it includes?

 Molecular Biology
Definition
 Molecular biology is the branch of biology that deals with the
structure and function of macromolecules and the
macromolecular mechanisms that occur in living organisms.
 Focuses mainly on the structure and function of the gene: the
molecular nature of the gene, gene replication, mutation, and
expression.
 A gene is a region of DNA that controls a discrete hereditary c
haracteristic, usually corresponding to a single mRNA which
will be translated into a protein.
Fig. From Cell to gene
 Historical Background

Discovery of the 'nucleic acid' substance.

• Friedrich Miescher (1844-1895) discovered in a
substance purified from pus cells =>a crude
extract of nuclei.
– From these nuclei he isolated an unknown compound
which he called "nuclein" (acidic in nature).
– high amounts of phosphorous.
• Altman (1889)
– the first to use the term 'nucleic acid'
• Piccard (1874)
– discovered the purine bases in nucleic acids.
• Kossel's work (1879 until 1888)
– Leads to the isolation of Adenine.
– Cytosine was isolated and identified in 1902-1903 by
Kossel, Studel & Levene.
• Ascoli(1900 )
– isolated Uracil from yeast nucleic acid.
 Frederick Griffith in 1928 described gene transformation
• In 1928, Griffith studied the bacterium Streptococcus
pneumoniae

• S. pneumoniae comes in two strains

– S  Smooth (strain IIIS)
o Secretes a polysaccharide capsule (evades
immune system)
o Produce smooth colonies on solid media

– R  Rough (strain IIR)

o Unable to secrete a capsule
o Produce colonies with a rough appearance
• Thus the bacteria had beenTransformed from the rough to the
smooth version.

• The ability of a substance to change the genetic characteristics of

an organism is known as transformation.

• Scientists set out to isolate this ‘transforming principle’ since they

were convinced it was the carrier of the genetic information.
 The Experiments of Avery, MacLeod & McCarty
• Suggests that “DNA is genetic material”
• Realized that Griffith’s observations could be used to identify
the genetic material or “transforming principle”
• In essence, the formation of the capsule is guided by the
bacteria’s genetic material
–Transformed bacteria acquired information to make the
capsule
–Variation exists in ability to make capsule
–The information required to create a capsule is replicated
and transmitted from mother to daughter cells
 The Experiments of Avery, MacLeod & McCarty

•At the time of their experimentation in the 1940s, it was known

that DNA, RNA, proteins and carbohydrates are the major
constituents of living cells

•Prepared cell extracts from smooth cells (IIIS) and added to

rough cells (IIR) for transformation in culture medium

•Only the DNA enriched extract was able to convert rough cells
into smooth cells
The Experiments of Avery, MacLeod & McCarty
Discovery of the Structure of DNA

• In 1953, James Watson and Francis Crick

discovered the double helical structure of DNA.
Watson and Crick proposed a double helix with
sugar-phosphate backbones on the outside and
bases aligned to the interior.

• The scientific framework for their breakthrough

was provided primarily by:

– Rosalind Franklin (X-ray diffraction)

– Erwin Chargaff (chemical composition)

Rosalind Franklin

• She used X-ray diffraction to study wet fibers of DNA

• The diffraction pattern she obtained suggested several structural

features of DNA

– Helical

– More than one strand

– 10 base pairs per complete turn

The diffraction pattern is interpreted
(using mathematical theory)
This can ultimately provide
information concerning the
structure of the molecule
Erwin Chargaff’s Experiment
• Chargaff pioneered many of the biochemical techniques for the
isolation, purification and measurement of nucleic acids from living cells
• It was already known then that DNA contained the four bases: A, G, C
and T
• Chargaff analyzed the base composition of DNA in different species to
see if there was a pattern
Chargaff’s rule
• Percent of adenine = percent of thymine (A=T)
• Percent of cytosine = percent of guanine (C=G)
• A+G = T+C (or purines = pyrimidines)
A Brief and Incomplete History of Molecular Biology
Historical Background
 Genetic material
• is responsible for the storage and transmission of hereditary
information. It can be DNA or RNA

• Organisms that have DNA as genetic material store its genetic

material either in nucleus for eukaryotic organisms (have true
nucleus) or in nucleoid region for prokaryotic organisms.

• DNA is stored in structures called chromosomes, which differ

from organisms in number and structure for each organism

– Eg. A human cell normally contains 46 chromosomes.

 Genetic material
• Each chromosome contains one molecule of DNA bound to a
group of proteins called histones.

• A gene is a segment of DNA that carries a single, specific

command.

– E.g. make a globin molecule”.

