Molecular Biology and Genetics

BIOL1018

Paula Tennant- weeks 7-9

Dwight Robinson- weeks 10-12

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 There are four basic kinds of biological
macromolecules. They are carbohydrates, lipids,
proteins and nucleic acids. These polymers are
composed of different monomers and serve different
functions.

• CARBOHYDRATES - composed of sugar monomers; necessary

for energy storage; structural roles

• LIPIDS – fatty acids and glycerol; energy storage, structural roles,

insulation

• PROTEINS - composed of amino acid monomers; structural

support, protection, transport, catalysis, defense, regulation,
movement

• NUCLEIC ACIDS - include DNA and RNA; composed of monomers

nucleotides; information storage. Nucleic acids contain instructions
for protein synthesis and allow organisms to transfer genetic
information from one generation to the next. ***
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 DNA
structure
1953 • Molecular Biology was
born April 25, 1953
when Watson & Crick
announced the
Recombinant
DNA
structure of DNA

• The science came of

age in 2001 with the
Gene cloning/
Genetic publication of a draft of
engineering the human genome

Human genome
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2001
• Analysis of the flow of
information among
DNA, RNA & protein
= Molecular Biology

• DNA
(deoxyribonucleic
acid) is the master
molecule in whose
structure is encoded
all the information
needed to create and
direct the chemical
machinery of life
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• Molecular Biology is one of 3 primary
molecular scale biological sciences

– Biochemistry; functions of proteins

– Genetics; how genes are inherited and
propagated

– Molecular Biology; process of DNA

replication, transcription and translation of
genes

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 Molecular Biology
• Structure of DNA
• Function of DNA
• DNA replication
• Transcription & translation
• Control of gene expression
• Recombinant DNA technology

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General house keeping rules to remember:
• Lecture outlines & reading materials
– http://ourvle.mona.uwi/
– Tutorial questions & Lab notes

• SAME TUTORIAL STREAMS AS in BIOL1017

• SAME LAB STREAMS AS in BIOL1017

– Lab manual - http://ourvle.mona.uwi/

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General house keeping rules to remember:

• Incourse Test (November 27)

– 30 mcqs
– 1 hour
– Based on material covered in lectures AND labs

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 General notices
Final grade: a composite of coursework &
final exam

• 50% Coursework
– 20% Lab reports/assignments
– 10% Tutorial quizzes
– 20% Incourse test

• 50% Final exam December

– 30 mcqs, 4 saqs, 2 eqs
– 2 hours 9
• Analysis of the flow of
information among
DNA, RNA & protein
= Molecular Biology

• DNA
(deoxyribonucleic
acid) is the master
molecule in whose
structure is encoded
all the information
needed to create and
direct the chemical
machinery of life
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 In the early twentieth century, geneticists associated
the presence of genes with chromosomes.

Chromatin: DNA + protein complex, unwound DNA

Chromosome: tightly packed DNA, genetic element
carrying genes essential to cellular function. Eukaryotic cells
have several chromosomes, each containing a linear DNA
molecule. Bacterial cells typically have a single chromosome
consisting of a circular DNA molecule (+ plasmids).
Gene: unit of heredity, stored information  a segment of
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DNA that specifies the structure of a single polypeptide chain
Griffith & the transforming principle (1928): Work with the bacterium
Streptococcus pneumoniae showed that genetic material could be
transferred; molecule of inheritance (transforming principle).

R strain: no capsule
 rough appearance, non-virulent

S strain: smooth capsule

 virulent, fatal infection

The presence of the dead S strain resulted

in the transformation of the R strain.
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Follow up experiments by Avery and coworkers in the 1940s established that
DNA was the mechanism for this transfer of genetic information between
the two bacteria.

*RNase
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*Protease
 Having established the identity of the transforming
principle & DNA as the genetic material, the next
important questions were …

• How are genetic messages encoded in DNA?

• What is the chemical structure of DNA?

