Introduction to DNA
Lecture 1 – Structure of DNA
Within most cells (with the exception of red blood cells) is the nucleus which houses all the
genetic material for the entire organism. This genetic material is known as Deoxy ribonucleic
acid or DNA. It contains all the genetic information a living organism needs to survive. In
order to survive, DNA enables the production of proteins (how this happens will be covered
in detail later). Proteins are produced in response to environmental and biological queues.
The DNA contains information for which proteins to create, when to create them and how
they are made. Proteins are important because they carry out many functions within the cell
and the organism overall.
Nucleus containing DNA
Cell
Because DNA contains so much information it is actually very long. In fact, there is a total of
1.8 metres of DNA in the nucleus of a human cell, which itself is only 0.6 nanometres in size!
In order to fit it inside the nucleus, the DNA must be condensed into a more practical format.
To do this the DNA wraps around proteins called histones. These proteins allow the DNA to
coil around them and then curl up on itself, in a format we call supercoiling (a little bit like a
spool of thread but lots of them all bound together). In this form we refer to the DNA as
chromatin. Chromatin condenses further to make up a single chromosome, a term you are
probably familiar with and you may be aware of the fact that humans have 46 chromosomes.
DNA is stored as chromosomes not only so that it fits inside the cell but also it makes
replication easier (we will discuss this later).
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Introduction to DNA
Magnified
chromosome
Histone
Supercoiled
Chromatin DNA
DNA strand
Nucleus with
chromosomes
Cell
How DNA is condensed into a cell
Before any modifications such as DNA replication can occur, the DNA must first be unwound
and separated into a single strand. This enables it to be accessed by various components
within the cell which would otherwise be impossible in the condensed format.
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Introduction to DNA
DNA exists in the well documented form known as a double helix as shown below
DNA double helix
The helix is composed of two strands of DNA running antiparallel to each other (opposite
directions). If we break down the DNA helix, we will see there is a lot of important features
involved which are responsible for holding it together
Each DNA strand is made of subunits known as nucleotides. Nucleotides consist of a 5-
carbon sugar called deoxyribose, a phosphate and a nitrogenous base.
Phosphate
Nitrogenous
base
Deoxyribose
sugar
DNA nucleotide
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Introduction to DNA
Pyrimidine Bases Purine Bases
Cytosine Thymine Adenine Guanine
The chemical structure of the 4 Nitrogenous bases
There are 4 nitrogenous bases in DNA and they are responsible for creating the genetic code,
while the sugar and the phosphate make up the DNA backbone. The 4 nitrogenous bases
are called adenine, thymine, cytosine and guanine. Adenine and guanine are purine bases
due to their multiple ring structure and thymine and cytosine are pyrimidine bases due to
their single ring structure
When it comes to working out the directionality of the DNA strands, we use the carbon
numbering on the sugar molecule as a base. The carbons are counted as one prime (1’), two
prime (2’) and so on. That is just how it is done based on the naming convention. The
nitrogenous base will always bind to the 1’ carbon of the sugar molecule and then the
numbering starts from there. The phosphate group will from a bond between the 3’ carbon
of one sugar and the neighbouring 5’ carbon on another sugar. This bond between the
phosphate and the sugar is what is known as a phosphodiester bond and is responsible for
holding the DNA backbone together.
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Introduction to DNA
Simplified image of DNA backbone showing molecular
structure and carbon numbering
DNA strands are always read left to right. This means when you read the bases off the
strand you will read them from left to right. One strand of DNA will run 5’ to 3’ while the
other will run 3’ to 5’. This is what is known as running antiparallel. You can think of this as
a two-way street running in opposite direction to each other.
Simplified image of DNA backbone showing two strands
running antiparallel
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Introduction to DNA
The nitrogenous bases interact by what is referred to as base-pairs across the two
antiparallel strands of DNA. Adenine forms a base-pair with thymine and guanine forms a
base-pair with cytosine. I should note here that we call them complementary as this is how
they interact naturally and unless there is a mutation, they will not form a base pair in any
other format.
Simplified image of DNA backbone showing two strands
running antiparallel with bases pairs interacting across strands
Do not forget that the structure of DNA is three dimensional so it is a bit more complex than
the images shown above. The nitrogenous bases interact with each other across the DNA
strands by hydrogen bonding. Hydrogen bonding is a type of chemical interaction which
occurs between hydrogen with oxygen, nitrogen, fluorine or other hydrogen atoms on
neighbouring molecules. The nitrogenous bases must interact in this way to ensure
regularity and geometry of the helix is maintained enabling the structure of the DNA to
molecule keep its form.