• Every cell in the body of an organism has the same genetic

makeup, it is crucial that the genetic material be faithfully
replicated at every cell division
RNA can also serve as the genetic material in many viruses
Genes reside on chromosomes
 Genetic information
• DNA: is a Nucleic acid that
contains the genetic
instructions specifying the
biological development of
all cellular forms of life.
• Chromosomes: storage units
of genes.
• Gene: basic unit of genetic
information.
– Genes determine the
inherited characters.
• Genome: an organism’s
genetic material .
Genetic information
Structure and Order in Nucleic Acids
(DNA and RNA structure)

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Objectives of the lesson
•To explain what is nucleic acid and what it includes.

•To describe the chemical composition of nucleic acids.

•To be familiar about the double helix structure DNA.

•To identify the different types of RNA.

•To understand to difference between DNA and RNA.

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Structure and Order in Nucleic Acids
• Nucleic Acids (DNA and RNA) are linear polymers made of
subunits known as nucleotides.
• There are two types of nucleic acid, DNA and RNA.
– Store genetic information
– Transmitting genetic information to the cell machinery.
• There are four different nucleotides in each type of nucleic acid
and their order determines the genetic information.

Figure. The Order of the

Nucleotides Encodes the
Genetic Information

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 • Each nucleotide has three components: a phosphate group, a
five-carbon sugar, and a nitrogen-containing base.
• The phosphate groups and the sugars form the backbone of
each strand of DNA or RNA.
• The bases are joined to the sugars and stick out sideways.

Figure. Three Views of a Nucleotide

The three components of a nucleotide are shown to the left. The structures on the
right show the pentose sugar (deoxyribose) connected to the phosphate and the
base. 31
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Chemical composition of NA
1. The Bases: Pyrimidine and Purine
 The nitrogenous bases fall into two types:
– Pyrimidines
• a six-member ring (a single ring)
– Purines
• fused five-member imidazole and
six-member pyrimidine rings (double).

 Each NA is synthesized mainly from only four types of base.

– The same two purines, adenine and guanine, are present in both DNA
and RNA.
– The two pyrimidines
 DNA = Cytosine and Thymine;
 RNA = Cytosine and Uracil (is found instead of Thymine).
 The only difference
between Uracil and
thymine is the presence of
a methyl substituent at C5.

Figure. The Bases of the Nucleic Acids

The four bases of DNA are adenine, guanine, cytosine and thymine. In RNA, uracil replaces
thymine. Pyrimidine bases contain one-ring structures, whereas purine bases contain two-
ring structures.

The bases adenine, guanine, cytosine, thymine and Uracil are often abbreviated to A, G,
C, T and U, respectively.

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2. The sugars
• In nucleic acid, two types of sugars are present, both are
pentoses, or five-carbon sugars.
• In DNA, the sugar is always deoxyribose; whereas, in RNA, it
is ribose.
• Deoxyribose has one less oxygen than ribose. It is this chemical
difference that gave rise to the names deoxyribonucleic acid and
ribonucleic acid.

Figure. The Sugars Composing RNA and DNA

Ribose is the five-carbon sugar (pentose) found in
RNA. Deoxyribose is the pentose of DNA. It has one
less oxygen than ribose as it has a hydrogen in place
of the hydroxyl group on position 2¢ of the ribose
ring.
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 The difference between the two pentoses
(ribose and deoxyribose) lies on
 the absence/presence of the hydroxyl (OH) group at
position C2' of the sugar ring
– Ribose contains a hydroxyl (OH) group
– Deoxyribose lacks the oxygen and simply has a hydrogen (H)
– The deoxy prefix indicates that the 2‘-carbon atom of the
sugar lacks the oxygen atom

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• Both sugars have five-membered rings consisting of four
carbon atoms and an oxygen. The fifth carbon forms a side
chain to the ring. The five carbon atoms of the sugar are
numbered 1´, 2´, 3´, 4´ and 5´.

• By convention, in nucleic acids, numbers with prime marks

refer to the sugars and numbers without prime marks refer to
the positions around the rings of the bases.

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3. Phosphoric acid
• the sugars are connected to each other in the
polymerised RNA and DNA molecules.
• two pentose rings are joined by a phosphoric acid
molecule which is forming an ester bond with the 5'
and 3' C.
• The phosphate group linking the sugars has a
negative charge.
 Figure. Nucleotides Are Joined by
Phosphodiester Linkages. The nucleotides that form
the backbone of DNA and RNA are joined together
by linkage involving their phosphate groups. One
nucleotide is linked via its 5′- carbon to the oxygen
of the phosphate group and another nucleotide is
linked via its 3′-carbon to the other side of the
central phosphate. These linkages are termed
phosphodiester groups.

