Lecture 1
An introduction to DNA Topology
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The human cell contains
23 pairs of chromosomes
If we scale the cell
nucleus to the size of
Basketball then the DNA
scales to 200km in
length.
The cell nucleus is only 10
micrometres in diameter
The bacteria is made up
of only one DNA
molecule (which is a
closed loop)
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DNA stands for
Deoxyribonucleic acid
DNA is often called the
blueprint of life (the secret of
life).
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In simple terms, DNA
contains the instructions for
making proteins within the
cell.
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Its double helix structure was
discovered by Crick and
Watson 1953 (Nobel prize)
Mainly because of:
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its central importance to all
life on Earth (it contains all
genetic information)
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genetic tests
medical benefits such as
cures for diseases,
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genetically modified Food
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The DNA consists of two
long molecules arranged
into a ladder like
structure called the
double Helix
The two Backbones
(strands) are bonded
together by ladder
rungs which are made
up of pairs of bases.
Structure(video)
Each strand consists of:
1) A Sugar Phosphate Backbone
2) Four Base Chemicals
(Attached in Pairs)
 http://video.parajsa.com/video/1681/How-
DNA-Works
 DNA packing
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DNA of Bacteria consists of
closed loop
It is made up of two circular
strands which wrap around
each other
The backbones are circular
and the base pairs are the
same as in the case of
linear DNA (human)
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Bacteria and
viruses are often
made up of a
single DNA circular
molecule!
 Supercoil
(Animation)
 Super coiling
means coiling
of a coil
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Circular DNA, has
one helical turn
every 10.5 bp in
“relaxed”, form
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Super coiling
appears when two
points are twisted in
opposite directions
An electron micrograph of
The DNA molecule in
Relaxed and super-coiled
States
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For a cell to divide, it must first replicate its DNA
Each strand of the original double-stranded DNA serves as
template for the reproduction of the complementary strand.
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DNA in Cell (replication 1)
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Replication2(Youtube)
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Replication(circular) (DNA Tube)
What is DNA topology
about?
An electron
micrograph
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Corresponding
mathematical object
Circular DNA molecules
can be knotted as
Knotting may lead to
cell Death.
Certain Enzymes are
responsible of that
phenomena
(topoinsomerase)
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Enzymes are proteins that catalyze (i.e., increase
or decrease the rates of) chemical reactions
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In enzymatic reactions, the molecules at the
beginning of the process are called substrates,
after the transformation they are called the
products
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Almost all processes in a biological cell need
enzymes to occur at significant rates
Topoisomerase (video 1)
Topoisomerase (video 2)
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Mathematics: Deduce enzyme binding
and mechanism from observed products
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Molecular basis of heredity. It is a complex giant molecule that contains, in chemically coded
form, the information needed for a cell to make proteins. In other words it determines the order
in which amino acids are joined to make a specific protein in a cell. DNA is a ladder-like doublestranded nucleic acid, which forms the basis of genetic inheritance in all organisms, except for a
few viruses that have only RNA. DNA is organized into chromosomes and, in organisms other
than bacteria, it is found only in the cell nucleus.
DNA is a ladder-like molecule, which means that it is made up of two halves (the ladder sides),
formed of chains of nucleotide subunits. Each nucleotide contains a deoxyribose sugar, a
phosphate, and a base. A set of three bases – known as a codon – acts as a blueprint for the
incorporation of a particular amino acid, the subunit of a protein molecule. The two halves are
joined together by the bases – a purine (adenine or guanine) or pyrimidine (cytosine or thymine) –
forming pairs (the rungs). The bases form into two specific base pairs: adenine with thymine and
guanine with cytosine. The sequence of base pairs along the DNA acts as a code carrying
information about the sequence of amino acids in proteins. Three base pairs in sequence (triplet)
name an amino acid and the next three name the next amino acid that needs to be joined and so
on, to make a specific protein. The specific way in which the pairs form means that the base
sequence is preserved from generation to generation. Hereditary information is stored as a
specific sequence of bases.
Reference: http://encyclopedia.farlex.com/Circular+DNA