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Introduction to DNA
Two strands of DNA running antiparallel with bases pairs
interacting across the strands via hydrogen bonding
The DNA molecule is organised in such a way that the base pairs stack on top of each other
and this enables them to interact using what we call pi-pi interactions. This is a result of the
ring structures in the bases stacking on top of each other. Within each base is free electrons
which interacts with the free electrons from the base both above and below and gives the
DNA molecule further stability
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Introduction to DNA
Simplified DNA backbone showing two strands running
antiparallel illustrating the pi-pi interactions between stacked
bases
If we look at the length of the DNA helix, we always measure DNA in base-pairs so we will
say a gene for example will run over a length of X base-pairs.
Another important feature of DNA is the major and minor grooves. This applies to the three-
dimensional structure of the helix. If we look at the image below the major groove is the
large gap in the structure while the minor groove is the small gap.
Minor groove
Major groove
3-D DNA helix demonstrating the positions of the major and
minor grooves
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Introduction to DNA
These alternating major and minor grooves are important to the DNA as they enable proteins
to bind to the DNA which will help with DNA replication and further protein production. We
will discuss this in further detail later but for now all you need to know is that the major
groove contains base pair specific information, while the minor groove contains base pair
non-specific information. This results simply from the proteins are able in interact with the
bases within the grooves of the DNA when binding to the DNA. These grooves enable
proteins to correctly locate the region of DNA they need to bind to carry out important
functions within the genome.
Reference:
1. Molecular Biology of the Cell. 4th edition, Alberts B, Johnson A, Lewis J, et [Link]
York: Garland Science; 2002.
2. Biochemistry, Fifth Edition. Reginald H. Garrett, Charles M. Grisham. Publisher: Mary
Finch. Senior Developmental Editor: Peter McGahey.
Exercise Questions
1. What does DNA stand for?
___________________________________
2. What are the four nitrogenous bases in DNA?
________________________________________
3. ___________ molecules and deoxyribose form the backbone of the DNA molecule and
interact via______________________ bonds. (fill in the gaps)
4. What type of bond is formed between the base pairs stabilising the DNA molecule?
____________________
5. What is the shape taken on by the DNA molecule?
_________________________
6. The two strands of DNA are said to run ________________. (Fill in the gaps)
Answers
1. Deoxyribonucleic acid
2. Adenine, cytosine, thymine
and guanine
3. Phosphate, phosphodiester
4. Hydrogen
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5. Double helix
6. Anti-parallel
Introduction to DNA
Congratulations you completed chapter 1!
DEFFINITIONS LIST
Antiparallel – a term used to describe the directionality of double stranded DNA. The two
strands run in opposite directions to each other. The 5’ end of one strand aligns with the 3’
end of the other.
Chromosome – name given to the form a singular structure of super condensed DNA and the
proteins which keep it in this formation. Each chromosome codes for specific genes.
Chromatin – the name given to DNA when it is in the supercoiled format
Deoxyribose – the sugar which makes up the backbone of DNA. This sugar is made of 5 carbon
molecules which is why it is refed to a 5-carbon sugar.
Double helix – the name of the shape taken on by double stranded DNA
DNA – Deoxyribonucleic acid (contains all genetic information).
Free electrons – electrons are subunits of atoms and have a negative charge. They are
continually moving and are able to give atoms charge and when atoms bond together it is the
electrons which are involved in this process. Free electrons are those electrons which are
currently not forming interactions with anything.
Hydrogen bond – a hydrogen bond is a special type of bond we see in chemistry and it is very
strong. It takes place between hydrogen with oxygen, nitrogen, fluorine or other hydrogen
atoms on neighbouring molecules.
Nitrogenous base - contains nitrogen and is a building block of DNA. There are 4 nitrogenous
bases in DNA (adenine, thymine, cytosine and guanine)
Major groove – a structural feature of DNA which is important for enabling proteins to bind
to it.
Minor Groove - a structural feature of DNA which is important for enabling proteins to bind
to it.
Nucleus – region of the cell where the DNA is stored. (note: Not all cells have a nucleus)
Nucleotide – a subunit of DNA made up of deoxyribose, phosphate and one of the
nitrogenous bases.
Pi-pi interactions – a type of electrostatic interaction (a bond held in place by electrons)
Purine base – a nitrogenous base containing a purine ring (this name was given due to its
chemical structure).
Phosphodiester bond – the bond that holds the DNA backbone in place. The bond forms
between the phosphate and the 5’carbond on two different sugar molecules.
Pyrimidine base - a nitrogenous base containing a pyrimidine ring (this name was given due
to its chemical structure).
Super coiling – a format in which DNA is stored inside cells so as to fit all of it inside the
nucleus.
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