– Chemical composition of DNA
– X ray crystallography
– Model building

 work of Chargaff and Watson & Crick

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 Chemical structure of DNA
• DNA consists of
alternating units of
phosphate and sugar
(deoxyribose),
connected to each
sugar is one of the
nitrogenous bases
– Purine bases
– Pyrimidine bases

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 Nitrogen bases
• The nitrogen bases of
nucleic acids belong
to either of 2 chemical
classes

– Pyrimidine bases
• T&C
– Purine bases
• A&G

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 dATP deoxyadenosine triphosphate
dCTP deoxycytidine triphosphate
dGTP deoxyguanosine triphosphate
dTTP deoxythymidine triphosphate

• In a nucleotide, a base is attached to a pentose

sugar by a glycosidic linkage between the C1’ of the
sugar and a N of the base. Without a PO4, a base
bonded to its sugar is referred to as a nucleoside.
Nucleotides are nucleosides containing 1 or more PO4.

• DNA is a polynucleotide; a polymer in which nucleotides

are bonded to each other in a defined sequence.
• The succession of the letters AGTC indicate the
order of nucleotides within a DNA molecule. * 17
 The Deoxyribose Sugar
• A pentose, a 5-carbon sugar.
• 4 carbons and an oxygen make up
the 5-membered ring; the other
carbon branches off the ring.

• Carbon constituents of the sugar

ring are numbered 1'-4'
(pronounced "one-prime carbon"),
starting with the carbon to the right
of the oxygen going clockwise.
The fifth carbon (5') branches from
the 4' carbon.
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• The PO4 connecting 2
sugars spans from the 3’
carbon of one sugar to
the 5’ carbon of the
adjacent sugar

• The PO4 linkage in DNA

is a phosphodiester bond

• An important structural feature DNA is the orientation of

the nucleotides.*
– The 5’ end of a DNA strand has a phosphate group while the 3’
end has an –OH group
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• The PO4 connecting 2
sugars spans from the 3’
carbon of one sugar to
the 5’ carbon of the
adjacent sugar

• The PO4 linkage in DNA

is a phosphodiester

• An important structural feature DNA is the orientation of

the nucleotides.
– The 5’ end of a DNA strand has a phosphate group while the 3’
end has an –OH group
– Directionality or polarity 20
• An important structural
feature DNA is the
orientation of the
nucleotides.
– The 5’ end of a DNA
strand has a phosphate
group while the 3’ end
has an –OH group
– Directionality or polarity
– The succession of the
letters AGTC indicate
the order of nucleotides
within a DNA molecule.
By convention the
sequences are
5’ TCG 3’
presented from the 5’ to
3’ end.
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• DNA does not exist as a ss polynucleotide, but
as 2 polynucleotides that are not identical in
base sequence but are complementary
• The complementarity
arises because of the
specific pairing of the
purine and the
pyrimidine bases 
antiparallel
arrangement
• The strands are
wrapped around each
other  double helix 5’ TCG 3’
3’ AGC 5’ 22
• The size of a DNA molecule is expressed
in terms of …
– Molecular weight
• Single nucleotide = 330  because DNA
consists of many nucleotides the mw
mounts rapidly
– Number of nucleotides or base pairs
 e.g. a double helix of 6000 bp in length or
6 kilobase pairs (kb)
Base pair = a pair of complementary bases
in dsDNA molecules
5’ TCG 3’
3’ AGC 5’ 23
 Chargaff & Watson and Crick …..

• How are genetic messages encoded in DNA?

• What is the chemical structure of DNA?