• The phosphate group is joined to the sugar on either side by ester

linkages, and the overall structure is therefore a phosphodiester
linkage.
• The chain of sugars linked by phosphodiester bridges => backbone
of the nucleic acid
• The backbone is constant in a nucleic acid, but the bases vary from
one monomer to the next
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Nucleosides.
• Purine or Pyrimidine base is linked to ribose or deoxyribose
the resulting compound is known as a nucleoside.

• Depending on whether A, G, C or U (T) are condensed with

a ribose (deoxyribose) we talk about adenosine
(deoxyadenosine), guanosine (deoxyguanosine), cytidine
(deoxycytidine) or uridine (deoxythymidine).

• In the pyrimidine nucleosides, the sugar and base are joined

by a β-glycosidic link from the C1' of the pentose to the N1 of
the pyrimidine base.

• In the purine nucleosides, the C1' of the sugar is connected

through the β-glycosydic link to the N9 of the purine base.
Base + sugar = nucleoside
Nucleotides.
• The polymeric forms of RNA and DNA contain phosphoric
acid esters of the nucleosides= Nucleotides.

• When DNA is broken into its constituent nucleotides, the

cleavage may take place on either side of the phosphodiester
bonds.
• Nucleotides can be released:
– the nucleoside-3'-monophosphate and
– the nucleoside-5'-monophosphate.
– The ribonucleoside 5'-phosphates may be further phosphorylated at
position 5' to yield 5'-di- and -tri-phosphates.

• Thus, adenosine 5'-phosphate (AMP) yields adenosine 5'-

diphosphate (ADP) and adenosine 5'-triphosphate (ATP).
Figure : nucleoside + phosphate = nucleotide
 Nucleosides Are Bases Plus Sugars; Nucleotides
Are Nucleosides Plus Phosphate

• Three-letter abbreviations for the bases such as ade, gua, etc., are
sometimes used when writing biochemical pathways or for the
names of genes involved in nucleotide metabolism.
• When writing the sequence of a nucleic acid, the single letter
abbreviations are used (A, T, G and C for DNA or A, U, G and C
for RNA).
• The letter N is often used to refer to an unspecified base.
1. DNA Structure
• DNA is composed of two polynucleotide
chains (double stranded molecule).

• The two strands of a DNA molecule are

antiparallel, as they point in opposite
directions.

• This means that the 5’ -end of one strand

is opposite the 3’ -end of the other strand
i.e. one runs in the 5’ to 3’ direction and
the other 3’ to 5’

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• The two separate strands are wound
around each other in a helical
arrangement.
• There are 10 bases per complete twist
• This is the famous double helix first
proposed by Francis Crick and James
Watson in 1953.

• The DNA double helix is stabilized both

by hydrogen bonds between the bases
and by stacking of the aromatic rings of
the bases in the center of the helix.

• In double stranded DNA, the bases on each strand protrude into

the center of the double helix where they are paired with the bases
in the other strand by means of hydrogen bonds.
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• Each base pair consists of one larger purine base paired with a
smaller pyrimidine base.

• So, although the bases themselves differ in size, all of the allowed
base pairs are the same width, providing for a uniform width of the
helix.

• Adenine (A) in one strand is always paired with thymine (T) in the
other, and guanine (G) is always paired with cytosine (C).

• Consequently, the number of adenines in DNA is equal to the

number of thymines, and similarly the numbers of guanine and
cytosine are equal.

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• The A-T base pair has two hydrogen bonds and the G-C base pair is
held together by three.

Figure. Base Pairing by Hydrogen Bond Formation

Purines (adenine and guanine) pair with pyrimidines (thymine and cytosine) by hydrogen bonding
(colored regions).When the purines and pyrimidines first come together, they form the bonds indicated
by the dotted lines.

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• The two chains of the double helix have complementary
sequences

– Pairing between A and T and G and C on the two intertwined

chains.

– Due to the rules for base pairing, the sequence of a DNA strand
can be deduced if the sequence of its partner is known.

Example: 5’-ATGTC-3’ on one chain, the opposite chain must

have the complementary sequence 3’-TACAG-5’

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 The double-bonded structure is stabilized by

1. Base stacking

• Within the DNA, the bases are oriented at the

interior, and the flattened regions are face each
other

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 2. Hydrogen bonding between complementary bases
• A bonded to T (A:T) by two hydrogen bonds

• between amino group at C6 on A and the carbonyl at

C4 in T;
• between N1 of A and N3 of T

• G bonded to C (G:C) by three hydrogen bonds

• between amino group at C2 on G and the carbonyl at

C2 in C;
• between N1 of G and N3 of C;
• carbonyl at C6 of G and amine group at C4 of C

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