– Chemical composition of DNA
– X ray crystallography
– Model building

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Relative amounts of nitrogen bases in different
samples of DNA

(Chargaff & Davidson 1955)

Source Adenine Guanine Cytosine Thymine

T2 virus 32.5 18.2 16.7 32.6
Bull sperm 28.7 22.2 22.0 27.2
Yeast cells 31.3 18.7 17.1 32.9
Human 30.7 19.3 18.8 31.2
sperm

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 Relative amounts of nitrogen bases in different samples of DNA
(Chargaff & Davidson 1955)

Source Adenine Guanine Cytosine Thymine

T2 virus 32.5 18.2 16.7 32.6

Bull sperm 28.7 22.2 22.0 27.2
Yeast 31.3 18.7 17.1 32.9

Human sperm 30.7 19.3 18.8 31.2

According to Chargaff’s rules, if the DNA content of a cell was

composed of 15% A, then C would make up ______%, G would
make up ______%, and T would make up_____ % of the cell’s DNA.
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 Relative amounts of nitrogen bases in different samples of DNA
(Chargaff & Davidson 1955)

Source Adenine Guanine Cytosine Thymine

T2 virus 32.5 18.2 16.7 32.6

Bull sperm 28.7 22.2 22.0 27.2

Yeast 31.3 18.7 17.1 32.9

Human sperm 30.7 19.3 18.8 31.2

Chargaff’s rules

DNA carries genetic information in the form of specific nucleotide base sequences.
5’ TCAGGA 3’ differs from 5’ AGGCTA 3’
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In the 1950s, the 3-D arrangement of the subunits in DNA was determined
from data obtained from X-ray crystallography and by model building.

X-ray diffraction was also a key experimental tool that led to the discovery of the
DNA double helix. When a substance is exposed to radiation, such as X-rays,
the atoms in the substance will cause the X-rays to be scattered.

If the substance has a repeating structure, the pattern of scattering, known as

the diffraction pattern, is mathematically related to the structural
arrangement of the atoms causing the scattering.

Previous knowledge of the composition of DNA and the base pairing of

nucleotides along with X-ray data from Rosalind Franklin and Maurice Wilkins
helped Watson and Crick to put together and coherent model. 28
In the 1950s, the 3-D arrangement of the subunits in DNA was determined
from data obtained from X-ray crystallography and by model building.
(i) Maurice Wilkins (ii) Rosalind Franklin (iii) James Watson and Francis Crick

http://dnalc.org/view/15014-Franklin-s-X-ray-diffraction-explanation-of-X-ray-pattern-.html

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The X pattern suggested a
ds helical structure.

The diamond pattern

suggested continuous
ds helical structure (2 nm
diameter & a rise of 3.4 nm
up the axis)

The dark regions indicated

stacking of the bases
perpendicular to the fibre
axis. 30
Main points of the Watson & Crick model:

• Two polynucleotide chains coiled

around a central axis.
• Two chains are antiparallel.
• The bases of both strand are
lying inside of the structure and
stacking flat on one another,
0.34 nm apart.
• The two strands are held
together by hydrogen bonds.
• One complete turn of the helix is
3.4 nm long and contains 10
bases.
• The double helix measures 2 nm
in diameter.
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DNA stores information in the sequence of its
bases.

e.g. the information encoded in the sequence

5’ TCAGGA 3’ is different from the information in the
sequence 5’ AGGCTA 3’

As a carrier of information, DNA has two important

functions:
– HETEROCATALYTIC: directs the synthesis of other molecules
– AUTOCATALYTIC: directs the synthesis of itself

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 RNA (ribonucleic acid) is another type of nucleic acid.
(i) Genetic - i.e. makes up the genome
(ii) non-genetic - i.e. carries out the instructions of DNA, no genetic role

Alternating pentose sugar &

phosphates, 4 bases are attached
to the sugars and project from
the chain.

The nucleotides are referred to as

Ribonucleotides.

ATP adenosine triphosphate

CTP cytidine triphosphate
GTP guanosine triphosphate
UTP uridine triphosphate

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Some double stranded RNA molecules do exist (not helical though). Even
single stranded RNA can form double stranded base paired stretches within
the molecule.
This occurs when folding brings 2 oppositely oriented regions alongside
each other.
This means that compared to DNA with its relatively simple double helix,
many RNAs have a complicated structure of short double-stranded
segments interspersed with single stranded loops. 34